Note: the module "R" cannot be unloaded because it was not loaded.

WARNING: ignoring environment value of R_HOME

R Under development (unstable) (2025-10-22 r88969) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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> cargs <- commandArgs(trailingOnly=TRUE)
> if(length(cargs)==0){
+   ## before running interactively, make sure to start emacs/R with
+   ## environment defined in /scratch/...check_one.sh, particularly
+   ## R_LIBS_USER=/tmp/... otherwise we get error when installing
+   ## data.table.
+   base <- "/scratch/th798/data.table-revdeps/*"
+   cargs <- c(
+     Sys.glob(file.path(base,"deps.csv")),
+     "349",
+     Sys.glob(file.path(base, "data.table_release_*tar.gz")),
+     Sys.glob(file.path(base, "data.table_master_*tar.gz"))
+   )
+ }
> names(cargs) <- c("deps.csv", "task.str", "release", "master")
> dput(cargs)
c(deps.csv = "/scratch/th798/data.table-revdeps/2025-10-25/deps.csv", 
task.str = "439", release = "/scratch/th798/data.table-revdeps/2025-10-25/data.table_release_1.17.8.tar.gz", 
master = "/scratch/th798/data.table-revdeps/2025-10-25/data.table_master_1.17.99.b3acf2ad13848150e87c414f3edcc413c71fd977.tar.gz"
)
> (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers
[1] "/tmp/th798/24634860/R-devel/439"
> if(requireNamespace("R.cache"))R.cache::getCachePath()
Loading required namespace: R.cache
[1] "/tmp/th798/24634860/R-devel/439/R.cache"
> task.id <- as.integer(cargs[["task.str"]])
> deps.df <- read.csv(cargs[["deps.csv"]])
> (rev.dep <- deps.df$Package[task.id])
[1] "eyeris"
> job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id)
> setwd(task.dir)
> .libPaths()
[1] "/tmp/th798/24634860/R-devel/439/library"
[2] "/projects/genomic-ml/R/R-devel/library" 
> options(repos=c(#this should be in ~/.Rprofile too.
+   CRAN="http://cloud.r-project.org"))
> print(Sys.time())
[1] "2025-10-25 00:42:43 MST"
> install.time <- system.time({
+   install.packages(rev.dep, dep=TRUE)
+ })
Installing package into '/tmp/th798/24634860/R-devel/439/library'
(as 'lib' is unspecified)
also installing the dependencies 'eyelinker', 'gsignal'

trying URL 'http://cloud.r-project.org/src/contrib/eyelinker_0.2.1.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/gsignal_0.3-7.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/eyeris_3.0.1.tar.gz'
* installing *source* package 'eyelinker' ...
** this is package 'eyelinker' version '0.2.1'
** package 'eyelinker' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (eyelinker)
* installing *source* package 'gsignal' ...
** this is package 'gsignal' version '0.3-7'
** package 'gsignal' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c RcppExports.cpp -o RcppExports.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c conv2d.cpp -o conv2d.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c filter.cpp -o filter.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c fwht.cpp -o fwht.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c remez.cpp -o remez.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c sosfilt.cpp -o sosfilt.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c upfirdn.cpp -o upfirdn.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o gsignal.so RcppExports.o conv2d.o filter.o fwht.o remez.o sosfilt.o upfirdn.o
installing to /tmp/th798/24634860/R-devel/439/library/00LOCK-gsignal/00new/gsignal/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gsignal)
* installing *source* package 'eyeris' ...
** this is package 'eyeris' version '3.0.1'
** package 'eyeris' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (eyeris)

The downloaded source packages are in
	'/tmp/th798/24634860/RtmpAE094k/downloaded_packages'
> cat("Time to install revdep:\n")
Time to install revdep:
> print(install.time)
   user  system elapsed 
 59.338   3.473  68.143 
> print(Sys.time())
[1] "2025-10-25 00:43:51 MST"
> downloaded_packages <- file.path(
+   tempdir(),
+   "downloaded_packages")
> dl.glob <- file.path(
+   downloaded_packages,
+   paste0(rev.dep,"_*.tar.gz"))
> rev.dep.dl.row <- cbind(rev.dep, Sys.glob(dl.glob))
> colnames(rev.dep.dl.row) <- c("pkg","path")
> rev.dep.release.tar.gz <- normalizePath(rev.dep.dl.row[,"path"], mustWork=TRUE)
> pkg.Rcheck <- paste0(rev.dep, ".Rcheck")
> 
> proj.dir <- "~/genomic-ml/data.table-revdeps"
> source(file.path(proj.dir, "myStatus.R"))
> Rvers <- gsub("[()]", "", gsub(" ", "_", R.version[["version.string"]]))
> dir.create(Rvers, showWarnings=FALSE)
> Rcheck.list <- list()
> for(dt.version.short in c("release", "master")){
+   dt.tar.gz <- cargs[[dt.version.short]]
+   dt.version <- gsub(".tar.gz|/.*?_", "", dt.tar.gz)
+   print(Sys.time())
+   install.packages(dt.tar.gz, repos=NULL)
+   print(Sys.time())
+   check.cmd <- get_check_cmd(rev.dep.release.tar.gz)
+   system(check.cmd)
+   print(Sys.time())
+   dest.Rcheck <- file.path(
+     Rvers,
+     paste0(dt.version, ".Rcheck"))
+   unlink(dest.Rcheck, recursive=TRUE)
+   file.rename(pkg.Rcheck, dest.Rcheck)
+   Rcheck.list[[dt.version]] <- file.path(dest.Rcheck, "00check.log")
+ }
[1] "2025-10-25 00:43:51 MST"
Installing package into '/tmp/th798/24634860/R-devel/439/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** this is package 'data.table' version '1.17.8'
** package 'data.table' successfully unpacked and MD5 sums checked
** using staged installation
zlib 1.2.13 is available ok
* checking if R installation supports OpenMP without any extra hints... yes
** libs
using C compiler: 'gcc (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c assign.c -o assign.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c between.c -o between.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c bmerge.c -o bmerge.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c chmatch.c -o chmatch.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c cj.c -o cj.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c coalesce.c -o coalesce.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c dogroups.c -o dogroups.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fastmean.c -o fastmean.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fcast.c -o fcast.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fifelse.c -o fifelse.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fmelt.c -o fmelt.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c forder.c -o forder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frank.c -o frank.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fread.c -o fread.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c freadR.c -o freadR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c froll.c -o froll.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frollR.c -o frollR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frolladaptive.c -o frolladaptive.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fsort.c -o fsort.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwrite.c -o fwrite.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwriteR.c -o fwriteR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c gsumm.c -o gsumm.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c idatetime.c -o idatetime.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ijoin.c -o ijoin.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c init.c -o init.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c inrange.c -o inrange.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nafill.c -o nafill.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c negate.c -o negate.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nqrecreateindices.c -o nqrecreateindices.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c openmp-utils.c -o openmp-utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c programming.c -o programming.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c quickselect.c -o quickselect.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c rbindlist.c -o rbindlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c reorder.c -o reorder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c shift.c -o shift.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c snprintf.c -o snprintf.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c subset.c -o subset.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c transpose.c -o transpose.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c types.c -o types.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c uniqlist.c -o uniqlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c utils.c -o utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c vecseq.c -o vecseq.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c wrappers.c -o wrappers.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include
PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi
installing to /tmp/th798/24634860/R-devel/439/library/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (data.table)
[1] "2025-10-25 00:44:23 MST"
* using log directory '/tmp/th798/24634860/R-devel/439/eyeris.Rcheck'
* using R Under development (unstable) (2025-10-22 r88969)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Spack GCC) 12.2.0
    GNU Fortran (Spack GCC) 12.2.0
* running under: Red Hat Enterprise Linux 8.10 (Ootpa)
* using session charset: ASCII
* checking for file 'eyeris/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'eyeris' version '3.0.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'eyeris' can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   1.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
epoch 8.803  0.082    8.94
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(eyeris)
  
  eyeris v3.0.1 - Lumpy Space Princess <U+A4B0><U+2022><U+1D17><U+2022><U+FF61><U+A4B1><U+06F6>
  Welcome! Type ?`eyeris` to get started.
  
  > 
  > test_check("eyeris")
  i [2025-10-25 00:47:05] [INFO] Created output directory:
  /tmp/th798/24634860/RtmpkXnxps/test_chunked_output
  v [2025-10-25 00:47:05] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpkXnxps/bids_test/derivatives/test-db.eyerisdb
  i [2025-10-25 00:47:06] [INFO] Exporting data types: confounds_summary
  i [2025-10-25 00:47:06] [INFO] Processing data type: confounds_summary
  i [2025-10-25 00:47:06] [INFO] Grouping tables by epoch label...
  i [2025-10-25 00:47:06] [INFO] Found 1 epoch label groups for
  confounds_summary: _nolabel
  i [2025-10-25 00:47:06] [INFO] Analyzing column structures within epoch group
  '_nolabel'...
  i [2025-10-25 00:47:06] [INFO] Found 2 column-compatible groups within
  '_nolabel': goal, stim
  i [2025-10-25 00:47:06] [INFO] Processing confounds_summary group 'goal' (2
  tables)
  i [2025-10-25 00:47:06] [INFO] Using chunked processing (file size limit = 50MB
  < 500MB threshold)
  i [2025-10-25 00:47:06] [INFO] Processing with file size chunking enabled
  i [2025-10-25 00:47:06] [INFO] Starting chunked query processing (chunk size:
  50)
  i [2025-10-25 00:47:06] [INFO] Query: SELECT * FROM
  "confounds_summary_01_task_run01_goal" UNION ALL SELECT * FROM
  "confounds_summary_02_task_run01_goal"
  i [2025-10-25 00:47:06] [INFO] Processing chunk 1: 50 rows
  i [2025-10-25 00:47:06] [INFO] Created output file:
  test-db_confounds_summary_goal_chunked_01.csv
  i [2025-10-25 00:47:06] [INFO] Processing chunk 2: 50 rows
  i [2025-10-25 00:47:06] [INFO] Processing chunk 3: 50 rows
  i [2025-10-25 00:47:06] [INFO] No more data to process
  v [2025-10-25 00:47:06] [OKAY] Chunked processing complete:
  i [2025-10-25 00:47:06] [INFO] Total rows: 150
  i [2025-10-25 00:47:06] [INFO] Chunks: 3
  i [2025-10-25 00:47:06] [INFO] Processing time: 0 seconds
  i [2025-10-25 00:47:06] [INFO] Average rate: 4280 rows/second
  i [2025-10-25 00:47:06] [INFO] Processing confounds_summary group 'stim' (1
  tables)
  i [2025-10-25 00:47:06] [INFO] Using chunked processing (file size limit = 50MB
  < 500MB threshold)
  i [2025-10-25 00:47:06] [INFO] Processing with file size chunking enabled
  i [2025-10-25 00:47:06] [INFO] Starting chunked query processing (chunk size:
  50)
  i [2025-10-25 00:47:06] [INFO] Query: SELECT * FROM
  "confounds_summary_01_task_run01_stim"
  i [2025-10-25 00:47:06] [INFO] Processing chunk 1: 50 rows
  i [2025-10-25 00:47:06] [INFO] Created output file:
  test-db_confounds_summary_stim_chunked_01.csv
  i [2025-10-25 00:47:06] [INFO] Processing chunk 2: 50 rows
  i [2025-10-25 00:47:06] [INFO] No more data to process
  v [2025-10-25 00:47:06] [OKAY] Chunked processing complete:
  i [2025-10-25 00:47:06] [INFO] Total rows: 100
  i [2025-10-25 00:47:06] [INFO] Chunks: 2
  i [2025-10-25 00:47:06] [INFO] Processing time: 0 seconds
  i [2025-10-25 00:47:06] [INFO] Average rate: 2886 rows/second
  v [2025-10-25 00:47:06] [OKAY] Export complete!
  i [2025-10-25 00:47:06] [INFO] Data types exported: 2
  i [2025-10-25 00:47:06] [INFO] Total rows exported: 250
  i [2025-10-25 00:47:06] [INFO] Output directory:
  /tmp/th798/24634860/RtmpkXnxps/test_chunked_output
  i [2025-10-25 00:47:06] [INFO] Disconnected from eyeris database
  i [2025-10-25 00:47:07] [INFO] Created output directory:
  /tmp/th798/24634860/RtmpkXnxps/size_test_output
  v [2025-10-25 00:47:07] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpkXnxps/bids_size_test/derivatives/size-test.eyerisdb
  i [2025-10-25 00:47:07] [INFO] Exporting data types: timeseries
  i [2025-10-25 00:47:07] [INFO] Processing data type: timeseries
  i [2025-10-25 00:47:07] [INFO] Processing timeseries group 'all' (1 tables)
  i [2025-10-25 00:47:07] [INFO] Using chunked processing (file size limit =
  0.05MB < 500MB threshold)
  i [2025-10-25 00:47:07] [INFO] Processing with file size chunking enabled
  i [2025-10-25 00:47:07] [INFO] Starting chunked query processing (chunk size:
  500)
  i [2025-10-25 00:47:07] [INFO] Query: SELECT * FROM "timeseries_01_test_run01"
  i [2025-10-25 00:47:07] [INFO] Processing chunk 1: 500 rows
  i [2025-10-25 00:47:07] [INFO] Created output file:
  size-test_timeseries_chunked_01.csv
  i [2025-10-25 00:47:07] [INFO] Processing chunk 2: 500 rows
  i [2025-10-25 00:47:07] [INFO] Starting new file due to size limit:
  size-test_timeseries_chunked_02.csv
  i [2025-10-25 00:47:07] [INFO] Created output file:
  size-test_timeseries_chunked_02.csv
  i [2025-10-25 00:47:07] [INFO] Processing chunk 3: 500 rows
  i [2025-10-25 00:47:07] [INFO] Starting new file due to size limit:
  size-test_timeseries_chunked_03.csv
  i [2025-10-25 00:47:08] [INFO] Created output file:
  size-test_timeseries_chunked_03.csv
  i [2025-10-25 00:47:08] [INFO] Processing chunk 4: 500 rows
  i [2025-10-25 00:47:08] [INFO] Starting new file due to size limit:
  size-test_timeseries_chunked_04.csv
  i [2025-10-25 00:47:08] [INFO] Created output file:
  size-test_timeseries_chunked_04.csv
  i [2025-10-25 00:47:08] [INFO] No more data to process
  v [2025-10-25 00:47:08] [OKAY] Chunked processing complete:
  i [2025-10-25 00:47:08] [INFO] Total rows: 2000
  i [2025-10-25 00:47:08] [INFO] Chunks: 4
  i [2025-10-25 00:47:08] [INFO] Processing time: 0.1 seconds
  i [2025-10-25 00:47:08] [INFO] Average rate: 21768 rows/second
  i [2025-10-25 00:47:08] [INFO] Finalizing 4 output files with proper
  numbering...
  i [2025-10-25 00:47:08] [INFO] Renamed: size-test_timeseries_chunked_01.csv ->
  size-test_timeseries_chunked_01-of-04.csv
  i [2025-10-25 00:47:08] [INFO] Renamed: size-test_timeseries_chunked_02.csv ->
  size-test_timeseries_chunked_02-of-04.csv
  i [2025-10-25 00:47:08] [INFO] Renamed: size-test_timeseries_chunked_03.csv ->
  size-test_timeseries_chunked_03-of-04.csv
  i [2025-10-25 00:47:08] [INFO] Renamed: size-test_timeseries_chunked_04.csv ->
  size-test_timeseries_chunked_04-of-04.csv
  v [2025-10-25 00:47:08] [OKAY] Export complete!
  i [2025-10-25 00:47:08] [INFO] Data types exported: 1
  i [2025-10-25 00:47:08] [INFO] Total rows exported: 2000
  i [2025-10-25 00:47:08] [INFO] Output directory:
  /tmp/th798/24634860/RtmpkXnxps/size_test_output
  i [2025-10-25 00:47:08] [INFO] Disconnected from eyeris database
  v [2025-10-25 00:47:10] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpkXnxps/test_bids/derivatives/user-test.eyerisdb
  i [2025-10-25 00:47:11] [INFO] Executing query: SELECT * FROM (SELECT * FROM
  "epochs_002_02_memory_run01") as combined_data WHERE 1=1 AND subject_id = '002'
  i [2025-10-25 00:47:11] [INFO] Executing query: SELECT * FROM (SELECT * FROM
  "epochs_002_02_memory_run01") as combined_data WHERE 1=1 AND subject_id = '002'
  AND session_id = '02' AND task_name = 'memory'
  i [2025-10-25 00:47:11] [INFO] Disconnected from eyeris database
  i [2025-10-25 00:47:14] [INFO] Executing query: SELECT * FROM (SELECT * FROM
  "epoch_timeseries_005_01_epochtest_run01_prepostprobe") as combined_data WHERE
  1=1 AND subject_id = '005'
  v [2025-10-25 00:47:17] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 00:47:17] [INFO] Processing block: block_1
  v [2025-10-25 00:47:17] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 00:47:17] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 00:47:17] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 00:47:17] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 00:47:18] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 00:47:18] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 00:47:18] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 00:47:18] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 00:47:18] [INFO] Block processing summary:
  i [2025-10-25 00:47:18] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 00:47:18] [OKAY] Running eyeris::summarize_confounds()
  i [2025-10-25 00:47:19] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:20] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:21] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:21] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:21] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:22] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:22] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:23] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:23] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:24] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:24] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:24] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:25] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:25] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:26] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:26] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:26] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:27] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2025-10-25 00:47:31] [WARN] No detrend data found for run-01
  
  
  processing file: sub-001.Rmd
  output file: sub-001.knit.md
  
  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-001.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-001.html --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-devel/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-devel/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpkXnxps/rmarkdown-str1d86130cb4a5b.html 
  File  not found in resource path
  v [2025-10-25 00:47:33] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 00:47:33] [INFO] Processing block: block_1
  v [2025-10-25 00:47:33] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 00:47:33] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 00:47:33] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 00:47:34] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 00:47:34] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 00:47:34] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 00:47:34] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 00:47:34] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 00:47:34] [INFO] Block processing summary:
  i [2025-10-25 00:47:34] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 00:47:34] [OKAY] Running eyeris::summarize_confounds()
  i [2025-10-25 00:47:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:36] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:36] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:37] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:37] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:38] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:38] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:39] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:39] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:40] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:40] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:40] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:41] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:41] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:41] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:42] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:42] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:42] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2025-10-25 00:47:47] [WARN] No detrend data found for run-01
  
  
  processing file: sub-002.Rmd
  output file: sub-002.knit.md
  
  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-002.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-002.html --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-devel/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-devel/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpkXnxps/rmarkdown-str1d861504682fb.html 
  File  not found in resource path
  v [2025-10-25 00:47:47] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 00:47:48] [INFO] Processing block: block_1
  v [2025-10-25 00:47:48] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 00:47:48] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 00:47:48] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 00:47:48] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 00:47:48] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 00:47:48] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 00:47:48] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 00:47:48] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 00:47:48] [INFO] Block processing summary:
  i [2025-10-25 00:47:48] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 00:47:48] [OKAY] Running eyeris::summarize_confounds()
  i [2025-10-25 00:47:50] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:50] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:51] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:51] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:52] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:52] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:53] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:53] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:53] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:54] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:54] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:55] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:55] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:55] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:56] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:56] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:56] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:47:57] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2025-10-25 00:48:01] [WARN] No detrend data found for run-01
  
  
  processing file: sub-003.Rmd
  output file: sub-003.knit.md
  
  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-003.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-003.html --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-devel/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-devel/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpkXnxps/rmarkdown-str1d8612a17a512.html 
  File  not found in resource path
  v [2025-10-25 00:48:01] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 00:48:01] [INFO] Processing block: block_1
  v [2025-10-25 00:48:01] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 00:48:01] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 00:48:02] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 00:48:02] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 00:48:02] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 00:48:02] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 00:48:02] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 00:48:02] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 00:48:02] [INFO] Block processing summary:
  i [2025-10-25 00:48:02] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 00:48:02] [OKAY] Running eyeris::summarize_confounds()
  i [2025-10-25 00:48:03] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:48:04] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:48:04] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:48:05] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:48:05] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:48:06] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:48:06] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:48:07] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:48:07] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:48:07] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:48:08] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:48:08] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:48:09] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:48:09] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:48:09] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:48:10] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:48:10] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:48:10] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2025-10-25 00:48:14] [WARN] No detrend data found for run-01
  
  
  processing file: sub-004.Rmd
  output file: sub-004.knit.md
  
  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-004.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-004.html --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-devel/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-devel/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpkXnxps/rmarkdown-str1d8611963275c.html 
  File  not found in resource path
  i [2025-10-25 00:48:18] [INFO] Disconnected from eyeris database
  v [2025-10-25 00:48:18] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpkXnxps/test_bids/derivatives/test-study.eyerisdb
  i [2025-10-25 00:48:18] [INFO] Disconnected from eyeris database
  i [2025-10-25 00:48:19] [INFO] Disconnected from eyeris database
  v [2025-10-25 00:48:19] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpkXnxps/test_bids_read/derivatives/read-test.eyerisdb
  i [2025-10-25 00:48:20] [INFO] Disconnected from eyeris database
  i [2025-10-25 00:48:21] [INFO] Disconnected from eyeris database
  v [2025-10-25 00:48:21] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpkXnxps/test_bids_size/derivatives/size-test.eyerisdb
  i [2025-10-25 00:48:22] [INFO] Disconnected from eyeris database
  i [2025-10-25 00:48:22] [INFO] Disconnected from eyeris database
  v [2025-10-25 00:48:22] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpkXnxps/test_bids_empty/derivatives/empty-test.eyerisdb
  ! [2025-10-25 00:48:23] [WARN] No valid tables found in database (after
  excluding temp tables)
  i [2025-10-25 00:48:23] [INFO] Disconnected from eyeris database
  v [2025-10-25 00:48:23] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 00:48:23] [INFO] Processing block: block_1
  v [2025-10-25 00:48:23] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 00:48:23] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 00:48:24] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 00:48:24] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 00:48:24] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 00:48:24] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 00:48:24] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 00:48:24] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 00:48:24] [INFO] Block processing summary:
  i [2025-10-25 00:48:24] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 00:48:24] [OKAY] Running eyeris::summarize_confounds()
  v [2025-10-25 00:48:24] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 00:48:24] [INFO] Binocular data detected. Processing average
  mode.
  i [2025-10-25 00:48:24] [INFO] Processing block: block_1
  v [2025-10-25 00:48:24] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 00:48:25] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 00:48:25] [OKAY] Running eyeris::interpolate() for block_1
  ! [2025-10-25 00:48:25] [WARN] No NAs detected in pupil data... Skipping
  interpolation!
  v [2025-10-25 00:48:25] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 00:48:25] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 00:48:25] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 00:48:25] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 00:48:25] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 00:48:25] [INFO] Block processing summary:
  i [2025-10-25 00:48:25] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 00:48:25] [OKAY] Running eyeris::summarize_confounds()
  [ FAIL 4 | WARN 226 | SKIP 0 | PASS 192 ]
  
  == Failed tests ================================================================
  -- Failure ('test-parallel-database.R:10:7'): manual parallel processing flag enables temporary databases --
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    pandoc document conversion failed with error 99
  Backtrace:
      x
   1. +-withr::with_envvar(...) at test-parallel-database.R:4:3
   2. | \-base::force(code)
   3. \-testthat::expect_no_error(...) at test-parallel-database.R:9:5
  -- Failure ('test-parallel-database.R:32:7'): SLURM environment variables are detected for parallel processing --
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    pandoc document conversion failed with error 99
  Backtrace:
      x
   1. +-withr::with_envvar(...) at test-parallel-database.R:28:3
   2. | \-base::force(code)
   3. \-testthat::expect_no_error(...) at test-parallel-database.R:31:5
  -- Failure ('test-parallel-database.R:52:7'): PBS environment variables are detected for parallel processing --
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    pandoc document conversion failed with error 99
  Backtrace:
      x
   1. +-withr::with_envvar(...) at test-parallel-database.R:48:3
   2. | \-base::force(code)
   3. \-testthat::expect_no_error(...) at test-parallel-database.R:51:5
  -- Failure ('test-parallel-database.R:71:5'): normal database operation works without parallel processing --
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    pandoc document conversion failed with error 99
  
  [ FAIL 4 | WARN 226 | SKIP 0 | PASS 192 ]
  Error: Test failures
  In addition: Warning messages:
  1: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  2: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  Execution halted
  Warning messages:
  1: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  2: Connection is garbage-collected, use dbDisconnect() to avoid this. 
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  '/tmp/th798/24634860/R-devel/439/eyeris.Rcheck/00check.log'
for details.

