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

WARNING: ignoring environment value of R_HOME

R Under development (unstable) (2025-03-29 r88074) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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> 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/2025-03-30/deps.csv", 
task.str = "474", release = "/scratch/th798/data.table-revdeps/2025-03-30/data.table_release_1.17.0.tar.gz", 
master = "/scratch/th798/data.table-revdeps/2025-03-30/data.table_master_1.17.99.2cb03162a21328cc5f68a8c3b0e554f5edfcb5b9.tar.gz"
)
> (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers
[1] "/tmp/th798/16189510/R-devel/474"
> if(requireNamespace("R.cache"))R.cache::getCachePath()
Loading required namespace: R.cache
[1] "/tmp/th798/16189510/R-devel/474/R.cache"
> task.id <- as.integer(cargs[["task.str"]])
> deps.df <- read.csv(cargs[["deps.csv"]])
> (rev.dep <- deps.df$Package[task.id])
[1] "fixest"
> job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id)
> setwd(task.dir)
> .libPaths()
[1] "/tmp/th798/16189510/R-devel/474/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] "2025-03-30 01:01:12 MST"
> install.time <- system.time({
+   install.packages(rev.dep, dep=TRUE)
+ })
Installing package into '/tmp/th798/16189510/R-devel/474/library'
(as 'lib' is unspecified)
also installing the dependencies 'collapse', 'dreamerr', 'stringmagic', 'plm', 'lfe', 'AER'

trying URL 'http://cloud.r-project.org/src/contrib/collapse_2.1.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/dreamerr_1.4.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/stringmagic_1.1.2.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/plm_2.6-5.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/lfe_3.1.1.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/AER_1.2-14.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/fixest_0.12.1.tar.gz'
* installing *source* package 'collapse' ...
** this is package 'collapse' version '2.1.0'
** package 'collapse' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: 'gcc (Spack GCC) 12.2.0'
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ExportSymbols.c -o ExportSymbols.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c RcppExports.cpp -o RcppExports.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c TRA.c -o TRA.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c base_radixsort.c -o base_radixsort.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c data.table_init.c -o data.table_init.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c data.table_rbindlist.c -o data.table_rbindlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c data.table_subset.c -o data.table_subset.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c data.table_utils.c -o data.table_utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c extptr.c -o extptr.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c fbetween_fwithin.cpp -o fbetween_fwithin.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c fbstats.cpp -o fbstats.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fcumsum.c -o fcumsum.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c fdiff_fgrowth.cpp -o fdiff_fgrowth.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ffirst.c -o ffirst.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c flag.cpp -o flag.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c flast.c -o flast.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fmean.c -o fmean.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fmin_fmax.c -o fmin_fmax.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fmode.c -o fmode.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fndistinct.c -o fndistinct.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fnobs.c -o fnobs.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fnth_fmedian_fquantile.c -o fnth_fmedian_fquantile.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fprod.c -o fprod.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c fscale.cpp -o fscale.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fsum.c -o fsum.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c fvar_fsd.cpp -o fvar_fsd.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c gsplit.c -o gsplit.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c handle_attributes.c -o handle_attributes.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c join.c -o join.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c kit_dup.c -o kit_dup.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c match.c -o match.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c mrtl_mctl.cpp -o mrtl_mctl.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c pivot.c -o pivot.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c psmat.cpp -o psmat.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c pwnobs.cpp -o pwnobs.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c qF_qG.cpp -o qF_qG.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c seqid_groupid.cpp -o seqid_groupid.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c small_helper.c -o small_helper.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c stats_mAR.c -o stats_mAR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c stats_pacf.c -o stats_pacf.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c varying.cpp -o varying.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o collapse.so ExportSymbols.o RcppExports.o TRA.o base_radixsort.o data.table_init.o data.table_rbindlist.o data.table_subset.o data.table_utils.o extptr.o fbetween_fwithin.o fbstats.o fcumsum.o fdiff_fgrowth.o ffirst.o flag.o flast.o fmean.o fmin_fmax.o fmode.o fndistinct.o fnobs.o fnth_fmedian_fquantile.o fprod.o fscale.o fsum.o fvar_fsd.o gsplit.o handle_attributes.o join.o kit_dup.o match.o mrtl_mctl.o pivot.o programming.o psmat.o pwnobs.o qF_qG.o seqid_groupid.o small_helper.o stats_mAR.o stats_pacf.o varying.o -fopenmp
installing to /tmp/th798/16189510/R-devel/474/library/00LOCK-collapse/00new/collapse/libs
** 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
** 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 (collapse)
* installing *source* package 'stringmagic' ...
** this is package 'stringmagic' version '1.1.2'
** package 'stringmagic' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c RcppExports.cpp -o RcppExports.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c string_tools.cpp -o string_tools.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c stringmagic.cpp -o stringmagic.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c stringmagic_parser.cpp -o stringmagic_parser.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c to_integer.cpp -o to_integer.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o stringmagic.so RcppExports.o string_tools.o stringmagic.o stringmagic_parser.o to_integer.o
installing to /tmp/th798/16189510/R-devel/474/library/00LOCK-stringmagic/00new/stringmagic/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** 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 (stringmagic)
* installing *source* package 'lfe' ...
** this is package 'lfe' version '3.1.1'
** package 'lfe' successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... /packages/gcc/12.2.0-nnbserq/bin/gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether /packages/gcc/12.2.0-nnbserq/bin/gcc accepts -g... yes
checking for /packages/gcc/12.2.0-nnbserq/bin/gcc option to enable C11 features... none needed
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for a sed that does not truncate output... /usr/bin/sed
checking how to run the C preprocessor... /packages/gcc/12.2.0-nnbserq/bin/gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking whether /packages/gcc/12.2.0-nnbserq/bin/gcc is Clang... no
checking whether pthreads work with "-pthread" and "-lpthread"... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking for timed semaphore wait... yes
checking for library containing pthread_setname_np... none required
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
config.status: src/config.h is unchanged
** 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   -fvisibility=hidden -fopenmp -pthread  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c crowsum.c -o crowsum.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   -fvisibility=hidden -fopenmp -pthread  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c demean.c -o demean.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   -fvisibility=hidden -fopenmp -pthread  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c factor.c -o factor.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   -fvisibility=hidden -fopenmp -pthread  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c kaczmarz.c -o kaczmarz.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   -fvisibility=hidden -fopenmp -pthread  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c lfe.c -o lfe.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   -fvisibility=hidden -fopenmp -pthread  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -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 lfe.so crowsum.o demean.o factor.o kaczmarz.o lfe.o utils.o -lpthread -pthread -L/home/th798/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -fopenmp
installing to /tmp/th798/16189510/R-devel/474/library/00LOCK-lfe/00new/lfe/libs
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lfe)
* installing *source* package 'AER' ...
** this is package 'AER' version '1.2-14'
** package 'AER' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** demo
** 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 (AER)
* installing *source* package 'dreamerr' ...
** this is package 'dreamerr' version '1.4.0'
** package 'dreamerr' 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 (dreamerr)
* installing *source* package 'plm' ...
** this is package 'plm' version '2.6-5'
** package 'plm' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** 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 (plm)
* installing *source* package 'fixest' ...
** this is package 'fixest' version '0.12.1'
** package 'fixest' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c RcppExports.cpp -o RcppExports.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c convergence.cpp -o convergence.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c demeaning.cpp -o demeaning.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c dsb.cpp -o dsb.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c lm_related.cpp -o lm_related.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c misc_funs.cpp -o misc_funs.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c parallel_funs.cpp -o parallel_funs.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c quf.cpp -o quf.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c string_funs.cpp -o string_funs.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c vcov_related.cpp -o vcov_related.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o fixest.so RcppExports.o convergence.o demeaning.o dsb.o lm_related.o misc_funs.o parallel_funs.o quf.o string_funs.o vcov_related.o -fopenmp
installing to /tmp/th798/16189510/R-devel/474/library/00LOCK-fixest/00new/fixest/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** 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 (fixest)

The downloaded source packages are in
	'/tmp/th798/16189510/RtmpvJm0eT/downloaded_packages'
> cat("Time to install revdep:\n")
Time to install revdep:
> print(install.time)
   user  system elapsed 
154.183  10.366 289.093 
> print(Sys.time())
[1] "2025-03-30 01:06:01 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] "2025-03-30 01:06:01 MST"
Installing package into '/tmp/th798/16189510/R-devel/474/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** this is package 'data.table' version '1.17.0'
** 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/th798/16189510/R-devel/474/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] "2025-03-30 01:06:24 MST"
* using log directory '/tmp/th798/16189510/R-devel/474/fixest.Rcheck'
* using R Under development (unstable) (2025-03-29 r88074)
* 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 'fixest/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'fixest' version '0.12.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'fixest' can be installed ... OK
* used C++ compiler: 'g++ (Spack GCC) 12.2.0'
* checking installed package size ... INFO
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    3.6Mb
    libs   1.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'fixest_tests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

[1] "2025-03-30 01:11:38 MST"
[1] "2025-03-30 01:11:38 MST"
Installing package into '/tmp/th798/16189510/R-devel/474/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** this is package 'data.table' version '1.17.99'
** using staged installation
zlib 1.2.13 is available ok
* checking if R installation supports OpenMP without any extra hints... yes
** libs
using C compiler: 'gcc (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c assign.c -o assign.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c between.c -o between.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c bmerge.c -o bmerge.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c chmatch.c -o chmatch.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c cj.c -o cj.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c coalesce.c -o coalesce.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c dogroups.c -o dogroups.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fastmean.c -o fastmean.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fcast.c -o fcast.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fifelse.c -o fifelse.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fmelt.c -o fmelt.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c forder.c -o forder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frank.c -o frank.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fread.c -o fread.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c freadR.c -o freadR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c froll.c -o froll.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frollR.c -o frollR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frolladaptive.c -o frolladaptive.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c 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/th798/16189510/R-devel/474/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] "2025-03-30 01:12:00 MST"
* using log directory '/tmp/th798/16189510/R-devel/474/fixest.Rcheck'
* using R Under development (unstable) (2025-03-29 r88074)
* 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 'fixest/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'fixest' version '0.12.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'fixest' can be installed ... OK
* used C++ compiler: 'g++ (Spack GCC) 12.2.0'
* checking installed package size ... INFO
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    3.6Mb
    libs   1.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'fixest_tests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

[1] "2025-03-30 01:16:37 MST"
> 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 4.4.3 (2025-02-28) -- "Trophy Case"
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/2025-03-30/deps.csv", 
task.str = "474", release = "/scratch/th798/data.table-revdeps/2025-03-30/data.table_release_1.17.0.tar.gz", 
master = "/scratch/th798/data.table-revdeps/2025-03-30/data.table_master_1.17.99.2cb03162a21328cc5f68a8c3b0e554f5edfcb5b9.tar.gz"
)
> (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers
[1] "/tmp/th798/16189510/R-release/474"
> if(requireNamespace("R.cache"))R.cache::getCachePath()
Loading required namespace: R.cache
[1] "/tmp/th798/16189510/R-release/474/R.cache"
> task.id <- as.integer(cargs[["task.str"]])
> deps.df <- read.csv(cargs[["deps.csv"]])
> (rev.dep <- deps.df$Package[task.id])
[1] "fixest"
> job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id)
> setwd(task.dir)
> .libPaths()
[1] "/tmp/th798/16189510/R-release/474/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] "2025-03-30 01:16:42 MST"
> install.time <- system.time({
+   install.packages(rev.dep, dep=TRUE)
+ })
Installing package into '/tmp/th798/16189510/R-release/474/library'
(as 'lib' is unspecified)
also installing the dependencies 'dreamerr', 'stringmagic', 'lfe'

trying URL 'http://cloud.r-project.org/src/contrib/dreamerr_1.4.0.tar.gz'
Content type 'application/x-gzip' length 1122706 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'http://cloud.r-project.org/src/contrib/stringmagic_1.1.2.tar.gz'
Content type 'application/x-gzip' length 3340420 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

trying URL 'http://cloud.r-project.org/src/contrib/lfe_3.1.1.tar.gz'
Content type 'application/x-gzip' length 1126380 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'http://cloud.r-project.org/src/contrib/fixest_0.12.1.tar.gz'
Content type 'application/x-gzip' length 2325402 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

* installing *source* package 'stringmagic' ...
** package 'stringmagic' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c RcppExports.cpp -o RcppExports.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c string_tools.cpp -o string_tools.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c stringmagic.cpp -o stringmagic.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c stringmagic_parser.cpp -o stringmagic_parser.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c to_integer.cpp -o to_integer.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o stringmagic.so RcppExports.o string_tools.o stringmagic.o stringmagic_parser.o to_integer.o
installing to /tmp/th798/16189510/R-release/474/library/00LOCK-stringmagic/00new/stringmagic/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** 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 (stringmagic)
* installing *source* package 'lfe' ...
** package 'lfe' successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... /packages/gcc/12.2.0-nnbserq/bin/gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether /packages/gcc/12.2.0-nnbserq/bin/gcc accepts -g... yes
checking for /packages/gcc/12.2.0-nnbserq/bin/gcc option to enable C11 features... none needed
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for a sed that does not truncate output... /usr/bin/sed
checking how to run the C preprocessor... /packages/gcc/12.2.0-nnbserq/bin/gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking whether /packages/gcc/12.2.0-nnbserq/bin/gcc is Clang... no
checking whether pthreads work with "-pthread" and "-lpthread"... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking for timed semaphore wait... yes
checking for library containing pthread_setname_np... none required
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
config.status: src/config.h is unchanged
** 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   -fvisibility=hidden -fopenmp -pthread  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c crowsum.c -o crowsum.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   -fvisibility=hidden -fopenmp -pthread  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c demean.c -o demean.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   -fvisibility=hidden -fopenmp -pthread  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c factor.c -o factor.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   -fvisibility=hidden -fopenmp -pthread  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c kaczmarz.c -o kaczmarz.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   -fvisibility=hidden -fopenmp -pthread  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c lfe.c -o lfe.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   -fvisibility=hidden -fopenmp -pthread  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -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 lfe.so crowsum.o demean.o factor.o kaczmarz.o lfe.o utils.o -lpthread -pthread -L/home/th798/R/R-release/lib -lRblas -lgfortran -lm -lquadmath -fopenmp
installing to /tmp/th798/16189510/R-release/474/library/00LOCK-lfe/00new/lfe/libs
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lfe)
* installing *source* package 'dreamerr' ...
** package 'dreamerr' 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 (dreamerr)
* installing *source* package 'fixest' ...
** package 'fixest' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c RcppExports.cpp -o RcppExports.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c convergence.cpp -o convergence.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c demeaning.cpp -o demeaning.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c dsb.cpp -o dsb.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c lm_related.cpp -o lm_related.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c misc_funs.cpp -o misc_funs.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c parallel_funs.cpp -o parallel_funs.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c quf.cpp -o quf.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c string_funs.cpp -o string_funs.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -DSTRICT_R_HEADERS -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c vcov_related.cpp -o vcov_related.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o fixest.so RcppExports.o convergence.o demeaning.o dsb.o lm_related.o misc_funs.o parallel_funs.o quf.o string_funs.o vcov_related.o -fopenmp
installing to /tmp/th798/16189510/R-release/474/library/00LOCK-fixest/00new/fixest/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** 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 (fixest)

The downloaded source packages are in
	'/tmp/th798/16189510/Rtmpp8Ku4w/downloaded_packages'
> cat("Time to install revdep:\n")
Time to install revdep:
> print(install.time)
   user  system elapsed 
 98.624   4.760 111.801 
> print(Sys.time())
[1] "2025-03-30 01:18:34 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] "2025-03-30 01:18:34 MST"
Installing package into '/tmp/th798/16189510/R-release/474/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** 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/th798/16189510/R-release/474/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] "2025-03-30 01:18:53 MST"
* using log directory '/tmp/th798/16189510/R-release/474/fixest.Rcheck'
* using R version 4.4.3 (2025-02-28)
* 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 'fixest/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'fixest' version '0.12.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'fixest' can be installed ... OK
* used C++ compiler: 'g++ (Spack GCC) 12.2.0'
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    3.6Mb
    libs   1.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'fixest_tests.R'
 ERROR
Running the tests in 'tests/fixest_tests.R' failed.
Complete output:
  > #----------------------------------------------#
  > # Author: Laurent Berge
  > # Date creation: Fri Jul 10 09:03:06 2020
  > # ~: package sniff tests
  > #----------------------------------------------#
  > 
  > # Not everything is currently covered, but I'll improve it over time
  > 
  > # Some functions are not trivial to test properly though
  > 
  > library(fixest)
  > 
  > test = fixest:::test ; chunk = fixest:::chunk
  > vcovClust = fixest:::vcovClust
  > stvec = stringmagic::string_vec_alias()
  > 
  > setFixest_notes(FALSE)
  > 
  > if(fixest:::is_r_check()){
  +   if(requireNamespace("data.table", quietly = TRUE)){
  +     library(data.table)
  +     data.table::setDTthreads(1)
  +   }
  +   setFixest_nthreads(1)
  + }
  > 
  > ####
  > #### ESTIMATIONS ####
  > ####
  > 
  > ####
  > #### ... Main ####
  > ####
  > 
  > 
  > chunk("ESTIMATION")
  ESTIMATION
  
