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

WARNING: ignoring environment value of R_HOME

R Under development (unstable) (2025-08-21 r88668) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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You are welcome to redistribute it under certain conditions.
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/2025-08-22/deps.csv", 
task.str = "1174", release = "/scratch/th798/data.table-revdeps/2025-08-22/data.table_release_1.17.8.tar.gz", 
master = "/scratch/th798/data.table-revdeps/2025-08-22/data.table_master_1.17.99.c27ec26f0112c62d8c51e8c064409a82e7b0db9c.tar.gz"
)
> (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers
[1] "/tmp/th798/21033829/R-devel/1174"
> if(requireNamespace("R.cache"))R.cache::getCachePath()
Loading required namespace: R.cache
[1] "/tmp/th798/21033829/R-devel/1174/R.cache"
> task.id <- as.integer(cargs[["task.str"]])
> deps.df <- read.csv(cargs[["deps.csv"]])
> (rev.dep <- deps.df$Package[task.id])
[1] "RDML"
> job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id)
> setwd(task.dir)
> .libPaths()
[1] "/tmp/th798/21033829/R-devel/1174/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] "2025-08-22 00:23:43 MST"
> install.time <- system.time({
+   install.packages(rev.dep, dep=TRUE)
+ })
Installing package into '/tmp/th798/21033829/R-devel/1174/library'
(as 'lib' is unspecified)
also installing the dependencies 'Rfit', 'pipeR', 'chipPCR', 'qpcR', 'kfigr', 'MBmca'

trying URL 'http://cloud.r-project.org/src/contrib/Rfit_0.27.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/pipeR_0.6.1.3.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/chipPCR_1.0-2.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/qpcR_1.4-2.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/kfigr_1.2.1.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/MBmca_1.1-0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/RDML_1.1.tar.gz'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'Rfit' failed
* installing *source* package 'pipeR' ...
** this is package 'pipeR' version '0.6.1.3'
** package 'pipeR' successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (pipeR)
ERROR: dependency 'Rfit' is not available for package 'chipPCR'
Perhaps try a variation of:
install.packages('Rfit')
* removing '/tmp/th798/21033829/R-devel/1174/library/chipPCR'
* installing *source* package 'qpcR' ...
** this is package 'qpcR' version '1.4-2'
** package 'qpcR' successfully unpacked and MD5 sums checked
** using staged installation
** 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    -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 registerDynamicSymbol.c -o registerDynamicSymbol.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    -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 smth.c -o smth.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 qpcR.so registerDynamicSymbol.o smth.o -L/home/th798/R/R-devel/lib -lRlapack -L/home/th798/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
installing to /tmp/th798/21033829/R-devel/1174/library/00LOCK-qpcR/00new/qpcR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (qpcR)
* installing *source* package 'kfigr' ...
** this is package 'kfigr' version '1.2.1'
** package 'kfigr' successfully unpacked and MD5 sums checked
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (kfigr)
ERROR: dependency 'chipPCR' is not available for package 'MBmca'
Perhaps try a variation of:
install.packages('chipPCR')
* removing '/tmp/th798/21033829/R-devel/1174/library/MBmca'
* installing *source* package 'RDML' ...
** this is package 'RDML' version '1.1'
** package 'RDML' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (RDML)

The downloaded source packages are in
	'/tmp/th798/21033829/RtmpfFPYDe/downloaded_packages'
Warning messages:
1: In download.file(urls, destfiles, "libcurl", mode = "wb", ...) :
  URL 'http://cloud.r-project.org/src/contrib/Rfit_0.27.0.tar.gz': Timeout of 60 seconds was reached
2: In download.file(urls, destfiles, "libcurl", mode = "wb", ...) :
  some files were not downloaded
3: In install.packages(rev.dep, dep = TRUE) :
  installation of package 'chipPCR' had non-zero exit status
4: In install.packages(rev.dep, dep = TRUE) :
  installation of package 'MBmca' had non-zero exit status
> cat("Time to install revdep:\n")
Time to install revdep:
> print(install.time)
   user  system elapsed 
 44.255   3.222 135.935 
> print(Sys.time())
[1] "2025-08-22 00:25:59 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] "2025-08-22 00:25:59 MST"
Installing package into '/tmp/th798/21033829/R-devel/1174/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/th798/21033829/R-devel/1174/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] "2025-08-22 00:26:20 MST"
* using log directory '/tmp/th798/21033829/R-devel/1174/RDML.Rcheck'
* using R Under development (unstable) (2025-08-21 r88668)
* 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 'RDML/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RDML' version '1.1'
* checking package namespace information ... OK
* checking package dependencies ... INFO
Packages suggested but not available for checking: 'chipPCR', 'MBmca'
* 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 'RDML' can be installed ... OK
* checking installed package size ... OK
* checking package 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 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 examples ... ERROR
Running examples in 'RDML-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RDML
> ### Title: R6 class 'RDML' - contains methods to read and overview
> ###   fluorescence data from RDML v1.1 and v1.2 format files
> ### Aliases: RDML
> ### Keywords: Bio--Rad CFX96 IO LightCycler RDML StepOne file qPCR
> 
> ### ** Examples
> 
> ## EXAMPLE 1:
> ## internal dataset lc96_bACTXY.rdml (in 'data' directory)
> ## generated by Roche LightCycler 96. Contains qPCR data
> ## with four targets and two types.
> ## Import with default settings.
> PATH <- path.package("RDML")
> filename <- paste(PATH, "/extdata/", "lc96_bACTXY.rdml", sep ="")
> lc96 <- RDML$new(filename)