[1] "2025-10-25 00:49:09 MST"
[1] "2025-10-25 00:49:09 MST"
Installing package into '/tmp/th798/24634860/R-devel/439/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** this is package 'data.table' version '1.17.99'
** using staged installation
zlib 1.2.13 is available ok
* checking if R installation supports OpenMP without any extra hints... yes
** libs
using C compiler: 'gcc (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c assign.c -o assign.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c between.c -o between.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c bmerge.c -o bmerge.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c chmatch.c -o chmatch.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c cj.c -o cj.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c coalesce.c -o coalesce.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c dogroups.c -o dogroups.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fastmean.c -o fastmean.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fcast.c -o fcast.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fifelse.c -o fifelse.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fmelt.c -o fmelt.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c forder.c -o forder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frank.c -o frank.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fread.c -o fread.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c freadR.c -o freadR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c froll.c -o froll.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frollR.c -o frollR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frolladaptive.c -o frolladaptive.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frollapply.c -o frollapply.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fsort.c -o fsort.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwrite.c -o fwrite.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwriteR.c -o fwriteR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c gsumm.c -o gsumm.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c idatetime.c -o idatetime.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ijoin.c -o ijoin.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c init.c -o init.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c inrange.c -o inrange.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c mergelist.c -o mergelist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nafill.c -o nafill.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c negate.c -o negate.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nqrecreateindices.c -o nqrecreateindices.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c openmp-utils.c -o openmp-utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c programming.c -o programming.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c quickselect.c -o quickselect.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c rbindlist.c -o rbindlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c reorder.c -o reorder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c shellsort.c -o shellsort.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c shift.c -o shift.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c snprintf.c -o snprintf.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c subset.c -o subset.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c transpose.c -o transpose.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c types.c -o types.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c uniqlist.c -o uniqlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c utils.c -o utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c vecseq.c -o vecseq.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c wrappers.c -o wrappers.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include
PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi
installing to /tmp/th798/24634860/R-devel/439/library/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (data.table)
[1] "2025-10-25 00:49:38 MST"
* using log directory '/tmp/th798/24634860/R-devel/439/eyeris.Rcheck'
* using R Under development (unstable) (2025-10-22 r88969)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Spack GCC) 12.2.0
    GNU Fortran (Spack GCC) 12.2.0
* running under: Red Hat Enterprise Linux 8.10 (Ootpa)
* using session charset: ASCII
* checking for file 'eyeris/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'eyeris' version '3.0.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'eyeris' can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   1.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
epoch 8.855  0.095   9.001
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(eyeris)
  
  eyeris v3.0.1 - Lumpy Space Princess <U+A4B0><U+2022><U+1D17><U+2022><U+FF61><U+A4B1><U+06F6>
  Welcome! Type ?`eyeris` to get started.
  
  > 
  > test_check("eyeris")
  i [2025-10-25 00:52:15] [INFO] Created output directory:
  /tmp/th798/24634860/RtmpagBdnO/test_chunked_output
  v [2025-10-25 00:52:15] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpagBdnO/bids_test/derivatives/test-db.eyerisdb
  i [2025-10-25 00:52:16] [INFO] Exporting data types: confounds_summary
  i [2025-10-25 00:52:16] [INFO] Processing data type: confounds_summary
  i [2025-10-25 00:52:16] [INFO] Grouping tables by epoch label...
  i [2025-10-25 00:52:16] [INFO] Found 1 epoch label groups for
  confounds_summary: _nolabel
  i [2025-10-25 00:52:16] [INFO] Analyzing column structures within epoch group
  '_nolabel'...
  i [2025-10-25 00:52:16] [INFO] Found 2 column-compatible groups within
  '_nolabel': goal, stim
  i [2025-10-25 00:52:16] [INFO] Processing confounds_summary group 'goal' (2
  tables)
  i [2025-10-25 00:52:16] [INFO] Using chunked processing (file size limit = 50MB
  < 500MB threshold)
  i [2025-10-25 00:52:16] [INFO] Processing with file size chunking enabled
  i [2025-10-25 00:52:16] [INFO] Starting chunked query processing (chunk size:
  50)
  i [2025-10-25 00:52:16] [INFO] Query: SELECT * FROM
  "confounds_summary_01_task_run01_goal" UNION ALL SELECT * FROM
  "confounds_summary_02_task_run01_goal"
  i [2025-10-25 00:52:16] [INFO] Processing chunk 1: 50 rows
  i [2025-10-25 00:52:16] [INFO] Created output file:
  test-db_confounds_summary_goal_chunked_01.csv
  i [2025-10-25 00:52:16] [INFO] Processing chunk 2: 50 rows
  i [2025-10-25 00:52:16] [INFO] Processing chunk 3: 50 rows
  i [2025-10-25 00:52:16] [INFO] No more data to process
  v [2025-10-25 00:52:16] [OKAY] Chunked processing complete:
  i [2025-10-25 00:52:16] [INFO] Total rows: 150
  i [2025-10-25 00:52:16] [INFO] Chunks: 3
  i [2025-10-25 00:52:16] [INFO] Processing time: 0 seconds
  i [2025-10-25 00:52:16] [INFO] Average rate: 4153 rows/second
  i [2025-10-25 00:52:16] [INFO] Processing confounds_summary group 'stim' (1
  tables)
  i [2025-10-25 00:52:16] [INFO] Using chunked processing (file size limit = 50MB
  < 500MB threshold)
  i [2025-10-25 00:52:16] [INFO] Processing with file size chunking enabled
  i [2025-10-25 00:52:16] [INFO] Starting chunked query processing (chunk size:
  50)
  i [2025-10-25 00:52:16] [INFO] Query: SELECT * FROM
  "confounds_summary_01_task_run01_stim"
  i [2025-10-25 00:52:16] [INFO] Processing chunk 1: 50 rows
  i [2025-10-25 00:52:16] [INFO] Created output file:
  test-db_confounds_summary_stim_chunked_01.csv
  i [2025-10-25 00:52:16] [INFO] Processing chunk 2: 50 rows
  i [2025-10-25 00:52:16] [INFO] No more data to process
  v [2025-10-25 00:52:16] [OKAY] Chunked processing complete:
  i [2025-10-25 00:52:16] [INFO] Total rows: 100
  i [2025-10-25 00:52:16] [INFO] Chunks: 2
  i [2025-10-25 00:52:16] [INFO] Processing time: 0 seconds
  i [2025-10-25 00:52:16] [INFO] Average rate: 3929 rows/second
  v [2025-10-25 00:52:16] [OKAY] Export complete!
  i [2025-10-25 00:52:16] [INFO] Data types exported: 2
  i [2025-10-25 00:52:16] [INFO] Total rows exported: 250
  i [2025-10-25 00:52:16] [INFO] Output directory:
  /tmp/th798/24634860/RtmpagBdnO/test_chunked_output
  i [2025-10-25 00:52:16] [INFO] Disconnected from eyeris database
  i [2025-10-25 00:52:16] [INFO] Created output directory:
  /tmp/th798/24634860/RtmpagBdnO/size_test_output
  v [2025-10-25 00:52:16] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpagBdnO/bids_size_test/derivatives/size-test.eyerisdb
  i [2025-10-25 00:52:17] [INFO] Exporting data types: timeseries
  i [2025-10-25 00:52:17] [INFO] Processing data type: timeseries
  i [2025-10-25 00:52:17] [INFO] Processing timeseries group 'all' (1 tables)
  i [2025-10-25 00:52:17] [INFO] Using chunked processing (file size limit =
  0.05MB < 500MB threshold)
  i [2025-10-25 00:52:17] [INFO] Processing with file size chunking enabled
  i [2025-10-25 00:52:17] [INFO] Starting chunked query processing (chunk size:
  500)
  i [2025-10-25 00:52:17] [INFO] Query: SELECT * FROM "timeseries_01_test_run01"
  i [2025-10-25 00:52:17] [INFO] Processing chunk 1: 500 rows
  i [2025-10-25 00:52:17] [INFO] Created output file:
  size-test_timeseries_chunked_01.csv
  i [2025-10-25 00:52:17] [INFO] Processing chunk 2: 500 rows
  i [2025-10-25 00:52:17] [INFO] Starting new file due to size limit:
  size-test_timeseries_chunked_02.csv
  i [2025-10-25 00:52:17] [INFO] Created output file:
  size-test_timeseries_chunked_02.csv
  i [2025-10-25 00:52:17] [INFO] Processing chunk 3: 500 rows
  i [2025-10-25 00:52:17] [INFO] Starting new file due to size limit:
  size-test_timeseries_chunked_03.csv
  i [2025-10-25 00:52:17] [INFO] Created output file:
  size-test_timeseries_chunked_03.csv
  i [2025-10-25 00:52:17] [INFO] Processing chunk 4: 500 rows
  i [2025-10-25 00:52:17] [INFO] Starting new file due to size limit:
  size-test_timeseries_chunked_04.csv
  i [2025-10-25 00:52:17] [INFO] Created output file:
  size-test_timeseries_chunked_04.csv
  i [2025-10-25 00:52:17] [INFO] No more data to process
  v [2025-10-25 00:52:17] [OKAY] Chunked processing complete:
  i [2025-10-25 00:52:17] [INFO] Total rows: 2000
  i [2025-10-25 00:52:17] [INFO] Chunks: 4
  i [2025-10-25 00:52:17] [INFO] Processing time: 0.1 seconds
  i [2025-10-25 00:52:17] [INFO] Average rate: 21349 rows/second
  i [2025-10-25 00:52:17] [INFO] Finalizing 4 output files with proper
  numbering...
  i [2025-10-25 00:52:17] [INFO] Renamed: size-test_timeseries_chunked_01.csv ->
  size-test_timeseries_chunked_01-of-04.csv
  i [2025-10-25 00:52:17] [INFO] Renamed: size-test_timeseries_chunked_02.csv ->
  size-test_timeseries_chunked_02-of-04.csv
  i [2025-10-25 00:52:17] [INFO] Renamed: size-test_timeseries_chunked_03.csv ->
  size-test_timeseries_chunked_03-of-04.csv
  i [2025-10-25 00:52:17] [INFO] Renamed: size-test_timeseries_chunked_04.csv ->
  size-test_timeseries_chunked_04-of-04.csv
  v [2025-10-25 00:52:17] [OKAY] Export complete!
  i [2025-10-25 00:52:17] [INFO] Data types exported: 1
  i [2025-10-25 00:52:17] [INFO] Total rows exported: 2000
  i [2025-10-25 00:52:17] [INFO] Output directory:
  /tmp/th798/24634860/RtmpagBdnO/size_test_output
  i [2025-10-25 00:52:17] [INFO] Disconnected from eyeris database
  v [2025-10-25 00:52:20] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpagBdnO/test_bids/derivatives/user-test.eyerisdb
  i [2025-10-25 00:52:21] [INFO] Executing query: SELECT * FROM (SELECT * FROM
  "epochs_002_02_memory_run01") as combined_data WHERE 1=1 AND subject_id = '002'
  i [2025-10-25 00:52:21] [INFO] Executing query: SELECT * FROM (SELECT * FROM
  "epochs_002_02_memory_run01") as combined_data WHERE 1=1 AND subject_id = '002'
  AND session_id = '02' AND task_name = 'memory'
  i [2025-10-25 00:52:21] [INFO] Disconnected from eyeris database
  i [2025-10-25 00:52:24] [INFO] Executing query: SELECT * FROM (SELECT * FROM
  "epoch_timeseries_005_01_epochtest_run01_prepostprobe") as combined_data WHERE
  1=1 AND subject_id = '005'
  v [2025-10-25 00:52:26] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 00:52:26] [INFO] Processing block: block_1
  v [2025-10-25 00:52:27] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 00:52:27] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 00:52:27] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 00:52:27] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 00:52:27] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 00:52:27] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 00:52:27] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 00:52:27] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 00:52:27] [INFO] Block processing summary:
  i [2025-10-25 00:52:27] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 00:52:27] [OKAY] Running eyeris::summarize_confounds()
  i [2025-10-25 00:52:29] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:29] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:30] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:30] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:30] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:31] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:31] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:32] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:32] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:33] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:33] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:33] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:34] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:34] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:36] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2025-10-25 00:52:40] [WARN] No detrend data found for run-01
  
  
  processing file: sub-001.Rmd
  output file: sub-001.knit.md
  
  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-001.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-001.html --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-devel/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-devel/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpagBdnO/rmarkdown-str2d4fe626a832d.html 
  File  not found in resource path
  v [2025-10-25 00:52:41] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 00:52:41] [INFO] Processing block: block_1
  v [2025-10-25 00:52:41] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 00:52:41] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 00:52:42] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 00:52:42] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 00:52:42] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 00:52:42] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 00:52:42] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 00:52:42] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 00:52:42] [INFO] Block processing summary:
  i [2025-10-25 00:52:42] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 00:52:42] [OKAY] Running eyeris::summarize_confounds()
  i [2025-10-25 00:52:43] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:44] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:44] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:45] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:45] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:46] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:46] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:46] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:47] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:47] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:49] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:49] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:49] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:50] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:50] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:50] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2025-10-25 00:52:54] [WARN] No detrend data found for run-01
  
  
  processing file: sub-002.Rmd
  output file: sub-002.knit.md
  
  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-002.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-002.html --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-devel/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-devel/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpagBdnO/rmarkdown-str2d4fe6c20258d.html 
  File  not found in resource path
  v [2025-10-25 00:52:55] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 00:52:55] [INFO] Processing block: block_1
  v [2025-10-25 00:52:55] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 00:52:55] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 00:52:56] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 00:52:56] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 00:52:56] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 00:52:56] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 00:52:56] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 00:52:56] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 00:52:56] [INFO] Block processing summary:
  i [2025-10-25 00:52:56] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 00:52:56] [OKAY] Running eyeris::summarize_confounds()
  i [2025-10-25 00:52:57] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:58] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:58] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:59] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:52:59] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:00] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:00] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:01] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:01] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:01] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:02] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:02] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:03] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:03] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:03] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:04] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:04] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:04] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2025-10-25 00:53:08] [WARN] No detrend data found for run-01
  
  
  processing file: sub-003.Rmd
  output file: sub-003.knit.md
  
  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-003.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-003.html --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-devel/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-devel/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpagBdnO/rmarkdown-str2d4fe2619b420.html 
  File  not found in resource path
  v [2025-10-25 00:53:09] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 00:53:09] [INFO] Processing block: block_1
  v [2025-10-25 00:53:09] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 00:53:09] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 00:53:10] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 00:53:10] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 00:53:10] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 00:53:10] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 00:53:10] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 00:53:10] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 00:53:10] [INFO] Block processing summary:
  i [2025-10-25 00:53:10] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 00:53:10] [OKAY] Running eyeris::summarize_confounds()
  i [2025-10-25 00:53:11] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:12] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:12] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:13] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:13] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:14] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:14] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:14] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:15] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:15] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:16] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:16] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:17] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:17] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:17] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:18] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:18] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:53:18] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2025-10-25 00:53:22] [WARN] No detrend data found for run-01
  
  
  processing file: sub-004.Rmd
  output file: sub-004.knit.md
  
  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-004.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-004.html --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-devel/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-devel/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpagBdnO/rmarkdown-str2d4fe71cb701d.html 
  File  not found in resource path
  i [2025-10-25 00:53:26] [INFO] Disconnected from eyeris database
  v [2025-10-25 00:53:26] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpagBdnO/test_bids/derivatives/test-study.eyerisdb
  i [2025-10-25 00:53:27] [INFO] Disconnected from eyeris database
  i [2025-10-25 00:53:28] [INFO] Disconnected from eyeris database
  v [2025-10-25 00:53:28] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpagBdnO/test_bids_read/derivatives/read-test.eyerisdb
  i [2025-10-25 00:53:28] [INFO] Disconnected from eyeris database
  i [2025-10-25 00:53:29] [INFO] Disconnected from eyeris database
  v [2025-10-25 00:53:29] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpagBdnO/test_bids_size/derivatives/size-test.eyerisdb
  i [2025-10-25 00:53:30] [INFO] Disconnected from eyeris database
  i [2025-10-25 00:53:30] [INFO] Disconnected from eyeris database
  v [2025-10-25 00:53:30] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpagBdnO/test_bids_empty/derivatives/empty-test.eyerisdb
  ! [2025-10-25 00:53:31] [WARN] No valid tables found in database (after
  excluding temp tables)
  i [2025-10-25 00:53:31] [INFO] Disconnected from eyeris database
  v [2025-10-25 00:53:31] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 00:53:32] [INFO] Processing block: block_1
  v [2025-10-25 00:53:32] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 00:53:32] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 00:53:32] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 00:53:32] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 00:53:32] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 00:53:32] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 00:53:32] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 00:53:32] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 00:53:32] [INFO] Block processing summary:
  i [2025-10-25 00:53:32] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 00:53:32] [OKAY] Running eyeris::summarize_confounds()
  v [2025-10-25 00:53:33] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 00:53:33] [INFO] Binocular data detected. Processing average
  mode.
  i [2025-10-25 00:53:34] [INFO] Processing block: block_1
  v [2025-10-25 00:53:34] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 00:53:34] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 00:53:34] [OKAY] Running eyeris::interpolate() for block_1
  ! [2025-10-25 00:53:34] [WARN] No NAs detected in pupil data... Skipping
  interpolation!
  v [2025-10-25 00:53:34] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 00:53:34] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 00:53:34] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 00:53:34] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 00:53:34] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 00:53:34] [INFO] Block processing summary:
  i [2025-10-25 00:53:34] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 00:53:34] [OKAY] Running eyeris::summarize_confounds()
  [ FAIL 4 | WARN 226 | SKIP 0 | PASS 192 ]
  
  == Failed tests ================================================================
  -- Failure ('test-parallel-database.R:10:7'): manual parallel processing flag enables temporary databases --
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    pandoc document conversion failed with error 99
  Backtrace:
      x
   1. +-withr::with_envvar(...) at test-parallel-database.R:4:3
   2. | \-base::force(code)
   3. \-testthat::expect_no_error(...) at test-parallel-database.R:9:5
  -- Failure ('test-parallel-database.R:32:7'): SLURM environment variables are detected for parallel processing --
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    pandoc document conversion failed with error 99
  Backtrace:
      x
   1. +-withr::with_envvar(...) at test-parallel-database.R:28:3
   2. | \-base::force(code)
   3. \-testthat::expect_no_error(...) at test-parallel-database.R:31:5
  -- Failure ('test-parallel-database.R:52:7'): PBS environment variables are detected for parallel processing --
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    pandoc document conversion failed with error 99
  Backtrace:
      x
   1. +-withr::with_envvar(...) at test-parallel-database.R:48:3
   2. | \-base::force(code)
   3. \-testthat::expect_no_error(...) at test-parallel-database.R:51:5
  -- Failure ('test-parallel-database.R:71:5'): normal database operation works without parallel processing --
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    pandoc document conversion failed with error 99
  
  [ FAIL 4 | WARN 226 | SKIP 0 | PASS 192 ]
  Error: Test failures
  In addition: Warning messages:
  1: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  2: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  3: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  4: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  '/tmp/th798/24634860/R-devel/439/eyeris.Rcheck/00check.log'
for details.