  > 
  > set.seed(0)
  > 
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > base$fe_2 = rep(1:5, 30)
  > base$fe_3 = sample(15, 150, TRUE)
  > base$constant = 5
  > base$y_int = as.integer(base$y)
  > base$w = as.vector(unclass(base$species) - 0.95)
  > base$offset_value = unclass(base$species) - 0.95
  > base$y_01 = 1 * ((scale(base$x1) + rnorm(150)) > 0)
  > # what follows to avoid removal of fixed-effects (logit is pain in the neck)
  > base$y_01[1:5 + rep(c(0, 50, 100), each = 5)] = 1
  > base$y_01[6:10 + rep(c(0, 50, 100), each = 5)] = 0
  > # We enforce the removal of observations
  > base$y_int_null = base$y_int
  > base$y_int_null[base$fe_3 %in% 1:5] = 0
  > 
  > for(model in c("ols", "pois", "logit", "negbin", "Gamma")){
  +   cat("Model: ", format(model, width = 6), sep = "")
  +   for(use_weights in c(FALSE, TRUE)){
  +     my_weight = NULL
  +     if(use_weights) my_weight = base$w
  + 
  +     for(use_offset in c(FALSE, TRUE)){
  +       my_offset = NULL
  +       if(use_offset) my_offset = base$offset_value
  + 
  +       for(id_fe in 0:9){
  + 
  +         cat(".")
  + 
  +         tol = switch(model, "negbin" = 1e-2, "logit" = 3e-5, 1e-5)
  + 
  +         # Setting up the formula to accommodate FEs
  +         if(id_fe == 0){
  +           fml_fixest = fml_stats = y ~ x1
  +         } else if(id_fe == 1){
  +           fml_fixest = y ~ x1 | species
  +           fml_stats = y ~ x1 + factor(species)
  +         } else if(id_fe == 2){
  +           fml_fixest = y ~ x1 | species + fe_2
  +           fml_stats = y ~ x1 + factor(species) + factor(fe_2)
  +         } else if(id_fe == 3){
  +           # varying slope
  +           fml_fixest = y ~ x1 | species[[x2]]
  +           fml_stats = y ~ x1 + x2:species
  +         } else if(id_fe == 4){
  +           # varying slope -- 1 VS, 1 FE
  +           fml_fixest = y ~ x1 | species[[x2]] + fe_2
  +           fml_stats = y ~ x1 + x2:species + factor(fe_2)
  +         } else if(id_fe == 5){
  +           # varying slope -- 2 VS
  +           fml_fixest = y ~ x1 | species[x2]
  +           fml_stats = y ~ x1 + x2:species + species
  +         } else if(id_fe == 6){
  +           # varying slope -- 2 VS bis
  +           fml_fixest = y ~ x1 | species[[x2]] + fe_2[[x3]]
  +           fml_stats = y ~ x1 + x2:species + x3:factor(fe_2)
  +         } else if(id_fe == 7){
  +           # Combined clusters
  +           fml_fixest = y ~ x1 + x2 | species^fe_2
  +           fml_stats = y ~ x1 + x2 + paste(species, fe_2)
  +         } else if(id_fe == 8){
  +           fml_fixest = y ~ x1 | species[x2] + fe_2[x3] + fe_3
  +           fml_stats = y ~ x1 + species + i(species, x2) + factor(fe_2) + i(fe_2, x3) + factor(fe_3)
  +         } else if(id_fe == 9){
  +           fml_fixest = y ~ x1 | species + fe_2[x2,x3] + fe_3
  +           fml_stats = y ~ x1 + species + factor(fe_2) + i(fe_2, x2) + i(fe_2, x3) + factor(fe_3)
  +         }
  + 
  +         # ad hoc modifications of the formula
  +         if(model == "logit"){
  +           fml_fixest = xpd(y_01 ~ ..rhs, ..rhs = fml_fixest[[3]])
  +           fml_stats = xpd(y_01 ~ ..rhs, ..rhs = fml_stats[[3]])
  + 
  +           # The estimations are OK, conv differences out of my control
  +           if(id_fe %in% 8:9) tol = 0.5
  + 
  +         } else if(model == "pois"){
  +           fml_fixest = xpd(y_int_null ~ ..rhs, ..rhs = fml_fixest[[3]])
  +           fml_stats = xpd(y_int_null ~ ..rhs, ..rhs = fml_stats[[3]])
  + 
  +         } else if(model %in% c("negbin", "Gamma")){
  +           fml_fixest = xpd(y_int ~ ..rhs, ..rhs = fml_fixest[[3]])
  +           fml_stats = xpd(y_int ~ ..rhs, ..rhs = fml_stats[[3]])
  +         }
  + 
  +         adj = 1
  +         if(model == "ols"){
  +           res = feols(fml_fixest, base, weights = my_weight, offset = my_offset)
  +           res_bis = lm(fml_stats, base, weights = my_weight, offset = my_offset)
  + 
  +         } else if(model %in% c("pois", "logit", "Gamma")){
  +           adj = 0
  +           if(model == "Gamma" && use_offset) next
  + 
  +           my_family = switch(model, pois = poisson(), logit = binomial(), Gamma = Gamma())
  + 
  +           res = feglm(fml_fixest, base, family = my_family, weights = my_weight, offset = my_offset)
  + 
  +           if(!is.null(res$obs_selection$obsRemoved)){
  +             qui = res$obs_selection$obsRemoved
  + 
  +             # I MUST do that.... => subset does not work...
  +             base_tmp = base[qui, ]
  +             base_tmp$my_offset = my_offset[qui]
  +             base_tmp$my_weight = my_weight[qui]
  +             res_bis = glm(fml_stats, base_tmp, family = my_family, weights = my_weight, offset = my_offset)
  +           } else {
  +             res_bis = glm(fml_stats, data = base, family = my_family, weights = my_weight, offset = my_offset)
  +           }
  + 
  +         } else if(model == "negbin"){
  +           # no offset in glm.nb + no VS in fenegbin + no weights in fenegbin
  +           if(use_weights || use_offset || id_fe > 2) next
  + 
  +           res = fenegbin(fml_fixest, base, notes = FALSE)
  +           res_bis = MASS::glm.nb(fml_stats, base)
  + 
  +         }
  + 
  +         test(coef(res)["x1"], coef(res_bis)["x1"], "~", tol)
  +         test(se(res, se = "st", ssc = ssc(adj = adj))["x1"], se(res_bis)["x1"], "~", tol)
  +         test(pvalue(res, se = "st", ssc = ssc(adj = adj))["x1"], pvalue(res_bis)["x1"], "~", tol*10**(model == "negbin"))
  +         # cat("Model: ", model, ", FE: ", id_fe, ", weight: ", use_weights,  ", offset: ", use_offset, "\n", sep="")
  + 
  +       }
  +       cat("|")
  +     }
  +   }
  +   cat("\n")
  + }
  Model: ols   ..........|..........|..........|..........|
  Model: pois  ..........|..........|..........|..........|
  Model: logit ..........|..........|..........|..........|
  Model: negbin..........|..........|..........|..........|
  Model: Gamma ..........|..........|..........|..........|
  There were 36 warnings (use warnings() to see them)
  > 
  > ####
  > #### ... Corner cases ####
  > ####
  > 
  > chunk("Corner cases")
  CORNER CASES
  
  > 
  > 
  > # We test the absence of bugs
  > 
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "fe1")
  > base$fe2 = rep(1:5, 30)
  > base$y[1:5] = NA
  > base$x1[4:8] = NA
  > base$x2[4:21] = NA
  > base$x3[110:111] = NA
  > base$fe1[110:118] = NA
  > base$fe2[base$fe2 == 1] = 0
  > base$fe3 = sample(letters[1:5], 150, TRUE)
  > base$period = rep(1:50, 3)
  > base$x_cst = 1
  > 
  > res = feols(y ~ 1 | csw(fe1, fe1^fe2), base)
  > 
  > res = feols(y ~ 1 + csw(x1, i(fe1)) | fe2, base)
  > 
  > res = feols(y ~ csw(f(x1, 1:2), x2) | sw0(fe2, fe2^fe3), base, panel.id = ~ fe1 + period)
  > 
  > res = feols(d(y) ~ -1 + d(x2), base, panel.id = ~ fe1 + period)
  > test(length(coef(res)), 1)
  > 
  > res = feols(c(y, x1) ~ 1 | fe1 | x2 ~ x3, base)
  > 
  > res = feols(y ~ x1 | fe1[x2] + fe2[x2], base)
  > 
  > #
  > # NA models (ie all variables are collinear with the FEs)
  > #
  > 
  > # Should work when warn = FALSE or multiple est
  > for(i in 1:2){
  +   fun = switch(i, "1" = feols, "2" = feglm)
  + 
  +   res = feols(y ~ x_cst | fe1, base, warn = FALSE)
  +   res         # => no error
  +   etable(res) # => no error
  + 
  +   # error when warn = TRUE
  +   test(feols(y ~ x_cst | fe1, base), "err")
  + 
  +   # multiple est => no error
  +   res = feols(c(y, x1) ~ x_cst | fe1, base)
  +   res         # => no error
  +   etable(res) # => no error
  + }
  > 
  > 
  > # Removing the intercept!!!
  > 
  > res = feols(y ~ -1 + x1 + i(fe1), base)
  > test("(Intercept)" %in% names(res$coefficients), FALSE)
  > 
  > res = feols(y ~ -1 + x1 + factor(fe1), base)
  > test("(Intercept)" %in% names(res$coefficients), FALSE)
  > 
  > res = feols(y ~ -1 + x1 + i(fe1) + i(fe2), base)
  > test("(Intercept)" %in% names(res$coefficients), FALSE)
  > test(is.null(res$collin.var), TRUE)
  > 
  > 
  > # IV + interacted FEs
  > res = feols(y ~ x1 | fe1^fe2 | x2 ~ x3, base)
  > 
  > # IVs no exo var
  > res = feols(y ~ 0 | x2 ~ x3, base)
  > # Same in stepwise
  > res = feols(y ~ 0 | sw0(fe1) | x2 ~ x3, base)
  > 
  > # IVs + lags
  > res = feols(y ~ x1 | fe1^fe2 | l(x2, -1:1) ~ l(x3, -1:1), base, panel.id = ~ fe1 + period)
  > 
  > # functions in interactions
  > res = feols(y ~ x1 | factor(fe1)^factor(fe2), base)
  > res = feols(y ~ x1 | round(x2^2), base)
  > test(feols(y ~ x1 | factor(fe1^fe2), base), "err")
  > 
  > res = feols(y ~ x1 | bin(x2, "bin::1")^fe1 + fe1^fe2, base)
  > 
  > # 1 obs (after FE removal) estimation
  > base_1obs = data.frame(y = c(1, 0), fe = c(1, 2), x = c(1, 0))
  > test(fepois(y ~ x | fe, base_1obs), "err")
  > # no error
  > res = fepois(y ~ 1 | fe, base_1obs)
  > 
  > # warning when demeaning algo reaches max iterations 
  > data(trade)
  > test(feols(Euros ~ log(dist_km) | Destination + Origin + Product, 
  +            trade, fixef.iter = 1), "warn")
  > 
  > 
  > ####
  > #### ... Fit methods ####
  > ####
  > 
  > chunk("Fit methods")
  FIT METHODS
  
  > 
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > base$y_int = as.integer(base$y)
  > base$y_log = sample(c(TRUE, FALSE), 150, TRUE)
  > 
  > res = feglm.fit(base$y, base[, 2:4])
  > res_bis = feglm(y ~ -1 + x1 + x2 + x3, base)
  > test(coef(res), coef(res_bis))
  > 
  > res = feglm.fit(base$y_int, base[, 2:4])
  > res_bis = feglm(y_int ~ -1 + x1 + x2 + x3, base)
  > test(coef(res), coef(res_bis))
  > 
  > res = feglm.fit(base$y_log, base[, 2:4])
  > res_bis = feglm(y_log ~ -1 + x1 + x2 + x3, base)
  > test(coef(res), coef(res_bis))
  > 
  > 
  > 
  > res = feglm.fit(base$y, base[, 2:4], family = "poisson")
  > res_bis = feglm(y ~ -1 + x1 + x2 + x3, base, family = "poisson")
  > test(coef(res), coef(res_bis))
  > 
  > res = feglm.fit(base$y_int, base[, 2:4], family = "poisson")
  > res_bis = feglm(y_int ~ -1 + x1 + x2 + x3, base, family = "poisson")
  > test(coef(res), coef(res_bis))
  > 
  > res = feglm.fit(base$y_log, base[, 2:4], family = "poisson")
  > res_bis = feglm(y_log ~ -1 + x1 + x2 + x3, base, family = "poisson")
  > test(coef(res), coef(res_bis))
  > 
  > ####
  > #### global variables ####
  > ####
  > 
  > chunk("globals")
  GLOBALS
  
  > 
  > est_reg = function(df, yvar, xvar, refgrp) {
  +   feols(.[yvar] ~ i(.[xvar], ref = refgrp), data = df)
  + }
  > 
  > (est = est_reg(iris, "Sepal.Length", "Species", ref = "setosa"))
  OLS estimation, Dep. Var.: Sepal.Length
  Observations: 150
  Standard-errors: IID 
                      Estimate Std. Error  t value   Pr(>|t|)    
  (Intercept)            5.006   0.072802 68.76164  < 2.2e-16 ***
  Species::versicolor    0.930   0.102958  9.03282 8.7702e-16 ***
  Species::virginica     1.582   0.102958 15.36551  < 2.2e-16 ***
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  RMSE: 0.509616   Adj. R2: 0.613518
  > 
  > # checking when it should not work
  > base = setNames(iris, c("y", "x1", "x2", "x3", "species"))
  > 
  > z = base$x1
  > test(feols(y ~ z, base), "err")
  > 
  > 
  > 
  > ####
  > #### ... Collinearity ####
  > ####
  > 
  > chunk("COLLINEARITY")
  COLLINEARITY
  
  > 
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > base$constant = 5
  > base$y_int = as.integer(base$y)
  > base$w = as.vector(unclass(base$species) - 0.95)
  > 
  > for(useWeights in c(FALSE, TRUE)){
  +   for(model in c("ols", "pois")){
  +     for(use_fe in c(FALSE, TRUE)){
  +       cat(".")
  + 
  +       my_weight = NULL
  +       if(useWeights) my_weight = base$w
  + 
  +       adj = 1
  +       if(model == "ols"){
  +         if(!use_fe){
  +           res = feols(y ~ x1 + constant, base, weights = my_weight)
  +           res_bis = lm(y ~ x1 + constant, base, weights = my_weight)
  +         } else {
  +           res = feols(y ~ x1 + constant | species, base, weights = my_weight)
  +           res_bis = lm(y ~ x1 + constant + species, base, weights = my_weight)
  +         }
  +       } else {
  +         if(!use_fe){
  +           res = fepois(y_int ~ x1 + constant, base, weights = my_weight)
  +           res_bis = glm(y_int ~ x1 + constant, base, weights = my_weight, family = poisson)
  +         } else {
  +           res = fepois(y_int ~ x1 + constant | species, base, weights = my_weight)
  +           res_bis = glm(y_int ~ x1 + constant + species, base, weights = my_weight, family = poisson)
  +         }
  +         adj = 0
  +       }
  + 
  +       test(coef(res)["x1"], coef(res_bis)["x1"], "~")
  +       test(se(res, se = "st", ssc = ssc(adj=adj))["x1"], se(res_bis)["x1"], "~")
  +       # cat("Weight: ", useWeights, ", model: ", model, ", FE: ", use_fe, "\n", sep="")
  + 
  +     }
  +   }
  + }
  ........> cat("\n")
  
  > 
  > 
  > ####
  > #### ... Non linear tests ####
  > ####
  > 
  > chunk("NON LINEAR")
  NON LINEAR
  
  > 
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > 
  > tab = c("versicolor" = 5, "setosa" = 0, "virginica" = -5)
  > 
  > fun_nl = function(a, b, spec){
  +   res = as.numeric(tab[spec])
  +   a*res + b*res^2
  + }
  > 
  > est_nl = feNmlm(y ~ x1, base, NL.fml = ~fun_nl(a, b, species), NL.start = 1, family = "gaussian")
  > 
  > base$var_spec = as.numeric(tab[base$species])
  > 
  > est_lin = feols(y ~ x1 + var_spec + I(var_spec^2), base)
  > 
  > test(coef(est_nl), coef(est_lin)[c(3, 4, 1, 2)], "~")
  > 
  > ####
  > #### ... Lagging ####
  > ####
  > 
  > # Different types of lag
  > # 1) check no error in wide variety of situations
  > # 2) check consistency
  > 
  > chunk("LAGGING")
  LAGGING
  