Loading experiment: ca1eb225-ecea-4793-9804-87bfbb45f81d
	run: 65aeb1ec-b377-4ef6-b03f-92898d47488b
> 
> tab <- lc96$AsTable(name.pattern = paste(sample[[react$sample$id]]$description,
+                                          react$id$id), 
+                     quantity = sample[[react$sample$id]]$quantity$value)
Warning in lc96$AsTable(name.pattern = paste(sample[[react$sample$id]]$description,  :
  fdata.name column has duplicates! Try another 'name.pattern'.
> ## Show dyes names
> unique(tab$target.dyeId)
[1] "FAM"       "Hex"       "Texas Red" "Cy5"      
> ## Show types of the samples for dye 'FAM'
> library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> unique(filter(tab, target.dyeId == "FAM")$sample.type)
[1] "std"  "unkn"
> 
> ## Show template quantities for dye 'FAM' type 'std' 
> COPIES <- filter(tab, target.dyeId == "FAM", sample.type == "std")$quantity
> ## Define calibration curves (type of the samples - 'std').
> ## No replicates.
> library(qpcR)
Loading required package: MASS

Attaching package: 'MASS'

The following object is masked from 'package:dplyr':

    select

Loading required package: minpack.lm
Loading required package: rgl
This build of rgl does not include OpenGL functions.  Use
 rglwidget() to display results, e.g. via options(rgl.printRglwidget = TRUE).
Loading required package: robustbase
Loading required package: Matrix
> CAL <- modlist(lc96$GetFData(filter(tab,
+                                     target.dyeId == "FAM", 
+                                     sample.type == "std")),
+                baseline="lin", basecyc=8:15)
Making model for Sample 39 39 (l4)
 => Fitting passed...

Making model for Sample 39 40 (l4)
 => Fitting passed...

Making model for Sample 41 41 (l4)
 => Fitting passed...

Making model for Sample 41 42 (l4)
 => Fitting passed...

Making model for Sample 43 43 (l4)
 => Fitting passed...

Making model for Sample 43 44 (l4)
 => Fitting passed...

Making model for Sample 45 45 (l4)
 => Fitting passed...

Making model for Sample 45 46 (l4)
 => Fitting passed...

Making model for Sample 51 51 (l4)
 => Fitting passed...

Making model for Sample 51 52 (l4)
 => Fitting passed...

Calculating delta of first/second derivative maxima...
.........10
> ## Define samples to predict (first two samples with the type - 'unkn').
> PRED <- modlist(lc96$GetFData(filter(tab, 
+                                     target.dyeId == "FAM", 
+                                     sample.type == "unkn")),
+                baseline="lin", basecyc=8:15)
Making model for Sample 53 53 (l4)
 => Fitting passed...

Making model for Sample 54 54 (l4)
 => Fitting passed...

Making model for Sample 55 55 (l4)
 => Fitting passed...

Making model for Sample 56 56 (l4)
 => Fitting passed...

Making model for Sample 57 57 (l4)
 => Fitting passed...

Making model for Sample 58 58 (l4)
 => Fitting passed...

Calculating delta of first/second derivative maxima...
......
> ## Conduct quantification.
> calib(refcurve = CAL, predcurve = PRED, thresh = "cpD2",
+       dil = COPIES)
[1] "Calculating threshold cycles of reference curves..."
[1] "Calculating threshold cycles of prediction curves..."
$eff
         [,1]     [,2]     [,3]     [,4]     [,5]     [,6]     [,7]     [,8]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
         [,9]    [,10]    [,11]    [,12]    [,13]    [,14]    [,15]    [,16]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,17]    [,18]    [,19]    [,20]    [,21]    [,22]    [,23]    [,24]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,25]    [,26]    [,27]    [,28]    [,29]    [,30]    [,31]    [,32]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,33]    [,34]    [,35]    [,36]    [,37]    [,38]    [,39]    [,40]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,41]    [,42]    [,43]    [,44]    [,45]    [,46]    [,47]    [,48]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,49]    [,50]    [,51]    [,52]    [,53]    [,54]    [,55]    [,56]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,57]    [,58]    [,59]    [,60]    [,61]    [,62]    [,63]    [,64]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,65]    [,66]    [,67]    [,68]    [,69]    [,70]    [,71]    [,72]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,73]    [,74]    [,75]    [,76]    [,77]    [,78]    [,79]    [,80]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,81]    [,82]    [,83]    [,84]    [,85]    [,86]    [,87]    [,88]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,89]    [,90]    [,91]    [,92]    [,93]    [,94]    [,95]    [,96]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,97]    [,98]    [,99]   [,100]   [,101]   [,102]   [,103]   [,104]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,105]   [,106]   [,107]   [,108]   [,109]   [,110]   [,111]   [,112]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,113]   [,114]   [,115]   [,116]   [,117]   [,118]   [,119]   [,120]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,121]   [,122]   [,123]   [,124]   [,125]   [,126]   [,127]   [,128]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,129]   [,130]   [,131]   [,132]   [,133]   [,134]   [,135]   [,136]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,137]   [,138]   [,139]   [,140]   [,141]   [,142]   [,143]   [,144]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,145]   [,146]   [,147]   [,148]   [,149]   [,150]   [,151]   [,152]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,153]   [,154]   [,155]   [,156]   [,157]   [,158]   [,159]   [,160]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,161]   [,162]   [,163]   [,164]   [,165]   [,166]   [,167]   [,168]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,169]   [,170]   [,171]   [,172]   [,173]   [,174]   [,175]   [,176]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,177]   [,178]   [,179]   [,180]   [,181]   [,182]   [,183]   [,184]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,185]   [,186]   [,187]   [,188]   [,189]   [,190]   [,191]   [,192]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,193]   [,194]   [,195]   [,196]   [,197]   [,198]   [,199]   [,200]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251