[1] "2025-10-25 00:54:35 MST"
> system(paste(c("diff -u", Rcheck.list), collapse=" "))
--- R_Under_development_unstable_2025-10-22_r88969/release_1.17.8.Rcheck/00check.log	2025-10-25 00:49:09.725528197 -0700
+++ R_Under_development_unstable_2025-10-22_r88969/master_1.17.99.b3acf2ad13848150e87c414f3edcc413c71fd977.Rcheck/00check.log	2025-10-25 00:54:35.862440148 -0700
@@ -58,7 +58,7 @@
 * checking examples ... OK
 Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
-epoch 8.803  0.082    8.94
+epoch 8.855  0.095   9.001
 * checking for unstated dependencies in 'tests' ... OK
 * checking tests ... ERROR
   Running 'testthat.R'
@@ -80,411 +80,411 @@
   
   > 
   > test_check("eyeris")
-  i [2025-10-25 00:47:05] [INFO] Created output directory:
-  /tmp/th798/24634860/RtmpkXnxps/test_chunked_output
-  v [2025-10-25 00:47:05] [OKAY] Connected to eyeris database:
-  /tmp/th798/24634860/RtmpkXnxps/bids_test/derivatives/test-db.eyerisdb
-  i [2025-10-25 00:47:06] [INFO] Exporting data types: confounds_summary
-  i [2025-10-25 00:47:06] [INFO] Processing data type: confounds_summary
-  i [2025-10-25 00:47:06] [INFO] Grouping tables by epoch label...
-  i [2025-10-25 00:47:06] [INFO] Found 1 epoch label groups for
+  i [2025-10-25 00:52:15] [INFO] Created output directory:
+  /tmp/th798/24634860/RtmpagBdnO/test_chunked_output
+  v [2025-10-25 00:52:15] [OKAY] Connected to eyeris database:
+  /tmp/th798/24634860/RtmpagBdnO/bids_test/derivatives/test-db.eyerisdb
+  i [2025-10-25 00:52:16] [INFO] Exporting data types: confounds_summary
+  i [2025-10-25 00:52:16] [INFO] Processing data type: confounds_summary
+  i [2025-10-25 00:52:16] [INFO] Grouping tables by epoch label...
+  i [2025-10-25 00:52:16] [INFO] Found 1 epoch label groups for
   confounds_summary: _nolabel
-  i [2025-10-25 00:47:06] [INFO] Analyzing column structures within epoch group
+  i [2025-10-25 00:52:16] [INFO] Analyzing column structures within epoch group
   '_nolabel'...
-  i [2025-10-25 00:47:06] [INFO] Found 2 column-compatible groups within
+  i [2025-10-25 00:52:16] [INFO] Found 2 column-compatible groups within
   '_nolabel': goal, stim
-  i [2025-10-25 00:47:06] [INFO] Processing confounds_summary group 'goal' (2
+  i [2025-10-25 00:52:16] [INFO] Processing confounds_summary group 'goal' (2
   tables)
-  i [2025-10-25 00:47:06] [INFO] Using chunked processing (file size limit = 50MB
+  i [2025-10-25 00:52:16] [INFO] Using chunked processing (file size limit = 50MB
   < 500MB threshold)
-  i [2025-10-25 00:47:06] [INFO] Processing with file size chunking enabled
-  i [2025-10-25 00:47:06] [INFO] Starting chunked query processing (chunk size:
+  i [2025-10-25 00:52:16] [INFO] Processing with file size chunking enabled
+  i [2025-10-25 00:52:16] [INFO] Starting chunked query processing (chunk size:
   50)
-  i [2025-10-25 00:47:06] [INFO] Query: SELECT * FROM
+  i [2025-10-25 00:52:16] [INFO] Query: SELECT * FROM
   "confounds_summary_01_task_run01_goal" UNION ALL SELECT * FROM
   "confounds_summary_02_task_run01_goal"
-  i [2025-10-25 00:47:06] [INFO] Processing chunk 1: 50 rows
-  i [2025-10-25 00:47:06] [INFO] Created output file:
+  i [2025-10-25 00:52:16] [INFO] Processing chunk 1: 50 rows
+  i [2025-10-25 00:52:16] [INFO] Created output file:
   test-db_confounds_summary_goal_chunked_01.csv
-  i [2025-10-25 00:47:06] [INFO] Processing chunk 2: 50 rows
-  i [2025-10-25 00:47:06] [INFO] Processing chunk 3: 50 rows
-  i [2025-10-25 00:47:06] [INFO] No more data to process
-  v [2025-10-25 00:47:06] [OKAY] Chunked processing complete:
-  i [2025-10-25 00:47:06] [INFO] Total rows: 150
-  i [2025-10-25 00:47:06] [INFO] Chunks: 3
-  i [2025-10-25 00:47:06] [INFO] Processing time: 0 seconds
-  i [2025-10-25 00:47:06] [INFO] Average rate: 4280 rows/second
-  i [2025-10-25 00:47:06] [INFO] Processing confounds_summary group 'stim' (1
+  i [2025-10-25 00:52:16] [INFO] Processing chunk 2: 50 rows
+  i [2025-10-25 00:52:16] [INFO] Processing chunk 3: 50 rows
+  i [2025-10-25 00:52:16] [INFO] No more data to process
+  v [2025-10-25 00:52:16] [OKAY] Chunked processing complete:
+  i [2025-10-25 00:52:16] [INFO] Total rows: 150
+  i [2025-10-25 00:52:16] [INFO] Chunks: 3
+  i [2025-10-25 00:52:16] [INFO] Processing time: 0 seconds
+  i [2025-10-25 00:52:16] [INFO] Average rate: 4153 rows/second
+  i [2025-10-25 00:52:16] [INFO] Processing confounds_summary group 'stim' (1
   tables)
-  i [2025-10-25 00:47:06] [INFO] Using chunked processing (file size limit = 50MB
+  i [2025-10-25 00:52:16] [INFO] Using chunked processing (file size limit = 50MB
   < 500MB threshold)
-  i [2025-10-25 00:47:06] [INFO] Processing with file size chunking enabled
-  i [2025-10-25 00:47:06] [INFO] Starting chunked query processing (chunk size:
+  i [2025-10-25 00:52:16] [INFO] Processing with file size chunking enabled
+  i [2025-10-25 00:52:16] [INFO] Starting chunked query processing (chunk size:
   50)
-  i [2025-10-25 00:47:06] [INFO] Query: SELECT * FROM
+  i [2025-10-25 00:52:16] [INFO] Query: SELECT * FROM
   "confounds_summary_01_task_run01_stim"
-  i [2025-10-25 00:47:06] [INFO] Processing chunk 1: 50 rows
-  i [2025-10-25 00:47:06] [INFO] Created output file:
+  i [2025-10-25 00:52:16] [INFO] Processing chunk 1: 50 rows
+  i [2025-10-25 00:52:16] [INFO] Created output file:
   test-db_confounds_summary_stim_chunked_01.csv
-  i [2025-10-25 00:47:06] [INFO] Processing chunk 2: 50 rows
-  i [2025-10-25 00:47:06] [INFO] No more data to process
-  v [2025-10-25 00:47:06] [OKAY] Chunked processing complete:
-  i [2025-10-25 00:47:06] [INFO] Total rows: 100
-  i [2025-10-25 00:47:06] [INFO] Chunks: 2
-  i [2025-10-25 00:47:06] [INFO] Processing time: 0 seconds
-  i [2025-10-25 00:47:06] [INFO] Average rate: 2886 rows/second
-  v [2025-10-25 00:47:06] [OKAY] Export complete!
-  i [2025-10-25 00:47:06] [INFO] Data types exported: 2
-  i [2025-10-25 00:47:06] [INFO] Total rows exported: 250
-  i [2025-10-25 00:47:06] [INFO] Output directory:
-  /tmp/th798/24634860/RtmpkXnxps/test_chunked_output
-  i [2025-10-25 00:47:06] [INFO] Disconnected from eyeris database
-  i [2025-10-25 00:47:07] [INFO] Created output directory:
-  /tmp/th798/24634860/RtmpkXnxps/size_test_output
-  v [2025-10-25 00:47:07] [OKAY] Connected to eyeris database:
-  /tmp/th798/24634860/RtmpkXnxps/bids_size_test/derivatives/size-test.eyerisdb
-  i [2025-10-25 00:47:07] [INFO] Exporting data types: timeseries
-  i [2025-10-25 00:47:07] [INFO] Processing data type: timeseries
-  i [2025-10-25 00:47:07] [INFO] Processing timeseries group 'all' (1 tables)
-  i [2025-10-25 00:47:07] [INFO] Using chunked processing (file size limit =
+  i [2025-10-25 00:52:16] [INFO] Processing chunk 2: 50 rows
+  i [2025-10-25 00:52:16] [INFO] No more data to process
+  v [2025-10-25 00:52:16] [OKAY] Chunked processing complete:
+  i [2025-10-25 00:52:16] [INFO] Total rows: 100
+  i [2025-10-25 00:52:16] [INFO] Chunks: 2
+  i [2025-10-25 00:52:16] [INFO] Processing time: 0 seconds
+  i [2025-10-25 00:52:16] [INFO] Average rate: 3929 rows/second
+  v [2025-10-25 00:52:16] [OKAY] Export complete!
+  i [2025-10-25 00:52:16] [INFO] Data types exported: 2
+  i [2025-10-25 00:52:16] [INFO] Total rows exported: 250
+  i [2025-10-25 00:52:16] [INFO] Output directory:
+  /tmp/th798/24634860/RtmpagBdnO/test_chunked_output
+  i [2025-10-25 00:52:16] [INFO] Disconnected from eyeris database
+  i [2025-10-25 00:52:16] [INFO] Created output directory:
+  /tmp/th798/24634860/RtmpagBdnO/size_test_output
+  v [2025-10-25 00:52:16] [OKAY] Connected to eyeris database:
+  /tmp/th798/24634860/RtmpagBdnO/bids_size_test/derivatives/size-test.eyerisdb
+  i [2025-10-25 00:52:17] [INFO] Exporting data types: timeseries
+  i [2025-10-25 00:52:17] [INFO] Processing data type: timeseries
+  i [2025-10-25 00:52:17] [INFO] Processing timeseries group 'all' (1 tables)
+  i [2025-10-25 00:52:17] [INFO] Using chunked processing (file size limit =
   0.05MB < 500MB threshold)
-  i [2025-10-25 00:47:07] [INFO] Processing with file size chunking enabled
-  i [2025-10-25 00:47:07] [INFO] Starting chunked query processing (chunk size:
+  i [2025-10-25 00:52:17] [INFO] Processing with file size chunking enabled
+  i [2025-10-25 00:52:17] [INFO] Starting chunked query processing (chunk size:
   500)
-  i [2025-10-25 00:47:07] [INFO] Query: SELECT * FROM "timeseries_01_test_run01"
-  i [2025-10-25 00:47:07] [INFO] Processing chunk 1: 500 rows
-  i [2025-10-25 00:47:07] [INFO] Created output file:
+  i [2025-10-25 00:52:17] [INFO] Query: SELECT * FROM "timeseries_01_test_run01"
+  i [2025-10-25 00:52:17] [INFO] Processing chunk 1: 500 rows
+  i [2025-10-25 00:52:17] [INFO] Created output file:
   size-test_timeseries_chunked_01.csv
-  i [2025-10-25 00:47:07] [INFO] Processing chunk 2: 500 rows
-  i [2025-10-25 00:47:07] [INFO] Starting new file due to size limit:
+  i [2025-10-25 00:52:17] [INFO] Processing chunk 2: 500 rows
+  i [2025-10-25 00:52:17] [INFO] Starting new file due to size limit:
   size-test_timeseries_chunked_02.csv
-  i [2025-10-25 00:47:07] [INFO] Created output file:
+  i [2025-10-25 00:52:17] [INFO] Created output file:
   size-test_timeseries_chunked_02.csv
-  i [2025-10-25 00:47:07] [INFO] Processing chunk 3: 500 rows
-  i [2025-10-25 00:47:07] [INFO] Starting new file due to size limit:
+  i [2025-10-25 00:52:17] [INFO] Processing chunk 3: 500 rows
+  i [2025-10-25 00:52:17] [INFO] Starting new file due to size limit:
   size-test_timeseries_chunked_03.csv
-  i [2025-10-25 00:47:08] [INFO] Created output file:
+  i [2025-10-25 00:52:17] [INFO] Created output file:
   size-test_timeseries_chunked_03.csv
-  i [2025-10-25 00:47:08] [INFO] Processing chunk 4: 500 rows
-  i [2025-10-25 00:47:08] [INFO] Starting new file due to size limit:
+  i [2025-10-25 00:52:17] [INFO] Processing chunk 4: 500 rows
+  i [2025-10-25 00:52:17] [INFO] Starting new file due to size limit:
   size-test_timeseries_chunked_04.csv
-  i [2025-10-25 00:47:08] [INFO] Created output file:
+  i [2025-10-25 00:52:17] [INFO] Created output file:
   size-test_timeseries_chunked_04.csv
-  i [2025-10-25 00:47:08] [INFO] No more data to process
-  v [2025-10-25 00:47:08] [OKAY] Chunked processing complete:
-  i [2025-10-25 00:47:08] [INFO] Total rows: 2000
-  i [2025-10-25 00:47:08] [INFO] Chunks: 4
-  i [2025-10-25 00:47:08] [INFO] Processing time: 0.1 seconds
-  i [2025-10-25 00:47:08] [INFO] Average rate: 21768 rows/second
-  i [2025-10-25 00:47:08] [INFO] Finalizing 4 output files with proper
+  i [2025-10-25 00:52:17] [INFO] No more data to process
+  v [2025-10-25 00:52:17] [OKAY] Chunked processing complete:
+  i [2025-10-25 00:52:17] [INFO] Total rows: 2000
+  i [2025-10-25 00:52:17] [INFO] Chunks: 4
+  i [2025-10-25 00:52:17] [INFO] Processing time: 0.1 seconds
+  i [2025-10-25 00:52:17] [INFO] Average rate: 21349 rows/second
+  i [2025-10-25 00:52:17] [INFO] Finalizing 4 output files with proper
   numbering...
-  i [2025-10-25 00:47:08] [INFO] Renamed: size-test_timeseries_chunked_01.csv ->
+  i [2025-10-25 00:52:17] [INFO] Renamed: size-test_timeseries_chunked_01.csv ->
   size-test_timeseries_chunked_01-of-04.csv
-  i [2025-10-25 00:47:08] [INFO] Renamed: size-test_timeseries_chunked_02.csv ->
+  i [2025-10-25 00:52:17] [INFO] Renamed: size-test_timeseries_chunked_02.csv ->
   size-test_timeseries_chunked_02-of-04.csv
-  i [2025-10-25 00:47:08] [INFO] Renamed: size-test_timeseries_chunked_03.csv ->
+  i [2025-10-25 00:52:17] [INFO] Renamed: size-test_timeseries_chunked_03.csv ->
   size-test_timeseries_chunked_03-of-04.csv
-  i [2025-10-25 00:47:08] [INFO] Renamed: size-test_timeseries_chunked_04.csv ->
+  i [2025-10-25 00:52:17] [INFO] Renamed: size-test_timeseries_chunked_04.csv ->
   size-test_timeseries_chunked_04-of-04.csv
-  v [2025-10-25 00:47:08] [OKAY] Export complete!
-  i [2025-10-25 00:47:08] [INFO] Data types exported: 1
-  i [2025-10-25 00:47:08] [INFO] Total rows exported: 2000
-  i [2025-10-25 00:47:08] [INFO] Output directory:
-  /tmp/th798/24634860/RtmpkXnxps/size_test_output
-  i [2025-10-25 00:47:08] [INFO] Disconnected from eyeris database
-  v [2025-10-25 00:47:10] [OKAY] Connected to eyeris database:
-  /tmp/th798/24634860/RtmpkXnxps/test_bids/derivatives/user-test.eyerisdb
-  i [2025-10-25 00:47:11] [INFO] Executing query: SELECT * FROM (SELECT * FROM
+  v [2025-10-25 00:52:17] [OKAY] Export complete!
+  i [2025-10-25 00:52:17] [INFO] Data types exported: 1
+  i [2025-10-25 00:52:17] [INFO] Total rows exported: 2000
+  i [2025-10-25 00:52:17] [INFO] Output directory:
+  /tmp/th798/24634860/RtmpagBdnO/size_test_output
+  i [2025-10-25 00:52:17] [INFO] Disconnected from eyeris database
+  v [2025-10-25 00:52:20] [OKAY] Connected to eyeris database:
+  /tmp/th798/24634860/RtmpagBdnO/test_bids/derivatives/user-test.eyerisdb
+  i [2025-10-25 00:52:21] [INFO] Executing query: SELECT * FROM (SELECT * FROM
   "epochs_002_02_memory_run01") as combined_data WHERE 1=1 AND subject_id = '002'
-  i [2025-10-25 00:47:11] [INFO] Executing query: SELECT * FROM (SELECT * FROM
+  i [2025-10-25 00:52:21] [INFO] Executing query: SELECT * FROM (SELECT * FROM
   "epochs_002_02_memory_run01") as combined_data WHERE 1=1 AND subject_id = '002'
   AND session_id = '02' AND task_name = 'memory'
-  i [2025-10-25 00:47:11] [INFO] Disconnected from eyeris database
-  i [2025-10-25 00:47:14] [INFO] Executing query: SELECT * FROM (SELECT * FROM
+  i [2025-10-25 00:52:21] [INFO] Disconnected from eyeris database
+  i [2025-10-25 00:52:24] [INFO] Executing query: SELECT * FROM (SELECT * FROM
   "epoch_timeseries_005_01_epochtest_run01_prepostprobe") as combined_data WHERE
   1=1 AND subject_id = '005'
-  v [2025-10-25 00:47:17] [OKAY] Running eyeris::load_asc()
-  i [2025-10-25 00:47:17] [INFO] Processing block: block_1
-  v [2025-10-25 00:47:17] [OKAY] Running eyeris::deblink() for block_1
-  v [2025-10-25 00:47:17] [OKAY] Running eyeris::detransient() for block_1
-  v [2025-10-25 00:47:17] [OKAY] Running eyeris::interpolate() for block_1
-  v [2025-10-25 00:47:17] [OKAY] Running eyeris::lpfilt() for block_1
-  ! [2025-10-25 00:47:18] [WARN] Skipping eyeris::downsample() for block_1
-  ! [2025-10-25 00:47:18] [WARN] Skipping eyeris::bin() for block_1
-  ! [2025-10-25 00:47:18] [WARN] Skipping eyeris::detrend() for block_1
-  v [2025-10-25 00:47:18] [OKAY] Running eyeris::zscore() for block_1
-  i [2025-10-25 00:47:18] [INFO] Block processing summary:
-  i [2025-10-25 00:47:18] [INFO] block_1: OK (steps: 6, latest:
+  v [2025-10-25 00:52:26] [OKAY] Running eyeris::load_asc()
+  i [2025-10-25 00:52:26] [INFO] Processing block: block_1
+  v [2025-10-25 00:52:27] [OKAY] Running eyeris::deblink() for block_1
+  v [2025-10-25 00:52:27] [OKAY] Running eyeris::detransient() for block_1
+  v [2025-10-25 00:52:27] [OKAY] Running eyeris::interpolate() for block_1
+  v [2025-10-25 00:52:27] [OKAY] Running eyeris::lpfilt() for block_1
+  ! [2025-10-25 00:52:27] [WARN] Skipping eyeris::downsample() for block_1
+  ! [2025-10-25 00:52:27] [WARN] Skipping eyeris::bin() for block_1
+  ! [2025-10-25 00:52:27] [WARN] Skipping eyeris::detrend() for block_1
+  v [2025-10-25 00:52:27] [OKAY] Running eyeris::zscore() for block_1
+  i [2025-10-25 00:52:27] [INFO] Block processing summary:
+  i [2025-10-25 00:52:27] [INFO] block_1: OK (steps: 6, latest:
   pupil_raw_deblink_detransient_interpolate_lpfilt_z)
-  v [2025-10-25 00:47:18] [OKAY] Running eyeris::summarize_confounds()
-  i [2025-10-25 00:47:19] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  v [2025-10-25 00:52:27] [OKAY] Running eyeris::summarize_confounds()
+  i [2025-10-25 00:52:29] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:20] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:29] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:21] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:30] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:21] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:30] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:21] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:30] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:22] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:31] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:22] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:31] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:23] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:32] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:23] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:32] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:24] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:33] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:24] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:33] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:24] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:33] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:25] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:34] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:25] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:34] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:26] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:26] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:26] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:27] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:36] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  ! [2025-10-25 00:47:31] [WARN] No detrend data found for run-01
+  ! [2025-10-25 00:52:40] [WARN] No detrend data found for run-01
   
   
   processing file: sub-001.Rmd
   output file: sub-001.knit.md
   
-  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-001.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-001.html --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-devel/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-devel/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpkXnxps/rmarkdown-str1d86130cb4a5b.html 
+  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-001.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-001.html --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-devel/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-devel/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpagBdnO/rmarkdown-str2d4fe626a832d.html 
   File  not found in resource path
-  v [2025-10-25 00:47:33] [OKAY] Running eyeris::load_asc()
-  i [2025-10-25 00:47:33] [INFO] Processing block: block_1
-  v [2025-10-25 00:47:33] [OKAY] Running eyeris::deblink() for block_1
-  v [2025-10-25 00:47:33] [OKAY] Running eyeris::detransient() for block_1
-  v [2025-10-25 00:47:33] [OKAY] Running eyeris::interpolate() for block_1
-  v [2025-10-25 00:47:34] [OKAY] Running eyeris::lpfilt() for block_1
-  ! [2025-10-25 00:47:34] [WARN] Skipping eyeris::downsample() for block_1
-  ! [2025-10-25 00:47:34] [WARN] Skipping eyeris::bin() for block_1
-  ! [2025-10-25 00:47:34] [WARN] Skipping eyeris::detrend() for block_1
-  v [2025-10-25 00:47:34] [OKAY] Running eyeris::zscore() for block_1
-  i [2025-10-25 00:47:34] [INFO] Block processing summary:
-  i [2025-10-25 00:47:34] [INFO] block_1: OK (steps: 6, latest:
+  v [2025-10-25 00:52:41] [OKAY] Running eyeris::load_asc()
+  i [2025-10-25 00:52:41] [INFO] Processing block: block_1
+  v [2025-10-25 00:52:41] [OKAY] Running eyeris::deblink() for block_1
+  v [2025-10-25 00:52:41] [OKAY] Running eyeris::detransient() for block_1
+  v [2025-10-25 00:52:42] [OKAY] Running eyeris::interpolate() for block_1
+  v [2025-10-25 00:52:42] [OKAY] Running eyeris::lpfilt() for block_1
+  ! [2025-10-25 00:52:42] [WARN] Skipping eyeris::downsample() for block_1
+  ! [2025-10-25 00:52:42] [WARN] Skipping eyeris::bin() for block_1
+  ! [2025-10-25 00:52:42] [WARN] Skipping eyeris::detrend() for block_1
+  v [2025-10-25 00:52:42] [OKAY] Running eyeris::zscore() for block_1
+  i [2025-10-25 00:52:42] [INFO] Block processing summary:
+  i [2025-10-25 00:52:42] [INFO] block_1: OK (steps: 6, latest:
   pupil_raw_deblink_detransient_interpolate_lpfilt_z)
-  v [2025-10-25 00:47:34] [OKAY] Running eyeris::summarize_confounds()
-  i [2025-10-25 00:47:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  v [2025-10-25 00:52:42] [OKAY] Running eyeris::summarize_confounds()
+  i [2025-10-25 00:52:43] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:36] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:44] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:36] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:44] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:37] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:45] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:37] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:45] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:38] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:46] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:38] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:46] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:39] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:46] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:39] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:47] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:40] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:47] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:40] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:40] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:41] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:49] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:41] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:49] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:41] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:49] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:42] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:50] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:42] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:50] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:42] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:50] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  ! [2025-10-25 00:47:47] [WARN] No detrend data found for run-01
+  ! [2025-10-25 00:52:54] [WARN] No detrend data found for run-01
   