  > 
  > data(base_did)
  > base = base_did
  > 
  > n = nrow(base)
  > 
  > set.seed(0)
  > base$y_na = base$y ; base$y_na[sample(n, 50)] = NA
  > base$period_txt = letters[base$period]
  > ten_dates = c("1960-01-15", "1960-01-16", "1960-03-31", "1960-04-05", "1960-05-12", "1960-05-25", "1960-06-20", "1960-07-30", "1965-01-02", "2002-12-05")
  > base$period_date = as.Date(ten_dates, "%Y-%m-%d")[base$period]
  > base$y_0 = base$y**2 ; base$y_0[base$id == 1] = 0
  > 
  > # We compute the lags "by hand"
  > base = base[order(base$id, base$period), ]
  > base$x1_lag = c(NA, base$x1[-n]) ; base$x1_lag[base$period == 1] = NA
  > base$x1_lead = c(base$x1[-1], NA) ; base$x1_lead[base$period == 10] = NA
  > base$x1_diff = base$x1 - base$x1_lag
  > 
  > # we create holes
  > base$period_bis = base$period ; base$period_bis[base$period_bis == 5] = 50
  > base$x1_lag_hole = base$x1_lag ; base$x1_lag_hole[base$period %in% c(5, 6)] = NA
  > base$x1_lead_hole = base$x1_lead ; base$x1_lead_hole[base$period %in% c(4, 5)] = NA
  > 
  > # we reshuffle the base
  > base = base[sample(n), ]
  > 
  > #
  > # Checks consistency
  > #
  > 
  > cat("consistentcy...")
  consistentcy...> 
  > test(lag(x1 ~ id + period, data = base), base$x1_lag)
  > test(lag(x1 ~ id + period, -1, data = base), base$x1_lead)
  > 
  > test(lag(x1 ~ id + period_bis, data = base), base$x1_lag_hole)
  > test(lag(x1 ~ id + period_bis, -1, data = base), base$x1_lead_hole)
  > 
  > test(lag(x1 ~ id + period_txt, data = base), base$x1_lag)
  > test(lag(x1 ~ id + period_txt, -1, data = base), base$x1_lead)
  > 
  > test(lag(x1 ~ id + period_date, data = base), base$x1_lag)
  > test(lag(x1 ~ id + period_date, -1, data = base), base$x1_lead)
  > 
  > cat("done.\nEstimations...")
  done.
  Estimations...> 
  > #
  > # Estimations
  > #
  > 
  > # Poisson
  > 
  > for(depvar in c("y", "y_na", "y_0")){
  +   for(p in c("period", "period_txt", "period_date")){
  + 
  +     base$per = base[[p]]
  + 
  +     cat(".")
  + 
  +     base$y_dep = base[[depvar]]
  +     pdat = panel(base, ~ id + period)
  + 
  +     if(depvar == "y_0"){
  +       estfun = fepois
  +     } else {
  +       estfun = feols
  +     }
  + 
  +     est_raw  = estfun(y_dep ~ x1 + x1_lag + x1_lead, base)
  +     est      = estfun(y_dep ~ x1 + l(x1) + f(x1), base, panel.id = "id,per")
  +     est_pdat = estfun(y_dep ~ x1 + l(x1, 1) + f(x1, 1), pdat)
  +     test(coef(est_raw), coef(est))
  +     test(coef(est_raw), coef(est_pdat))
  + 
  +     # Now diff
  +     est_raw  = estfun(y_dep ~ x1 + x1_diff, base)
  +     est      = estfun(y_dep ~ x1 + d(x1), base, panel.id = "id,per")
  +     est_pdat = estfun(y_dep ~ x1 + d(x1, 1), pdat)
  +     test(coef(est_raw), coef(est))
  +     test(coef(est_raw), coef(est_pdat))
  + 
  +     # Now we just check that calls to l/f works without checking coefs
  + 
  +     est = estfun(y_dep ~ x1 + l(x1) + f(x1), base, panel.id = "id,per")
  +     est = estfun(y_dep ~ l(x1, -1:1) + f(x1, 2), base, panel.id = c("id", "per"))
  +     est = estfun(y_dep ~ l(x1, -1:1, fill = 1), base, panel.id = ~ id + per)
  +     if(depvar == "y") test(est$nobs, n)
  +     est = estfun(f(y_dep) ~ f(x1, -1:1), base, panel.id = ~ id + per)
  +   }
  + }
  .........> 
  > cat("done.\n\n")
  done.
  
  > 
  > #
  > # Data table
  > #
  > 
  > cat("data.table...")
  data.table...> # We just check there is no bug (consistency should be OK)
  > 
  > library(data.table)
  > 
  > base_dt = data.table(id = c("A", "A", "B", "B"),
  +            time = c(1, 2, 1, 3),
  +            x = c(5, 6, 7, 8))
  > 
  > base_dt = panel(base_dt, ~id + time)
  > 
  > base_dt[, x_l := l(x)]
  > test(base_dt$x_l, c(NA, 5, NA, NA))
  > 
  > lag_creator = function(dt) {
  +   dt2 = panel(dt, ~id + time)
  +   dt2[, x_l := l(x)]
  +   return(dt2)
  + }
  > 
  > base_bis = lag_creator(base_dt)
  > 
  > base_bis[, x_d := d(x)]
  > 
  > cat("done.\n\n")
  done.
  
  > 
  > #
  > # Panel
  > #
  > 
  > # We ensure we get the right SEs whether we use the panel() or the panel.id method
  > data(base_did)
  > 
  > # Setting a data set as a panel...
  > pdat = panel(base_did, ~id+period)
  > pdat$fe = sample(15, nrow(pdat), replace = TRUE)
  > 
  > base_panel = unpanel(pdat)
  > 
  > est_pdat = feols(y ~ x1 | fe, pdat)
  > est_panel = feols(y ~ x1 | fe, base_panel, panel.id = ~id+period)
  > 
  > test(attr(vcov(est_pdat, attr = TRUE), "type"),
  +    attr(vcov(est_panel, attr = TRUE), "type"))
  > 
  > ####
  > #### ... subset ####
  > ####
  > 
  > chunk("SUBSET")
  SUBSET
  
  > 
  > set.seed(5)
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > base$fe_bis = sample(letters, 150, TRUE)
  > base$x4 = rnorm(150)
  > base$x1[sample(150, 5)] = NA
  > 
  > fml = y ~ x1 + x2
  > 
  > # Errors
  > test(feols(fml, base, subset = ~species), "err")
  > test(feols(fml, base, subset = -1:15), "err")
  > test(feols(fml, base, subset = integer(0)), "err")
  > test(feols(fml, base, subset = c(TRUE, TRUE, FALSE)), "err")
  > 
  > # Valid use
  > for(id_fun in 1:6){
  +   estfun = switch(as.character(id_fun),
  +           "1" = feols,
  +           "2" = feglm,
  +           "3" = fepois,
  +           "4" = femlm,
  +           "5" = fenegbin,
  +           "6" = feNmlm)
  + 
  +   for(id_fe in 1:5){
  + 
  +     cat(".")
  + 
  +     fml = switch(as.character(id_fe),
  +            "1" = y ~ x1 + x2,
  +            "2" = y ~ x1 + x2 | species,
  +            "3" = y ~ x1 + x2 | fe_bis,
  +            "4" = y ~ x1 + x2 + i(fe_bis),
  +            "5" = y ~ x1 + x2 | fe_bis[x3])
  + 
  +     if(id_fe == 5 && id_fun %in% 4:6) next
  + 
  +     if(id_fun == 6){
  +       res_sub_a = estfun(fml, base, subset = ~species == "setosa", NL.fml = ~ a*x4, NL.start = 0)
  +       res_sub_b = estfun(fml, base, subset = base$species == "setosa", NL.fml = ~ a*x4, NL.start = 0)
  +       res_sub_c = estfun(fml, base, subset = which(base$species == "setosa"), NL.fml = ~ a*x4, NL.start = 0)
  +       res       = estfun(fml, base[base$species == "setosa", ], NL.fml = ~ a*x4, NL.start = 0)
  +     } else {
  +       res_sub_a = estfun(fml, base, subset = ~species == "setosa")
  +       res_sub_b = estfun(fml, base, subset = base$species == "setosa")
  +       res_sub_c = estfun(fml, base, subset = which(base$species == "setosa"))
  +       res       = estfun(fml, base[base$species == "setosa", ])
  +     }
  + 
  +     test(coef(res_sub_a), coef(res))
  +     test(coef(res_sub_b), coef(res))
  +     test(coef(res_sub_c), coef(res))
  +     test(se(res_sub_c, cluster = "fe_bis"), se(res, cluster = "fe_bis"))
  +   }
  +   cat("|")
  + }
  .....|.....|.....|.....|.....|.....|> cat("\n")
  
  > 
  > 
  > ####
  > #### ... split ####
  > ####
  > 
  > chunk("split")
  SPLIT
  
  > 
  > base = setNames(iris, c("y", "x1", "x2", "x3", "species"))
  > 
  > # simple: formula
  > est = feols(y ~ x.[1:3], base, split = ~species %keep% "@^v")
  > test(length(est), 2)
  > 
  > est = feols(y ~ x.[1:3], base, fsplit = ~species %keep% c("set", "vers"))
  > test(length(est), 3)
  > 
  > est = feols(y ~ x.[1:3], base, split = ~species %drop% "set")
  > test(length(est), 2)
  > 
  > # simple: vector
  > est = feols(y ~ x.[1:3], base, split = base$species %keep% "@^v")
  > test(length(est), 2)
  > 
  > est = feols(y ~ x.[1:3], base, split = base$species %keep% c("set", "vers"))
  > test(length(est), 2)
  > 
  > est = feols(y ~ x.[1:3], base, split = base$species %drop% "set")
  > test(length(est), 2)
  > 
  > # with bin
  > est = feols(y ~ x.[1:2], base,
  +       split = ~bin(x3, c("cut::5", "saint emilion", "pessac leognan",
  +                  "margaux", "saint julien", "entre deux mers")) %keep% c("saint e", "pe"))
  > test(length(est), 2)
  > 
  > est = feols(y ~ x.[1:2], base,
  +       split = ~bin(x3, c("cut::5", "saint emilion", "pessac leognan", NA)) %drop% "@\\d")
  > test(length(est), 2)
  > 
  > # with argument
  > est = feols(y ~ x.[1:3], base, split = ~species, split.keep = "@^v")
  > test(length(est), 2)
  > 
  > est = feols(y ~ x.[1:3], base, fsplit = ~species, split.keep = c("set", "vers"))
  > test(length(est), 3)
  > 
  > est = feols(y ~ x.[1:3], base, split = ~species, split.drop = "set")
  > test(length(est), 2)
  > 
  > 
  > ####
  > #### ... Multiple estimations ####
  > ####
  > 
  > chunk("Multiple")
  MULTIPLE
  
  > 
  > set.seed(2)
  > base = iris
  > names(base) = c("y1", "x1", "x2", "x3", "species")
  > base$y2 = 10 + rnorm(150) + 0.5 * base$x1
  > base$x4 = rnorm(150) + 0.5 * base$y1
  > base$fe2 = rep(letters[1:15], 10)
  > base$fe2[50:51] = NA
  > base$y2[base$fe2 == "a" & !is.na(base$fe2)] = 0
  > base$x2[1:5] = NA
  > base$x3[6] = NA
  > base$x5 = rnorm(150)
  > base$x6 = rnorm(150) + base$y1 * 0.25
  > base$fe3 = rep(letters[1:10], 15)
  > 
  > 
  > for(id_fun in 1:5){
  +   estfun = switch(as.character(id_fun),
  +                   "1" = feols,
  +                   "2" = feglm,
  +                   "3" = fepois,
  +                   "4" = femlm,
  +                   "5" = feNmlm)
  + 
  +   # Following weird bug ASAN on CRAN I cannot replicate, check 4/5 not performed on non Windows
  +   if(Sys.info()["sysname"] != "Windows"){
  +     if(id_fun %in% 4:5) next
  +   }
  + 
  + 
  +   est_multi = estfun(c(y1, y2) ~ x1 + sw(x2, x3), base, split = ~species)
  + 
  +   k = 1
  +   for(s in c("setosa", "versicolor", "virginica")){
  +     for(lhs in c("y1", "y2")){
  +       for(rhs in c("x2", "x3")){
  +         res = estfun(.[lhs] ~ x1 + .[rhs], base[base$species == s, ], notes = FALSE)
  + 
  +         test(coef(est_multi[[k]]), coef(res))
  +         test(se(est_multi[[k]], cluster = "fe3"), se(res, cluster = "fe3"))
  +         k = k + 1
  +       }
  +     }
  +   }
  + 
  +   cat("__")
  + 
  +   est_multi = estfun(c(y1, y2) ~ x1 + csw0(x2, x3) + x4 | species + fe2, base, fsplit = ~species)
  +   k = 1
  +   all_rhs = c("", "x2", "x3")
  +   for(s in c("all", "setosa", "versicolor", "virginica")){
  +     for(lhs in c("y1", "y2")){
  +       for(n_rhs in 1:3){
  +         if(s == "all"){
  +           res = estfun(xpd(..lhs ~ x1 + ..rhs + x4 | species + fe2, ..lhs = lhs, ..rhs = all_rhs[1:n_rhs]), base, notes = FALSE)
  +         } else {
  +           res = estfun(xpd(..lhs ~ x1 + ..rhs + x4 | species + fe2, ..lhs = lhs, ..rhs = all_rhs[1:n_rhs]), base[base$species == s, ], notes = FALSE)
  +         }
  + 
  +         vname = names(coef(res))
  +         test(coef(est_multi[[k]])[vname], coef(res), "~" , 1e-6)
  +         test(se(est_multi[[k]], cluster = "fe3")[vname], se(res, cluster = "fe3"), "~" , 1e-6)
  +         k = k + 1
  +       }
  +     }
  +   }
  + 
  +   cat("|")
  + }
  __|__|__|> cat("\n")
  
  > 
  > 
  > # No error tests
  > # We test with IV + possible corner cases
  > 
  > base$left = rnorm(150)
  > base$right = rnorm(150)
  > 
  > est_multi = feols(c(y1, y2) ~ sw0(x1) | sw0(species) | x2 ~ x3, base)
  > 
  > # We check a few
  > est_a = feols(y1 ~ 1 | x2 ~ x3, base)
  > est_b = feols(y1 ~ x1 | species | x2 ~ x3, base)
  > est_c = feols(y2 ~ 1 | x2 ~ x3, base)
  > 
  > test(coef(est_multi[lhs = "y1", rhs = "^1", fixef = "1", drop = TRUE]), coef(est_a))
  > test(coef(est_multi[lhs = "y1", rhs = "x1", fixef = "spe", drop = TRUE]), coef(est_b))
  > test(coef(est_multi[lhs = "y2", rhs = "^1", fixef = "1", drop = TRUE]), coef(est_c))
  > 
  > # with fixed covariates
  > est_multi_LR = feols(c(y1, y2) ~ left + sw0(x1*x4) + right | sw0(species) | x2 ~ x3, base)
  > 
  > est_a = feols(y1 ~ left + right | x2 ~ x3, base)
  > est_b = feols(y1 ~ left + x1*x4 + right | species | x2 ~ x3, base)
  > est_c = feols(y2 ~ left + right | x2 ~ x3, base)
  > 
  > test(coef(est_multi_LR[lhs = "y1", rhs = "!x1", fixef = "1", drop = TRUE]), coef(est_a))
  > user_name = c("fit_x2", "left", "x1", "x4", "x1:x4", "right")
  > test(names(coef(est_multi_LR[lhs = "y1", rhs = "x1", fixef = "spe", drop = TRUE])), user_name)
  > test(coef(est_multi_LR[lhs = "y1", rhs = "x1", fixef = "spe", drop = TRUE]), coef(est_b)[user_name])
  > test(coef(est_multi_LR[lhs = "y2", rhs = "!x1", fixef = "1", drop = TRUE]), coef(est_c))
  > 
  > 
  > # mvsw
  > 
  > est_mvsw = feols(y1 ~ mvsw(x1, x2), base)
  > est_mvsw_fe = feols(y1 ~ mvsw(x1, x2) | mvsw(species, fe2), base)
  > est_mvsw_fe_iv = feols(y1 ~ mvsw(x1, x2) | mvsw(species, fe2) | x3 ~ x4, base)
  > 
  > test(length(est_mvsw), 4)
  > test(length(as.list(est_mvsw_fe)), 16)
  > test(length(as.list(est_mvsw_fe_iv)), 16)
  > 
  > # Summary of multiple endo vars
  > est_multi_iv = feols(c(y1, y2) ~ sw0(x1) | sw0(species) | x3 + x4 ~ x5 + x6, base)
  > test(length(est_multi_iv), 8)
  > test(length(summary(est_multi_iv, stage = 1)), 16)
  > 
  > # IV without exo var:
  > est_mult_no_exo = feols(c(y1, y2) ~ 0 | x3 + x4 ~ x5 + x6, base)
  > est_no_exo_y2 = feols(y2 ~ 0 | x3 + x4 ~ x5 + x6, base)
  > test(coef(est_mult_no_exo[[2]]), coef(est_no_exo_y2))
  > 
  > # proper ordering
  > est_multi = feols(c(y1, y2) ~ sw0(x1) | sw0(fe2), base, split = ~species)
  > test(names(models(est_multi[fixef = TRUE, sample = FALSE])),
  +    stvec("id, fixef, lhs, rhs, sample.var, sample"))
  > 
  > test(names(models(est_multi[fixef = "fe2", sample = "seto"])),
  +    stvec("id, fixef, sample.var, sample, lhs, rhs"))
  > 
  > test(names(models(est_multi[fixef = "fe2", sample = "seto", reorder = FALSE])),
  +    stvec("id, sample.var, sample, fixef, lhs, rhs"))
  > 
  > # NA models
  > base$y_0 = base$x1 ** 2 + rnorm(150)
  > base$y_0[base$species == "setosa"] = 0
  > 
  > est_pois = fepois(y_0 ~ csw(x.[,1:4]), base, split = ~species)
  > 
  > base$x1_bis = base$x1
  > est_pois = fepois(y_0 ~ x.[1:3] + x1_bis | sw0(species), base)
  > 
  > # Different ways .[]
  > base = setNames(iris, c("y", "x1", "x2", "x3", "species"))
  > 
  > dep_all = list(stvec("y, x1, x2"), ~y + x1 + x2)
  > for(dep in dep_all){
  +   m = feols(.[dep] ~ x3, base)
  +   test(length(m), 3)
  + 
  +   m = feols(x3 ~ .[dep], base)
  +   test(length(m$coefficients), 4)
  + 
  +   m = feols(x3 ~ csw(.[,dep]), base)
  +   test(length(m), 3)
  + }
  > 
  > # offset in multiple outcomes // no error test
  > 
  > offset_single_ols = feols(am ~ hp, offset = ~ log(qsec), data = mtcars)
  > offset_mult_ols = feols(c(mpg, am) ~ hp, offset = ~ log(qsec), data = mtcars)
  > 
  > test(coef(offset_mult_ols[[2]]), coef(offset_single_ols))
  > 
  > offset_single_glm = feglm(am ~ hp, offset = ~ log(qsec), data = mtcars)
  > offset_mult_glm = feglm(c(mpg, am) ~ hp, offset = ~ log(qsec), data = mtcars)
  > 
  > test(coef(offset_mult_glm[[2]]), coef(offset_single_glm))
  > 
  > # LHS expansion with IVs
  > 
  > lhs = c("mpg", "wt")
  > est_lhs = feols(.[lhs] ~ disp | hp ~ qsec, data = mtcars)
  > test(length(est_lhs), 2)
  > 
  > est_lhs = feols(..("mpg|wt") ~ disp | hp ~ qsec, data = mtcars)
  > test(length(est_lhs), 2)
  > 
  > 
  > ####
  > #### ... IV ####
  > ####
  > 
  > chunk("IV")
  IV
  