$AICc
          [,1]      [,2]      [,3]      [,4]      [,5]      [,6]      [,7]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
          [,8]      [,9]     [,10]     [,11]     [,12]     [,13]     [,14]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,15]     [,16]     [,17]     [,18]     [,19]     [,20]     [,21]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,22]     [,23]     [,24]     [,25]     [,26]     [,27]     [,28]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,29]     [,30]     [,31]     [,32]     [,33]     [,34]     [,35]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,36]     [,37]     [,38]     [,39]     [,40]     [,41]     [,42]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,43]     [,44]     [,45]     [,46]     [,47]     [,48]     [,49]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,50]     [,51]     [,52]     [,53]     [,54]     [,55]     [,56]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,57]     [,58]     [,59]     [,60]     [,61]     [,62]     [,63]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,64]     [,65]     [,66]     [,67]     [,68]     [,69]     [,70]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,71]     [,72]     [,73]     [,74]     [,75]     [,76]     [,77]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,78]     [,79]     [,80]     [,81]     [,82]     [,83]     [,84]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,85]     [,86]     [,87]     [,88]     [,89]     [,90]     [,91]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,92]     [,93]     [,94]     [,95]     [,96]     [,97]     [,98]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,99]    [,100]    [,101]    [,102]    [,103]    [,104]    [,105]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,106]    [,107]    [,108]    [,109]    [,110]    [,111]    [,112]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,113]    [,114]    [,115]    [,116]    [,117]    [,118]    [,119]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,120]    [,121]    [,122]    [,123]    [,124]    [,125]    [,126]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,127]    [,128]    [,129]    [,130]    [,131]    [,132]    [,133]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,134]    [,135]    [,136]    [,137]    [,138]    [,139]    [,140]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,141]    [,142]    [,143]    [,144]    [,145]    [,146]    [,147]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,148]    [,149]    [,150]    [,151]    [,152]    [,153]    [,154]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,155]    [,156]    [,157]    [,158]    [,159]    [,160]    [,161]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,162]    [,163]    [,164]    [,165]    [,166]    [,167]    [,168]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,169]    [,170]    [,171]    [,172]    [,173]    [,174]    [,175]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,176]    [,177]    [,178]    [,179]    [,180]    [,181]    [,182]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,183]    [,184]    [,185]    [,186]    [,187]    [,188]    [,189]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,190]    [,191]    [,192]    [,193]    [,194]    [,195]    [,196]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,197]    [,198]    [,199]    [,200]
[1,] -13.92692 -13.92692 -13.92692 -13.92692

$Rsq.ad
          [,1]      [,2]      [,3]      [,4]      [,5]      [,6]      [,7]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
          [,8]      [,9]     [,10]     [,11]     [,12]     [,13]     [,14]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,15]     [,16]     [,17]     [,18]     [,19]     [,20]     [,21]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,22]     [,23]     [,24]     [,25]     [,26]     [,27]     [,28]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,29]     [,30]     [,31]     [,32]     [,33]     [,34]     [,35]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,36]     [,37]     [,38]     [,39]     [,40]     [,41]     [,42]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,43]     [,44]     [,45]     [,46]     [,47]     [,48]     [,49]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,50]     [,51]     [,52]     [,53]     [,54]     [,55]     [,56]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,57]     [,58]     [,59]     [,60]     [,61]     [,62]     [,63]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,64]     [,65]     [,66]     [,67]     [,68]     [,69]     [,70]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,71]     [,72]     [,73]     [,74]     [,75]     [,76]     [,77]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,78]     [,79]     [,80]     [,81]     [,82]     [,83]     [,84]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,85]     [,86]     [,87]     [,88]     [,89]     [,90]     [,91]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,92]     [,93]     [,94]     [,95]     [,96]     [,97]     [,98]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,99]    [,100]    [,101]    [,102]    [,103]    [,104]    [,105]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,106]    [,107]    [,108]    [,109]    [,110]    [,111]    [,112]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,113]    [,114]    [,115]    [,116]    [,117]    [,118]    [,119]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,120]    [,121]    [,122]    [,123]    [,124]    [,125]    [,126]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,127]    [,128]    [,129]    [,130]    [,131]    [,132]    [,133]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,134]    [,135]    [,136]    [,137]    [,138]    [,139]    [,140]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,141]    [,142]    [,143]    [,144]    [,145]    [,146]    [,147]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,148]    [,149]    [,150]    [,151]    [,152]    [,153]    [,154]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,155]    [,156]    [,157]    [,158]    [,159]    [,160]    [,161]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,162]    [,163]    [,164]    [,165]    [,166]    [,167]    [,168]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,169]    [,170]    [,171]    [,172]    [,173]    [,174]    [,175]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,176]    [,177]    [,178]    [,179]    [,180]    [,181]    [,182]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,183]    [,184]    [,185]    [,186]    [,187]    [,188]    [,189]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,190]    [,191]    [,192]    [,193]    [,194]    [,195]    [,196]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,197]    [,198]    [,199]    [,200]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956