   
   processing file: sub-002.Rmd
   output file: sub-002.knit.md
   
-  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-002.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-002.html --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-devel/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-devel/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpkXnxps/rmarkdown-str1d861504682fb.html 
+  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-002.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-002.html --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-devel/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-devel/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpagBdnO/rmarkdown-str2d4fe6c20258d.html 
   File  not found in resource path
-  v [2025-10-25 00:47:47] [OKAY] Running eyeris::load_asc()
-  i [2025-10-25 00:47:48] [INFO] Processing block: block_1
-  v [2025-10-25 00:47:48] [OKAY] Running eyeris::deblink() for block_1
-  v [2025-10-25 00:47:48] [OKAY] Running eyeris::detransient() for block_1
-  v [2025-10-25 00:47:48] [OKAY] Running eyeris::interpolate() for block_1
-  v [2025-10-25 00:47:48] [OKAY] Running eyeris::lpfilt() for block_1
-  ! [2025-10-25 00:47:48] [WARN] Skipping eyeris::downsample() for block_1
-  ! [2025-10-25 00:47:48] [WARN] Skipping eyeris::bin() for block_1
-  ! [2025-10-25 00:47:48] [WARN] Skipping eyeris::detrend() for block_1
-  v [2025-10-25 00:47:48] [OKAY] Running eyeris::zscore() for block_1
-  i [2025-10-25 00:47:48] [INFO] Block processing summary:
-  i [2025-10-25 00:47:48] [INFO] block_1: OK (steps: 6, latest:
+  v [2025-10-25 00:52:55] [OKAY] Running eyeris::load_asc()
+  i [2025-10-25 00:52:55] [INFO] Processing block: block_1
+  v [2025-10-25 00:52:55] [OKAY] Running eyeris::deblink() for block_1
+  v [2025-10-25 00:52:55] [OKAY] Running eyeris::detransient() for block_1
+  v [2025-10-25 00:52:56] [OKAY] Running eyeris::interpolate() for block_1
+  v [2025-10-25 00:52:56] [OKAY] Running eyeris::lpfilt() for block_1
+  ! [2025-10-25 00:52:56] [WARN] Skipping eyeris::downsample() for block_1
+  ! [2025-10-25 00:52:56] [WARN] Skipping eyeris::bin() for block_1
+  ! [2025-10-25 00:52:56] [WARN] Skipping eyeris::detrend() for block_1
+  v [2025-10-25 00:52:56] [OKAY] Running eyeris::zscore() for block_1
+  i [2025-10-25 00:52:56] [INFO] Block processing summary:
+  i [2025-10-25 00:52:56] [INFO] block_1: OK (steps: 6, latest:
   pupil_raw_deblink_detransient_interpolate_lpfilt_z)
-  v [2025-10-25 00:47:48] [OKAY] Running eyeris::summarize_confounds()
-  i [2025-10-25 00:47:50] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  v [2025-10-25 00:52:56] [OKAY] Running eyeris::summarize_confounds()
+  i [2025-10-25 00:52:57] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:50] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:58] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:51] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:58] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:51] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:59] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:52] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:52:59] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:52] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:00] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:53] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:00] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:53] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:01] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:53] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:01] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:54] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:01] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:54] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:02] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:55] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:02] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:55] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:03] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:55] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:03] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:56] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:03] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:56] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:04] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:56] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:04] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:47:57] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:04] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  ! [2025-10-25 00:48:01] [WARN] No detrend data found for run-01
+  ! [2025-10-25 00:53:08] [WARN] No detrend data found for run-01
   
   
   processing file: sub-003.Rmd
   output file: sub-003.knit.md
   
-  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-003.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-003.html --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-devel/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-devel/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpkXnxps/rmarkdown-str1d8612a17a512.html 
+  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-003.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-003.html --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-devel/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-devel/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpagBdnO/rmarkdown-str2d4fe2619b420.html 
   File  not found in resource path
-  v [2025-10-25 00:48:01] [OKAY] Running eyeris::load_asc()
-  i [2025-10-25 00:48:01] [INFO] Processing block: block_1
-  v [2025-10-25 00:48:01] [OKAY] Running eyeris::deblink() for block_1
-  v [2025-10-25 00:48:01] [OKAY] Running eyeris::detransient() for block_1
-  v [2025-10-25 00:48:02] [OKAY] Running eyeris::interpolate() for block_1
-  v [2025-10-25 00:48:02] [OKAY] Running eyeris::lpfilt() for block_1
-  ! [2025-10-25 00:48:02] [WARN] Skipping eyeris::downsample() for block_1
-  ! [2025-10-25 00:48:02] [WARN] Skipping eyeris::bin() for block_1
-  ! [2025-10-25 00:48:02] [WARN] Skipping eyeris::detrend() for block_1
-  v [2025-10-25 00:48:02] [OKAY] Running eyeris::zscore() for block_1
-  i [2025-10-25 00:48:02] [INFO] Block processing summary:
-  i [2025-10-25 00:48:02] [INFO] block_1: OK (steps: 6, latest:
+  v [2025-10-25 00:53:09] [OKAY] Running eyeris::load_asc()
+  i [2025-10-25 00:53:09] [INFO] Processing block: block_1
+  v [2025-10-25 00:53:09] [OKAY] Running eyeris::deblink() for block_1
+  v [2025-10-25 00:53:09] [OKAY] Running eyeris::detransient() for block_1
+  v [2025-10-25 00:53:10] [OKAY] Running eyeris::interpolate() for block_1
+  v [2025-10-25 00:53:10] [OKAY] Running eyeris::lpfilt() for block_1
+  ! [2025-10-25 00:53:10] [WARN] Skipping eyeris::downsample() for block_1
+  ! [2025-10-25 00:53:10] [WARN] Skipping eyeris::bin() for block_1
+  ! [2025-10-25 00:53:10] [WARN] Skipping eyeris::detrend() for block_1
+  v [2025-10-25 00:53:10] [OKAY] Running eyeris::zscore() for block_1
+  i [2025-10-25 00:53:10] [INFO] Block processing summary:
+  i [2025-10-25 00:53:10] [INFO] block_1: OK (steps: 6, latest:
   pupil_raw_deblink_detransient_interpolate_lpfilt_z)
-  v [2025-10-25 00:48:02] [OKAY] Running eyeris::summarize_confounds()
-  i [2025-10-25 00:48:03] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  v [2025-10-25 00:53:10] [OKAY] Running eyeris::summarize_confounds()
+  i [2025-10-25 00:53:11] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:48:04] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:12] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:48:04] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:12] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:48:05] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:13] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:48:05] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:13] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:48:06] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:14] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:48:06] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:14] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:48:07] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:14] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:48:07] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:15] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:48:07] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:15] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:48:08] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:16] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:48:08] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:16] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:48:09] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:17] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:48:09] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:17] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:48:09] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:17] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:48:10] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:18] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:48:10] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:18] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:48:10] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 00:53:18] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  ! [2025-10-25 00:48:14] [WARN] No detrend data found for run-01
+  ! [2025-10-25 00:53:22] [WARN] No detrend data found for run-01
   
   
   processing file: sub-004.Rmd
   output file: sub-004.knit.md
   
-  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-004.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-004.html --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-devel/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-devel/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpkXnxps/rmarkdown-str1d8611963275c.html 
+  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-004.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-004.html --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-devel/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-devel/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-devel/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpagBdnO/rmarkdown-str2d4fe71cb701d.html 
   File  not found in resource path
-  i [2025-10-25 00:48:18] [INFO] Disconnected from eyeris database
-  v [2025-10-25 00:48:18] [OKAY] Connected to eyeris database:
-  /tmp/th798/24634860/RtmpkXnxps/test_bids/derivatives/test-study.eyerisdb
-  i [2025-10-25 00:48:18] [INFO] Disconnected from eyeris database
-  i [2025-10-25 00:48:19] [INFO] Disconnected from eyeris database
-  v [2025-10-25 00:48:19] [OKAY] Connected to eyeris database:
-  /tmp/th798/24634860/RtmpkXnxps/test_bids_read/derivatives/read-test.eyerisdb
-  i [2025-10-25 00:48:20] [INFO] Disconnected from eyeris database
-  i [2025-10-25 00:48:21] [INFO] Disconnected from eyeris database
-  v [2025-10-25 00:48:21] [OKAY] Connected to eyeris database:
-  /tmp/th798/24634860/RtmpkXnxps/test_bids_size/derivatives/size-test.eyerisdb
-  i [2025-10-25 00:48:22] [INFO] Disconnected from eyeris database
-  i [2025-10-25 00:48:22] [INFO] Disconnected from eyeris database
-  v [2025-10-25 00:48:22] [OKAY] Connected to eyeris database:
-  /tmp/th798/24634860/RtmpkXnxps/test_bids_empty/derivatives/empty-test.eyerisdb
-  ! [2025-10-25 00:48:23] [WARN] No valid tables found in database (after
+  i [2025-10-25 00:53:26] [INFO] Disconnected from eyeris database
+  v [2025-10-25 00:53:26] [OKAY] Connected to eyeris database:
+  /tmp/th798/24634860/RtmpagBdnO/test_bids/derivatives/test-study.eyerisdb
+  i [2025-10-25 00:53:27] [INFO] Disconnected from eyeris database
+  i [2025-10-25 00:53:28] [INFO] Disconnected from eyeris database
+  v [2025-10-25 00:53:28] [OKAY] Connected to eyeris database:
+  /tmp/th798/24634860/RtmpagBdnO/test_bids_read/derivatives/read-test.eyerisdb
+  i [2025-10-25 00:53:28] [INFO] Disconnected from eyeris database
+  i [2025-10-25 00:53:29] [INFO] Disconnected from eyeris database
+  v [2025-10-25 00:53:29] [OKAY] Connected to eyeris database:
+  /tmp/th798/24634860/RtmpagBdnO/test_bids_size/derivatives/size-test.eyerisdb
+  i [2025-10-25 00:53:30] [INFO] Disconnected from eyeris database
+  i [2025-10-25 00:53:30] [INFO] Disconnected from eyeris database
+  v [2025-10-25 00:53:30] [OKAY] Connected to eyeris database:
+  /tmp/th798/24634860/RtmpagBdnO/test_bids_empty/derivatives/empty-test.eyerisdb
+  ! [2025-10-25 00:53:31] [WARN] No valid tables found in database (after
   excluding temp tables)
-  i [2025-10-25 00:48:23] [INFO] Disconnected from eyeris database
-  v [2025-10-25 00:48:23] [OKAY] Running eyeris::load_asc()
-  i [2025-10-25 00:48:23] [INFO] Processing block: block_1
-  v [2025-10-25 00:48:23] [OKAY] Running eyeris::deblink() for block_1
-  v [2025-10-25 00:48:23] [OKAY] Running eyeris::detransient() for block_1
-  v [2025-10-25 00:48:24] [OKAY] Running eyeris::interpolate() for block_1
-  v [2025-10-25 00:48:24] [OKAY] Running eyeris::lpfilt() for block_1
-  ! [2025-10-25 00:48:24] [WARN] Skipping eyeris::downsample() for block_1
-  ! [2025-10-25 00:48:24] [WARN] Skipping eyeris::bin() for block_1
-  ! [2025-10-25 00:48:24] [WARN] Skipping eyeris::detrend() for block_1
-  v [2025-10-25 00:48:24] [OKAY] Running eyeris::zscore() for block_1
-  i [2025-10-25 00:48:24] [INFO] Block processing summary:
-  i [2025-10-25 00:48:24] [INFO] block_1: OK (steps: 6, latest:
+  i [2025-10-25 00:53:31] [INFO] Disconnected from eyeris database
+  v [2025-10-25 00:53:31] [OKAY] Running eyeris::load_asc()
+  i [2025-10-25 00:53:32] [INFO] Processing block: block_1
+  v [2025-10-25 00:53:32] [OKAY] Running eyeris::deblink() for block_1
+  v [2025-10-25 00:53:32] [OKAY] Running eyeris::detransient() for block_1
+  v [2025-10-25 00:53:32] [OKAY] Running eyeris::interpolate() for block_1
+  v [2025-10-25 00:53:32] [OKAY] Running eyeris::lpfilt() for block_1
+  ! [2025-10-25 00:53:32] [WARN] Skipping eyeris::downsample() for block_1
+  ! [2025-10-25 00:53:32] [WARN] Skipping eyeris::bin() for block_1
+  ! [2025-10-25 00:53:32] [WARN] Skipping eyeris::detrend() for block_1
+  v [2025-10-25 00:53:32] [OKAY] Running eyeris::zscore() for block_1
+  i [2025-10-25 00:53:32] [INFO] Block processing summary:
+  i [2025-10-25 00:53:32] [INFO] block_1: OK (steps: 6, latest:
   pupil_raw_deblink_detransient_interpolate_lpfilt_z)
-  v [2025-10-25 00:48:24] [OKAY] Running eyeris::summarize_confounds()
-  v [2025-10-25 00:48:24] [OKAY] Running eyeris::load_asc()
-  i [2025-10-25 00:48:24] [INFO] Binocular data detected. Processing average
+  v [2025-10-25 00:53:32] [OKAY] Running eyeris::summarize_confounds()
+  v [2025-10-25 00:53:33] [OKAY] Running eyeris::load_asc()
+  i [2025-10-25 00:53:33] [INFO] Binocular data detected. Processing average
   mode.
-  i [2025-10-25 00:48:24] [INFO] Processing block: block_1
-  v [2025-10-25 00:48:24] [OKAY] Running eyeris::deblink() for block_1
-  v [2025-10-25 00:48:25] [OKAY] Running eyeris::detransient() for block_1
-  v [2025-10-25 00:48:25] [OKAY] Running eyeris::interpolate() for block_1
-  ! [2025-10-25 00:48:25] [WARN] No NAs detected in pupil data... Skipping
+  i [2025-10-25 00:53:34] [INFO] Processing block: block_1
+  v [2025-10-25 00:53:34] [OKAY] Running eyeris::deblink() for block_1
+  v [2025-10-25 00:53:34] [OKAY] Running eyeris::detransient() for block_1
+  v [2025-10-25 00:53:34] [OKAY] Running eyeris::interpolate() for block_1
+  ! [2025-10-25 00:53:34] [WARN] No NAs detected in pupil data... Skipping
   interpolation!
-  v [2025-10-25 00:48:25] [OKAY] Running eyeris::lpfilt() for block_1
-  ! [2025-10-25 00:48:25] [WARN] Skipping eyeris::downsample() for block_1
-  ! [2025-10-25 00:48:25] [WARN] Skipping eyeris::bin() for block_1
-  ! [2025-10-25 00:48:25] [WARN] Skipping eyeris::detrend() for block_1
-  v [2025-10-25 00:48:25] [OKAY] Running eyeris::zscore() for block_1
-  i [2025-10-25 00:48:25] [INFO] Block processing summary:
-  i [2025-10-25 00:48:25] [INFO] block_1: OK (steps: 6, latest:
+  v [2025-10-25 00:53:34] [OKAY] Running eyeris::lpfilt() for block_1
+  ! [2025-10-25 00:53:34] [WARN] Skipping eyeris::downsample() for block_1
+  ! [2025-10-25 00:53:34] [WARN] Skipping eyeris::bin() for block_1
+  ! [2025-10-25 00:53:34] [WARN] Skipping eyeris::detrend() for block_1
+  v [2025-10-25 00:53:34] [OKAY] Running eyeris::zscore() for block_1
+  i [2025-10-25 00:53:34] [INFO] Block processing summary:
+  i [2025-10-25 00:53:34] [INFO] block_1: OK (steps: 6, latest:
   pupil_raw_deblink_detransient_interpolate_lpfilt_z)
-  v [2025-10-25 00:48:25] [OKAY] Running eyeris::summarize_confounds()
+  v [2025-10-25 00:53:34] [OKAY] Running eyeris::summarize_confounds()
   [ FAIL 4 | WARN 226 | SKIP 0 | PASS 192 ]
   
   == Failed tests ================================================================
@@ -525,10 +525,9 @@
   In addition: Warning messages:
   1: Connection is garbage-collected, use dbDisconnect() to avoid this. 
   2: Connection is garbage-collected, use dbDisconnect() to avoid this. 
+  3: Connection is garbage-collected, use dbDisconnect() to avoid this. 
+  4: Connection is garbage-collected, use dbDisconnect() to avoid this. 
   Execution halted
-  Warning messages:
-  1: Connection is garbage-collected, use dbDisconnect() to avoid this. 
-  2: Connection is garbage-collected, use dbDisconnect() to avoid this. 
 * checking for unstated dependencies in vignettes ... OK
 * checking package vignettes ... OK
 * checking re-building of vignette outputs ... OK
> library(data.table, lib.loc=R.home("library"))
> (sig.diff.dt <- myDiff(Rvers))
Key: <checking>
Empty data.table (0 rows and 3 cols): checking,master,release
> 
> ## If there are significant differences, use git bisect to find when
> ## they started.
> if(nrow(sig.diff.dt)){
+   dt.git <- file.path(task.dir, "data.table.git")
+   unlink(dt.git, recursive=TRUE, force=TRUE)
+   system(paste("cd ~/R/data.table && git fetch --tags"))
+   system(paste("git clone ~/R/data.table", dt.git))
+   release.tag <- gsub(".tar.gz|.*_", "", cargs[["release"]])
+   rev.parse.cmd <- paste(
+     "cd", dt.git, "&& git rev-parse master")
+   master.sha <- system(rev.parse.cmd, intern=TRUE)
+   merge.base.cmd <- paste(
+     "cd", dt.git, "&& git merge-base master", release.tag)
+   merge.base.sha <- system(merge.base.cmd, intern=TRUE)
+   old.sha <- merge.base.sha
+   run_R <- file.path(proj.dir, "install_dt_then_check_dep.R")
+   sig.diff.dt[, first.bad.commit := NA_character_]
+   sig.diff.dt[, comments := NA_character_]
+   for(diff.i in 1:nrow(sig.diff.dt)){
+     sig.diff.row <- sig.diff.dt[diff.i]
+     bisect.cmd <- paste(
+       "cd", dt.git, "&&",
+       "git bisect start &&",
+       "git bisect old", old.sha, "&&",
+       "git bisect new master &&",
+       "git bisect run",
+       R.home('bin/Rscript'),
+       run_R,
+       shQuote(sig.diff.row$checking),
+       sig.diff.row$release,
+       rev.dep.release.tar.gz,
+       release.tag)
+     print(bisect.cmd)
+     bisect.out <- system(bisect.cmd, intern=TRUE)
+     cat(bisect.out,sep="\n")
+     if(is.null(attr(bisect.out,"status"))){
+       first.bad.sha <- nc::capture_all_str(
+         bisect.out,
+         sha="[0-9a-f]+",
+         " is the first new commit")$sha
+       parent.cmd <- paste(
+         "cd ~/R/data.table && git log --pretty=%P -n 1",
+         first.bad.sha)
+       parent.sha <- system(parent.cmd, intern=TRUE)
+       sig.diff.dt[diff.i, first.bad.commit := first.bad.sha]
+       parent.msg <- paste0("parent=", parent.sha)
+       this.comment <- if(parent.sha==old.sha){
+         paste(parent.msg, "same as git bisect old")
+       }else if(first.bad.sha==master.sha){
+         paste("same as git bisect new=master,", parent.msg)
+       }else{
+         parent.msg
+       }
+       sig.diff.dt[diff.i, comments := this.comment]
+     }
+   }
+   ## add CRAN column.
+   sig.diff.dt[, CRAN := {
+     flavor <- get_flavor(Rvers)
+     details <- data.table(flavor=unique(flavor))[, {
+       base <- "https://www.r-project.org/nosvn/R.check/"
+       u <- paste0(base, flavor, "/", rev.dep, "-00check.txt")
+       check.txt <- tempfile()
+       tryCatch({
+         download.file(u, check.txt, quiet=TRUE)
+       }, error=function(e){
+         NULL
+       })
+       check.lines <- if(file.exists(check.txt)){
+         readLines(check.txt,encoding="UTF-8")
+       }else{
+         ""
+       }
+       repl.lines <- gsub("[\u2018\u2019]", "'", check.lines)
+       ##gsub("[‘’]", "'", check.lines) does not work with LC_ALL=C.
+       myStatus(line.vec=repl.lines)
+     }, by=flavor]
+     select.dt <- data.table(flavor, checking)
+     details[select.dt, msg, on=.(flavor, checking)]
+   }]
+   dir.create(file.path(job.dir, Rvers))
+   diffs.csv <- file.path(job.dir, Rvers, "significant_differences.csv")
+   data.table::fwrite(sig.diff.dt, diffs.csv)
+   print(sig.diff.dt)
+ }
> 
WARNING: ignoring environment value of R_HOME