  > 
  > base = iris
  > names(base) = c("y", "x1", "x_endo_1", "x_inst_1", "fe")
  > set.seed(2)
  > base$x_inst_2 = 0.2 * base$y + 0.2 * base$x_endo_1 + rnorm(150, sd = 0.5)
  > base$x_endo_2 = 0.2 * base$y - 0.2 * base$x_inst_1 + rnorm(150, sd = 0.5)
  > 
  > # Checking a basic estimation
  > 
  > setFixest_vcov(all = "iid")
  > 
  > est_iv = feols(y ~ x1 | x_endo_1 + x_endo_2 ~ x_inst_1 + x_inst_2, base)
  > 
  > res_f1 = feols(x_endo_1 ~ x1 + x_inst_1 + x_inst_2, base)
  > res_f2 = feols(x_endo_2 ~ x1 + x_inst_1 + x_inst_2, base)
  > 
  > base$fit_x_endo_1 = predict(res_f1)
  > base$fit_x_endo_2 = predict(res_f2)
  > 
  > res_2nd = feols(y ~ fit_x_endo_1 + fit_x_endo_2 + x1, base)
  > 
  > # the coef
  > test(coef(est_iv), coef(res_2nd))
  > 
  > # the SE
  > resid_iv = base$y - predict(res_2nd, data.frame(x1 = base$x1, fit_x_endo_1 = base$x_endo_1, fit_x_endo_2 = base$x_endo_2))
  > sigma2_iv = sum(resid_iv**2) / (res_2nd$nobs - res_2nd$nparams)
  > 
  > sum_2nd = summary(res_2nd, .vcov = res_2nd$cov.iid / res_2nd$sigma2 * sigma2_iv)
  > 
  > # We only check that on Windows => avoids super odd bug in fedora devel
  > # The worst is that I just can't debug it.... so that's the way it's done.
  > if(Sys.info()["sysname"] == "Windows"){
  +   test(se(sum_2nd), se(est_iv))
  + }
  > 
  > # check no bug when all exogenous vars are removed bc of collinearity
  > df = data.frame(x = rnorm(8), y = rnorm(8),
  +                 z = rnorm(8), fe = rep(0:1, each = 4))
  > 
  > est_iv = feols(y ~ fe | fe | x ~ z, df)
  > est_iv = feols(y ~ sw(fe, fe) | fe | x ~ z, df)
  > 
  > # check no bug
  > etable(summary(est_iv, stage = 1:2))
                  summary(est_..1 summary(es..2 summary(est_..3 summary(es..4
  Dependent Var.:               x             y               x             y
                                                                             
  z               0.1127 (0.5532)               0.1127 (0.5532)              
  x                               1.110 (6.499)                 1.110 (6.499)
  Fixed-Effects:  --------------- ------------- --------------- -------------
  fe                          Yes           Yes             Yes           Yes
  _______________ _______________ _____________ _______________ _____________
  S.E. type                   IID           IID             IID           IID
  Observations                  8             8               8             8
  R2                      0.35875      -0.08261         0.35875      -0.08261
  Within R2               0.00823      -0.33354         0.00823      -0.33354
  ---
  Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  > 
  > setFixest_vcov(reset = TRUE)
  > 
  > ####
  > #### ... VCOV at estimation ####
  > ####
  > 
  > chunk("vcov at estimation")
  VCOV AT ESTIMATION
  
  > 
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > base$clu = sample(6, 150, TRUE)
  > base$clu[1:5] = NA
  > 
  > est = feols(y ~ x1 | species, base, cluster = ~clu, ssc = ssc(adj = FALSE))
  > 
  > # The three should be identical
  > v1 = est$cov.scaled
  > v1b = vcov(est)
  > v1c = summary(est)$cov.scaled
  > 
  > test(v1, v1b)
  > test(v1, v1c)
  > 
  > # Only ssc change
  > v2 = summary(est, ssc = ssc())$cov.scaled
  > v2b = vcov(est, ssc = ssc())
  > 
  > test(v2, v2b)
  > test(max(abs(v1 - v2)) == 0, FALSE)
  > 
  > # vcov change only
  > v3 = summary(est, se = "hetero")$cov.scaled
  > v3b = vcov(est, se = "hetero")
  > 
  > test(v3, v3b)
  > test(max(abs(v1 - v3)) == 0, FALSE)
  > test(max(abs(v2 - v3)) == 0, FALSE)
  > 
  > # feols.fit
  > 
  > ymat = base$y
  > xmat = base[, 2:3]
  > fe = base$species
  > 
  > for(use_fe in c(TRUE, FALSE)){
  +   all_vcov = stvec("iid, hetero")
  +   if(use_fe){
  +     setFixest_fml(..fe = ~ 1 | species)
  +     all_vcov = c(all_vcov, "cluster")
  +   } else {
  +     setFixest_fml(..fe = ~ 1)
  +   }
  + 
  +   for(v in all_vcov){
  + 
  +     if(use_fe){
  +       est_fit = feols.fit(ymat, xmat, fe, vcov = v)
  +     } else {
  +       est_fit = feols.fit(ymat, cbind(1, xmat), vcov = v)
  +     }
  + 
  +     est = feols(y ~ x1 + x2 + ..fe, base, vcov = v)
  + 
  +     test(vcov(est), vcov(est_fit))
  +   }
  + }
  > 
  > 
  > 
  > 
  > ####
  > #### ... Argument sliding ####
  > ####
  > 
  > chunk("argument sliding")
  ARGUMENT SLIDING
  
  > 
  > base = setNames(iris, c("y", "x1", "x2", "x3", "species"))
  > 
  > setFixest_estimation(data = base)
  > 
  > raw = feols(y ~ x1 + x2, base, ~species)
  > slided = feols(y ~ x1 + x2, ~species)
  > 
  > test(coef(raw), coef(slided))
  > 
  > # Error, with error msg relative to 'data'
  > test(feols(y ~ x1 + x2, 1:5), "err")
  > 
  > # should be another estimation
  > other_est = feols(y ~ x1 + x2, head(base, 50))
  > test(nobs(other_est), 50)
  > 
  > setFixest_estimation(reset = TRUE)
  > 
  > ####
  > #### ... Offset ####
  > ####
  > 
  > chunk("offset")
  OFFSET
  
  > 
  > # we test the different ways to set an offset
  > 
  > base = setNames(iris, c("y", "x1", "x2", "x3", "species"))
  > 
  > o1 = feols(y ~ x1 + offset(x2) + offset(x3^2 + 3), base)
  > o2 = feols(y ~ x1, base, offset = ~x2 + x3^2 + 3)
  > test(coef(o1), coef(o2))
  > 
  > test(predict(o1, newdata = head(base)), 
  +      predict(o2, newdata = head(base)))
  > 
  > # error
  > test(feols(y ~ x1 + offset(x2), base, offset = ~x3), "err")
  > 
  > 
  > ####
  > #### ... Only Coef ####
  > ####
  > 
  > chunk("only.coef")
  ONLY.COEF
  
  > 
  > 
  > base = setNames(iris, c("y", "x1", "x2", "x3", "species"))
  > base$x4 = base$x1 + 5
  > 
  > m = feols(y ~ x1 + x2 + x4, base, only.coef = TRUE)
  > test(length(m), 4)
  > test(sum(is.na(m)), 1)
  > 
  > m = fepois(y ~ x1 + x2 + x4, base, only.coef = TRUE)
  > test(length(m), 4)
  > test(sum(is.na(m)), 1)
  > 
  > m = femlm(y ~ x1 + x2, base, only.coef = TRUE)
  > test(length(m), 3)
  > test(sum(is.na(m)), 0)
  > 
  > test(feols(y ~ sw(x1, x2), base, only.coef = TRUE), "err")
  > 
  > 
  > ####
  > #### Standard-errors ####
  > ####
  > 
  > chunk("STANDARD ERRORS")
  STANDARD ERRORS
  
  > 
  > #
  > # Fixed-effects corrections
  > #
  > 
  > # We create "irregular" FEs
  > set.seed(0)
  > base = data.frame(x = rnorm(20))
  > base$y = base$x + rnorm(20)
  > base$fe1 = rep(rep(1:3, c(4, 3, 3)), 2)
  > base$fe2 = rep(rep(1:5, each = 2), 2)
  > est = feols(y ~ x | fe1 + fe2, base)
  > 
  > # fe1: 3 FEs
  > # fe2: 5 FEs
  > 
  > #
  > # Clustered standard-errors: by fe1
  > #
  > 
  > # Default: fixef.K = "nested"
  > #  => adjustment K = 1 + 5 (i.e. x + fe2)
  > test(attr(vcov(est, ssc = ssc(fixef.K = "nested"), attr = TRUE), "dof.K"), 6)
  > 
  > # fixef.K = FALSE
  > #  => adjustment K = 1 (i.e. only x)
  > test(attr(vcov(est, ssc = ssc(fixef.K = "none"), attr = TRUE), "dof.K"), 1)
  > 
  > # fixef.K = TRUE
  > #  => adjustment K = 1 + 3 + 5 - 1 (i.e. x + fe1 + fe2 - 1 restriction)
  > test(attr(vcov(est, ssc = ssc(fixef.K = "full"), attr = TRUE), "dof.K"), 8)
  > 
  > # fixef.K = TRUE & fixef.exact = TRUE
  > #  => adjustment K = 1 + 3 + 5 - 2 (i.e. x + fe1 + fe2 - 2 restrictions)
  > test(attr(vcov(est, ssc = ssc(fixef.K = "full", fixef.force_exact = TRUE), attr = TRUE), "dof.K"), 7)
  > 
  > #
  > # Manual checks of the SEs
  > #
  > 
  > n = est$nobs
  > VCOV_raw = est$cov.iid / ((n - 1) / (n - est$nparams))
  > 
  > # standard
  > for(k_val in c("none", "nested", "full")){
  +   for(adj in c(FALSE, TRUE)){
  + 
  +     K = switch(k_val, none = 1, nested = 8, full = 8)
  +     my_adj = ifelse(adj, (n - 1) / (n - K), 1)
  + 
  +     test(vcov(est, se = "standard", ssc = ssc(adj = adj, fixef.K = k_val)), VCOV_raw * my_adj)
  + 
  +     # cat("adj = ", adj, " ; fixef.K = ", k_val, "\n", sep = "")
  +   }
  + }
  > 
  > # Clustered, fe1
  > VCOV_raw = est$cov.iid / est$sigma2
  > H = vcovClust(est$fixef_id$fe1, VCOV_raw, scores = est$scores, adj = FALSE)
  > n = nobs(est)
  > 
  > for(tdf in c("conventional", "min")){
  +   for(k_val in c("none", "nested", "full")){
  +     for(c_adj in c(FALSE, TRUE)){
  +       for(adj in c(FALSE, TRUE)){
  + 
  +         K = switch(k_val, none = 1, nested = 6, full = 8)
  +         cluster_factor = ifelse(c_adj, 3/2, 1)
  +         df = ifelse(tdf == "min", 2, 20 - K)
  +         my_adj = ifelse(adj, (n - 1) / (n - K), 1)
  + 
  +         V = H * cluster_factor
  + 
  +         # test SE
  +         test(vcov(est, se = "cluster", ssc = ssc(adj = adj, fixef.K = k_val, cluster.adj = c_adj)), V * my_adj)
  + 
  +         # test pvalue
  +         my_tstat = tstat(est, se = "cluster", ssc = ssc(adj = adj, fixef.K = k_val, cluster.adj = c_adj))
  +         test(pvalue(est, se = "cluster", ssc = ssc(adj = adj, fixef.K = k_val, cluster.adj = c_adj, t.df = tdf)), 2*pt(-abs(my_tstat), df))
  + 
  +         # cat("adj = ", adj, " ; fixef.K = ", k_val, " ; cluster.adj = ", c_adj, " t.df = ", tdf, "\n", sep = "")
  +       }
  +     }
  +   }
  + }
  > 
  > 
  > # 2-way Clustered, fe1 fe2
  > VCOV_raw = est$cov.iid / est$sigma2
  > M_i  = vcovClust(est$fixef_id$fe1, VCOV_raw, scores = est$scores, adj = FALSE)
  > M_t  = vcovClust(est$fixef_id$fe2, VCOV_raw, scores = est$scores, adj = FALSE)
  > M_it = vcovClust(paste(base$fe1, base$fe2), VCOV_raw, scores = est$scores, adj = FALSE, do.unclass = TRUE)
  > 
  > M_i + M_t - M_it
              [,1]
  [1,] 0.005391594
  > vcov(est, se = "two", ssc = ssc(adj = FALSE, cluster.adj = FALSE))
              x
  x 0.005391594
  > 
  > for(cdf in c("conventional", "min")){
  +   for(tdf in c("conventional", "min")){
  +     for(k_val in c("none", "nested", "full")){
  +       for(c_adj in c(FALSE, TRUE)){
  +         for(adj in c(FALSE, TRUE)){
  + 
  +           K = switch(k_val, none = 1, nested = 2, full = 8)
  + 
  +           if(c_adj){
  +             if(cdf == "min"){
  +               V = (M_i + M_t - M_it) * 3/2
  +             } else {
  +               V = M_i  * 3/2 + M_t * 5/4 - M_it * 6/5
  +             }
  +           } else {
  +             V = M_i + M_t - M_it
  +           }
  + 
  +           df = ifelse(tdf == "min", 2, 20 - K)
  +           my_adj = ifelse(adj, (n - 1) / (n - K), 1)
  + 
  +           # test SE
  +           test(vcov(est, se = "two", ssc = ssc(adj = adj, fixef.K = k_val, cluster.adj = c_adj, cluster.df = cdf)),
  +              V * my_adj)
  + 
  +           # test pvalue
  +           my_tstat = tstat(est, se = "two", ssc = ssc(adj = adj, fixef.K = k_val, cluster.adj = c_adj, cluster.df = cdf))
  +           test(pvalue(est, se = "two", ssc = ssc(adj = adj, fixef.K = k_val, cluster.adj = c_adj, cluster.df = cdf, t.df = tdf)),
  +              2*pt(-abs(my_tstat), df))
  + 
  +           # cat("adj = ", adj, " ; fixef.K = ", k_val, " ; cluster.adj = ", c_adj, " t.df = ", tdf, "\n", sep = "")
  +         }
  +       }
  +     }
  +   }
  + }
  > 
  > 
  > #
  > # Comparison with sandwich and plm
  > #
  > 
  > library(sandwich)
  
  Attaching package: 'sandwich'
  