$predconc
            [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
  [1,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
  [2,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
  [3,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
  [4,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
  [5,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
  [6,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
  [7,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
  [8,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
  [9,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [10,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [11,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [12,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [13,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [14,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [15,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [16,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [17,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [18,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [19,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [20,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [21,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [22,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [23,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [24,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [25,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [26,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [27,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [28,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [29,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [30,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [31,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [32,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [33,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [34,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [35,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [36,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [37,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [38,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [39,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [40,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [41,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [42,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [43,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [44,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
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 [47,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [48,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [49,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [50,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [51,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [52,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [53,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [54,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [55,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [56,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [57,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [58,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [59,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [60,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [61,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [62,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [63,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [64,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [65,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [66,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [67,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [68,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [69,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [70,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [71,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [72,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [73,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [74,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [75,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [76,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
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 [80,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [81,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [82,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
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 [88,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [89,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [90,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [91,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [92,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [93,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [94,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [95,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [96,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [97,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [98,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
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[100,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[101,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[102,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[103,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[104,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[105,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[106,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[107,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[108,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[109,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[110,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[111,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[112,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
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[126,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
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[128,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[129,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[130,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[131,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[132,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[133,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[134,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[135,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[136,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[137,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[138,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
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[140,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[141,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
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[153,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[154,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[155,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[156,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[157,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[158,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[159,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[160,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[161,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[162,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[163,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[164,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[165,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[166,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[167,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[168,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[169,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[170,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[171,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[172,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[173,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[174,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[175,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[176,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[177,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[178,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[179,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[180,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[181,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[182,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[183,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[184,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[185,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[186,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[187,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[188,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[189,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[190,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[191,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[192,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[193,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[194,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[195,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[196,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[197,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[198,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[199,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[200,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271

$conf.boot
$conf.boot$conf.eff
    2.5%    97.5% 
2.003251 2.003251 

$conf.boot$conf.AICc
     2.5%     97.5% 
-13.92692 -13.92692 

$conf.boot$conf.Rsq.ad
     2.5%     97.5% 
0.9992956 0.9992956 

$conf.boot$conf.predconc
           [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
2.5%  -1.478644 -1.487835 -3.381348 -3.584075 -3.172497 -2.979023
97.5% -1.410774 -1.419676 -3.247246 -3.442560 -3.045994 -2.859519


> 
> ## EXAMPLE 2:
> ## EXAMPLE 3:
> ## internal dataset BioRad_qPCR_melt.rdml (in 'data' directory)
> ## generated by Bio-Rad CFX96. Contains qPCR and melting data.
> ## Import with custom name pattern.
> PATH <- path.package("RDML")
> filename <- paste(PATH, "/extdata/", "BioRad_qPCR_melt.rdml", sep ="")
> cfx96 <- RDML$new(filename)

Loading experiment: All Wells
	run: Amp Step 3_FAM

	run: Amp Step 3_Cy5

Combining Bio-Rad runs
> ## Use plotCurves function from the chipPCR package to 
> ## get an overview of the amplification curves
> library(chipPCR)
Error in library(chipPCR) : there is no package called 'chipPCR'
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  '/tmp/th798/21033829/R-devel/1174/RDML.Rcheck/00check.log'
for details.

[1] "2025-08-22 00:27:49 MST"
[1] "2025-08-22 00:27:49 MST"
Installing package into '/tmp/th798/21033829/R-devel/1174/library'
(as 'lib' is unspecified)
Warning: invalid package '/scratch/th798/data.table-revdeps/2025-08-22/data.table_master_1.17.99.c27ec26f0112c62d8c51e8c064409a82e7b0db9c.tar.gz'
Error: ERROR: no packages specified
[1] "2025-08-22 00:27:50 MST"
* using log directory '/tmp/th798/21033829/R-devel/1174/RDML.Rcheck'
* using R Under development (unstable) (2025-08-21 r88668)
* 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 'RDML/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RDML' version '1.1'
* checking package namespace information ... OK
* checking package dependencies ... INFO
Packages suggested but not available for checking: 'chipPCR', 'MBmca'
* 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 'RDML' can be installed ... OK
* checking installed package size ... OK
* checking package 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 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 examples ... ERROR
Running examples in 'RDML-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RDML
> ### Title: R6 class 'RDML' - contains methods to read and overview
> ###   fluorescence data from RDML v1.1 and v1.2 format files
> ### Aliases: RDML
> ### Keywords: Bio--Rad CFX96 IO LightCycler RDML StepOne file qPCR
> 
> ### ** Examples
> 
> ## EXAMPLE 1:
> ## internal dataset lc96_bACTXY.rdml (in 'data' directory)
> ## generated by Roche LightCycler 96. Contains qPCR data
> ## with four targets and two types.
> ## Import with default settings.
> PATH <- path.package("RDML")
> filename <- paste(PATH, "/extdata/", "lc96_bACTXY.rdml", sep ="")
> lc96 <- RDML$new(filename)