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> cargs <- commandArgs(trailingOnly=TRUE)
> if(length(cargs)==0){
+   ## before running interactively, make sure to start emacs/R with
+   ## environment defined in /scratch/...check_one.sh, particularly
+   ## R_LIBS_USER=/tmp/... otherwise we get error when installing
+   ## data.table.
+   base <- "/scratch/th798/data.table-revdeps/*"
+   cargs <- c(
+     Sys.glob(file.path(base,"deps.csv")),
+     "349",
+     Sys.glob(file.path(base, "data.table_release_*tar.gz")),
+     Sys.glob(file.path(base, "data.table_master_*tar.gz"))
+   )
+ }
> names(cargs) <- c("deps.csv", "task.str", "release", "master")
> dput(cargs)
c(deps.csv = "/scratch/th798/data.table-revdeps/2025-10-25/deps.csv", 
task.str = "439", release = "/scratch/th798/data.table-revdeps/2025-10-25/data.table_release_1.17.8.tar.gz", 
master = "/scratch/th798/data.table-revdeps/2025-10-25/data.table_master_1.17.99.b3acf2ad13848150e87c414f3edcc413c71fd977.tar.gz"
)
> (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers
[1] "/tmp/th798/24634860/R-release/439"
> if(requireNamespace("R.cache"))R.cache::getCachePath()
Loading required namespace: R.cache
[1] "/tmp/th798/24634860/R-release/439/R.cache"
> task.id <- as.integer(cargs[["task.str"]])
> deps.df <- read.csv(cargs[["deps.csv"]])
> (rev.dep <- deps.df$Package[task.id])
[1] "eyeris"
> job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id)
> setwd(task.dir)
> .libPaths()
[1] "/tmp/th798/24634860/R-release/439/library"
[2] "/projects/genomic-ml/R/R-release/library" 
> options(repos=c(#this should be in ~/.Rprofile too.
+   CRAN="http://cloud.r-project.org"))
> print(Sys.time())
[1] "2025-10-25 00:54:45 MST"
> install.time <- system.time({
+   install.packages(rev.dep, dep=TRUE)
+ })
Installing package into '/tmp/th798/24634860/R-release/439/library'
(as 'lib' is unspecified)
also installing the dependencies 'eyelinker', 'gsignal'

trying URL 'http://cloud.r-project.org/src/contrib/eyelinker_0.2.1.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/gsignal_0.3-7.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/eyeris_3.0.1.tar.gz'
* installing *source* package 'eyelinker' ...
** this is package 'eyelinker' version '0.2.1'
** package 'eyelinker' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (eyelinker)
* installing *source* package 'gsignal' ...
** this is package 'gsignal' version '0.3-7'
** package 'gsignal' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c RcppExports.cpp -o RcppExports.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c conv2d.cpp -o conv2d.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c filter.cpp -o filter.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c fwht.cpp -o fwht.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c remez.cpp -o remez.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c sosfilt.cpp -o sosfilt.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c upfirdn.cpp -o upfirdn.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o gsignal.so RcppExports.o conv2d.o filter.o fwht.o remez.o sosfilt.o upfirdn.o
installing to /tmp/th798/24634860/R-release/439/library/00LOCK-gsignal/00new/gsignal/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gsignal)
* installing *source* package 'eyeris' ...
** this is package 'eyeris' version '3.0.1'
** package 'eyeris' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (eyeris)

The downloaded source packages are in
	'/tmp/th798/24634860/Rtmpohv5j4/downloaded_packages'
> cat("Time to install revdep:\n")
Time to install revdep:
> print(install.time)
   user  system elapsed 
 72.243   3.770  83.769 
> print(Sys.time())
[1] "2025-10-25 00:56:08 MST"
> downloaded_packages <- file.path(
+   tempdir(),
+   "downloaded_packages")
> dl.glob <- file.path(
+   downloaded_packages,
+   paste0(rev.dep,"_*.tar.gz"))
> rev.dep.dl.row <- cbind(rev.dep, Sys.glob(dl.glob))
> colnames(rev.dep.dl.row) <- c("pkg","path")
> rev.dep.release.tar.gz <- normalizePath(rev.dep.dl.row[,"path"], mustWork=TRUE)
> pkg.Rcheck <- paste0(rev.dep, ".Rcheck")
> 
> proj.dir <- "~/genomic-ml/data.table-revdeps"
> source(file.path(proj.dir, "myStatus.R"))
> Rvers <- gsub("[()]", "", gsub(" ", "_", R.version[["version.string"]]))
> dir.create(Rvers, showWarnings=FALSE)
> Rcheck.list <- list()
> for(dt.version.short in c("release", "master")){
+   dt.tar.gz <- cargs[[dt.version.short]]
+   dt.version <- gsub(".tar.gz|/.*?_", "", dt.tar.gz)
+   print(Sys.time())
+   install.packages(dt.tar.gz, repos=NULL)
+   print(Sys.time())
+   check.cmd <- get_check_cmd(rev.dep.release.tar.gz)
+   system(check.cmd)
+   print(Sys.time())
+   dest.Rcheck <- file.path(
+     Rvers,
+     paste0(dt.version, ".Rcheck"))
+   unlink(dest.Rcheck, recursive=TRUE)
+   file.rename(pkg.Rcheck, dest.Rcheck)
+   Rcheck.list[[dt.version]] <- file.path(dest.Rcheck, "00check.log")
+ }
[1] "2025-10-25 00:56:09 MST"
Installing package into '/tmp/th798/24634860/R-release/439/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** this is package 'data.table' version '1.17.8'
** package 'data.table' successfully unpacked and MD5 sums checked
** using staged installation
zlib 1.2.13 is available ok
* checking if R installation supports OpenMP without any extra hints... yes
** libs
using C compiler: 'gcc (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c assign.c -o assign.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c between.c -o between.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c bmerge.c -o bmerge.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c chmatch.c -o chmatch.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c cj.c -o cj.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c coalesce.c -o coalesce.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c dogroups.c -o dogroups.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fastmean.c -o fastmean.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fcast.c -o fcast.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fifelse.c -o fifelse.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fmelt.c -o fmelt.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c forder.c -o forder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frank.c -o frank.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fread.c -o fread.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c freadR.c -o freadR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c froll.c -o froll.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frollR.c -o frollR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frolladaptive.c -o frolladaptive.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fsort.c -o fsort.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwrite.c -o fwrite.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwriteR.c -o fwriteR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c gsumm.c -o gsumm.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c idatetime.c -o idatetime.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ijoin.c -o ijoin.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c init.c -o init.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c inrange.c -o inrange.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nafill.c -o nafill.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c negate.c -o negate.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nqrecreateindices.c -o nqrecreateindices.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c openmp-utils.c -o openmp-utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c programming.c -o programming.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c quickselect.c -o quickselect.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c rbindlist.c -o rbindlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c reorder.c -o reorder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c shift.c -o shift.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c snprintf.c -o snprintf.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c subset.c -o subset.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c transpose.c -o transpose.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c types.c -o types.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c uniqlist.c -o uniqlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c utils.c -o utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c vecseq.c -o vecseq.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c wrappers.c -o wrappers.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include
PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi
installing to /tmp/th798/24634860/R-release/439/library/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (data.table)
[1] "2025-10-25 00:56:37 MST"
* using log directory '/tmp/th798/24634860/R-release/439/eyeris.Rcheck'
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Spack GCC) 12.2.0
    GNU Fortran (Spack GCC) 12.2.0
* running under: Red Hat Enterprise Linux 8.10 (Ootpa)
* using session charset: ASCII
* checking for file 'eyeris/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'eyeris' version '3.0.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'eyeris' can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   1.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
epoch 8.659  0.098   8.827
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(eyeris)
  
  eyeris v3.0.1 - Lumpy Space Princess <U+A4B0><U+2022><U+1D17><U+2022><U+FF61><U+A4B1><U+06F6>
  Welcome! Type ?`eyeris` to get started.
  
  > 
  > test_check("eyeris")
  i [2025-10-25 00:59:06] [INFO] Created output directory:
  /tmp/th798/24634860/Rtmpt8pqLX/test_chunked_output
  v [2025-10-25 00:59:07] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/Rtmpt8pqLX/bids_test/derivatives/test-db.eyerisdb
  i [2025-10-25 00:59:07] [INFO] Exporting data types: confounds_summary
  i [2025-10-25 00:59:07] [INFO] Processing data type: confounds_summary
  i [2025-10-25 00:59:07] [INFO] Grouping tables by epoch label...
  i [2025-10-25 00:59:07] [INFO] Found 1 epoch label groups for
  confounds_summary: _nolabel
  i [2025-10-25 00:59:07] [INFO] Analyzing column structures within epoch group
  '_nolabel'...
  i [2025-10-25 00:59:07] [INFO] Found 2 column-compatible groups within
  '_nolabel': goal, stim
  i [2025-10-25 00:59:07] [INFO] Processing confounds_summary group 'goal' (2
  tables)
  i [2025-10-25 00:59:07] [INFO] Using chunked processing (file size limit = 50MB
  < 500MB threshold)
  i [2025-10-25 00:59:07] [INFO] Processing with file size chunking enabled
  i [2025-10-25 00:59:07] [INFO] Starting chunked query processing (chunk size:
  50)
  i [2025-10-25 00:59:07] [INFO] Query: SELECT * FROM
  "confounds_summary_01_task_run01_goal" UNION ALL SELECT * FROM
  "confounds_summary_02_task_run01_goal"
  i [2025-10-25 00:59:07] [INFO] Processing chunk 1: 50 rows
  i [2025-10-25 00:59:07] [INFO] Created output file:
  test-db_confounds_summary_goal_chunked_01.csv
  i [2025-10-25 00:59:07] [INFO] Processing chunk 2: 50 rows
  i [2025-10-25 00:59:07] [INFO] Processing chunk 3: 50 rows
  i [2025-10-25 00:59:07] [INFO] No more data to process
  v [2025-10-25 00:59:07] [OKAY] Chunked processing complete:
  i [2025-10-25 00:59:07] [INFO] Total rows: 150
  i [2025-10-25 00:59:07] [INFO] Chunks: 3
  i [2025-10-25 00:59:07] [INFO] Processing time: 0 seconds
  i [2025-10-25 00:59:07] [INFO] Average rate: 4562 rows/second
  i [2025-10-25 00:59:07] [INFO] Processing confounds_summary group 'stim' (1
  tables)
  i [2025-10-25 00:59:07] [INFO] Using chunked processing (file size limit = 50MB
  < 500MB threshold)
  i [2025-10-25 00:59:07] [INFO] Processing with file size chunking enabled
  i [2025-10-25 00:59:07] [INFO] Starting chunked query processing (chunk size:
  50)
  i [2025-10-25 00:59:07] [INFO] Query: SELECT * FROM
  "confounds_summary_01_task_run01_stim"
  i [2025-10-25 00:59:07] [INFO] Processing chunk 1: 50 rows
  i [2025-10-25 00:59:07] [INFO] Created output file:
  test-db_confounds_summary_stim_chunked_01.csv
  i [2025-10-25 00:59:07] [INFO] Processing chunk 2: 50 rows
  i [2025-10-25 00:59:07] [INFO] No more data to process
  v [2025-10-25 00:59:07] [OKAY] Chunked processing complete:
  i [2025-10-25 00:59:07] [INFO] Total rows: 100
  i [2025-10-25 00:59:07] [INFO] Chunks: 2
  i [2025-10-25 00:59:08] [INFO] Processing time: 0 seconds
  i [2025-10-25 00:59:08] [INFO] Average rate: 3916 rows/second
  v [2025-10-25 00:59:08] [OKAY] Export complete!
  i [2025-10-25 00:59:08] [INFO] Data types exported: 2
  i [2025-10-25 00:59:08] [INFO] Total rows exported: 250
  i [2025-10-25 00:59:08] [INFO] Output directory:
  /tmp/th798/24634860/Rtmpt8pqLX/test_chunked_output
  i [2025-10-25 00:59:08] [INFO] Disconnected from eyeris database
  i [2025-10-25 00:59:08] [INFO] Created output directory:
  /tmp/th798/24634860/Rtmpt8pqLX/size_test_output
  v [2025-10-25 00:59:08] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/Rtmpt8pqLX/bids_size_test/derivatives/size-test.eyerisdb
  i [2025-10-25 00:59:09] [INFO] Exporting data types: timeseries
  i [2025-10-25 00:59:09] [INFO] Processing data type: timeseries
  i [2025-10-25 00:59:09] [INFO] Processing timeseries group 'all' (1 tables)
  i [2025-10-25 00:59:09] [INFO] Using chunked processing (file size limit =
  0.05MB < 500MB threshold)
  i [2025-10-25 00:59:09] [INFO] Processing with file size chunking enabled
  i [2025-10-25 00:59:09] [INFO] Starting chunked query processing (chunk size:
  500)
  i [2025-10-25 00:59:09] [INFO] Query: SELECT * FROM "timeseries_01_test_run01"
  i [2025-10-25 00:59:09] [INFO] Processing chunk 1: 500 rows
  i [2025-10-25 00:59:09] [INFO] Created output file:
  size-test_timeseries_chunked_01.csv
  i [2025-10-25 00:59:09] [INFO] Processing chunk 2: 500 rows
  i [2025-10-25 00:59:09] [INFO] Starting new file due to size limit:
  size-test_timeseries_chunked_02.csv
  i [2025-10-25 00:59:09] [INFO] Created output file:
  size-test_timeseries_chunked_02.csv
  i [2025-10-25 00:59:09] [INFO] Processing chunk 3: 500 rows
  i [2025-10-25 00:59:09] [INFO] Starting new file due to size limit:
  size-test_timeseries_chunked_03.csv
  i [2025-10-25 00:59:09] [INFO] Created output file:
  size-test_timeseries_chunked_03.csv
  i [2025-10-25 00:59:09] [INFO] Processing chunk 4: 500 rows
  i [2025-10-25 00:59:09] [INFO] Starting new file due to size limit:
  size-test_timeseries_chunked_04.csv
  i [2025-10-25 00:59:09] [INFO] Created output file:
  size-test_timeseries_chunked_04.csv
  i [2025-10-25 00:59:09] [INFO] No more data to process
  v [2025-10-25 00:59:09] [OKAY] Chunked processing complete:
  i [2025-10-25 00:59:09] [INFO] Total rows: 2000
  i [2025-10-25 00:59:09] [INFO] Chunks: 4
  i [2025-10-25 00:59:09] [INFO] Processing time: 0.1 seconds
  i [2025-10-25 00:59:09] [INFO] Average rate: 21692 rows/second
  i [2025-10-25 00:59:09] [INFO] Finalizing 4 output files with proper
  numbering...
  i [2025-10-25 00:59:09] [INFO] Renamed: size-test_timeseries_chunked_01.csv ->
  size-test_timeseries_chunked_01-of-04.csv
  i [2025-10-25 00:59:09] [INFO] Renamed: size-test_timeseries_chunked_02.csv ->
  size-test_timeseries_chunked_02-of-04.csv
  i [2025-10-25 00:59:09] [INFO] Renamed: size-test_timeseries_chunked_03.csv ->
  size-test_timeseries_chunked_03-of-04.csv
  i [2025-10-25 00:59:09] [INFO] Renamed: size-test_timeseries_chunked_04.csv ->
  size-test_timeseries_chunked_04-of-04.csv
  v [2025-10-25 00:59:09] [OKAY] Export complete!
  i [2025-10-25 00:59:09] [INFO] Data types exported: 1
  i [2025-10-25 00:59:09] [INFO] Total rows exported: 2000
  i [2025-10-25 00:59:09] [INFO] Output directory:
  /tmp/th798/24634860/Rtmpt8pqLX/size_test_output
  i [2025-10-25 00:59:09] [INFO] Disconnected from eyeris database
  v [2025-10-25 00:59:11] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/Rtmpt8pqLX/test_bids/derivatives/user-test.eyerisdb
  i [2025-10-25 00:59:12] [INFO] Executing query: SELECT * FROM (SELECT * FROM
  "epochs_002_02_memory_run01") as combined_data WHERE 1=1 AND subject_id = '002'
  i [2025-10-25 00:59:13] [INFO] Executing query: SELECT * FROM (SELECT * FROM
  "epochs_002_02_memory_run01") as combined_data WHERE 1=1 AND subject_id = '002'
  AND session_id = '02' AND task_name = 'memory'
  i [2025-10-25 00:59:13] [INFO] Disconnected from eyeris database
  i [2025-10-25 00:59:16] [INFO] Executing query: SELECT * FROM (SELECT * FROM
  "epoch_timeseries_005_01_epochtest_run01_prepostprobe") as combined_data WHERE
  1=1 AND subject_id = '005'
  v [2025-10-25 00:59:17] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 00:59:18] [INFO] Processing block: block_1
  v [2025-10-25 00:59:18] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 00:59:18] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 00:59:18] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 00:59:18] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 00:59:18] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 00:59:18] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 00:59:18] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 00:59:18] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 00:59:18] [INFO] Block processing summary:
  i [2025-10-25 00:59:18] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 00:59:18] [OKAY] Running eyeris::summarize_confounds()
  i [2025-10-25 00:59:20] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:20] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:21] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:21] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:22] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:22] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:23] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:23] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:24] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:24] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:24] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:25] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:25] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:26] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:26] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:26] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:27] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:27] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2025-10-25 00:59:32] [WARN] No detrend data found for run-01
  
  
  processing file: sub-001.Rmd
  output file: sub-001.knit.md
  
  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-001.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-001.html --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-release/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-release/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/Rtmpt8pqLX/rmarkdown-str404551ae11511.html 
  File  not found in resource path
  v [2025-10-25 00:59:32] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 00:59:33] [INFO] Processing block: block_1
  v [2025-10-25 00:59:33] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 00:59:33] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 00:59:33] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 00:59:33] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 00:59:33] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 00:59:33] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 00:59:33] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 00:59:33] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 00:59:33] [INFO] Block processing summary:
  i [2025-10-25 00:59:33] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 00:59:33] [OKAY] Running eyeris::summarize_confounds()
  i [2025-10-25 00:59:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:36] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:36] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:36] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:37] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:37] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:38] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:38] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:39] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:39] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:39] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:40] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:40] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:41] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:41] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:41] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:41] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2025-10-25 00:59:45] [WARN] No detrend data found for run-01
  
  
  processing file: sub-002.Rmd
  output file: sub-002.knit.md
  
  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-002.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-002.html --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-release/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-release/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/Rtmpt8pqLX/rmarkdown-str404556912c775.html 
  File  not found in resource path
  v [2025-10-25 00:59:46] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 00:59:46] [INFO] Processing block: block_1
  v [2025-10-25 00:59:46] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 00:59:46] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 00:59:46] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 00:59:46] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 00:59:46] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 00:59:46] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 00:59:46] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 00:59:46] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 00:59:46] [INFO] Block processing summary:
  i [2025-10-25 00:59:46] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 00:59:46] [OKAY] Running eyeris::summarize_confounds()
  i [2025-10-25 00:59:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:49] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:49] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:50] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:50] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:51] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:51] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:52] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:52] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:52] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:53] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:53] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:54] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:54] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:54] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:55] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 00:59:55] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2025-10-25 00:59:59] [WARN] No detrend data found for run-01
  
  
  processing file: sub-003.Rmd
  output file: sub-003.knit.md
  
  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-003.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-003.html --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-release/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-release/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/Rtmpt8pqLX/rmarkdown-str40455579081f5.html 
  File  not found in resource path
  v [2025-10-25 00:59:59] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 00:59:59] [INFO] Processing block: block_1
  v [2025-10-25 00:59:59] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 00:59:59] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 00:59:59] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 00:59:59] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 01:00:00] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 01:00:00] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 01:00:00] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 01:00:00] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 01:00:00] [INFO] Block processing summary:
  i [2025-10-25 01:00:00] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 01:00:00] [OKAY] Running eyeris::summarize_confounds()
  i [2025-10-25 01:00:01] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:00:02] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:00:02] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:00:02] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:00:03] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:00:03] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:00:04] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:00:04] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:00:05] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:00:05] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:00:06] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:00:06] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:00:06] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:00:07] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:00:07] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:00:07] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:00:08] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:00:08] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2025-10-25 01:00:12] [WARN] No detrend data found for run-01
  
  
  processing file: sub-004.Rmd
  output file: sub-004.knit.md
  
  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-004.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-004.html --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-release/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-release/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/Rtmpt8pqLX/rmarkdown-str404555cd5f266.html 
  File  not found in resource path
  i [2025-10-25 01:00:15] [INFO] Disconnected from eyeris database
  v [2025-10-25 01:00:16] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/Rtmpt8pqLX/test_bids/derivatives/test-study.eyerisdb
  i [2025-10-25 01:00:16] [INFO] Disconnected from eyeris database
  i [2025-10-25 01:00:17] [INFO] Disconnected from eyeris database
  v [2025-10-25 01:00:17] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/Rtmpt8pqLX/test_bids_read/derivatives/read-test.eyerisdb
  i [2025-10-25 01:00:18] [INFO] Disconnected from eyeris database
  i [2025-10-25 01:00:19] [INFO] Disconnected from eyeris database
  v [2025-10-25 01:00:19] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/Rtmpt8pqLX/test_bids_size/derivatives/size-test.eyerisdb
  i [2025-10-25 01:00:19] [INFO] Disconnected from eyeris database
  i [2025-10-25 01:00:20] [INFO] Disconnected from eyeris database
  v [2025-10-25 01:00:20] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/Rtmpt8pqLX/test_bids_empty/derivatives/empty-test.eyerisdb
  ! [2025-10-25 01:00:20] [WARN] No valid tables found in database (after
  excluding temp tables)
  i [2025-10-25 01:00:20] [INFO] Disconnected from eyeris database
  v [2025-10-25 01:00:21] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 01:00:21] [INFO] Processing block: block_1
  v [2025-10-25 01:00:21] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 01:00:21] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 01:00:21] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 01:00:21] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 01:00:21] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 01:00:21] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 01:00:21] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 01:00:21] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 01:00:21] [INFO] Block processing summary:
  i [2025-10-25 01:00:21] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 01:00:21] [OKAY] Running eyeris::summarize_confounds()
  v [2025-10-25 01:00:22] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 01:00:22] [INFO] Binocular data detected. Processing average
  mode.
  i [2025-10-25 01:00:22] [INFO] Processing block: block_1
  v [2025-10-25 01:00:22] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 01:00:22] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 01:00:22] [OKAY] Running eyeris::interpolate() for block_1
  ! [2025-10-25 01:00:22] [WARN] No NAs detected in pupil data... Skipping
  interpolation!
  v [2025-10-25 01:00:22] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 01:00:22] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 01:00:22] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 01:00:22] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 01:00:22] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 01:00:22] [INFO] Block processing summary:
  i [2025-10-25 01:00:22] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 01:00:22] [OKAY] Running eyeris::summarize_confounds()
  [ FAIL 4 | WARN 226 | SKIP 0 | PASS 192 ]
  
  == Failed tests ================================================================
  -- Failure ('test-parallel-database.R:10:7'): manual parallel processing flag enables temporary databases --
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    pandoc document conversion failed with error 99
  Backtrace:
      x
   1. +-withr::with_envvar(...) at test-parallel-database.R:4:3
   2. | \-base::force(code)
   3. \-testthat::expect_no_error(...) at test-parallel-database.R:9:5
  -- Failure ('test-parallel-database.R:32:7'): SLURM environment variables are detected for parallel processing --
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    pandoc document conversion failed with error 99
  Backtrace:
      x
   1. +-withr::with_envvar(...) at test-parallel-database.R:28:3
   2. | \-base::force(code)
   3. \-testthat::expect_no_error(...) at test-parallel-database.R:31:5
  -- Failure ('test-parallel-database.R:52:7'): PBS environment variables are detected for parallel processing --
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    pandoc document conversion failed with error 99
  Backtrace:
      x
   1. +-withr::with_envvar(...) at test-parallel-database.R:48:3
   2. | \-base::force(code)
   3. \-testthat::expect_no_error(...) at test-parallel-database.R:51:5
  -- Failure ('test-parallel-database.R:71:5'): normal database operation works without parallel processing --
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    pandoc document conversion failed with error 99
  
  [ FAIL 4 | WARN 226 | SKIP 0 | PASS 192 ]
  Error: Test failures
  In addition: Warning messages:
  1: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  2: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  3: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  Execution halted
  Warning message:
  Connection is garbage-collected, use dbDisconnect() to avoid this. 
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  '/tmp/th798/24634860/R-release/439/eyeris.Rcheck/00check.log'
for details.