  The following object is masked _by_ '.GlobalEnv':
  
      estfun
  
  > 
  > # Data generation
  > set.seed(0)
  > N = 20; G = N/5; T = N/G
  > d = data.frame( y=rnorm(N), x=rnorm(N), grp=rep(1:G,T), tm=rep(1:T,each=G) )
  > 
  > # Estimations
  > est_lm    = lm(y ~ x + as.factor(grp) + as.factor(tm), data=d)
  > est_feols = feols(y ~ x | grp + tm, data=d)
  > 
  > #
  > # Standard
  > #
  > 
  > test(se(est_feols, se = "st")["x"], se(est_lm)["x"])
  > 
  > #
  > # Clustered
  > #
  > 
  > # Clustered by grp
  > se_CL_grp_lm_HC1 = sqrt(vcovCL(est_lm, cluster = d$grp, type = "HC1")["x", "x"])
  > se_CL_grp_lm_HC0 = sqrt(vcovCL(est_lm, cluster = d$grp, type = "HC0")["x", "x"])
  > 
  > # How to get the lm
  > test(se(est_feols, ssc = ssc(fixef.K = "full")), se_CL_grp_lm_HC1)
  > test(se(est_feols, ssc = ssc(adj = FALSE, fixef.K = "full")), se_CL_grp_lm_HC0)
  > 
  > #
  > # Heteroskedasticity-robust
  > #
  > 
  > se_white_lm_HC1 = sqrt(vcovHC(est_lm, type = "HC1")["x", "x"])
  > se_white_lm_HC0 = sqrt(vcovHC(est_lm, type = "HC0")["x", "x"])
  > 
  > test(se(est_feols, se = "hetero"), se_white_lm_HC1)
  > test(se(est_feols, se = "hetero", ssc = ssc(adj = FALSE, cluster.adj = FALSE)), se_white_lm_HC0)
  > 
  > #
  > # Two way
  > #
  > 
  > # Clustered by grp & tm
  > se_CL_2w_lm    = sqrt(vcovCL(est_lm, cluster = ~ grp + tm, type = "HC1")["x", "x"])
  > se_CL_2w_feols = se(est_feols, se = "twoway")
  > 
  > test(se(est_feols, se = "twoway", ssc = ssc(fixef.K = "full", cluster.df = "conv")), se_CL_2w_lm)
  > 
  > #
  > # Checking the calls work properly
  > #
  > 
  > data(trade)
  > 
  > est_pois = femlm(Euros ~ log(dist_km)|Origin+Destination, trade)
  > 
  > se_clust = se(est_pois, se = "cluster", cluster = "Product")
  > test(se(est_pois, cluster = trade$Product), se_clust)
  > test(se(est_pois, cluster = ~Product), se_clust)
  > 
  > se_two = se(est_pois, se = "twoway", cluster = trade[, c("Product", "Destination")])
  > test(se_two, se(est_pois, cluster = c("Product", "Destination")))
  > test(se_two, se(est_pois, cluster = ~Product+Destination))
  > 
  > se_clu_comb = se(est_pois, cluster = "Product^Destination")
  > test(se_clu_comb, se(est_pois, cluster = paste(trade$Product, trade$Destination)))
  > test(se_clu_comb, se(est_pois, cluster = ~Product^Destination))
  > 
  > se_two_comb = se(est_pois, cluster = c("Origin^Destination", "Product"))
  > test(se_two_comb, se(est_pois, cluster = list(paste(trade$Origin, trade$Destination), trade$Product)))
  > test(se_two_comb, se(est_pois, cluster = ~Origin^Destination + Product))
  > 
  > # With cluster removed
  > base = trade
  > base$Euros[base$Origin == "FR"] = 0
  > est_pois = femlm(Euros ~ log(dist_km)|Origin+Destination, base)
  > 
  > se_clust = se(est_pois, se = "cluster", cluster = "Product")
  > test(se(est_pois, cluster = base$Product), se_clust)
  > test(se(est_pois, cluster = ~Product), se_clust)
  > 
  > se_two = se(est_pois, se = "twoway", cluster = base[, c("Product", "Destination")])
  > test(se_two, se(est_pois, cluster = c("Product", "Destination")))
  > test(se_two, se(est_pois, cluster = ~Product+Destination))
  > 
  > se_clu_comb = se(est_pois, cluster = "Product^Destination")
  > test(se_clu_comb, se(est_pois, cluster = paste(base$Product, base$Destination)))
  > test(se_clu_comb, se(est_pois, cluster = ~Product^Destination))
  > 
  > se_two_comb = se(est_pois, cluster = c("Origin^Destination", "Product"))
  > test(se_two_comb, se(est_pois, cluster = list(paste(base$Origin, base$Destination), base$Product)))
  > test(se_two_comb, se(est_pois, cluster = ~Origin^Destination + Product))
  > 
  > # With cluster removed and NAs
  > base = trade
  > base$Euros[base$Origin == "FR"] = 0
  > base$Euros_na = base$Euros ; base$Euros_na[sample(nrow(base), 50)] = NA
  > base$Destination_na = base$Destination ; base$Destination_na[sample(nrow(base), 50)] = NA
  > base$Origin_na = base$Origin ; base$Origin_na[sample(nrow(base), 50)] = NA
  > base$Product_na = base$Product ; base$Product_na[sample(nrow(base), 50)] = NA
  > 
  > est_pois = femlm(Euros ~ log(dist_km)|Origin+Destination_na, base)
  > 
  > se_clust = se(est_pois, se = "cluster", cluster = "Product")
  > test(se(est_pois, cluster = base$Product), se_clust)
  > test(se(est_pois, cluster = ~Product), se_clust)
  > 
  > se_two = se(est_pois, se = "twoway", cluster = base[, c("Product", "Destination")])
  > test(se_two, se(est_pois, cluster = c("Product", "Destination")))
  > test(se_two, se(est_pois, cluster = ~Product+Destination))
  > 
  > se_clu_comb = se(est_pois, cluster = "Product^Destination")
  > test(se_clu_comb, se(est_pois, cluster = paste(base$Product, base$Destination)))
  > test(se_clu_comb, se(est_pois, cluster = ~Product^Destination))
  > 
  > se_two_comb = se(est_pois, cluster = c("Origin^Destination", "Product"))
  > test(se_two_comb, se(est_pois, cluster = list(paste(base$Origin, base$Destination), base$Product)))
  > test(se_two_comb, se(est_pois, cluster = ~Origin^Destination + Product))
  > 
  > #
  > # Checking errors
  > #
  > 
  > # Should report error
  > test(se(est_pois, cluster = "Origin_na"), "err")
  > test(se(est_pois, cluster = base$Origin_na), "err")
  > test(se(est_pois, cluster = list(base$Origin_na)), "err")
  > test(se(est_pois, cluster = ~Origin_na^Destination), "err")
  > 
  > test(se(est_pois, se = "cluster", cluster = ~Origin_na^not_there), "err")
  > 
  > #
  > # Checking that the aliases work fine
  > #
  > 
  > se_hetero = se(est_pois, se = "hetero")
  > se_hc1    = se(est_pois, se = "hc1")
  > se_white  = se(est_pois, se = "white")
  > 
  > test(se_hetero, se_hc1)
  > test(se_hetero, se_white)
  > 
  > #
  > # New argument vcov
  > #
  > 
  > # We mostly check the absence of errors
  > data(base_did)
  > 
  > est_panel = feols(y ~ x1, base_did, panel.id = ~id + period, subset = 1:500)
  > 
  > se_est = se(est_panel)
  > test(se(est_panel, ~id), se_est)
  > 
  > # changing ssc argument
  > test(se(est_panel, ssc = ssc(adj = FALSE)), se(est_panel, ~id + ssc(adj = FALSE)))
  > 
  > # using vcov_cluster
  > test(se_est, se(est_panel, vcov_cluster("id")))
  > test(se_est, se(vcov_cluster(est_panel, "id")))
  > 
  > # NW
  > se_NW = se(est_panel, "NW")
  > test(se_NW, se(est_panel, NW ~ id + period))
  > test(se_NW, se(est_panel, newey ~ id + period))
  > test(se_NW, se(est_panel, vcov_NW("id", "period")))
  > test(se_NW, se(est_panel, vcov_NW(time = "period"))) # here unit is deduced
  > 
  > se_NW2 = se(est_panel, NW(2))
  > test(se_NW2, se(est_panel, NW(2) ~ id + period))
  > test(se_NW2, se(est_panel, vcov_NW(lag = 2)))
  > 
  > # errors
  > est = feols(y ~ x1, base_did)
  > test(se(est, NW ~ period), "err")
  > 
  > # DK
  > se_DK = se(est_panel, "DK")
  > test(se_DK, se(est_panel, DK ~ period))
  > test(se_DK, se(est_panel, dris ~ period))
  > test(se_DK, se(est_panel, vcov_DK("period")))
  > 
  > se_DK2 = se(est_panel, DK(2))
  > test(se_DK2, se(est_panel, DK(2) ~ period))
  > test(se_DK2, se(est_panel, vcov_DK(lag = 2)))
  > 
  > 
  > # Conley
  > data(quakes)
  > 
  > est = feols(depth ~ mag, quakes, "conley")
  > 
  > se_conley = se(est)
  > test(se_conley, se(est, conley(90) ~ 1))
  > test(se_conley, se(est, conley(90) ~ lat + long))
  > 
  > se_conley200 = se(est, conley(200) ~ lat + long)
  > test(se_conley200, se(est, vcov_conley(cutoff = 200)))
  > test(se_conley200, se(est, vcov_conley("lat", "long", cutoff = 200)))
  > 
  > se_conleyExtra = se(est, conley(pixel = 20, distance = "spherical"))
  > test(se_conleyExtra, se(vcov_conley(est, pixel = 20, distance = "spherical")))
  > 
  > 
  > # Checking the value of Conley SEs with equivalences
  > # we generate data that leads to simple values
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > 
  > # scattered along 111km
  > base$lat = rep(seq(-0.5, 0.5, length.out = 50), 3)
  > 
  > # scattered across very long distances
  > base$lon = rep(c(0, 80, 160), each = 50)
  > 
  > est = feols(y ~ x1, base)
  > 
  > # Equivalence 1 -- clustered SEs
  > se_clu = se(est, ~lon + ssc(adj = FALSE, cluster.adj = FALSE))
  > test(se_clu, se(est, conley(200) ~ ssc(adj = FALSE)))
  > 
  > # Equivalence 2 -- White SEs
  > se_hc1 = se(est, hetero ~ ssc(adj = FALSE, cluster.adj = FALSE))
  > test(se_hc1, se(est, conley(1) ~ ssc(adj = FALSE)))
  > 
  > 
  > #
  > # ssc with custom t.df values
  > #
  > 
  > est = feols(y ~ x1 + x2, base)
  > 
  > m = summary(est, ssc = ssc(t.df = 5))
  > 
  > test(m$coeftable[, 4], 2*pt(-abs(m$coeftable[, 3]), 5))
  > 
  > #
  > # feols.fit
  > #
  > 
  > 
  > base = setNames(iris, c("y", "x1", "x2", "x3", "species"))
  > 
  > est = feols(y ~ x1 | species, base, vcov = "hete")
  > est_fit = feols.fit(base$y, base$x1, base$species, vcov = "hete")
  > 
  > test(se(est), se(est_fit))
  > 
  > est = feols(y ~ x1 | species, base, cluster = base$species)
  > est_fit = feols.fit(base$y, base$x1, base$species, cluster = base$species)
  > 
  > test(se(est), se(est_fit))
  > 
  > est = feols(y ~ x1 | species, base, vcov = "cluster")
  > est_fit = feols.fit(base$y, base$x1, base$species, vcov = "cluster")
  > 
  > test(se(est), se(est_fit))
  > 
  > 
  > # error for the other VCOVs
  > test(feols.fit(base$y, base$x1, base$species, vcov = "hac"), "err")
  > test(feols.fit(base$y, base$x1, base$species, vcov = "conley"), "err")
  > 
  > ####
  > #### Residuals ####
  > ####
  > 
  > chunk("RESIDUALS")
  RESIDUALS
  
  > 
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > base$y_int = as.integer(base$y) + 1
  > 
  > # OLS + GLM + FENMLM
  > 
  > for(method in c("ols", "feglm", "femlm", "fenegbin")){
  +   cat("Method: ", format(method, width = 8))
  +   for(do_weight in c(FALSE, TRUE)){
  +     cat(".")
  + 
  +     if(do_weight){
  +       w = unclass(as.factor(base$species))
  +     } else {
  +       w = NULL
  +     }
  + 
  +     if(method == "ols"){
  +       m = feols(y_int ~ x1 | species, base, weights = w)
  +       mm = lm(y_int ~ x1 + species, base, weights = w)
  + 
  +     } else if(method == "feglm"){
  +       m = feglm(y_int ~ x1 | species, base, weights = w, family = "poisson")
  +       mm = glm(y_int ~ x1 + species, base, weights = w, family = poisson())
  + 
  +     } else if(method == "femlm"){
  +       if(!is.null(w)) next
  +       m = femlm(y_int ~ x1 | species, base)
  +       mm = glm(y_int ~ x1 + species, base, family = poisson())
  + 
  +     } else if(method == "fenegbin"){
  +       if(!is.null(w)) next
  +       m = fenegbin(y_int ~ x1 | species, base, notes = FALSE)
  +       mm = MASS::glm.nb(y_int ~ x1 + species, base)
  +     }
  + 
  +     tol = ifelse(method == "fenegbin", 1e-2, 1e-6)
  + 
  +     test(resid(m, "r"), resid(mm, "resp"), "~", tol = tol)
  +     test(resid(m, "d"), resid(mm, "d"), "~", tol = tol)
  +     test(resid(m, "p"), resid(mm, "pearson"), "~", tol = tol)
  + 
  +     test(deviance(m), deviance(mm), "~", tol = tol)
  +   }
  +   cat("\n")
  + }
  Method:  ols     ..
  Method:  feglm   ..
  Method:  femlm   ..
  Method:  fenegbin..
  Warning messages:
  1: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
    iteration limit reached
  2: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
    iteration limit reached
  > cat("\n")
  
  > 
  > 
  > ####
  > #### fixef ####
  > ####
  > 
  > chunk("FIXEF")
  FIXEF
  
  > 
  > set.seed(0)
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > base$x4 = rnorm(150) + 0.25*base$y
  > base$fe_bis = sample(10, 150, TRUE)
  > base$fe_ter = sample(15, 150, TRUE)
  > 
  > get_coef = function(all_coef, x){
  +   res = all_coef[grepl(x, names(all_coef), perl = TRUE)]
  +   names(res) = gsub(x, "", names(res), perl = TRUE)
  +   res
  + }
  > 
  > #
  > # With 2 x 1 FE
  > #
  > 
  > m = feols(y ~ x1 + x2 | species + fe_bis, base)
  > all_coef = coef(feols(y ~ -1 + x1 + x2 + species + factor(fe_bis), base))
  > 
  > m_fe = fixef(m)
  > c1  = get_coef(all_coef, "species")
  > test(var(c1 - m_fe$species[names(c1)]), 0)
  > 
  > c2  = get_coef(all_coef, "factor\\(fe_bis\\)")
  > test(var(c2 - m_fe$fe_bis[names(c2)]), 0)
  > 
  > 
  > #
  > # With 1 FE + 1 FE 1 VS
  > #
  > 
  > m = feols(y ~ x1 + x2 | species + fe_bis[x3], base)
  > all_coef = coef(feols(y ~ -1 + x1 + x2 + species + factor(fe_bis) + i(fe_bis, x3), base))
  > 
  > m_fe = fixef(m)
  > c1  = get_coef(all_coef, "species")
  > test(var(c1 - m_fe$species[names(c1)]), 0, "~")
  > 
  > c2  = get_coef(all_coef, "factor\\(fe_bis\\)")
  > test(var(c2 - m_fe$fe_bis[names(c2)]), 0, "~")
  > 
  > c3  = get_coef(all_coef, "fe_bis::|:x3")
  > test(c3, m_fe[["fe_bis[[x3]]"]][names(c3)], "~", tol = 1e-5)
  > # This test does not pass in R 3.5.0.... why?
  > # diff: 6.56851425546723e-05
  > 
  > #
  > # With 2 x (1 FE + 1 VS) + 1 FE
  > #
  > 
  > m = feols(y ~ x1 | species[x2] + fe_bis[x3] + fe_ter, base)
  > all_coef = coef(feols(y ~ -1 + x1 + species + i(species, x2) + factor(fe_bis) + i(fe_bis, x3) + factor(fe_ter), base))
  > 
  > m_fe = fixef(m)
  > c1  = get_coef(all_coef, "^species(?=[^:])")
  > test(var(c1 - m_fe$species[names(c1)]), 0, "~")
  > 
  > c2  = get_coef(all_coef, "^factor\\(fe_bis\\)")
  > test(var(c2 - m_fe$fe_bis[names(c2)]), 0, "~")
  > 
  > c3  = get_coef(all_coef, "fe_bis::|:x3")
  > test(c3, m_fe[["fe_bis[[x3]]"]][names(c3)], "~", tol = 2e-4)
  > 
  > c4  = get_coef(all_coef, "species::|:x2")
  > test(c4, m_fe[["species[[x2]]"]][names(c4)], "~", tol = 2e-4)
  > 
  > #
  > # With 2 x (1 FE) + 1 FE 2 VS
  > #
  > 
  > m = feols(y ~ x1 | species + fe_bis[x2,x3] + fe_ter, base)
  > all_coef = coef(feols(y ~ x1 + species + factor(fe_bis) + i(fe_bis, x2) + i(fe_bis, x3) + factor(fe_ter), base))
  > 
  > m_fe = fixef(m)
  > c1  = get_coef(all_coef, "^species")
  > test(var(c1 - m_fe$species[names(c1)]), 0, "~")
  > 
  > c2  = get_coef(all_coef, "^factor\\(fe_bis\\)")
  > test(var(c2 - m_fe$fe_bis[names(c2)]), 0, "~")
  > 
  > c3  = get_coef(all_coef, "fe_bis::(?=.+x2)|:x2")
  > test(c3, m_fe[["fe_bis[[x2]]"]][names(c3)], "~", tol = 2e-4)
  > 
  > c4  = get_coef(all_coef, "fe_bis::(?=.+x3)|:x3")
  > test(c4, m_fe[["fe_bis[[x3]]"]][names(c4)], "~", tol = 2e-4)
  > # This test does not pass in R 3.5.0.... why?
  > # diff: 0.000239702137861342
  > 
  > #
  > # With weights
  > #
  > 
  > w = 3 * (as.integer(base$species) - 0.95)
  > m = feols(y ~ x1 | species + fe_bis[x2,x3] + fe_ter, base, weights = w)
  > all_coef = coef(feols(y ~ x1 + species + factor(fe_bis) + i(fe_bis, x2) + i(fe_bis, x3) + factor(fe_ter), base, weights = w))
  > 
  > m_fe = fixef(m)
  > c1  = get_coef(all_coef, "^species")
  > test(var(c1 - m_fe$species[names(c1)]), 0, "~")
  > 
  > c2  = get_coef(all_coef, "^factor\\(fe_bis\\)")
  > test(var(c2 - m_fe$fe_bis[names(c2)]), 0, "~")
  > 
  > c3  = get_coef(all_coef, "fe_bis::(?=.+x2)|:x2")
  > test(c3, m_fe[["fe_bis[[x2]]"]][names(c3)], "~", tol = 2e-4)
  > 
  > c4  = get_coef(all_coef, "fe_bis::(?=.+x3)|:x3")
  > test(c4, m_fe[["fe_bis[[x3]]"]][names(c4)], "~", tol = 2e-4)
  > 
  > 
  > ####
  > #### To Integer ####
  > ####
  > 
  > chunk("TO_INTEGER")
  TO_INTEGER
  