Loading experiment: ca1eb225-ecea-4793-9804-87bfbb45f81d
	run: 65aeb1ec-b377-4ef6-b03f-92898d47488b
> 
> tab <- lc96$AsTable(name.pattern = paste(sample[[react$sample$id]]$description,
+                                          react$id$id), 
+                     quantity = sample[[react$sample$id]]$quantity$value)
Warning in lc96$AsTable(name.pattern = paste(sample[[react$sample$id]]$description,  :
  fdata.name column has duplicates! Try another 'name.pattern'.
> ## Show dyes names
> unique(tab$target.dyeId)
[1] "FAM"       "Hex"       "Texas Red" "Cy5"      
> ## Show types of the samples for dye 'FAM'
> library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> unique(filter(tab, target.dyeId == "FAM")$sample.type)
[1] "std"  "unkn"
> 
> ## Show template quantities for dye 'FAM' type 'std' 
> COPIES <- filter(tab, target.dyeId == "FAM", sample.type == "std")$quantity
> ## Define calibration curves (type of the samples - 'std').
> ## No replicates.
> library(qpcR)
Loading required package: MASS

Attaching package: 'MASS'

The following object is masked from 'package:dplyr':

    select

Loading required package: minpack.lm
Loading required package: rgl
This build of rgl does not include OpenGL functions.  Use
 rglwidget() to display results, e.g. via options(rgl.printRglwidget = TRUE).
Loading required package: robustbase
Loading required package: Matrix
> CAL <- modlist(lc96$GetFData(filter(tab,
+                                     target.dyeId == "FAM", 
+                                     sample.type == "std")),
+                baseline="lin", basecyc=8:15)
Making model for Sample 39 39 (l4)
 => Fitting passed...

Making model for Sample 39 40 (l4)
 => Fitting passed...

Making model for Sample 41 41 (l4)
 => Fitting passed...

Making model for Sample 41 42 (l4)
 => Fitting passed...

Making model for Sample 43 43 (l4)
 => Fitting passed...

Making model for Sample 43 44 (l4)
 => Fitting passed...

Making model for Sample 45 45 (l4)
 => Fitting passed...

Making model for Sample 45 46 (l4)
 => Fitting passed...

Making model for Sample 51 51 (l4)
 => Fitting passed...

Making model for Sample 51 52 (l4)
 => Fitting passed...

Calculating delta of first/second derivative maxima...
.........10
> ## Define samples to predict (first two samples with the type - 'unkn').
> PRED <- modlist(lc96$GetFData(filter(tab, 
+                                     target.dyeId == "FAM", 
+                                     sample.type == "unkn")),
+                baseline="lin", basecyc=8:15)
Making model for Sample 53 53 (l4)
 => Fitting passed...

Making model for Sample 54 54 (l4)
 => Fitting passed...

Making model for Sample 55 55 (l4)
 => Fitting passed...

Making model for Sample 56 56 (l4)
 => Fitting passed...

Making model for Sample 57 57 (l4)
 => Fitting passed...

Making model for Sample 58 58 (l4)
 => Fitting passed...

Calculating delta of first/second derivative maxima...
......
> ## Conduct quantification.
> calib(refcurve = CAL, predcurve = PRED, thresh = "cpD2",
+       dil = COPIES)
[1] "Calculating threshold cycles of reference curves..."
[1] "Calculating threshold cycles of prediction curves..."
$eff
         [,1]     [,2]     [,3]     [,4]     [,5]     [,6]     [,7]     [,8]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
         [,9]    [,10]    [,11]    [,12]    [,13]    [,14]    [,15]    [,16]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,17]    [,18]    [,19]    [,20]    [,21]    [,22]    [,23]    [,24]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,25]    [,26]    [,27]    [,28]    [,29]    [,30]    [,31]    [,32]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,33]    [,34]    [,35]    [,36]    [,37]    [,38]    [,39]    [,40]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,41]    [,42]    [,43]    [,44]    [,45]    [,46]    [,47]    [,48]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,49]    [,50]    [,51]    [,52]    [,53]    [,54]    [,55]    [,56]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,57]    [,58]    [,59]    [,60]    [,61]    [,62]    [,63]    [,64]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,65]    [,66]    [,67]    [,68]    [,69]    [,70]    [,71]    [,72]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,73]    [,74]    [,75]    [,76]    [,77]    [,78]    [,79]    [,80]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,81]    [,82]    [,83]    [,84]    [,85]    [,86]    [,87]    [,88]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,89]    [,90]    [,91]    [,92]    [,93]    [,94]    [,95]    [,96]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
        [,97]    [,98]    [,99]   [,100]   [,101]   [,102]   [,103]   [,104]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,105]   [,106]   [,107]   [,108]   [,109]   [,110]   [,111]   [,112]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,113]   [,114]   [,115]   [,116]   [,117]   [,118]   [,119]   [,120]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,121]   [,122]   [,123]   [,124]   [,125]   [,126]   [,127]   [,128]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,129]   [,130]   [,131]   [,132]   [,133]   [,134]   [,135]   [,136]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,137]   [,138]   [,139]   [,140]   [,141]   [,142]   [,143]   [,144]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,145]   [,146]   [,147]   [,148]   [,149]   [,150]   [,151]   [,152]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,153]   [,154]   [,155]   [,156]   [,157]   [,158]   [,159]   [,160]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,161]   [,162]   [,163]   [,164]   [,165]   [,166]   [,167]   [,168]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,169]   [,170]   [,171]   [,172]   [,173]   [,174]   [,175]   [,176]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,177]   [,178]   [,179]   [,180]   [,181]   [,182]   [,183]   [,184]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,185]   [,186]   [,187]   [,188]   [,189]   [,190]   [,191]   [,192]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251
       [,193]   [,194]   [,195]   [,196]   [,197]   [,198]   [,199]   [,200]
[1,] 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251 2.003251