[1] "2025-10-25 01:01:05 MST"
[1] "2025-10-25 01:01:05 MST"
Installing package into '/tmp/th798/24634860/R-release/439/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** this is package 'data.table' version '1.17.99'
** using staged installation
zlib 1.2.13 is available ok
* checking if R installation supports OpenMP without any extra hints... yes
** libs
using C compiler: 'gcc (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c assign.c -o assign.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c between.c -o between.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c bmerge.c -o bmerge.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c chmatch.c -o chmatch.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c cj.c -o cj.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c coalesce.c -o coalesce.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c dogroups.c -o dogroups.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fastmean.c -o fastmean.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fcast.c -o fcast.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fifelse.c -o fifelse.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fmelt.c -o fmelt.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c forder.c -o forder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frank.c -o frank.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fread.c -o fread.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c freadR.c -o freadR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c froll.c -o froll.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frollR.c -o frollR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frolladaptive.c -o frolladaptive.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frollapply.c -o frollapply.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fsort.c -o fsort.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwrite.c -o fwrite.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwriteR.c -o fwriteR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c gsumm.c -o gsumm.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c idatetime.c -o idatetime.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ijoin.c -o ijoin.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c init.c -o init.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c inrange.c -o inrange.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c mergelist.c -o mergelist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nafill.c -o nafill.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c negate.c -o negate.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nqrecreateindices.c -o nqrecreateindices.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c openmp-utils.c -o openmp-utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c programming.c -o programming.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c quickselect.c -o quickselect.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c rbindlist.c -o rbindlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c reorder.c -o reorder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c shellsort.c -o shellsort.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c shift.c -o shift.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c snprintf.c -o snprintf.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c subset.c -o subset.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c transpose.c -o transpose.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c types.c -o types.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c uniqlist.c -o uniqlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c utils.c -o utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c vecseq.c -o vecseq.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c wrappers.c -o wrappers.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include
PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi
installing to /tmp/th798/24634860/R-release/439/library/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (data.table)
[1] "2025-10-25 01:01:34 MST"
* using log directory '/tmp/th798/24634860/R-release/439/eyeris.Rcheck'
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Spack GCC) 12.2.0
    GNU Fortran (Spack GCC) 12.2.0
* running under: Red Hat Enterprise Linux 8.10 (Ootpa)
* using session charset: ASCII
* checking for file 'eyeris/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'eyeris' version '3.0.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'eyeris' can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   1.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
      user system elapsed
epoch 8.63  0.102   8.783
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(eyeris)
  
  eyeris v3.0.1 - Lumpy Space Princess <U+A4B0><U+2022><U+1D17><U+2022><U+FF61><U+A4B1><U+06F6>
  Welcome! Type ?`eyeris` to get started.
  
  > 
  > test_check("eyeris")
  i [2025-10-25 01:04:01] [INFO] Created output directory:
  /tmp/th798/24634860/RtmpfSfMz2/test_chunked_output
  v [2025-10-25 01:04:01] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpfSfMz2/bids_test/derivatives/test-db.eyerisdb
  i [2025-10-25 01:04:01] [INFO] Exporting data types: confounds_summary
  i [2025-10-25 01:04:01] [INFO] Processing data type: confounds_summary
  i [2025-10-25 01:04:01] [INFO] Grouping tables by epoch label...
  i [2025-10-25 01:04:01] [INFO] Found 1 epoch label groups for
  confounds_summary: _nolabel
  i [2025-10-25 01:04:01] [INFO] Analyzing column structures within epoch group
  '_nolabel'...
  i [2025-10-25 01:04:01] [INFO] Found 2 column-compatible groups within
  '_nolabel': goal, stim
  i [2025-10-25 01:04:01] [INFO] Processing confounds_summary group 'goal' (2
  tables)
  i [2025-10-25 01:04:01] [INFO] Using chunked processing (file size limit = 50MB
  < 500MB threshold)
  i [2025-10-25 01:04:01] [INFO] Processing with file size chunking enabled
  i [2025-10-25 01:04:01] [INFO] Starting chunked query processing (chunk size:
  50)
  i [2025-10-25 01:04:01] [INFO] Query: SELECT * FROM
  "confounds_summary_01_task_run01_goal" UNION ALL SELECT * FROM
  "confounds_summary_02_task_run01_goal"
  i [2025-10-25 01:04:01] [INFO] Processing chunk 1: 50 rows
  i [2025-10-25 01:04:01] [INFO] Created output file:
  test-db_confounds_summary_goal_chunked_01.csv
  i [2025-10-25 01:04:01] [INFO] Processing chunk 2: 50 rows
  i [2025-10-25 01:04:01] [INFO] Processing chunk 3: 50 rows
  i [2025-10-25 01:04:01] [INFO] No more data to process
  v [2025-10-25 01:04:01] [OKAY] Chunked processing complete:
  i [2025-10-25 01:04:01] [INFO] Total rows: 150
  i [2025-10-25 01:04:01] [INFO] Chunks: 3
  i [2025-10-25 01:04:01] [INFO] Processing time: 0 seconds
  i [2025-10-25 01:04:01] [INFO] Average rate: 4739 rows/second
  i [2025-10-25 01:04:01] [INFO] Processing confounds_summary group 'stim' (1
  tables)
  i [2025-10-25 01:04:01] [INFO] Using chunked processing (file size limit = 50MB
  < 500MB threshold)
  i [2025-10-25 01:04:01] [INFO] Processing with file size chunking enabled
  i [2025-10-25 01:04:01] [INFO] Starting chunked query processing (chunk size:
  50)
  i [2025-10-25 01:04:01] [INFO] Query: SELECT * FROM
  "confounds_summary_01_task_run01_stim"
  i [2025-10-25 01:04:01] [INFO] Processing chunk 1: 50 rows
  i [2025-10-25 01:04:01] [INFO] Created output file:
  test-db_confounds_summary_stim_chunked_01.csv
  i [2025-10-25 01:04:01] [INFO] Processing chunk 2: 50 rows
  i [2025-10-25 01:04:01] [INFO] No more data to process
  v [2025-10-25 01:04:01] [OKAY] Chunked processing complete:
  i [2025-10-25 01:04:01] [INFO] Total rows: 100
  i [2025-10-25 01:04:01] [INFO] Chunks: 2
  i [2025-10-25 01:04:01] [INFO] Processing time: 0 seconds
  i [2025-10-25 01:04:01] [INFO] Average rate: 4034 rows/second
  v [2025-10-25 01:04:01] [OKAY] Export complete!
  i [2025-10-25 01:04:01] [INFO] Data types exported: 2
  i [2025-10-25 01:04:01] [INFO] Total rows exported: 250
  i [2025-10-25 01:04:01] [INFO] Output directory:
  /tmp/th798/24634860/RtmpfSfMz2/test_chunked_output
  i [2025-10-25 01:04:02] [INFO] Disconnected from eyeris database
  i [2025-10-25 01:04:02] [INFO] Created output directory:
  /tmp/th798/24634860/RtmpfSfMz2/size_test_output
  v [2025-10-25 01:04:02] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpfSfMz2/bids_size_test/derivatives/size-test.eyerisdb
  i [2025-10-25 01:04:03] [INFO] Exporting data types: timeseries
  i [2025-10-25 01:04:03] [INFO] Processing data type: timeseries
  i [2025-10-25 01:04:03] [INFO] Processing timeseries group 'all' (1 tables)
  i [2025-10-25 01:04:03] [INFO] Using chunked processing (file size limit =
  0.05MB < 500MB threshold)
  i [2025-10-25 01:04:03] [INFO] Processing with file size chunking enabled
  i [2025-10-25 01:04:03] [INFO] Starting chunked query processing (chunk size:
  500)
  i [2025-10-25 01:04:03] [INFO] Query: SELECT * FROM "timeseries_01_test_run01"
  i [2025-10-25 01:04:03] [INFO] Processing chunk 1: 500 rows
  i [2025-10-25 01:04:03] [INFO] Created output file:
  size-test_timeseries_chunked_01.csv
  i [2025-10-25 01:04:03] [INFO] Processing chunk 2: 500 rows
  i [2025-10-25 01:04:03] [INFO] Starting new file due to size limit:
  size-test_timeseries_chunked_02.csv
  i [2025-10-25 01:04:03] [INFO] Created output file:
  size-test_timeseries_chunked_02.csv
  i [2025-10-25 01:04:03] [INFO] Processing chunk 3: 500 rows
  i [2025-10-25 01:04:03] [INFO] Starting new file due to size limit:
  size-test_timeseries_chunked_03.csv
  i [2025-10-25 01:04:03] [INFO] Created output file:
  size-test_timeseries_chunked_03.csv
  i [2025-10-25 01:04:03] [INFO] Processing chunk 4: 500 rows
  i [2025-10-25 01:04:03] [INFO] Starting new file due to size limit:
  size-test_timeseries_chunked_04.csv
  i [2025-10-25 01:04:03] [INFO] Created output file:
  size-test_timeseries_chunked_04.csv
  i [2025-10-25 01:04:03] [INFO] No more data to process
  v [2025-10-25 01:04:03] [OKAY] Chunked processing complete:
  i [2025-10-25 01:04:03] [INFO] Total rows: 2000
  i [2025-10-25 01:04:03] [INFO] Chunks: 4
  i [2025-10-25 01:04:03] [INFO] Processing time: 0.1 seconds
  i [2025-10-25 01:04:03] [INFO] Average rate: 21787 rows/second
  i [2025-10-25 01:04:03] [INFO] Finalizing 4 output files with proper
  numbering...
  i [2025-10-25 01:04:03] [INFO] Renamed: size-test_timeseries_chunked_01.csv ->
  size-test_timeseries_chunked_01-of-04.csv
  i [2025-10-25 01:04:03] [INFO] Renamed: size-test_timeseries_chunked_02.csv ->
  size-test_timeseries_chunked_02-of-04.csv
  i [2025-10-25 01:04:03] [INFO] Renamed: size-test_timeseries_chunked_03.csv ->
  size-test_timeseries_chunked_03-of-04.csv
  i [2025-10-25 01:04:03] [INFO] Renamed: size-test_timeseries_chunked_04.csv ->
  size-test_timeseries_chunked_04-of-04.csv
  v [2025-10-25 01:04:03] [OKAY] Export complete!
  i [2025-10-25 01:04:03] [INFO] Data types exported: 1
  i [2025-10-25 01:04:03] [INFO] Total rows exported: 2000
  i [2025-10-25 01:04:03] [INFO] Output directory:
  /tmp/th798/24634860/RtmpfSfMz2/size_test_output
  i [2025-10-25 01:04:03] [INFO] Disconnected from eyeris database
  v [2025-10-25 01:04:05] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpfSfMz2/test_bids/derivatives/user-test.eyerisdb
  i [2025-10-25 01:04:06] [INFO] Executing query: SELECT * FROM (SELECT * FROM
  "epochs_002_02_memory_run01") as combined_data WHERE 1=1 AND subject_id = '002'
  i [2025-10-25 01:04:07] [INFO] Executing query: SELECT * FROM (SELECT * FROM
  "epochs_002_02_memory_run01") as combined_data WHERE 1=1 AND subject_id = '002'
  AND session_id = '02' AND task_name = 'memory'
  i [2025-10-25 01:04:07] [INFO] Disconnected from eyeris database
  i [2025-10-25 01:04:10] [INFO] Executing query: SELECT * FROM (SELECT * FROM
  "epoch_timeseries_005_01_epochtest_run01_prepostprobe") as combined_data WHERE
  1=1 AND subject_id = '005'
  v [2025-10-25 01:04:11] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 01:04:12] [INFO] Processing block: block_1
  v [2025-10-25 01:04:12] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 01:04:12] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 01:04:12] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 01:04:12] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 01:04:12] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 01:04:12] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 01:04:12] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 01:04:12] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 01:04:12] [INFO] Block processing summary:
  i [2025-10-25 01:04:12] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 01:04:12] [OKAY] Running eyeris::summarize_confounds()
  i [2025-10-25 01:04:14] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:14] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:15] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:15] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:16] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:16] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:17] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:17] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:18] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:18] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:18] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:19] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:19] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:19] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:20] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:20] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:21] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:21] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2025-10-25 01:04:26] [WARN] No detrend data found for run-01
  
  
  processing file: sub-001.Rmd
  output file: sub-001.knit.md
  
  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-001.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-001.html --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-release/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-release/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpfSfMz2/rmarkdown-str4efb768802ad3.html 
  File  not found in resource path
  v [2025-10-25 01:04:26] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 01:04:27] [INFO] Processing block: block_1
  v [2025-10-25 01:04:27] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 01:04:27] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 01:04:27] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 01:04:27] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 01:04:27] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 01:04:27] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 01:04:27] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 01:04:27] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 01:04:27] [INFO] Block processing summary:
  i [2025-10-25 01:04:27] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 01:04:27] [OKAY] Running eyeris::summarize_confounds()
  i [2025-10-25 01:04:28] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:29] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:29] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:30] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:30] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:31] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:31] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:32] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:32] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:32] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:33] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:33] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:34] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:34] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:34] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2025-10-25 01:04:39] [WARN] No detrend data found for run-01
  
  
  processing file: sub-002.Rmd
  output file: sub-002.knit.md
  
  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-002.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-002.html --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-release/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-release/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpfSfMz2/rmarkdown-str4efb741106070.html 
  File  not found in resource path
  v [2025-10-25 01:04:40] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 01:04:40] [INFO] Processing block: block_1
  v [2025-10-25 01:04:40] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 01:04:40] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 01:04:40] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 01:04:40] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 01:04:40] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 01:04:40] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 01:04:40] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 01:04:40] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 01:04:40] [INFO] Block processing summary:
  i [2025-10-25 01:04:40] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 01:04:40] [OKAY] Running eyeris::summarize_confounds()
  i [2025-10-25 01:04:42] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:42] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:43] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:43] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:44] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:44] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:45] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:45] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:45] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:46] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:46] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:47] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:47] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:47] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:49] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2025-10-25 01:04:52] [WARN] No detrend data found for run-01
  
  
  processing file: sub-003.Rmd
  output file: sub-003.knit.md
  
  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-003.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-003.html --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-release/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-release/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpfSfMz2/rmarkdown-str4efb7b8ec4ae.html 
  File  not found in resource path
  v [2025-10-25 01:04:53] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 01:04:53] [INFO] Processing block: block_1
  v [2025-10-25 01:04:53] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 01:04:53] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 01:04:53] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 01:04:53] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 01:04:53] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 01:04:53] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 01:04:53] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 01:04:53] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 01:04:53] [INFO] Block processing summary:
  i [2025-10-25 01:04:53] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 01:04:53] [OKAY] Running eyeris::summarize_confounds()
  i [2025-10-25 01:04:55] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:55] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:56] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:56] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:57] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:57] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:58] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:58] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:59] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:04:59] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:05:00] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:05:00] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:05:00] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:05:01] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:05:01] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:05:01] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:05:02] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  i [2025-10-25 01:05:02] [INFO] Plotting block 1 with sampling rate 1000 Hz from
  possible blocks: 1
  ! [2025-10-25 01:05:06] [WARN] No detrend data found for run-01
  
  
  processing file: sub-004.Rmd
  output file: sub-004.knit.md
  
  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-004.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-004.html --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-release/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-release/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpfSfMz2/rmarkdown-str4efb74745c43e.html 
  File  not found in resource path
  i [2025-10-25 01:05:09] [INFO] Disconnected from eyeris database
  v [2025-10-25 01:05:09] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpfSfMz2/test_bids/derivatives/test-study.eyerisdb
  i [2025-10-25 01:05:10] [INFO] Disconnected from eyeris database
  i [2025-10-25 01:05:11] [INFO] Disconnected from eyeris database
  v [2025-10-25 01:05:11] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpfSfMz2/test_bids_read/derivatives/read-test.eyerisdb
  i [2025-10-25 01:05:12] [INFO] Disconnected from eyeris database
  i [2025-10-25 01:05:13] [INFO] Disconnected from eyeris database
  v [2025-10-25 01:05:13] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpfSfMz2/test_bids_size/derivatives/size-test.eyerisdb
  i [2025-10-25 01:05:13] [INFO] Disconnected from eyeris database
  i [2025-10-25 01:05:13] [INFO] Disconnected from eyeris database
  v [2025-10-25 01:05:14] [OKAY] Connected to eyeris database:
  /tmp/th798/24634860/RtmpfSfMz2/test_bids_empty/derivatives/empty-test.eyerisdb
  ! [2025-10-25 01:05:14] [WARN] No valid tables found in database (after
  excluding temp tables)
  i [2025-10-25 01:05:14] [INFO] Disconnected from eyeris database
  v [2025-10-25 01:05:14] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 01:05:15] [INFO] Processing block: block_1
  v [2025-10-25 01:05:15] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 01:05:15] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 01:05:15] [OKAY] Running eyeris::interpolate() for block_1
  v [2025-10-25 01:05:15] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 01:05:15] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 01:05:15] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 01:05:15] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 01:05:15] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 01:05:15] [INFO] Block processing summary:
  i [2025-10-25 01:05:15] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 01:05:15] [OKAY] Running eyeris::summarize_confounds()
  v [2025-10-25 01:05:16] [OKAY] Running eyeris::load_asc()
  i [2025-10-25 01:05:16] [INFO] Binocular data detected. Processing average
  mode.
  i [2025-10-25 01:05:16] [INFO] Processing block: block_1
  v [2025-10-25 01:05:16] [OKAY] Running eyeris::deblink() for block_1
  v [2025-10-25 01:05:16] [OKAY] Running eyeris::detransient() for block_1
  v [2025-10-25 01:05:16] [OKAY] Running eyeris::interpolate() for block_1
  ! [2025-10-25 01:05:16] [WARN] No NAs detected in pupil data... Skipping
  interpolation!
  v [2025-10-25 01:05:16] [OKAY] Running eyeris::lpfilt() for block_1
  ! [2025-10-25 01:05:16] [WARN] Skipping eyeris::downsample() for block_1
  ! [2025-10-25 01:05:16] [WARN] Skipping eyeris::bin() for block_1
  ! [2025-10-25 01:05:16] [WARN] Skipping eyeris::detrend() for block_1
  v [2025-10-25 01:05:16] [OKAY] Running eyeris::zscore() for block_1
  i [2025-10-25 01:05:16] [INFO] Block processing summary:
  i [2025-10-25 01:05:16] [INFO] block_1: OK (steps: 6, latest:
  pupil_raw_deblink_detransient_interpolate_lpfilt_z)
  v [2025-10-25 01:05:16] [OKAY] Running eyeris::summarize_confounds()
  [ FAIL 4 | WARN 226 | SKIP 0 | PASS 192 ]
  
  == Failed tests ================================================================
  -- Failure ('test-parallel-database.R:10:7'): manual parallel processing flag enables temporary databases --
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    pandoc document conversion failed with error 99
  Backtrace:
      x
   1. +-withr::with_envvar(...) at test-parallel-database.R:4:3
   2. | \-base::force(code)
   3. \-testthat::expect_no_error(...) at test-parallel-database.R:9:5
  -- Failure ('test-parallel-database.R:32:7'): SLURM environment variables are detected for parallel processing --
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    pandoc document conversion failed with error 99
  Backtrace:
      x
   1. +-withr::with_envvar(...) at test-parallel-database.R:28:3
   2. | \-base::force(code)
   3. \-testthat::expect_no_error(...) at test-parallel-database.R:31:5
  -- Failure ('test-parallel-database.R:52:7'): PBS environment variables are detected for parallel processing --
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    pandoc document conversion failed with error 99
  Backtrace:
      x
   1. +-withr::with_envvar(...) at test-parallel-database.R:48:3
   2. | \-base::force(code)
   3. \-testthat::expect_no_error(...) at test-parallel-database.R:51:5
  -- Failure ('test-parallel-database.R:71:5'): normal database operation works without parallel processing --
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    pandoc document conversion failed with error 99
  
  [ FAIL 4 | WARN 226 | SKIP 0 | PASS 192 ]
  Error: Test failures
  In addition: Warning messages:
  1: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  2: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  3: Connection is garbage-collected, use dbDisconnect() to avoid this. 
  Execution halted
  Warning message:
  Connection is garbage-collected, use dbDisconnect() to avoid this. 
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  '/tmp/th798/24634860/R-release/439/eyeris.Rcheck/00check.log'
for details.