  > 
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > base$z = sample(5, 150, TRUE)
  > 
  > # Normal
  > m = to_integer(base$species)
  > test(length(unique(m)), 3)
  > 
  > m = to_integer(base$species, base$z)
  > test(length(unique(m)), 15)
  > 
  > # with NA
  > base$species_na = base$species
  > base$species_na[base$species == "setosa"] = NA
  > 
  > m = to_integer(base$species_na, base$z)
  > test(length(unique(m)), 11)
  > 
  > m = to_integer(base$species_na, base$z, add_items = TRUE, items.list = TRUE)
  > test(length(m$items), 10)
  > 
  > 
  > 
  > ####
  > #### Interact ####
  > ####
  > 
  > 
  > chunk("Interact")
  INTERACT
  
  > 
  > base = setNames(iris, c("y", "x1", "x2", "x3", "species"))
  > base$fe_2 = round(seq(-5, 5, length.out = 150))
  > 
  > #
  > # We just ensure it works without error
  > #
  > 
  > m = feols(y ~ x1 + i(fe_2), base)
  > coefplot(m)
  > etable(m, dict = c("0" = "zero"))
                                   m
  Dependent Var.:                  y
                                    
  Constant         2.367*** (0.4683)
  x1              0.7513*** (0.1275)
  fe_2 = -4          0.0679 (0.2247)
  fe_2 = -3          0.1381 (0.2239)
  fe_2 = -2         0.4083. (0.2242)
  fe_2 = -1        1.406*** (0.2389)
  fe_2 = zero      1.693*** (0.2423)
  fe_2 = 1         1.319*** (0.2366)
  fe_2 = 2         1.827*** (0.2323)
  fe_2 = 3         2.047*** (0.2314)
  fe_2 = 4         2.072*** (0.2285)
  fe_2 = 5         1.732*** (0.2601)
  _______________ __________________
  S.E. type                      IID
  Observations                   150
  R2                         0.64694
  Adj. R2                    0.61880
  ---
  Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  > 
  > m = feols(y ~ x1 + i(fe_2) + i(fe_2, x2), base)
  > coefplot(m)
  > etable(m, dict = c("0" = "zero"))
                                    m
  Dependent Var.:                   y
                                     
  Constant              2.290 (1.400)
  x1               0.4049*** (0.0835)
  fe_2 = -4            0.1078 (1.520)
  fe_2 = -3             2.222 (1.594)
  fe_2 = -2            0.3446 (1.414)
  fe_2 = -1           -0.7139 (1.587)
  fe_2 = zero          0.3448 (1.587)
  fe_2 = 1             0.1762 (1.630)
  fe_2 = 2            -0.3183 (1.467)
  fe_2 = 3             -1.715 (1.538)
  fe_2 = 4             -2.226 (1.721)
  fe_2 = 5             0.1711 (2.374)
  x2 x fe_2 = -5      0.8629 (0.9673)
  x2 x fe_2 = -4     0.8919* (0.4045)
  x2 x fe_2 = -3     -0.5411 (0.4828)
  x2 x fe_2 = -2   0.6065*** (0.0600)
  x2 x fe_2 = -1   0.7534*** (0.1848)
  x2 x fe_2 = zero  0.5449** (0.1746)
  x2 x fe_2 = 1      0.5115* (0.1984)
  x2 x fe_2 = 2    0.6090*** (0.0846)
  x2 x fe_2 = 3    0.8699*** (0.1164)
  x2 x fe_2 = 4    0.9780*** (0.1816)
  x2 x fe_2 = 5       0.5037 (0.3634)
  ________________ __________________
  S.E. type                       IID
  Observations                    150
  R2                          0.88552
  Adj. R2                     0.86569
  ---
  Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  > 
  > a = i(base$fe_2)
  > b = i(base$fe_2, ref = 0:1)
  > d = i(base$fe_2, keep = 0:1)
  > 
  > test(ncol(a), ncol(b) + 2)
  > test(ncol(d), 2)
  > 
  > #
  > # binning
  > #
  > 
  > m = feols(y ~ x1 + i(fe_2, bin = list("0" = -1:1)), base)
  > test(length(coef(m)), 12 - 2)
  > 
  > # SA
  > data(base_stagg)
  > res_sunab = feols(y ~ x1 + sunab(year_treated, year, bin = "bin::2"), base_stagg)
  > iplot(res_sunab)
  > test(length(coef(res_sunab)), 15)
  > 
  > res_sunab = feols(y ~ x1 + sunab(year_treated, year, bin.rel = "bin::2"), base_stagg)
  > iplot(res_sunab)
  > test(length(coef(res_sunab)), 12)
  > 
  > 
  > ####
  > #### bin ####
  > ####
  > 
  > chunk("BIN")
  BIN
  
  > 
  > plen = iris$Petal.Length
  > years = round(rnorm(1000, 2000, 5))
  > 
  > my_cuts = c("cut::3", "cut::2]5]", "cut::q1]q2]q3]", "cut::p20]p50]p70]p90]", "cut::2[q2]p90]")
  > 
  > for(type in 1:2){
  + 
  +   x = switch(type, "1" = plen, "2" = years)
  + 
  +   for(cut in my_cuts){
  + 
  +     my_bin = bin(x, cut)
  +     bin_char = as.character(my_bin)
  + 
  +     if(grepl("[", bin_char[1], fixed = TRUE)){
  +       all_min = as.numeric(gsub("(^\\[)|(;.+)", "", bin_char))
  +       all_max = as.numeric(gsub(".+; |\\]", "", bin_char))
  +     } else {
  +       all_min = as.numeric(gsub("-.+", "", bin_char))
  +       all_max = as.numeric(gsub(".+-", "", bin_char))
  +     }
  + 
  +     test(all(x >= all_min), TRUE)
  +     test(all(x <= all_max), TRUE)
  +   }
  + }
  > 
  > 
  > 
  > 
  > 
  > 
  > 
  > ####
  > #### demean ####
  > ####
  > 
  > chunk("DEMEAN")
  DEMEAN
  
  > 
  > data(trade)
  > 
  > base = trade
  > base$ln_euros = log(base$Euros)
  > base$ln_dist = log(base$dist_km)
  > 
  > X = base[, c("ln_euros", "ln_dist")]
  > fe = base[, c("Origin", "Destination")]
  > 
  > base_new = demean(X, fe)
  > 
  > a = feols(ln_euros ~ ln_dist, base_new)
  > b = feols(ln_euros ~ ln_dist | Origin + Destination, base, demeaned = TRUE)
  > 
  > test(coef(a)[-1], coef(b), "~", 1e-12)
  > 
  > test(base_new$ln_euros, b$y_demeaned)
  > test(base_new$ln_dist, b$X_demeaned)
  > 
  > # Now we just check there's no error
  > 
  > # NAs
  > X_NA = X
  > fe_NA = fe
  > X_NA[1:5, 1] = NA
  > fe_NA[6:10, 1] = NA
  > X_demean = demean(X_NA, fe_NA, na.rm = FALSE)
  > test(nrow(X_demean), nrow(X))
  > 
  > # integer
  > X_int = X
  > X_int[[1]] = as.integer(X_int[[1]])
  > X_demean = demean(X_int, fe)
  > 
  > # matrix/DF
  > X_demean = demean(X_int, fe, as.matrix = TRUE)
  > test(is.matrix(X_demean), TRUE)
  > 
  > X_demean = demean(as.matrix(X_int), fe, as.matrix = FALSE)
  > test(is.matrix(X_demean), FALSE)
  > 
  > # slopes
  > X_dm_slopes = demean(ln_dist ~ Origin + Destination[ln_euros], data = base)
  > X_dm_slopes_bis = demean(base$ln_dist, fe, slope.vars = base$ln_euros, slope.flag = c(0, 1))
  > 
  > test(X_dm_slopes[[1]], X_dm_slopes_bis)
  > 
  > # with data table + formula call
  > trade_dt = as.data.table(trade)
  > trade_dt$ln_dist = log(trade_dt$dist_km)
  > 
  > dist_dm_dt = demean(ln_dist ~ Origin + Destination, data = trade_dt)
  > dist_dm_df = demean(ln_dist ~ Origin + Destination, data = base)
  > 
  > ####
  > #### hatvalues ####
  > ####
  > 
  > 
  > chunk("HATVALUES")
  HATVALUES
  
  > 
  > base = setNames(iris, c("y", "x1", "x2", "x3", "species"))
  > base$y_int = as.integer(base$y)
  > base$y_bin = 1 * (base$y > mean(base$y))
  > 
  > fm  = lm(y ~ x1 + x2, base)
  > ffm = feols(y ~ x1 + x2, base)
  > test(hatvalues(ffm), hatvalues(fm))
  > 
  > glm_poi  = glm(y_int ~ x1 + x2, family = poisson(), base)
  > feglm_poi = fepois(y_int ~ x1 + x2, base)
  > test(hatvalues(feglm_poi), hatvalues(glm_poi))
  > 
  > 
  > glm_logit  = glm(y_bin ~ x1 + x2, family = binomial(), base)
  > feglm_logit = feglm(y_bin ~ x1 + x2, base, binomial())
  > test(hatvalues(feglm_logit), hatvalues(glm_logit))
  > 
  > glm_probit  = glm(y_bin ~ x1 + x2, family = binomial("probit"), base)
  > feglm_probit = feglm(y_bin ~ x1 + x2, base, binomial("probit"))
  > test(hatvalues(feglm_probit), hatvalues(glm_probit))
  > 
  > 
  > ####
  > #### sandwich ####
  > ####
  > 
  > chunk("SANDWICH")
  SANDWICH
  
  > 
  > # Compatibility with sandwich
  > 
  > library(sandwich)
  > 
  > data(base_did)
  > est = feols(y ~ x1 + I(x1**2) + factor(id), base_did)
  > 
  > test(vcov(est, cluster = ~id), vcovCL(est, cluster = ~id, type = "HC1"))
  > 
  > est_pois = fepois(as.integer(y) + 20 ~ x1 + I(x1**2) + factor(id), base_did)
  > 
  > test(vcov(est_pois, cluster = ~id), vcovCL(est_pois, cluster = ~id, type = "HC1"))
  > 
  > # With FEs
  > 
  > est = feols(y ~ x1 + I(x1**2) | id, base_did)
  > 
  > test(vcov(est, cluster = ~id, ssc = ssc(adj = FALSE)), vcovCL(est, cluster = ~id))
  Error in test(vcov(est, cluster = ~id, ssc = ssc(adj = FALSE)), vcovCL(est,  : 
    Difference > tol: Max abs. diff: 2.13414988018377e-06 (in position 1)
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  '/tmp/th798/16189510/R-release/474/fixest.Rcheck/00check.log'
for details.

[1] "2025-03-30 01:23:16 MST"
[1] "2025-03-30 01:23:16 MST"
Installing package into '/tmp/th798/16189510/R-release/474/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** 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/th798/16189510/R-release/474/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] "2025-03-30 01:23:34 MST"
* using log directory '/tmp/th798/16189510/R-release/474/fixest.Rcheck'
* using R version 4.4.3 (2025-02-28)
* 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 'fixest/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'fixest' version '0.12.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'fixest' can be installed ... OK
* used C++ compiler: 'g++ (Spack GCC) 12.2.0'
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    3.6Mb
    libs   1.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'fixest_tests.R'
 ERROR
Running the tests in 'tests/fixest_tests.R' failed.
Complete output:
  > #----------------------------------------------#
  > # Author: Laurent Berge
  > # Date creation: Fri Jul 10 09:03:06 2020
  > # ~: package sniff tests
  > #----------------------------------------------#
  > 
  > # Not everything is currently covered, but I'll improve it over time
  > 
  > # Some functions are not trivial to test properly though
  > 
  > library(fixest)
  > 
  > test = fixest:::test ; chunk = fixest:::chunk
  > vcovClust = fixest:::vcovClust
  > stvec = stringmagic::string_vec_alias()
  > 
  > setFixest_notes(FALSE)
  > 
  > if(fixest:::is_r_check()){
  +   if(requireNamespace("data.table", quietly = TRUE)){
  +     library(data.table)
  +     data.table::setDTthreads(1)
  +   }
  +   setFixest_nthreads(1)
  + }
  > 
  > ####
  > #### ESTIMATIONS ####
  > ####
  > 
  > ####
  > #### ... Main ####
  > ####
  > 
  > 
  > chunk("ESTIMATION")
  ESTIMATION
  