$AICc
          [,1]      [,2]      [,3]      [,4]      [,5]      [,6]      [,7]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
          [,8]      [,9]     [,10]     [,11]     [,12]     [,13]     [,14]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,15]     [,16]     [,17]     [,18]     [,19]     [,20]     [,21]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,22]     [,23]     [,24]     [,25]     [,26]     [,27]     [,28]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,29]     [,30]     [,31]     [,32]     [,33]     [,34]     [,35]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,36]     [,37]     [,38]     [,39]     [,40]     [,41]     [,42]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,43]     [,44]     [,45]     [,46]     [,47]     [,48]     [,49]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,50]     [,51]     [,52]     [,53]     [,54]     [,55]     [,56]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,57]     [,58]     [,59]     [,60]     [,61]     [,62]     [,63]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,64]     [,65]     [,66]     [,67]     [,68]     [,69]     [,70]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,71]     [,72]     [,73]     [,74]     [,75]     [,76]     [,77]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,78]     [,79]     [,80]     [,81]     [,82]     [,83]     [,84]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,85]     [,86]     [,87]     [,88]     [,89]     [,90]     [,91]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,92]     [,93]     [,94]     [,95]     [,96]     [,97]     [,98]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
         [,99]    [,100]    [,101]    [,102]    [,103]    [,104]    [,105]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,106]    [,107]    [,108]    [,109]    [,110]    [,111]    [,112]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,113]    [,114]    [,115]    [,116]    [,117]    [,118]    [,119]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,120]    [,121]    [,122]    [,123]    [,124]    [,125]    [,126]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,127]    [,128]    [,129]    [,130]    [,131]    [,132]    [,133]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,134]    [,135]    [,136]    [,137]    [,138]    [,139]    [,140]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,141]    [,142]    [,143]    [,144]    [,145]    [,146]    [,147]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,148]    [,149]    [,150]    [,151]    [,152]    [,153]    [,154]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,155]    [,156]    [,157]    [,158]    [,159]    [,160]    [,161]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,162]    [,163]    [,164]    [,165]    [,166]    [,167]    [,168]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,169]    [,170]    [,171]    [,172]    [,173]    [,174]    [,175]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,176]    [,177]    [,178]    [,179]    [,180]    [,181]    [,182]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,183]    [,184]    [,185]    [,186]    [,187]    [,188]    [,189]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,190]    [,191]    [,192]    [,193]    [,194]    [,195]    [,196]
[1,] -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692 -13.92692
        [,197]    [,198]    [,199]    [,200]
[1,] -13.92692 -13.92692 -13.92692 -13.92692

$Rsq.ad
          [,1]      [,2]      [,3]      [,4]      [,5]      [,6]      [,7]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
          [,8]      [,9]     [,10]     [,11]     [,12]     [,13]     [,14]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,15]     [,16]     [,17]     [,18]     [,19]     [,20]     [,21]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,22]     [,23]     [,24]     [,25]     [,26]     [,27]     [,28]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,29]     [,30]     [,31]     [,32]     [,33]     [,34]     [,35]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,36]     [,37]     [,38]     [,39]     [,40]     [,41]     [,42]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,43]     [,44]     [,45]     [,46]     [,47]     [,48]     [,49]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,50]     [,51]     [,52]     [,53]     [,54]     [,55]     [,56]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,57]     [,58]     [,59]     [,60]     [,61]     [,62]     [,63]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,64]     [,65]     [,66]     [,67]     [,68]     [,69]     [,70]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,71]     [,72]     [,73]     [,74]     [,75]     [,76]     [,77]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,78]     [,79]     [,80]     [,81]     [,82]     [,83]     [,84]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,85]     [,86]     [,87]     [,88]     [,89]     [,90]     [,91]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,92]     [,93]     [,94]     [,95]     [,96]     [,97]     [,98]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
         [,99]    [,100]    [,101]    [,102]    [,103]    [,104]    [,105]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,106]    [,107]    [,108]    [,109]    [,110]    [,111]    [,112]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,113]    [,114]    [,115]    [,116]    [,117]    [,118]    [,119]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,120]    [,121]    [,122]    [,123]    [,124]    [,125]    [,126]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,127]    [,128]    [,129]    [,130]    [,131]    [,132]    [,133]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,134]    [,135]    [,136]    [,137]    [,138]    [,139]    [,140]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,141]    [,142]    [,143]    [,144]    [,145]    [,146]    [,147]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,148]    [,149]    [,150]    [,151]    [,152]    [,153]    [,154]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,155]    [,156]    [,157]    [,158]    [,159]    [,160]    [,161]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,162]    [,163]    [,164]    [,165]    [,166]    [,167]    [,168]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,169]    [,170]    [,171]    [,172]    [,173]    [,174]    [,175]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,176]    [,177]    [,178]    [,179]    [,180]    [,181]    [,182]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,183]    [,184]    [,185]    [,186]    [,187]    [,188]    [,189]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,190]    [,191]    [,192]    [,193]    [,194]    [,195]    [,196]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956 0.9992956
        [,197]    [,198]    [,199]    [,200]
[1,] 0.9992956 0.9992956 0.9992956 0.9992956