[1] "2025-10-25 01:06:00 MST"
> system(paste(c("diff -u", Rcheck.list), collapse=" "))
--- R_version_4.5.1_2025-06-13/release_1.17.8.Rcheck/00check.log	2025-10-25 01:01:05.372931090 -0700
+++ R_version_4.5.1_2025-06-13/master_1.17.99.b3acf2ad13848150e87c414f3edcc413c71fd977.Rcheck/00check.log	2025-10-25 01:06:00.498046724 -0700
@@ -57,8 +57,8 @@
 * checking files in 'vignettes' ... OK
 * checking examples ... OK
 Examples with CPU (user + system) or elapsed time > 5s
-       user system elapsed
-epoch 8.659  0.098   8.827
+      user system elapsed
+epoch 8.63  0.102   8.783
 * checking for unstated dependencies in 'tests' ... OK
 * checking tests ... ERROR
   Running 'testthat.R'
@@ -80,411 +80,411 @@
   
   > 
   > test_check("eyeris")
-  i [2025-10-25 00:59:06] [INFO] Created output directory:
-  /tmp/th798/24634860/Rtmpt8pqLX/test_chunked_output
-  v [2025-10-25 00:59:07] [OKAY] Connected to eyeris database:
-  /tmp/th798/24634860/Rtmpt8pqLX/bids_test/derivatives/test-db.eyerisdb
-  i [2025-10-25 00:59:07] [INFO] Exporting data types: confounds_summary
-  i [2025-10-25 00:59:07] [INFO] Processing data type: confounds_summary
-  i [2025-10-25 00:59:07] [INFO] Grouping tables by epoch label...
-  i [2025-10-25 00:59:07] [INFO] Found 1 epoch label groups for
+  i [2025-10-25 01:04:01] [INFO] Created output directory:
+  /tmp/th798/24634860/RtmpfSfMz2/test_chunked_output
+  v [2025-10-25 01:04:01] [OKAY] Connected to eyeris database:
+  /tmp/th798/24634860/RtmpfSfMz2/bids_test/derivatives/test-db.eyerisdb
+  i [2025-10-25 01:04:01] [INFO] Exporting data types: confounds_summary
+  i [2025-10-25 01:04:01] [INFO] Processing data type: confounds_summary
+  i [2025-10-25 01:04:01] [INFO] Grouping tables by epoch label...
+  i [2025-10-25 01:04:01] [INFO] Found 1 epoch label groups for
   confounds_summary: _nolabel
-  i [2025-10-25 00:59:07] [INFO] Analyzing column structures within epoch group
+  i [2025-10-25 01:04:01] [INFO] Analyzing column structures within epoch group
   '_nolabel'...
-  i [2025-10-25 00:59:07] [INFO] Found 2 column-compatible groups within
+  i [2025-10-25 01:04:01] [INFO] Found 2 column-compatible groups within
   '_nolabel': goal, stim
-  i [2025-10-25 00:59:07] [INFO] Processing confounds_summary group 'goal' (2
+  i [2025-10-25 01:04:01] [INFO] Processing confounds_summary group 'goal' (2
   tables)
-  i [2025-10-25 00:59:07] [INFO] Using chunked processing (file size limit = 50MB
+  i [2025-10-25 01:04:01] [INFO] Using chunked processing (file size limit = 50MB
   < 500MB threshold)
-  i [2025-10-25 00:59:07] [INFO] Processing with file size chunking enabled
-  i [2025-10-25 00:59:07] [INFO] Starting chunked query processing (chunk size:
+  i [2025-10-25 01:04:01] [INFO] Processing with file size chunking enabled
+  i [2025-10-25 01:04:01] [INFO] Starting chunked query processing (chunk size:
   50)
-  i [2025-10-25 00:59:07] [INFO] Query: SELECT * FROM
+  i [2025-10-25 01:04:01] [INFO] Query: SELECT * FROM
   "confounds_summary_01_task_run01_goal" UNION ALL SELECT * FROM
   "confounds_summary_02_task_run01_goal"
-  i [2025-10-25 00:59:07] [INFO] Processing chunk 1: 50 rows
-  i [2025-10-25 00:59:07] [INFO] Created output file:
+  i [2025-10-25 01:04:01] [INFO] Processing chunk 1: 50 rows
+  i [2025-10-25 01:04:01] [INFO] Created output file:
   test-db_confounds_summary_goal_chunked_01.csv
-  i [2025-10-25 00:59:07] [INFO] Processing chunk 2: 50 rows
-  i [2025-10-25 00:59:07] [INFO] Processing chunk 3: 50 rows
-  i [2025-10-25 00:59:07] [INFO] No more data to process
-  v [2025-10-25 00:59:07] [OKAY] Chunked processing complete:
-  i [2025-10-25 00:59:07] [INFO] Total rows: 150
-  i [2025-10-25 00:59:07] [INFO] Chunks: 3
-  i [2025-10-25 00:59:07] [INFO] Processing time: 0 seconds
-  i [2025-10-25 00:59:07] [INFO] Average rate: 4562 rows/second
-  i [2025-10-25 00:59:07] [INFO] Processing confounds_summary group 'stim' (1
+  i [2025-10-25 01:04:01] [INFO] Processing chunk 2: 50 rows
+  i [2025-10-25 01:04:01] [INFO] Processing chunk 3: 50 rows
+  i [2025-10-25 01:04:01] [INFO] No more data to process
+  v [2025-10-25 01:04:01] [OKAY] Chunked processing complete:
+  i [2025-10-25 01:04:01] [INFO] Total rows: 150
+  i [2025-10-25 01:04:01] [INFO] Chunks: 3
+  i [2025-10-25 01:04:01] [INFO] Processing time: 0 seconds
+  i [2025-10-25 01:04:01] [INFO] Average rate: 4739 rows/second
+  i [2025-10-25 01:04:01] [INFO] Processing confounds_summary group 'stim' (1
   tables)
-  i [2025-10-25 00:59:07] [INFO] Using chunked processing (file size limit = 50MB
+  i [2025-10-25 01:04:01] [INFO] Using chunked processing (file size limit = 50MB
   < 500MB threshold)
-  i [2025-10-25 00:59:07] [INFO] Processing with file size chunking enabled
-  i [2025-10-25 00:59:07] [INFO] Starting chunked query processing (chunk size:
+  i [2025-10-25 01:04:01] [INFO] Processing with file size chunking enabled
+  i [2025-10-25 01:04:01] [INFO] Starting chunked query processing (chunk size:
   50)
-  i [2025-10-25 00:59:07] [INFO] Query: SELECT * FROM
+  i [2025-10-25 01:04:01] [INFO] Query: SELECT * FROM
   "confounds_summary_01_task_run01_stim"
-  i [2025-10-25 00:59:07] [INFO] Processing chunk 1: 50 rows
-  i [2025-10-25 00:59:07] [INFO] Created output file:
+  i [2025-10-25 01:04:01] [INFO] Processing chunk 1: 50 rows
+  i [2025-10-25 01:04:01] [INFO] Created output file:
   test-db_confounds_summary_stim_chunked_01.csv
-  i [2025-10-25 00:59:07] [INFO] Processing chunk 2: 50 rows
-  i [2025-10-25 00:59:07] [INFO] No more data to process
-  v [2025-10-25 00:59:07] [OKAY] Chunked processing complete:
-  i [2025-10-25 00:59:07] [INFO] Total rows: 100
-  i [2025-10-25 00:59:07] [INFO] Chunks: 2
-  i [2025-10-25 00:59:08] [INFO] Processing time: 0 seconds
-  i [2025-10-25 00:59:08] [INFO] Average rate: 3916 rows/second
-  v [2025-10-25 00:59:08] [OKAY] Export complete!
-  i [2025-10-25 00:59:08] [INFO] Data types exported: 2
-  i [2025-10-25 00:59:08] [INFO] Total rows exported: 250
-  i [2025-10-25 00:59:08] [INFO] Output directory:
-  /tmp/th798/24634860/Rtmpt8pqLX/test_chunked_output
-  i [2025-10-25 00:59:08] [INFO] Disconnected from eyeris database
-  i [2025-10-25 00:59:08] [INFO] Created output directory:
-  /tmp/th798/24634860/Rtmpt8pqLX/size_test_output
-  v [2025-10-25 00:59:08] [OKAY] Connected to eyeris database:
-  /tmp/th798/24634860/Rtmpt8pqLX/bids_size_test/derivatives/size-test.eyerisdb
-  i [2025-10-25 00:59:09] [INFO] Exporting data types: timeseries
-  i [2025-10-25 00:59:09] [INFO] Processing data type: timeseries
-  i [2025-10-25 00:59:09] [INFO] Processing timeseries group 'all' (1 tables)
-  i [2025-10-25 00:59:09] [INFO] Using chunked processing (file size limit =
+  i [2025-10-25 01:04:01] [INFO] Processing chunk 2: 50 rows
+  i [2025-10-25 01:04:01] [INFO] No more data to process
+  v [2025-10-25 01:04:01] [OKAY] Chunked processing complete:
+  i [2025-10-25 01:04:01] [INFO] Total rows: 100
+  i [2025-10-25 01:04:01] [INFO] Chunks: 2
+  i [2025-10-25 01:04:01] [INFO] Processing time: 0 seconds
+  i [2025-10-25 01:04:01] [INFO] Average rate: 4034 rows/second
+  v [2025-10-25 01:04:01] [OKAY] Export complete!
+  i [2025-10-25 01:04:01] [INFO] Data types exported: 2
+  i [2025-10-25 01:04:01] [INFO] Total rows exported: 250
+  i [2025-10-25 01:04:01] [INFO] Output directory:
+  /tmp/th798/24634860/RtmpfSfMz2/test_chunked_output
+  i [2025-10-25 01:04:02] [INFO] Disconnected from eyeris database
+  i [2025-10-25 01:04:02] [INFO] Created output directory:
+  /tmp/th798/24634860/RtmpfSfMz2/size_test_output
+  v [2025-10-25 01:04:02] [OKAY] Connected to eyeris database:
+  /tmp/th798/24634860/RtmpfSfMz2/bids_size_test/derivatives/size-test.eyerisdb
+  i [2025-10-25 01:04:03] [INFO] Exporting data types: timeseries
+  i [2025-10-25 01:04:03] [INFO] Processing data type: timeseries
+  i [2025-10-25 01:04:03] [INFO] Processing timeseries group 'all' (1 tables)
+  i [2025-10-25 01:04:03] [INFO] Using chunked processing (file size limit =
   0.05MB < 500MB threshold)
-  i [2025-10-25 00:59:09] [INFO] Processing with file size chunking enabled
-  i [2025-10-25 00:59:09] [INFO] Starting chunked query processing (chunk size:
+  i [2025-10-25 01:04:03] [INFO] Processing with file size chunking enabled
+  i [2025-10-25 01:04:03] [INFO] Starting chunked query processing (chunk size:
   500)
-  i [2025-10-25 00:59:09] [INFO] Query: SELECT * FROM "timeseries_01_test_run01"
-  i [2025-10-25 00:59:09] [INFO] Processing chunk 1: 500 rows
-  i [2025-10-25 00:59:09] [INFO] Created output file:
+  i [2025-10-25 01:04:03] [INFO] Query: SELECT * FROM "timeseries_01_test_run01"
+  i [2025-10-25 01:04:03] [INFO] Processing chunk 1: 500 rows
+  i [2025-10-25 01:04:03] [INFO] Created output file:
   size-test_timeseries_chunked_01.csv
-  i [2025-10-25 00:59:09] [INFO] Processing chunk 2: 500 rows
-  i [2025-10-25 00:59:09] [INFO] Starting new file due to size limit:
+  i [2025-10-25 01:04:03] [INFO] Processing chunk 2: 500 rows
+  i [2025-10-25 01:04:03] [INFO] Starting new file due to size limit:
   size-test_timeseries_chunked_02.csv
-  i [2025-10-25 00:59:09] [INFO] Created output file:
+  i [2025-10-25 01:04:03] [INFO] Created output file:
   size-test_timeseries_chunked_02.csv
-  i [2025-10-25 00:59:09] [INFO] Processing chunk 3: 500 rows
-  i [2025-10-25 00:59:09] [INFO] Starting new file due to size limit:
+  i [2025-10-25 01:04:03] [INFO] Processing chunk 3: 500 rows
+  i [2025-10-25 01:04:03] [INFO] Starting new file due to size limit:
   size-test_timeseries_chunked_03.csv
-  i [2025-10-25 00:59:09] [INFO] Created output file:
+  i [2025-10-25 01:04:03] [INFO] Created output file:
   size-test_timeseries_chunked_03.csv
-  i [2025-10-25 00:59:09] [INFO] Processing chunk 4: 500 rows
-  i [2025-10-25 00:59:09] [INFO] Starting new file due to size limit:
+  i [2025-10-25 01:04:03] [INFO] Processing chunk 4: 500 rows
+  i [2025-10-25 01:04:03] [INFO] Starting new file due to size limit:
   size-test_timeseries_chunked_04.csv
-  i [2025-10-25 00:59:09] [INFO] Created output file:
+  i [2025-10-25 01:04:03] [INFO] Created output file:
   size-test_timeseries_chunked_04.csv
-  i [2025-10-25 00:59:09] [INFO] No more data to process
-  v [2025-10-25 00:59:09] [OKAY] Chunked processing complete:
-  i [2025-10-25 00:59:09] [INFO] Total rows: 2000
-  i [2025-10-25 00:59:09] [INFO] Chunks: 4
-  i [2025-10-25 00:59:09] [INFO] Processing time: 0.1 seconds
-  i [2025-10-25 00:59:09] [INFO] Average rate: 21692 rows/second
-  i [2025-10-25 00:59:09] [INFO] Finalizing 4 output files with proper
+  i [2025-10-25 01:04:03] [INFO] No more data to process
+  v [2025-10-25 01:04:03] [OKAY] Chunked processing complete:
+  i [2025-10-25 01:04:03] [INFO] Total rows: 2000
+  i [2025-10-25 01:04:03] [INFO] Chunks: 4
+  i [2025-10-25 01:04:03] [INFO] Processing time: 0.1 seconds
+  i [2025-10-25 01:04:03] [INFO] Average rate: 21787 rows/second
+  i [2025-10-25 01:04:03] [INFO] Finalizing 4 output files with proper
   numbering...
-  i [2025-10-25 00:59:09] [INFO] Renamed: size-test_timeseries_chunked_01.csv ->
+  i [2025-10-25 01:04:03] [INFO] Renamed: size-test_timeseries_chunked_01.csv ->
   size-test_timeseries_chunked_01-of-04.csv
-  i [2025-10-25 00:59:09] [INFO] Renamed: size-test_timeseries_chunked_02.csv ->
+  i [2025-10-25 01:04:03] [INFO] Renamed: size-test_timeseries_chunked_02.csv ->
   size-test_timeseries_chunked_02-of-04.csv
-  i [2025-10-25 00:59:09] [INFO] Renamed: size-test_timeseries_chunked_03.csv ->
+  i [2025-10-25 01:04:03] [INFO] Renamed: size-test_timeseries_chunked_03.csv ->
   size-test_timeseries_chunked_03-of-04.csv
-  i [2025-10-25 00:59:09] [INFO] Renamed: size-test_timeseries_chunked_04.csv ->
+  i [2025-10-25 01:04:03] [INFO] Renamed: size-test_timeseries_chunked_04.csv ->
   size-test_timeseries_chunked_04-of-04.csv
-  v [2025-10-25 00:59:09] [OKAY] Export complete!
-  i [2025-10-25 00:59:09] [INFO] Data types exported: 1
-  i [2025-10-25 00:59:09] [INFO] Total rows exported: 2000
-  i [2025-10-25 00:59:09] [INFO] Output directory:
-  /tmp/th798/24634860/Rtmpt8pqLX/size_test_output
-  i [2025-10-25 00:59:09] [INFO] Disconnected from eyeris database
-  v [2025-10-25 00:59:11] [OKAY] Connected to eyeris database:
-  /tmp/th798/24634860/Rtmpt8pqLX/test_bids/derivatives/user-test.eyerisdb
-  i [2025-10-25 00:59:12] [INFO] Executing query: SELECT * FROM (SELECT * FROM
+  v [2025-10-25 01:04:03] [OKAY] Export complete!
+  i [2025-10-25 01:04:03] [INFO] Data types exported: 1
+  i [2025-10-25 01:04:03] [INFO] Total rows exported: 2000
+  i [2025-10-25 01:04:03] [INFO] Output directory:
+  /tmp/th798/24634860/RtmpfSfMz2/size_test_output
+  i [2025-10-25 01:04:03] [INFO] Disconnected from eyeris database
+  v [2025-10-25 01:04:05] [OKAY] Connected to eyeris database:
+  /tmp/th798/24634860/RtmpfSfMz2/test_bids/derivatives/user-test.eyerisdb
+  i [2025-10-25 01:04:06] [INFO] Executing query: SELECT * FROM (SELECT * FROM
   "epochs_002_02_memory_run01") as combined_data WHERE 1=1 AND subject_id = '002'
-  i [2025-10-25 00:59:13] [INFO] Executing query: SELECT * FROM (SELECT * FROM
+  i [2025-10-25 01:04:07] [INFO] Executing query: SELECT * FROM (SELECT * FROM
   "epochs_002_02_memory_run01") as combined_data WHERE 1=1 AND subject_id = '002'
   AND session_id = '02' AND task_name = 'memory'
-  i [2025-10-25 00:59:13] [INFO] Disconnected from eyeris database
-  i [2025-10-25 00:59:16] [INFO] Executing query: SELECT * FROM (SELECT * FROM
+  i [2025-10-25 01:04:07] [INFO] Disconnected from eyeris database
+  i [2025-10-25 01:04:10] [INFO] Executing query: SELECT * FROM (SELECT * FROM
   "epoch_timeseries_005_01_epochtest_run01_prepostprobe") as combined_data WHERE
   1=1 AND subject_id = '005'
-  v [2025-10-25 00:59:17] [OKAY] Running eyeris::load_asc()
-  i [2025-10-25 00:59:18] [INFO] Processing block: block_1
-  v [2025-10-25 00:59:18] [OKAY] Running eyeris::deblink() for block_1
-  v [2025-10-25 00:59:18] [OKAY] Running eyeris::detransient() for block_1
-  v [2025-10-25 00:59:18] [OKAY] Running eyeris::interpolate() for block_1
-  v [2025-10-25 00:59:18] [OKAY] Running eyeris::lpfilt() for block_1
-  ! [2025-10-25 00:59:18] [WARN] Skipping eyeris::downsample() for block_1
-  ! [2025-10-25 00:59:18] [WARN] Skipping eyeris::bin() for block_1
-  ! [2025-10-25 00:59:18] [WARN] Skipping eyeris::detrend() for block_1
-  v [2025-10-25 00:59:18] [OKAY] Running eyeris::zscore() for block_1
-  i [2025-10-25 00:59:18] [INFO] Block processing summary:
-  i [2025-10-25 00:59:18] [INFO] block_1: OK (steps: 6, latest:
+  v [2025-10-25 01:04:11] [OKAY] Running eyeris::load_asc()
+  i [2025-10-25 01:04:12] [INFO] Processing block: block_1
+  v [2025-10-25 01:04:12] [OKAY] Running eyeris::deblink() for block_1
+  v [2025-10-25 01:04:12] [OKAY] Running eyeris::detransient() for block_1
+  v [2025-10-25 01:04:12] [OKAY] Running eyeris::interpolate() for block_1
+  v [2025-10-25 01:04:12] [OKAY] Running eyeris::lpfilt() for block_1
+  ! [2025-10-25 01:04:12] [WARN] Skipping eyeris::downsample() for block_1
+  ! [2025-10-25 01:04:12] [WARN] Skipping eyeris::bin() for block_1
+  ! [2025-10-25 01:04:12] [WARN] Skipping eyeris::detrend() for block_1
+  v [2025-10-25 01:04:12] [OKAY] Running eyeris::zscore() for block_1
+  i [2025-10-25 01:04:12] [INFO] Block processing summary:
+  i [2025-10-25 01:04:12] [INFO] block_1: OK (steps: 6, latest:
   pupil_raw_deblink_detransient_interpolate_lpfilt_z)
-  v [2025-10-25 00:59:18] [OKAY] Running eyeris::summarize_confounds()
-  i [2025-10-25 00:59:20] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  v [2025-10-25 01:04:12] [OKAY] Running eyeris::summarize_confounds()
+  i [2025-10-25 01:04:14] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:20] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:14] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:21] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:15] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:21] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:15] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:22] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:16] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:22] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:16] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:23] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:17] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:23] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:17] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:24] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:18] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:24] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:18] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:24] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:18] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:25] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:19] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:25] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:19] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:26] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:19] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:26] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:20] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:26] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:20] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:27] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:21] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:27] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:21] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  ! [2025-10-25 00:59:32] [WARN] No detrend data found for run-01
+  ! [2025-10-25 01:04:26] [WARN] No detrend data found for run-01
   