  > 
  > set.seed(0)
  > 
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > base$fe_2 = rep(1:5, 30)
  > base$fe_3 = sample(15, 150, TRUE)
  > base$constant = 5
  > base$y_int = as.integer(base$y)
  > base$w = as.vector(unclass(base$species) - 0.95)
  > base$offset_value = unclass(base$species) - 0.95
  > base$y_01 = 1 * ((scale(base$x1) + rnorm(150)) > 0)
  > # what follows to avoid removal of fixed-effects (logit is pain in the neck)
  > base$y_01[1:5 + rep(c(0, 50, 100), each = 5)] = 1
  > base$y_01[6:10 + rep(c(0, 50, 100), each = 5)] = 0
  > # We enforce the removal of observations
  > base$y_int_null = base$y_int
  > base$y_int_null[base$fe_3 %in% 1:5] = 0
  > 
  > for(model in c("ols", "pois", "logit", "negbin", "Gamma")){
  +   cat("Model: ", format(model, width = 6), sep = "")
  +   for(use_weights in c(FALSE, TRUE)){
  +     my_weight = NULL
  +     if(use_weights) my_weight = base$w
  + 
  +     for(use_offset in c(FALSE, TRUE)){
  +       my_offset = NULL
  +       if(use_offset) my_offset = base$offset_value
  + 
  +       for(id_fe in 0:9){
  + 
  +         cat(".")
  + 
  +         tol = switch(model, "negbin" = 1e-2, "logit" = 3e-5, 1e-5)
  + 
  +         # Setting up the formula to accommodate FEs
  +         if(id_fe == 0){
  +           fml_fixest = fml_stats = y ~ x1
  +         } else if(id_fe == 1){
  +           fml_fixest = y ~ x1 | species
  +           fml_stats = y ~ x1 + factor(species)
  +         } else if(id_fe == 2){
  +           fml_fixest = y ~ x1 | species + fe_2
  +           fml_stats = y ~ x1 + factor(species) + factor(fe_2)
  +         } else if(id_fe == 3){
  +           # varying slope
  +           fml_fixest = y ~ x1 | species[[x2]]
  +           fml_stats = y ~ x1 + x2:species
  +         } else if(id_fe == 4){
  +           # varying slope -- 1 VS, 1 FE
  +           fml_fixest = y ~ x1 | species[[x2]] + fe_2
  +           fml_stats = y ~ x1 + x2:species + factor(fe_2)
  +         } else if(id_fe == 5){
  +           # varying slope -- 2 VS
  +           fml_fixest = y ~ x1 | species[x2]
  +           fml_stats = y ~ x1 + x2:species + species
  +         } else if(id_fe == 6){
  +           # varying slope -- 2 VS bis
  +           fml_fixest = y ~ x1 | species[[x2]] + fe_2[[x3]]
  +           fml_stats = y ~ x1 + x2:species + x3:factor(fe_2)
  +         } else if(id_fe == 7){
  +           # Combined clusters
  +           fml_fixest = y ~ x1 + x2 | species^fe_2
  +           fml_stats = y ~ x1 + x2 + paste(species, fe_2)
  +         } else if(id_fe == 8){
  +           fml_fixest = y ~ x1 | species[x2] + fe_2[x3] + fe_3
  +           fml_stats = y ~ x1 + species + i(species, x2) + factor(fe_2) + i(fe_2, x3) + factor(fe_3)
  +         } else if(id_fe == 9){
  +           fml_fixest = y ~ x1 | species + fe_2[x2,x3] + fe_3
  +           fml_stats = y ~ x1 + species + factor(fe_2) + i(fe_2, x2) + i(fe_2, x3) + factor(fe_3)
  +         }
  + 
  +         # ad hoc modifications of the formula
  +         if(model == "logit"){
  +           fml_fixest = xpd(y_01 ~ ..rhs, ..rhs = fml_fixest[[3]])
  +           fml_stats = xpd(y_01 ~ ..rhs, ..rhs = fml_stats[[3]])
  + 
  +           # The estimations are OK, conv differences out of my control
  +           if(id_fe %in% 8:9) tol = 0.5
  + 
  +         } else if(model == "pois"){
  +           fml_fixest = xpd(y_int_null ~ ..rhs, ..rhs = fml_fixest[[3]])
  +           fml_stats = xpd(y_int_null ~ ..rhs, ..rhs = fml_stats[[3]])
  + 
  +         } else if(model %in% c("negbin", "Gamma")){
  +           fml_fixest = xpd(y_int ~ ..rhs, ..rhs = fml_fixest[[3]])
  +           fml_stats = xpd(y_int ~ ..rhs, ..rhs = fml_stats[[3]])
  +         }
  + 
  +         adj = 1
  +         if(model == "ols"){
  +           res = feols(fml_fixest, base, weights = my_weight, offset = my_offset)
  +           res_bis = lm(fml_stats, base, weights = my_weight, offset = my_offset)
  + 
  +         } else if(model %in% c("pois", "logit", "Gamma")){
  +           adj = 0
  +           if(model == "Gamma" && use_offset) next
  + 
  +           my_family = switch(model, pois = poisson(), logit = binomial(), Gamma = Gamma())
  + 
  +           res = feglm(fml_fixest, base, family = my_family, weights = my_weight, offset = my_offset)
  + 
  +           if(!is.null(res$obs_selection$obsRemoved)){
  +             qui = res$obs_selection$obsRemoved
  + 
  +             # I MUST do that.... => subset does not work...
  +             base_tmp = base[qui, ]
  +             base_tmp$my_offset = my_offset[qui]
  +             base_tmp$my_weight = my_weight[qui]
  +             res_bis = glm(fml_stats, base_tmp, family = my_family, weights = my_weight, offset = my_offset)
  +           } else {
  +             res_bis = glm(fml_stats, data = base, family = my_family, weights = my_weight, offset = my_offset)
  +           }
  + 
  +         } else if(model == "negbin"){
  +           # no offset in glm.nb + no VS in fenegbin + no weights in fenegbin
  +           if(use_weights || use_offset || id_fe > 2) next
  + 
  +           res = fenegbin(fml_fixest, base, notes = FALSE)
  +           res_bis = MASS::glm.nb(fml_stats, base)
  + 
  +         }
  + 
  +         test(coef(res)["x1"], coef(res_bis)["x1"], "~", tol)
  +         test(se(res, se = "st", ssc = ssc(adj = adj))["x1"], se(res_bis)["x1"], "~", tol)
  +         test(pvalue(res, se = "st", ssc = ssc(adj = adj))["x1"], pvalue(res_bis)["x1"], "~", tol*10**(model == "negbin"))
  +         # cat("Model: ", model, ", FE: ", id_fe, ", weight: ", use_weights,  ", offset: ", use_offset, "\n", sep="")
  + 
  +       }
  +       cat("|")
  +     }
  +   }
  +   cat("\n")
  + }
  Model: ols   ..........|..........|..........|..........|
  Model: pois  ..........|..........|..........|..........|
  Model: logit ..........|..........|..........|..........|
  Model: negbin..........|..........|..........|..........|
  Model: Gamma ..........|..........|..........|..........|
  There were 36 warnings (use warnings() to see them)
  > 
  > ####
  > #### ... Corner cases ####
  > ####
  > 
  > chunk("Corner cases")
  CORNER CASES
  
  > 
  > 
  > # We test the absence of bugs
  > 
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "fe1")
  > base$fe2 = rep(1:5, 30)
  > base$y[1:5] = NA
  > base$x1[4:8] = NA
  > base$x2[4:21] = NA
  > base$x3[110:111] = NA
  > base$fe1[110:118] = NA
  > base$fe2[base$fe2 == 1] = 0
  > base$fe3 = sample(letters[1:5], 150, TRUE)
  > base$period = rep(1:50, 3)
  > base$x_cst = 1
  > 
  > res = feols(y ~ 1 | csw(fe1, fe1^fe2), base)
  > 
  > res = feols(y ~ 1 + csw(x1, i(fe1)) | fe2, base)
  > 
  > res = feols(y ~ csw(f(x1, 1:2), x2) | sw0(fe2, fe2^fe3), base, panel.id = ~ fe1 + period)
  > 
  > res = feols(d(y) ~ -1 + d(x2), base, panel.id = ~ fe1 + period)
  > test(length(coef(res)), 1)
  > 
  > res = feols(c(y, x1) ~ 1 | fe1 | x2 ~ x3, base)
  > 
  > res = feols(y ~ x1 | fe1[x2] + fe2[x2], base)
  > 
  > #
  > # NA models (ie all variables are collinear with the FEs)
  > #
  > 
  > # Should work when warn = FALSE or multiple est
  > for(i in 1:2){
  +   fun = switch(i, "1" = feols, "2" = feglm)
  + 
  +   res = feols(y ~ x_cst | fe1, base, warn = FALSE)
  +   res         # => no error
  +   etable(res) # => no error
  + 
  +   # error when warn = TRUE
  +   test(feols(y ~ x_cst | fe1, base), "err")
  + 
  +   # multiple est => no error
  +   res = feols(c(y, x1) ~ x_cst | fe1, base)
  +   res         # => no error
  +   etable(res) # => no error
  + }
  > 
  > 
  > # Removing the intercept!!!
  > 
  > res = feols(y ~ -1 + x1 + i(fe1), base)
  > test("(Intercept)" %in% names(res$coefficients), FALSE)
  > 
  > res = feols(y ~ -1 + x1 + factor(fe1), base)
  > test("(Intercept)" %in% names(res$coefficients), FALSE)
  > 
  > res = feols(y ~ -1 + x1 + i(fe1) + i(fe2), base)
  > test("(Intercept)" %in% names(res$coefficients), FALSE)
  > test(is.null(res$collin.var), TRUE)
  > 
  > 
  > # IV + interacted FEs
  > res = feols(y ~ x1 | fe1^fe2 | x2 ~ x3, base)
  > 
  > # IVs no exo var
  > res = feols(y ~ 0 | x2 ~ x3, base)
  > # Same in stepwise
  > res = feols(y ~ 0 | sw0(fe1) | x2 ~ x3, base)
  > 
  > # IVs + lags
  > res = feols(y ~ x1 | fe1^fe2 | l(x2, -1:1) ~ l(x3, -1:1), base, panel.id = ~ fe1 + period)
  > 
  > # functions in interactions
  > res = feols(y ~ x1 | factor(fe1)^factor(fe2), base)
  > res = feols(y ~ x1 | round(x2^2), base)
  > test(feols(y ~ x1 | factor(fe1^fe2), base), "err")
  > 
  > res = feols(y ~ x1 | bin(x2, "bin::1")^fe1 + fe1^fe2, base)
  > 
  > # 1 obs (after FE removal) estimation
  > base_1obs = data.frame(y = c(1, 0), fe = c(1, 2), x = c(1, 0))
  > test(fepois(y ~ x | fe, base_1obs), "err")
  > # no error
  > res = fepois(y ~ 1 | fe, base_1obs)
  > 
  > # warning when demeaning algo reaches max iterations 
  > data(trade)
  > test(feols(Euros ~ log(dist_km) | Destination + Origin + Product, 
  +            trade, fixef.iter = 1), "warn")
  > 
  > 
  > ####
  > #### ... Fit methods ####
  > ####
  > 
  > chunk("Fit methods")
  FIT METHODS
  
  > 
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > base$y_int = as.integer(base$y)
  > base$y_log = sample(c(TRUE, FALSE), 150, TRUE)
  > 
  > res = feglm.fit(base$y, base[, 2:4])
  > res_bis = feglm(y ~ -1 + x1 + x2 + x3, base)
  > test(coef(res), coef(res_bis))
  > 
  > res = feglm.fit(base$y_int, base[, 2:4])
  > res_bis = feglm(y_int ~ -1 + x1 + x2 + x3, base)
  > test(coef(res), coef(res_bis))
  > 
  > res = feglm.fit(base$y_log, base[, 2:4])
  > res_bis = feglm(y_log ~ -1 + x1 + x2 + x3, base)
  > test(coef(res), coef(res_bis))
  > 
  > 
  > 
  > res = feglm.fit(base$y, base[, 2:4], family = "poisson")
  > res_bis = feglm(y ~ -1 + x1 + x2 + x3, base, family = "poisson")
  > test(coef(res), coef(res_bis))
  > 
  > res = feglm.fit(base$y_int, base[, 2:4], family = "poisson")
  > res_bis = feglm(y_int ~ -1 + x1 + x2 + x3, base, family = "poisson")
  > test(coef(res), coef(res_bis))
  > 
  > res = feglm.fit(base$y_log, base[, 2:4], family = "poisson")
  > res_bis = feglm(y_log ~ -1 + x1 + x2 + x3, base, family = "poisson")
  > test(coef(res), coef(res_bis))
  > 
  > ####
  > #### global variables ####
  > ####
  > 
  > chunk("globals")
  GLOBALS
  
  > 
  > est_reg = function(df, yvar, xvar, refgrp) {
  +   feols(.[yvar] ~ i(.[xvar], ref = refgrp), data = df)
  + }
  > 
  > (est = est_reg(iris, "Sepal.Length", "Species", ref = "setosa"))
  OLS estimation, Dep. Var.: Sepal.Length
  Observations: 150
  Standard-errors: IID 
                      Estimate Std. Error  t value   Pr(>|t|)    
  (Intercept)            5.006   0.072802 68.76164  < 2.2e-16 ***
  Species::versicolor    0.930   0.102958  9.03282 8.7702e-16 ***
  Species::virginica     1.582   0.102958 15.36551  < 2.2e-16 ***
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  RMSE: 0.509616   Adj. R2: 0.613518
  > 
  > # checking when it should not work
  > base = setNames(iris, c("y", "x1", "x2", "x3", "species"))
  > 
  > z = base$x1
  > test(feols(y ~ z, base), "err")
  > 
  > 
  > 
  > ####
  > #### ... Collinearity ####
  > ####
  > 
  > chunk("COLLINEARITY")
  COLLINEARITY
  
  > 
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > base$constant = 5
  > base$y_int = as.integer(base$y)
  > base$w = as.vector(unclass(base$species) - 0.95)
  > 
  > for(useWeights in c(FALSE, TRUE)){
  +   for(model in c("ols", "pois")){
  +     for(use_fe in c(FALSE, TRUE)){
  +       cat(".")
  + 
  +       my_weight = NULL
  +       if(useWeights) my_weight = base$w
  + 
  +       adj = 1
  +       if(model == "ols"){
  +         if(!use_fe){
  +           res = feols(y ~ x1 + constant, base, weights = my_weight)
  +           res_bis = lm(y ~ x1 + constant, base, weights = my_weight)
  +         } else {
  +           res = feols(y ~ x1 + constant | species, base, weights = my_weight)
  +           res_bis = lm(y ~ x1 + constant + species, base, weights = my_weight)
  +         }
  +       } else {
  +         if(!use_fe){
  +           res = fepois(y_int ~ x1 + constant, base, weights = my_weight)
  +           res_bis = glm(y_int ~ x1 + constant, base, weights = my_weight, family = poisson)
  +         } else {
  +           res = fepois(y_int ~ x1 + constant | species, base, weights = my_weight)
  +           res_bis = glm(y_int ~ x1 + constant + species, base, weights = my_weight, family = poisson)
  +         }
  +         adj = 0
  +       }
  + 
  +       test(coef(res)["x1"], coef(res_bis)["x1"], "~")
  +       test(se(res, se = "st", ssc = ssc(adj=adj))["x1"], se(res_bis)["x1"], "~")
  +       # cat("Weight: ", useWeights, ", model: ", model, ", FE: ", use_fe, "\n", sep="")
  + 
  +     }
  +   }
  + }
  ........> cat("\n")
  
  > 
  > 
  > ####
  > #### ... Non linear tests ####
  > ####
  > 
  > chunk("NON LINEAR")
  NON LINEAR
  
  > 
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > 
  > tab = c("versicolor" = 5, "setosa" = 0, "virginica" = -5)
  > 
  > fun_nl = function(a, b, spec){
  +   res = as.numeric(tab[spec])
  +   a*res + b*res^2
  + }
  > 
  > est_nl = feNmlm(y ~ x1, base, NL.fml = ~fun_nl(a, b, species), NL.start = 1, family = "gaussian")
  > 
  > base$var_spec = as.numeric(tab[base$species])
  > 
  > est_lin = feols(y ~ x1 + var_spec + I(var_spec^2), base)
  > 
  > test(coef(est_nl), coef(est_lin)[c(3, 4, 1, 2)], "~")
  > 
  > ####
  > #### ... Lagging ####
  > ####
  > 
  > # Different types of lag
  > # 1) check no error in wide variety of situations
  > # 2) check consistency
  > 
  > chunk("LAGGING")
  LAGGING
  
  > 
  > data(base_did)
  > base = base_did
  > 
  > n = nrow(base)
  > 
  > set.seed(0)
  > base$y_na = base$y ; base$y_na[sample(n, 50)] = NA
  > base$period_txt = letters[base$period]
  > ten_dates = c("1960-01-15", "1960-01-16", "1960-03-31", "1960-04-05", "1960-05-12", "1960-05-25", "1960-06-20", "1960-07-30", "1965-01-02", "2002-12-05")
  > base$period_date = as.Date(ten_dates, "%Y-%m-%d")[base$period]
  > base$y_0 = base$y**2 ; base$y_0[base$id == 1] = 0
  > 
  > # We compute the lags "by hand"
  > base = base[order(base$id, base$period), ]
  > base$x1_lag = c(NA, base$x1[-n]) ; base$x1_lag[base$period == 1] = NA
  > base$x1_lead = c(base$x1[-1], NA) ; base$x1_lead[base$period == 10] = NA
  > base$x1_diff = base$x1 - base$x1_lag
  > 
  > # we create holes
  > base$period_bis = base$period ; base$period_bis[base$period_bis == 5] = 50
  > base$x1_lag_hole = base$x1_lag ; base$x1_lag_hole[base$period %in% c(5, 6)] = NA
  > base$x1_lead_hole = base$x1_lead ; base$x1_lead_hole[base$period %in% c(4, 5)] = NA
  > 
  > # we reshuffle the base
  > base = base[sample(n), ]
  > 
  > #
  > # Checks consistency
  > #
  > 
  > cat("consistentcy...")
  consistentcy...> 
  > test(lag(x1 ~ id + period, data = base), base$x1_lag)
  > test(lag(x1 ~ id + period, -1, data = base), base$x1_lead)
  > 
  > test(lag(x1 ~ id + period_bis, data = base), base$x1_lag_hole)
  > test(lag(x1 ~ id + period_bis, -1, data = base), base$x1_lead_hole)
  > 
  > test(lag(x1 ~ id + period_txt, data = base), base$x1_lag)
  > test(lag(x1 ~ id + period_txt, -1, data = base), base$x1_lead)
  > 
  > test(lag(x1 ~ id + period_date, data = base), base$x1_lag)
  > test(lag(x1 ~ id + period_date, -1, data = base), base$x1_lead)
  > 
  > cat("done.\nEstimations...")
  done.
  Estimations...> 
  > #
  > # Estimations
  > #
  > 
  > # Poisson
  > 
  > for(depvar in c("y", "y_na", "y_0")){
  +   for(p in c("period", "period_txt", "period_date")){
  + 
  +     base$per = base[[p]]
  + 
  +     cat(".")
  + 
  +     base$y_dep = base[[depvar]]
  +     pdat = panel(base, ~ id + period)
  + 
  +     if(depvar == "y_0"){
  +       estfun = fepois
  +     } else {
  +       estfun = feols
  +     }
  + 
  +     est_raw  = estfun(y_dep ~ x1 + x1_lag + x1_lead, base)
  +     est      = estfun(y_dep ~ x1 + l(x1) + f(x1), base, panel.id = "id,per")
  +     est_pdat = estfun(y_dep ~ x1 + l(x1, 1) + f(x1, 1), pdat)
  +     test(coef(est_raw), coef(est))
  +     test(coef(est_raw), coef(est_pdat))
  + 
  +     # Now diff
  +     est_raw  = estfun(y_dep ~ x1 + x1_diff, base)
  +     est      = estfun(y_dep ~ x1 + d(x1), base, panel.id = "id,per")
  +     est_pdat = estfun(y_dep ~ x1 + d(x1, 1), pdat)
  +     test(coef(est_raw), coef(est))
  +     test(coef(est_raw), coef(est_pdat))
  + 
  +     # Now we just check that calls to l/f works without checking coefs
  + 
  +     est = estfun(y_dep ~ x1 + l(x1) + f(x1), base, panel.id = "id,per")
  +     est = estfun(y_dep ~ l(x1, -1:1) + f(x1, 2), base, panel.id = c("id", "per"))
  +     est = estfun(y_dep ~ l(x1, -1:1, fill = 1), base, panel.id = ~ id + per)
  +     if(depvar == "y") test(est$nobs, n)
  +     est = estfun(f(y_dep) ~ f(x1, -1:1), base, panel.id = ~ id + per)
  +   }
  + }
  .........> 
  > cat("done.\n\n")
  done.
  