$predconc
            [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
  [1,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
  [2,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
  [3,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
  [4,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
  [5,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
  [6,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
  [7,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
  [8,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
  [9,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [10,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [11,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [12,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [13,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [14,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [15,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [16,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [17,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [18,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [19,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [20,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [21,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [22,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [23,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [24,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [25,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [26,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [27,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [28,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [29,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [30,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [31,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [32,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [33,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [34,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [35,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [36,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [37,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [38,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [39,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [40,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [41,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [42,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [43,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [44,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [45,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [46,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [47,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [48,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [49,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [50,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [51,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [52,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [53,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [54,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [55,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [56,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [57,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [58,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [59,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [60,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [61,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [62,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [63,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [64,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [65,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [66,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [67,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [68,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [69,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [70,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [71,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [72,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [73,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [74,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [75,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [76,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [77,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [78,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [79,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [80,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [81,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [82,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [83,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [84,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [85,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [86,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [87,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [88,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [89,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [90,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [91,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [92,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [93,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [94,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [95,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [96,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [97,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [98,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
 [99,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[100,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[101,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[102,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[103,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[104,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[105,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[106,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[107,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[108,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[109,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[110,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[111,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[112,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[113,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[114,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[115,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[116,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[117,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[118,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[119,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[120,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[121,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[122,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[123,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[124,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[125,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[126,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[127,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[128,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[129,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[130,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[131,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[132,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[133,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[134,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[135,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[136,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[137,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[138,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[139,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[140,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[141,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[142,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[143,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[144,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[145,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[146,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[147,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[148,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[149,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[150,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[151,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[152,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[153,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[154,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[155,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[156,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[157,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[158,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[159,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[160,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[161,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[162,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[163,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[164,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[165,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[166,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[167,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[168,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[169,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[170,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[171,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[172,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[173,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[174,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[175,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[176,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[177,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[178,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[179,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[180,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[181,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[182,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[183,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[184,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[185,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[186,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[187,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[188,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[189,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[190,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[191,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[192,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[193,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[194,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[195,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[196,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[197,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[198,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[199,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271
[200,] -1.444709 -1.453755 -3.314297 -3.513318 -3.109245 -2.919271

$conf.boot
$conf.boot$conf.eff
    2.5%    97.5% 
2.003251 2.003251 

$conf.boot$conf.AICc
     2.5%     97.5% 
-13.92692 -13.92692 

$conf.boot$conf.Rsq.ad
     2.5%     97.5% 
0.9992956 0.9992956 

$conf.boot$conf.predconc
           [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
2.5%  -1.478644 -1.487835 -3.381348 -3.584075 -3.172497 -2.979023
97.5% -1.410774 -1.419676 -3.247246 -3.442560 -3.045994 -2.859519


> 
> ## EXAMPLE 2:
> ## EXAMPLE 3:
> ## internal dataset BioRad_qPCR_melt.rdml (in 'data' directory)
> ## generated by Bio-Rad CFX96. Contains qPCR and melting data.
> ## Import with custom name pattern.
> PATH <- path.package("RDML")
> filename <- paste(PATH, "/extdata/", "BioRad_qPCR_melt.rdml", sep ="")
> cfx96 <- RDML$new(filename)

Loading experiment: All Wells
	run: Amp Step 3_FAM

	run: Amp Step 3_Cy5

Combining Bio-Rad runs
> ## Use plotCurves function from the chipPCR package to 
> ## get an overview of the amplification curves
> library(chipPCR)
Error in library(chipPCR) : there is no package called 'chipPCR'
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  '/tmp/th798/21033829/R-devel/1174/RDML.Rcheck/00check.log'
for details.

[1] "2025-08-22 00:29:10 MST"
Warning message:
In install.packages(dt.tar.gz, repos = NULL) :
  installation of package '/scratch/th798/data.table-revdeps/2025-08-22/data.table_master_1.17.99.c27ec26f0112c62d8c51e8c064409a82e7b0db9c.tar.gz' had non-zero exit status
> system(paste(c("diff -u", Rcheck.list), collapse=" "))
> 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")
+   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/2025-08-22/deps.csv", 
task.str = "1174", release = "/scratch/th798/data.table-revdeps/2025-08-22/data.table_release_1.17.8.tar.gz", 
master = "/scratch/th798/data.table-revdeps/2025-08-22/data.table_master_1.17.99.c27ec26f0112c62d8c51e8c064409a82e7b0db9c.tar.gz"
)
> (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers
[1] "/tmp/th798/21033829/R-release/1174"
> if(requireNamespace("R.cache"))R.cache::getCachePath()
Loading required namespace: R.cache
[1] "/tmp/th798/21033829/R-release/1174/R.cache"
> task.id <- as.integer(cargs[["task.str"]])
> deps.df <- read.csv(cargs[["deps.csv"]])
> (rev.dep <- deps.df$Package[task.id])
[1] "RDML"
> job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id)
> setwd(task.dir)
> .libPaths()
[1] "/tmp/th798/21033829/R-release/1174/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] "2025-08-22 00:29:16 MST"
> install.time <- system.time({
+   install.packages(rev.dep, dep=TRUE)
+ })
Installing package into '/tmp/th798/21033829/R-release/1174/library'
(as 'lib' is unspecified)
also installing the dependencies 'Rfit', 'pipeR', 'chipPCR', 'qpcR', 'kfigr', 'MBmca'