   
   processing file: sub-001.Rmd
   output file: sub-001.knit.md
   
-  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-001.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-001.html --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-release/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-release/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/Rtmpt8pqLX/rmarkdown-str404551ae11511.html 
+  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-001.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-001.html --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-release/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-release/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpfSfMz2/rmarkdown-str4efb768802ad3.html 
   File  not found in resource path
-  v [2025-10-25 00:59:32] [OKAY] Running eyeris::load_asc()
-  i [2025-10-25 00:59:33] [INFO] Processing block: block_1
-  v [2025-10-25 00:59:33] [OKAY] Running eyeris::deblink() for block_1
-  v [2025-10-25 00:59:33] [OKAY] Running eyeris::detransient() for block_1
-  v [2025-10-25 00:59:33] [OKAY] Running eyeris::interpolate() for block_1
-  v [2025-10-25 00:59:33] [OKAY] Running eyeris::lpfilt() for block_1
-  ! [2025-10-25 00:59:33] [WARN] Skipping eyeris::downsample() for block_1
-  ! [2025-10-25 00:59:33] [WARN] Skipping eyeris::bin() for block_1
-  ! [2025-10-25 00:59:33] [WARN] Skipping eyeris::detrend() for block_1
-  v [2025-10-25 00:59:33] [OKAY] Running eyeris::zscore() for block_1
-  i [2025-10-25 00:59:33] [INFO] Block processing summary:
-  i [2025-10-25 00:59:33] [INFO] block_1: OK (steps: 6, latest:
+  v [2025-10-25 01:04:26] [OKAY] Running eyeris::load_asc()
+  i [2025-10-25 01:04:27] [INFO] Processing block: block_1
+  v [2025-10-25 01:04:27] [OKAY] Running eyeris::deblink() for block_1
+  v [2025-10-25 01:04:27] [OKAY] Running eyeris::detransient() for block_1
+  v [2025-10-25 01:04:27] [OKAY] Running eyeris::interpolate() for block_1
+  v [2025-10-25 01:04:27] [OKAY] Running eyeris::lpfilt() for block_1
+  ! [2025-10-25 01:04:27] [WARN] Skipping eyeris::downsample() for block_1
+  ! [2025-10-25 01:04:27] [WARN] Skipping eyeris::bin() for block_1
+  ! [2025-10-25 01:04:27] [WARN] Skipping eyeris::detrend() for block_1
+  v [2025-10-25 01:04:27] [OKAY] Running eyeris::zscore() for block_1
+  i [2025-10-25 01:04:27] [INFO] Block processing summary:
+  i [2025-10-25 01:04:27] [INFO] block_1: OK (steps: 6, latest:
   pupil_raw_deblink_detransient_interpolate_lpfilt_z)
-  v [2025-10-25 00:59:33] [OKAY] Running eyeris::summarize_confounds()
-  i [2025-10-25 00:59:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  v [2025-10-25 01:04:27] [OKAY] Running eyeris::summarize_confounds()
+  i [2025-10-25 01:04:28] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:29] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:36] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:29] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:36] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:30] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:36] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:30] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:37] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:31] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:37] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:31] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:38] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:32] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:38] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:32] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:39] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:32] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:39] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:33] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:39] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:33] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:40] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:34] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:40] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:34] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:41] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:34] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:41] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:41] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:41] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:35] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  ! [2025-10-25 00:59:45] [WARN] No detrend data found for run-01
+  ! [2025-10-25 01:04:39] [WARN] No detrend data found for run-01
   
   
   processing file: sub-002.Rmd
   output file: sub-002.knit.md
   
-  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-002.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-002.html --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-release/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-release/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/Rtmpt8pqLX/rmarkdown-str404556912c775.html 
+  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-002.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-002.html --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-release/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-release/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpfSfMz2/rmarkdown-str4efb741106070.html 
   File  not found in resource path
-  v [2025-10-25 00:59:46] [OKAY] Running eyeris::load_asc()
-  i [2025-10-25 00:59:46] [INFO] Processing block: block_1
-  v [2025-10-25 00:59:46] [OKAY] Running eyeris::deblink() for block_1
-  v [2025-10-25 00:59:46] [OKAY] Running eyeris::detransient() for block_1
-  v [2025-10-25 00:59:46] [OKAY] Running eyeris::interpolate() for block_1
-  v [2025-10-25 00:59:46] [OKAY] Running eyeris::lpfilt() for block_1
-  ! [2025-10-25 00:59:46] [WARN] Skipping eyeris::downsample() for block_1
-  ! [2025-10-25 00:59:46] [WARN] Skipping eyeris::bin() for block_1
-  ! [2025-10-25 00:59:46] [WARN] Skipping eyeris::detrend() for block_1
-  v [2025-10-25 00:59:46] [OKAY] Running eyeris::zscore() for block_1
-  i [2025-10-25 00:59:46] [INFO] Block processing summary:
-  i [2025-10-25 00:59:46] [INFO] block_1: OK (steps: 6, latest:
+  v [2025-10-25 01:04:40] [OKAY] Running eyeris::load_asc()
+  i [2025-10-25 01:04:40] [INFO] Processing block: block_1
+  v [2025-10-25 01:04:40] [OKAY] Running eyeris::deblink() for block_1
+  v [2025-10-25 01:04:40] [OKAY] Running eyeris::detransient() for block_1
+  v [2025-10-25 01:04:40] [OKAY] Running eyeris::interpolate() for block_1
+  v [2025-10-25 01:04:40] [OKAY] Running eyeris::lpfilt() for block_1
+  ! [2025-10-25 01:04:40] [WARN] Skipping eyeris::downsample() for block_1
+  ! [2025-10-25 01:04:40] [WARN] Skipping eyeris::bin() for block_1
+  ! [2025-10-25 01:04:40] [WARN] Skipping eyeris::detrend() for block_1
+  v [2025-10-25 01:04:40] [OKAY] Running eyeris::zscore() for block_1
+  i [2025-10-25 01:04:40] [INFO] Block processing summary:
+  i [2025-10-25 01:04:40] [INFO] block_1: OK (steps: 6, latest:
   pupil_raw_deblink_detransient_interpolate_lpfilt_z)
-  v [2025-10-25 00:59:46] [OKAY] Running eyeris::summarize_confounds()
-  i [2025-10-25 00:59:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  v [2025-10-25 01:04:40] [OKAY] Running eyeris::summarize_confounds()
+  i [2025-10-25 01:04:42] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:42] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:49] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:43] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:49] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:43] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:50] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:44] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:50] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:44] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:51] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:45] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:51] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:45] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:52] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:45] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:52] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:46] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:52] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:46] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:53] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:47] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:53] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:47] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:54] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:47] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:54] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:54] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:55] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:48] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 00:59:55] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:49] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  ! [2025-10-25 00:59:59] [WARN] No detrend data found for run-01
+  ! [2025-10-25 01:04:52] [WARN] No detrend data found for run-01
   
   
   processing file: sub-003.Rmd
   output file: sub-003.knit.md
   
-  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-003.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-003.html --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-release/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-release/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/Rtmpt8pqLX/rmarkdown-str40455579081f5.html 
+  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-003.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-003.html --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-release/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-release/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpfSfMz2/rmarkdown-str4efb7b8ec4ae.html 
   File  not found in resource path
-  v [2025-10-25 00:59:59] [OKAY] Running eyeris::load_asc()
-  i [2025-10-25 00:59:59] [INFO] Processing block: block_1
-  v [2025-10-25 00:59:59] [OKAY] Running eyeris::deblink() for block_1
-  v [2025-10-25 00:59:59] [OKAY] Running eyeris::detransient() for block_1
-  v [2025-10-25 00:59:59] [OKAY] Running eyeris::interpolate() for block_1
-  v [2025-10-25 00:59:59] [OKAY] Running eyeris::lpfilt() for block_1
-  ! [2025-10-25 01:00:00] [WARN] Skipping eyeris::downsample() for block_1
-  ! [2025-10-25 01:00:00] [WARN] Skipping eyeris::bin() for block_1
-  ! [2025-10-25 01:00:00] [WARN] Skipping eyeris::detrend() for block_1
-  v [2025-10-25 01:00:00] [OKAY] Running eyeris::zscore() for block_1
-  i [2025-10-25 01:00:00] [INFO] Block processing summary:
-  i [2025-10-25 01:00:00] [INFO] block_1: OK (steps: 6, latest:
+  v [2025-10-25 01:04:53] [OKAY] Running eyeris::load_asc()
+  i [2025-10-25 01:04:53] [INFO] Processing block: block_1
+  v [2025-10-25 01:04:53] [OKAY] Running eyeris::deblink() for block_1
+  v [2025-10-25 01:04:53] [OKAY] Running eyeris::detransient() for block_1
+  v [2025-10-25 01:04:53] [OKAY] Running eyeris::interpolate() for block_1
+  v [2025-10-25 01:04:53] [OKAY] Running eyeris::lpfilt() for block_1
+  ! [2025-10-25 01:04:53] [WARN] Skipping eyeris::downsample() for block_1
+  ! [2025-10-25 01:04:53] [WARN] Skipping eyeris::bin() for block_1
+  ! [2025-10-25 01:04:53] [WARN] Skipping eyeris::detrend() for block_1
+  v [2025-10-25 01:04:53] [OKAY] Running eyeris::zscore() for block_1
+  i [2025-10-25 01:04:53] [INFO] Block processing summary:
+  i [2025-10-25 01:04:53] [INFO] block_1: OK (steps: 6, latest:
   pupil_raw_deblink_detransient_interpolate_lpfilt_z)
-  v [2025-10-25 01:00:00] [OKAY] Running eyeris::summarize_confounds()
-  i [2025-10-25 01:00:01] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  v [2025-10-25 01:04:53] [OKAY] Running eyeris::summarize_confounds()
+  i [2025-10-25 01:04:55] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 01:00:02] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:55] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 01:00:02] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:56] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 01:00:02] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:56] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 01:00:03] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:57] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 01:00:03] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:57] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 01:00:04] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:58] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 01:00:04] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:58] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 01:00:05] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:59] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 01:00:05] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:04:59] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 01:00:06] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:05:00] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 01:00:06] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:05:00] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 01:00:06] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:05:00] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 01:00:07] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:05:01] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 01:00:07] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:05:01] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 01:00:07] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:05:01] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 01:00:08] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:05:02] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  i [2025-10-25 01:00:08] [INFO] Plotting block 1 with sampling rate 1000 Hz from
+  i [2025-10-25 01:05:02] [INFO] Plotting block 1 with sampling rate 1000 Hz from
   possible blocks: 1
-  ! [2025-10-25 01:00:12] [WARN] No detrend data found for run-01
+  ! [2025-10-25 01:05:06] [WARN] No detrend data found for run-01
   
   
   processing file: sub-004.Rmd
   output file: sub-004.knit.md
   
-  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-004.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-004.html --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-release/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-release/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/Rtmpt8pqLX/rmarkdown-str404555cd5f266.html 
+  /home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS sub-004.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output sub-004.html --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/R-release/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 6 --variable toc_float=1 --variable toc_selectors=h1,h2,h3,h4,h5,h6 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /projects/genomic-ml/R/R-release/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css /tmp/th798/24634860/R-release/439/eyeris.Rcheck/eyeris/rmarkdown/css/report.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/24634860/RtmpfSfMz2/rmarkdown-str4efb74745c43e.html 
   File  not found in resource path
-  i [2025-10-25 01:00:15] [INFO] Disconnected from eyeris database
-  v [2025-10-25 01:00:16] [OKAY] Connected to eyeris database:
-  /tmp/th798/24634860/Rtmpt8pqLX/test_bids/derivatives/test-study.eyerisdb
-  i [2025-10-25 01:00:16] [INFO] Disconnected from eyeris database
-  i [2025-10-25 01:00:17] [INFO] Disconnected from eyeris database
-  v [2025-10-25 01:00:17] [OKAY] Connected to eyeris database:
-  /tmp/th798/24634860/Rtmpt8pqLX/test_bids_read/derivatives/read-test.eyerisdb
-  i [2025-10-25 01:00:18] [INFO] Disconnected from eyeris database
-  i [2025-10-25 01:00:19] [INFO] Disconnected from eyeris database
-  v [2025-10-25 01:00:19] [OKAY] Connected to eyeris database:
-  /tmp/th798/24634860/Rtmpt8pqLX/test_bids_size/derivatives/size-test.eyerisdb
-  i [2025-10-25 01:00:19] [INFO] Disconnected from eyeris database
-  i [2025-10-25 01:00:20] [INFO] Disconnected from eyeris database
-  v [2025-10-25 01:00:20] [OKAY] Connected to eyeris database:
-  /tmp/th798/24634860/Rtmpt8pqLX/test_bids_empty/derivatives/empty-test.eyerisdb
-  ! [2025-10-25 01:00:20] [WARN] No valid tables found in database (after
+  i [2025-10-25 01:05:09] [INFO] Disconnected from eyeris database
+  v [2025-10-25 01:05:09] [OKAY] Connected to eyeris database:
+  /tmp/th798/24634860/RtmpfSfMz2/test_bids/derivatives/test-study.eyerisdb
+  i [2025-10-25 01:05:10] [INFO] Disconnected from eyeris database
+  i [2025-10-25 01:05:11] [INFO] Disconnected from eyeris database
+  v [2025-10-25 01:05:11] [OKAY] Connected to eyeris database:
+  /tmp/th798/24634860/RtmpfSfMz2/test_bids_read/derivatives/read-test.eyerisdb
+  i [2025-10-25 01:05:12] [INFO] Disconnected from eyeris database
+  i [2025-10-25 01:05:13] [INFO] Disconnected from eyeris database
+  v [2025-10-25 01:05:13] [OKAY] Connected to eyeris database:
+  /tmp/th798/24634860/RtmpfSfMz2/test_bids_size/derivatives/size-test.eyerisdb
+  i [2025-10-25 01:05:13] [INFO] Disconnected from eyeris database
+  i [2025-10-25 01:05:13] [INFO] Disconnected from eyeris database
+  v [2025-10-25 01:05:14] [OKAY] Connected to eyeris database:
+  /tmp/th798/24634860/RtmpfSfMz2/test_bids_empty/derivatives/empty-test.eyerisdb
+  ! [2025-10-25 01:05:14] [WARN] No valid tables found in database (after
   excluding temp tables)
-  i [2025-10-25 01:00:20] [INFO] Disconnected from eyeris database
-  v [2025-10-25 01:00:21] [OKAY] Running eyeris::load_asc()
-  i [2025-10-25 01:00:21] [INFO] Processing block: block_1
-  v [2025-10-25 01:00:21] [OKAY] Running eyeris::deblink() for block_1
-  v [2025-10-25 01:00:21] [OKAY] Running eyeris::detransient() for block_1
-  v [2025-10-25 01:00:21] [OKAY] Running eyeris::interpolate() for block_1
-  v [2025-10-25 01:00:21] [OKAY] Running eyeris::lpfilt() for block_1
-  ! [2025-10-25 01:00:21] [WARN] Skipping eyeris::downsample() for block_1
-  ! [2025-10-25 01:00:21] [WARN] Skipping eyeris::bin() for block_1
-  ! [2025-10-25 01:00:21] [WARN] Skipping eyeris::detrend() for block_1
-  v [2025-10-25 01:00:21] [OKAY] Running eyeris::zscore() for block_1
-  i [2025-10-25 01:00:21] [INFO] Block processing summary:
-  i [2025-10-25 01:00:21] [INFO] block_1: OK (steps: 6, latest:
+  i [2025-10-25 01:05:14] [INFO] Disconnected from eyeris database
+  v [2025-10-25 01:05:14] [OKAY] Running eyeris::load_asc()
+  i [2025-10-25 01:05:15] [INFO] Processing block: block_1
+  v [2025-10-25 01:05:15] [OKAY] Running eyeris::deblink() for block_1
+  v [2025-10-25 01:05:15] [OKAY] Running eyeris::detransient() for block_1
+  v [2025-10-25 01:05:15] [OKAY] Running eyeris::interpolate() for block_1
+  v [2025-10-25 01:05:15] [OKAY] Running eyeris::lpfilt() for block_1
+  ! [2025-10-25 01:05:15] [WARN] Skipping eyeris::downsample() for block_1
+  ! [2025-10-25 01:05:15] [WARN] Skipping eyeris::bin() for block_1
+  ! [2025-10-25 01:05:15] [WARN] Skipping eyeris::detrend() for block_1
+  v [2025-10-25 01:05:15] [OKAY] Running eyeris::zscore() for block_1
+  i [2025-10-25 01:05:15] [INFO] Block processing summary:
+  i [2025-10-25 01:05:15] [INFO] block_1: OK (steps: 6, latest:
   pupil_raw_deblink_detransient_interpolate_lpfilt_z)
-  v [2025-10-25 01:00:21] [OKAY] Running eyeris::summarize_confounds()
-  v [2025-10-25 01:00:22] [OKAY] Running eyeris::load_asc()
-  i [2025-10-25 01:00:22] [INFO] Binocular data detected. Processing average
+  v [2025-10-25 01:05:15] [OKAY] Running eyeris::summarize_confounds()
+  v [2025-10-25 01:05:16] [OKAY] Running eyeris::load_asc()
+  i [2025-10-25 01:05:16] [INFO] Binocular data detected. Processing average
   mode.
-  i [2025-10-25 01:00:22] [INFO] Processing block: block_1
-  v [2025-10-25 01:00:22] [OKAY] Running eyeris::deblink() for block_1
-  v [2025-10-25 01:00:22] [OKAY] Running eyeris::detransient() for block_1
-  v [2025-10-25 01:00:22] [OKAY] Running eyeris::interpolate() for block_1
-  ! [2025-10-25 01:00:22] [WARN] No NAs detected in pupil data... Skipping
+  i [2025-10-25 01:05:16] [INFO] Processing block: block_1
+  v [2025-10-25 01:05:16] [OKAY] Running eyeris::deblink() for block_1
+  v [2025-10-25 01:05:16] [OKAY] Running eyeris::detransient() for block_1
+  v [2025-10-25 01:05:16] [OKAY] Running eyeris::interpolate() for block_1
+  ! [2025-10-25 01:05:16] [WARN] No NAs detected in pupil data... Skipping
   interpolation!
-  v [2025-10-25 01:00:22] [OKAY] Running eyeris::lpfilt() for block_1
-  ! [2025-10-25 01:00:22] [WARN] Skipping eyeris::downsample() for block_1
-  ! [2025-10-25 01:00:22] [WARN] Skipping eyeris::bin() for block_1
-  ! [2025-10-25 01:00:22] [WARN] Skipping eyeris::detrend() for block_1
-  v [2025-10-25 01:00:22] [OKAY] Running eyeris::zscore() for block_1
-  i [2025-10-25 01:00:22] [INFO] Block processing summary:
-  i [2025-10-25 01:00:22] [INFO] block_1: OK (steps: 6, latest:
+  v [2025-10-25 01:05:16] [OKAY] Running eyeris::lpfilt() for block_1
+  ! [2025-10-25 01:05:16] [WARN] Skipping eyeris::downsample() for block_1
+  ! [2025-10-25 01:05:16] [WARN] Skipping eyeris::bin() for block_1
+  ! [2025-10-25 01:05:16] [WARN] Skipping eyeris::detrend() for block_1
+  v [2025-10-25 01:05:16] [OKAY] Running eyeris::zscore() for block_1
+  i [2025-10-25 01:05:16] [INFO] Block processing summary:
+  i [2025-10-25 01:05:16] [INFO] block_1: OK (steps: 6, latest:
   pupil_raw_deblink_detransient_interpolate_lpfilt_z)
-  v [2025-10-25 01:00:22] [OKAY] Running eyeris::summarize_confounds()
+  v [2025-10-25 01:05:16] [OKAY] Running eyeris::summarize_confounds()
   [ FAIL 4 | WARN 226 | SKIP 0 | PASS 192 ]
   
   == Failed tests ================================================================
> library(data.table, lib.loc=R.home("library"))
> (sig.diff.dt <- myDiff(Rvers))
Key: <checking>
Empty data.table (0 rows and 3 cols): checking,master,release
> 
> ## If there are significant differences, use git bisect to find when
> ## they started.
> if(nrow(sig.diff.dt)){
+   dt.git <- file.path(task.dir, "data.table.git")
+   unlink(dt.git, recursive=TRUE, force=TRUE)
+   system(paste("cd ~/R/data.table && git fetch --tags"))
+   system(paste("git clone ~/R/data.table", dt.git))
+   release.tag <- gsub(".tar.gz|.*_", "", cargs[["release"]])
+   rev.parse.cmd <- paste(
+     "cd", dt.git, "&& git rev-parse master")
+   master.sha <- system(rev.parse.cmd, intern=TRUE)
+   merge.base.cmd <- paste(
+     "cd", dt.git, "&& git merge-base master", release.tag)
+   merge.base.sha <- system(merge.base.cmd, intern=TRUE)
+   old.sha <- merge.base.sha
+   run_R <- file.path(proj.dir, "install_dt_then_check_dep.R")
+   sig.diff.dt[, first.bad.commit := NA_character_]
+   sig.diff.dt[, comments := NA_character_]
+   for(diff.i in 1:nrow(sig.diff.dt)){
+     sig.diff.row <- sig.diff.dt[diff.i]
+     bisect.cmd <- paste(
+       "cd", dt.git, "&&",
+       "git bisect start &&",
+       "git bisect old", old.sha, "&&",
+       "git bisect new master &&",
+       "git bisect run",
+       R.home('bin/Rscript'),
+       run_R,
+       shQuote(sig.diff.row$checking),
+       sig.diff.row$release,
+       rev.dep.release.tar.gz,
+       release.tag)
+     print(bisect.cmd)
+     bisect.out <- system(bisect.cmd, intern=TRUE)
+     cat(bisect.out,sep="\n")
+     if(is.null(attr(bisect.out,"status"))){
+       first.bad.sha <- nc::capture_all_str(
+         bisect.out,
+         sha="[0-9a-f]+",
+         " is the first new commit")$sha
+       parent.cmd <- paste(
+         "cd ~/R/data.table && git log --pretty=%P -n 1",
+         first.bad.sha)
+       parent.sha <- system(parent.cmd, intern=TRUE)
+       sig.diff.dt[diff.i, first.bad.commit := first.bad.sha]
+       parent.msg <- paste0("parent=", parent.sha)
+       this.comment <- if(parent.sha==old.sha){
+         paste(parent.msg, "same as git bisect old")
+       }else if(first.bad.sha==master.sha){
+         paste("same as git bisect new=master,", parent.msg)
+       }else{
+         parent.msg
+       }
+       sig.diff.dt[diff.i, comments := this.comment]
+     }
+   }
+   ## add CRAN column.
+   sig.diff.dt[, CRAN := {
+     flavor <- get_flavor(Rvers)
+     details <- data.table(flavor=unique(flavor))[, {
+       base <- "https://www.r-project.org/nosvn/R.check/"
+       u <- paste0(base, flavor, "/", rev.dep, "-00check.txt")
+       check.txt <- tempfile()
+       tryCatch({
+         download.file(u, check.txt, quiet=TRUE)
+       }, error=function(e){
+         NULL
+       })
+       check.lines <- if(file.exists(check.txt)){
+         readLines(check.txt,encoding="UTF-8")
+       }else{
+         ""
+       }
+       repl.lines <- gsub("[\u2018\u2019]", "'", check.lines)
+       ##gsub("[‘’]", "'", check.lines) does not work with LC_ALL=C.
+       myStatus(line.vec=repl.lines)
+     }, by=flavor]
+     select.dt <- data.table(flavor, checking)
+     details[select.dt, msg, on=.(flavor, checking)]
+   }]
+   dir.create(file.path(job.dir, Rvers))
+   diffs.csv <- file.path(job.dir, Rvers, "significant_differences.csv")
+   data.table::fwrite(sig.diff.dt, diffs.csv)
+   print(sig.diff.dt)
+ }
>