trying URL 'http://cloud.r-project.org/src/contrib/Rfit_0.27.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/pipeR_0.6.1.3.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/chipPCR_1.0-2.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/qpcR_1.4-2.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/kfigr_1.2.1.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/MBmca_1.1-0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/RDML_1.1.tar.gz'
* installing *source* package 'Rfit' ...
** this is package 'Rfit' version '0.27.0'
** package 'Rfit' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: 'gcc (Spack GCC) 12.2.0'
using Fortran compiler: 'GNU Fortran (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/gfortran  -fpic  -g -O2  -c hfuncd.f -o hfuncd.o
/packages/gcc/12.2.0-nnbserq/bin/gfortran  -fpic  -g -O2  -c hubcor.f -o hubcor.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    -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/gfortran  -fpic  -g -O2  -c lin3.f -o lin3.o
/packages/gcc/12.2.0-nnbserq/bin/gfortran  -fpic  -g -O2  -c nscale.f -o nscale.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 Rfit.so hfuncd.o hubcor.o init.o lin3.o nscale.o -lgfortran -lm -lquadmath
installing to /tmp/th798/21033829/R-release/1174/library/00LOCK-Rfit/00new/Rfit/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (Rfit)
* installing *source* package 'pipeR' ...
** this is package 'pipeR' version '0.6.1.3'
** package 'pipeR' successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (pipeR)
* installing *source* package 'qpcR' ...
** this is package 'qpcR' version '1.4-2'
** package 'qpcR' successfully unpacked and MD5 sums checked
** using staged installation
** 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    -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 registerDynamicSymbol.c -o registerDynamicSymbol.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    -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 smth.c -o smth.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 qpcR.so registerDynamicSymbol.o smth.o -L/home/th798/R/R-release/lib -lRlapack -L/home/th798/R/R-release/lib -lRblas -lgfortran -lm -lquadmath
installing to /tmp/th798/21033829/R-release/1174/library/00LOCK-qpcR/00new/qpcR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (qpcR)
* installing *source* package 'kfigr' ...
** this is package 'kfigr' version '1.2.1'
** package 'kfigr' successfully unpacked and MD5 sums checked
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (kfigr)
* installing *source* package 'chipPCR' ...
** this is package 'chipPCR' version '1.0-2'
** package 'chipPCR' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'qqline' from package 'stats' in package 'chipPCR'
** help
*** installing help indices
** 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 (chipPCR)
* installing *source* package 'RDML' ...
** this is package 'RDML' version '1.1'
** package 'RDML' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (RDML)
* installing *source* package 'MBmca' ...
** this is package 'MBmca' version '1.1-0'
** package 'MBmca' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MBmca)

The downloaded source packages are in
	'/tmp/th798/21033829/RtmpHqIIC5/downloaded_packages'
> cat("Time to install revdep:\n")
Time to install revdep:
> print(install.time)
   user  system elapsed 
 66.959   3.179  74.631 
> print(Sys.time())
[1] "2025-08-22 00:30:30 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] "2025-08-22 00:30:30 MST"
Installing package into '/tmp/th798/21033829/R-release/1174/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/th798/21033829/R-release/1174/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] "2025-08-22 00:30:49 MST"
* using log directory '/tmp/th798/21033829/R-release/1174/RDML.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 'RDML/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RDML' version '1.1'
* 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 'RDML' can be installed ... OK
* checking installed package size ... OK
* checking package 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 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 examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
      user system elapsed
RDML 7.721  0.172   8.095
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: OK

[1] "2025-08-22 00:32:15 MST"
[1] "2025-08-22 00:32:15 MST"
Installing package into '/tmp/th798/21033829/R-release/1174/library'
(as 'lib' is unspecified)
Warning: invalid package '/scratch/th798/data.table-revdeps/2025-08-22/data.table_master_1.17.99.c27ec26f0112c62d8c51e8c064409a82e7b0db9c.tar.gz'
Error: ERROR: no packages specified
[1] "2025-08-22 00:32:16 MST"
* using log directory '/tmp/th798/21033829/R-release/1174/RDML.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 'RDML/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RDML' version '1.1'
* 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 'RDML' can be installed ... OK
* checking installed package size ... OK
* checking package 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 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 examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
      user system elapsed
RDML 7.701  0.163   8.066
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: OK

[1] "2025-08-22 00:33:39 MST"
Warning message:
In install.packages(dt.tar.gz, repos = NULL) :
  installation of package '/scratch/th798/data.table-revdeps/2025-08-22/data.table_master_1.17.99.c27ec26f0112c62d8c51e8c064409a82e7b0db9c.tar.gz' had non-zero exit status
> system(paste(c("diff -u", Rcheck.list), collapse=" "))
--- R_version_4.5.1_2025-06-13/release_1.17.8.Rcheck/00check.log	2025-08-22 00:32:15.975867976 -0700
+++ R_version_4.5.1_2025-06-13/master_1.17.99.c27ec26f0112c62d8c51e8c064409a82e7b0db9c.Rcheck/00check.log	2025-08-22 00:33:39.525339274 -0700
@@ -49,7 +49,7 @@
 * checking examples ... OK
 Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
-RDML 7.721  0.172   8.095
+RDML 7.701  0.163   8.066
 * checking for unstated dependencies in 'tests' ... OK
 * checking tests ... OK
   Running 'testthat.R'
> 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")
+   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)
+ }
>