  > 
  > #
  > # Data table
  > #
  > 
  > cat("data.table...")
  data.table...> # We just check there is no bug (consistency should be OK)
  > 
  > library(data.table)
  > 
  > base_dt = data.table(id = c("A", "A", "B", "B"),
  +            time = c(1, 2, 1, 3),
  +            x = c(5, 6, 7, 8))
  > 
  > base_dt = panel(base_dt, ~id + time)
  > 
  > base_dt[, x_l := l(x)]
  > test(base_dt$x_l, c(NA, 5, NA, NA))
  > 
  > lag_creator = function(dt) {
  +   dt2 = panel(dt, ~id + time)
  +   dt2[, x_l := l(x)]
  +   return(dt2)
  + }
  > 
  > base_bis = lag_creator(base_dt)
  > 
  > base_bis[, x_d := d(x)]
  > 
  > cat("done.\n\n")
  done.
  
  > 
  > #
  > # Panel
  > #
  > 
  > # We ensure we get the right SEs whether we use the panel() or the panel.id method
  > data(base_did)
  > 
  > # Setting a data set as a panel...
  > pdat = panel(base_did, ~id+period)
  > pdat$fe = sample(15, nrow(pdat), replace = TRUE)
  > 
  > base_panel = unpanel(pdat)
  > 
  > est_pdat = feols(y ~ x1 | fe, pdat)
  > est_panel = feols(y ~ x1 | fe, base_panel, panel.id = ~id+period)
  > 
  > test(attr(vcov(est_pdat, attr = TRUE), "type"),
  +    attr(vcov(est_panel, attr = TRUE), "type"))
  > 
  > ####
  > #### ... subset ####
  > ####
  > 
  > chunk("SUBSET")
  SUBSET
  
  > 
  > set.seed(5)
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > base$fe_bis = sample(letters, 150, TRUE)
  > base$x4 = rnorm(150)
  > base$x1[sample(150, 5)] = NA
  > 
  > fml = y ~ x1 + x2
  > 
  > # Errors
  > test(feols(fml, base, subset = ~species), "err")
  > test(feols(fml, base, subset = -1:15), "err")
  > test(feols(fml, base, subset = integer(0)), "err")
  > test(feols(fml, base, subset = c(TRUE, TRUE, FALSE)), "err")
  > 
  > # Valid use
  > for(id_fun in 1:6){
  +   estfun = switch(as.character(id_fun),
  +           "1" = feols,
  +           "2" = feglm,
  +           "3" = fepois,
  +           "4" = femlm,
  +           "5" = fenegbin,
  +           "6" = feNmlm)
  + 
  +   for(id_fe in 1:5){
  + 
  +     cat(".")
  + 
  +     fml = switch(as.character(id_fe),
  +            "1" = y ~ x1 + x2,
  +            "2" = y ~ x1 + x2 | species,
  +            "3" = y ~ x1 + x2 | fe_bis,
  +            "4" = y ~ x1 + x2 + i(fe_bis),
  +            "5" = y ~ x1 + x2 | fe_bis[x3])
  + 
  +     if(id_fe == 5 && id_fun %in% 4:6) next
  + 
  +     if(id_fun == 6){
  +       res_sub_a = estfun(fml, base, subset = ~species == "setosa", NL.fml = ~ a*x4, NL.start = 0)
  +       res_sub_b = estfun(fml, base, subset = base$species == "setosa", NL.fml = ~ a*x4, NL.start = 0)
  +       res_sub_c = estfun(fml, base, subset = which(base$species == "setosa"), NL.fml = ~ a*x4, NL.start = 0)
  +       res       = estfun(fml, base[base$species == "setosa", ], NL.fml = ~ a*x4, NL.start = 0)
  +     } else {
  +       res_sub_a = estfun(fml, base, subset = ~species == "setosa")
  +       res_sub_b = estfun(fml, base, subset = base$species == "setosa")
  +       res_sub_c = estfun(fml, base, subset = which(base$species == "setosa"))
  +       res       = estfun(fml, base[base$species == "setosa", ])
  +     }
  + 
  +     test(coef(res_sub_a), coef(res))
  +     test(coef(res_sub_b), coef(res))
  +     test(coef(res_sub_c), coef(res))
  +     test(se(res_sub_c, cluster = "fe_bis"), se(res, cluster = "fe_bis"))
  +   }
  +   cat("|")
  + }
  .....|.....|.....|.....|.....|.....|> cat("\n")
  
  > 
  > 
  > ####
  > #### ... split ####
  > ####
  > 
  > chunk("split")
  SPLIT
  
  > 
  > base = setNames(iris, c("y", "x1", "x2", "x3", "species"))
  > 
  > # simple: formula
  > est = feols(y ~ x.[1:3], base, split = ~species %keep% "@^v")
  > test(length(est), 2)
  > 
  > est = feols(y ~ x.[1:3], base, fsplit = ~species %keep% c("set", "vers"))
  > test(length(est), 3)
  > 
  > est = feols(y ~ x.[1:3], base, split = ~species %drop% "set")
  > test(length(est), 2)
  > 
  > # simple: vector
  > est = feols(y ~ x.[1:3], base, split = base$species %keep% "@^v")
  > test(length(est), 2)
  > 
  > est = feols(y ~ x.[1:3], base, split = base$species %keep% c("set", "vers"))
  > test(length(est), 2)
  > 
  > est = feols(y ~ x.[1:3], base, split = base$species %drop% "set")
  > test(length(est), 2)
  > 
  > # with bin
  > est = feols(y ~ x.[1:2], base,
  +       split = ~bin(x3, c("cut::5", "saint emilion", "pessac leognan",
  +                  "margaux", "saint julien", "entre deux mers")) %keep% c("saint e", "pe"))
  > test(length(est), 2)
  > 
  > est = feols(y ~ x.[1:2], base,
  +       split = ~bin(x3, c("cut::5", "saint emilion", "pessac leognan", NA)) %drop% "@\\d")
  > test(length(est), 2)
  > 
  > # with argument
  > est = feols(y ~ x.[1:3], base, split = ~species, split.keep = "@^v")
  > test(length(est), 2)
  > 
  > est = feols(y ~ x.[1:3], base, fsplit = ~species, split.keep = c("set", "vers"))
  > test(length(est), 3)
  > 
  > est = feols(y ~ x.[1:3], base, split = ~species, split.drop = "set")
  > test(length(est), 2)
  > 
  > 
  > ####
  > #### ... Multiple estimations ####
  > ####
  > 
  > chunk("Multiple")
  MULTIPLE
  
  > 
  > set.seed(2)
  > base = iris
  > names(base) = c("y1", "x1", "x2", "x3", "species")
  > base$y2 = 10 + rnorm(150) + 0.5 * base$x1
  > base$x4 = rnorm(150) + 0.5 * base$y1
  > base$fe2 = rep(letters[1:15], 10)
  > base$fe2[50:51] = NA
  > base$y2[base$fe2 == "a" & !is.na(base$fe2)] = 0
  > base$x2[1:5] = NA
  > base$x3[6] = NA
  > base$x5 = rnorm(150)
  > base$x6 = rnorm(150) + base$y1 * 0.25
  > base$fe3 = rep(letters[1:10], 15)
  > 
  > 
  > for(id_fun in 1:5){
  +   estfun = switch(as.character(id_fun),
  +                   "1" = feols,
  +                   "2" = feglm,
  +                   "3" = fepois,
  +                   "4" = femlm,
  +                   "5" = feNmlm)
  + 
  +   # Following weird bug ASAN on CRAN I cannot replicate, check 4/5 not performed on non Windows
  +   if(Sys.info()["sysname"] != "Windows"){
  +     if(id_fun %in% 4:5) next
  +   }
  + 
  + 
  +   est_multi = estfun(c(y1, y2) ~ x1 + sw(x2, x3), base, split = ~species)
  + 
  +   k = 1
  +   for(s in c("setosa", "versicolor", "virginica")){
  +     for(lhs in c("y1", "y2")){
  +       for(rhs in c("x2", "x3")){
  +         res = estfun(.[lhs] ~ x1 + .[rhs], base[base$species == s, ], notes = FALSE)
  + 
  +         test(coef(est_multi[[k]]), coef(res))
  +         test(se(est_multi[[k]], cluster = "fe3"), se(res, cluster = "fe3"))
  +         k = k + 1
  +       }
  +     }
  +   }
  + 
  +   cat("__")
  + 
  +   est_multi = estfun(c(y1, y2) ~ x1 + csw0(x2, x3) + x4 | species + fe2, base, fsplit = ~species)
  +   k = 1
  +   all_rhs = c("", "x2", "x3")
  +   for(s in c("all", "setosa", "versicolor", "virginica")){
  +     for(lhs in c("y1", "y2")){
  +       for(n_rhs in 1:3){
  +         if(s == "all"){
  +           res = estfun(xpd(..lhs ~ x1 + ..rhs + x4 | species + fe2, ..lhs = lhs, ..rhs = all_rhs[1:n_rhs]), base, notes = FALSE)
  +         } else {
  +           res = estfun(xpd(..lhs ~ x1 + ..rhs + x4 | species + fe2, ..lhs = lhs, ..rhs = all_rhs[1:n_rhs]), base[base$species == s, ], notes = FALSE)
  +         }
  + 
  +         vname = names(coef(res))
  +         test(coef(est_multi[[k]])[vname], coef(res), "~" , 1e-6)
  +         test(se(est_multi[[k]], cluster = "fe3")[vname], se(res, cluster = "fe3"), "~" , 1e-6)
  +         k = k + 1
  +       }
  +     }
  +   }
  + 
  +   cat("|")
  + }
  __|__|__|> cat("\n")
  
  > 
  > 
  > # No error tests
  > # We test with IV + possible corner cases
  > 
  > base$left = rnorm(150)
  > base$right = rnorm(150)
  > 
  > est_multi = feols(c(y1, y2) ~ sw0(x1) | sw0(species) | x2 ~ x3, base)
  > 
  > # We check a few
  > est_a = feols(y1 ~ 1 | x2 ~ x3, base)
  > est_b = feols(y1 ~ x1 | species | x2 ~ x3, base)
  > est_c = feols(y2 ~ 1 | x2 ~ x3, base)
  > 
  > test(coef(est_multi[lhs = "y1", rhs = "^1", fixef = "1", drop = TRUE]), coef(est_a))
  > test(coef(est_multi[lhs = "y1", rhs = "x1", fixef = "spe", drop = TRUE]), coef(est_b))
  > test(coef(est_multi[lhs = "y2", rhs = "^1", fixef = "1", drop = TRUE]), coef(est_c))
  > 
  > # with fixed covariates
  > est_multi_LR = feols(c(y1, y2) ~ left + sw0(x1*x4) + right | sw0(species) | x2 ~ x3, base)
  > 
  > est_a = feols(y1 ~ left + right | x2 ~ x3, base)
  > est_b = feols(y1 ~ left + x1*x4 + right | species | x2 ~ x3, base)
  > est_c = feols(y2 ~ left + right | x2 ~ x3, base)
  > 
  > test(coef(est_multi_LR[lhs = "y1", rhs = "!x1", fixef = "1", drop = TRUE]), coef(est_a))
  > user_name = c("fit_x2", "left", "x1", "x4", "x1:x4", "right")
  > test(names(coef(est_multi_LR[lhs = "y1", rhs = "x1", fixef = "spe", drop = TRUE])), user_name)
  > test(coef(est_multi_LR[lhs = "y1", rhs = "x1", fixef = "spe", drop = TRUE]), coef(est_b)[user_name])
  > test(coef(est_multi_LR[lhs = "y2", rhs = "!x1", fixef = "1", drop = TRUE]), coef(est_c))
  > 
  > 
  > # mvsw
  > 
  > est_mvsw = feols(y1 ~ mvsw(x1, x2), base)
  > est_mvsw_fe = feols(y1 ~ mvsw(x1, x2) | mvsw(species, fe2), base)
  > est_mvsw_fe_iv = feols(y1 ~ mvsw(x1, x2) | mvsw(species, fe2) | x3 ~ x4, base)
  > 
  > test(length(est_mvsw), 4)
  > test(length(as.list(est_mvsw_fe)), 16)
  > test(length(as.list(est_mvsw_fe_iv)), 16)
  > 
  > # Summary of multiple endo vars
  > est_multi_iv = feols(c(y1, y2) ~ sw0(x1) | sw0(species) | x3 + x4 ~ x5 + x6, base)
  > test(length(est_multi_iv), 8)
  > test(length(summary(est_multi_iv, stage = 1)), 16)
  > 
  > # IV without exo var:
  > est_mult_no_exo = feols(c(y1, y2) ~ 0 | x3 + x4 ~ x5 + x6, base)
  > est_no_exo_y2 = feols(y2 ~ 0 | x3 + x4 ~ x5 + x6, base)
  > test(coef(est_mult_no_exo[[2]]), coef(est_no_exo_y2))
  > 
  > # proper ordering
  > est_multi = feols(c(y1, y2) ~ sw0(x1) | sw0(fe2), base, split = ~species)
  > test(names(models(est_multi[fixef = TRUE, sample = FALSE])),
  +    stvec("id, fixef, lhs, rhs, sample.var, sample"))
  > 
  > test(names(models(est_multi[fixef = "fe2", sample = "seto"])),
  +    stvec("id, fixef, sample.var, sample, lhs, rhs"))
  > 
  > test(names(models(est_multi[fixef = "fe2", sample = "seto", reorder = FALSE])),
  +    stvec("id, sample.var, sample, fixef, lhs, rhs"))
  > 
  > # NA models
  > base$y_0 = base$x1 ** 2 + rnorm(150)
  > base$y_0[base$species == "setosa"] = 0
  > 
  > est_pois = fepois(y_0 ~ csw(x.[,1:4]), base, split = ~species)
  > 
  > base$x1_bis = base$x1
  > est_pois = fepois(y_0 ~ x.[1:3] + x1_bis | sw0(species), base)
  > 
  > # Different ways .[]
  > base = setNames(iris, c("y", "x1", "x2", "x3", "species"))
  > 
  > dep_all = list(stvec("y, x1, x2"), ~y + x1 + x2)
  > for(dep in dep_all){
  +   m = feols(.[dep] ~ x3, base)
  +   test(length(m), 3)
  + 
  +   m = feols(x3 ~ .[dep], base)
  +   test(length(m$coefficients), 4)
  + 
  +   m = feols(x3 ~ csw(.[,dep]), base)
  +   test(length(m), 3)
  + }
  > 
  > # offset in multiple outcomes // no error test
  > 
  > offset_single_ols = feols(am ~ hp, offset = ~ log(qsec), data = mtcars)
  > offset_mult_ols = feols(c(mpg, am) ~ hp, offset = ~ log(qsec), data = mtcars)
  > 
  > test(coef(offset_mult_ols[[2]]), coef(offset_single_ols))
  > 
  > offset_single_glm = feglm(am ~ hp, offset = ~ log(qsec), data = mtcars)
  > offset_mult_glm = feglm(c(mpg, am) ~ hp, offset = ~ log(qsec), data = mtcars)
  > 
  > test(coef(offset_mult_glm[[2]]), coef(offset_single_glm))
  > 
  > # LHS expansion with IVs
  > 
  > lhs = c("mpg", "wt")
  > est_lhs = feols(.[lhs] ~ disp | hp ~ qsec, data = mtcars)
  > test(length(est_lhs), 2)
  > 
  > est_lhs = feols(..("mpg|wt") ~ disp | hp ~ qsec, data = mtcars)
  > test(length(est_lhs), 2)
  > 
  > 
  > ####
  > #### ... IV ####
  > ####
  > 
  > chunk("IV")
  IV
  
  > 
  > base = iris
  > names(base) = c("y", "x1", "x_endo_1", "x_inst_1", "fe")
  > set.seed(2)
  > base$x_inst_2 = 0.2 * base$y + 0.2 * base$x_endo_1 + rnorm(150, sd = 0.5)
  > base$x_endo_2 = 0.2 * base$y - 0.2 * base$x_inst_1 + rnorm(150, sd = 0.5)
  > 
  > # Checking a basic estimation
  > 
  > setFixest_vcov(all = "iid")
  > 
  > est_iv = feols(y ~ x1 | x_endo_1 + x_endo_2 ~ x_inst_1 + x_inst_2, base)
  > 
  > res_f1 = feols(x_endo_1 ~ x1 + x_inst_1 + x_inst_2, base)
  > res_f2 = feols(x_endo_2 ~ x1 + x_inst_1 + x_inst_2, base)
  > 
  > base$fit_x_endo_1 = predict(res_f1)
  > base$fit_x_endo_2 = predict(res_f2)
  > 
  > res_2nd = feols(y ~ fit_x_endo_1 + fit_x_endo_2 + x1, base)
  > 
  > # the coef
  > test(coef(est_iv), coef(res_2nd))
  > 
  > # the SE
  > resid_iv = base$y - predict(res_2nd, data.frame(x1 = base$x1, fit_x_endo_1 = base$x_endo_1, fit_x_endo_2 = base$x_endo_2))
  > sigma2_iv = sum(resid_iv**2) / (res_2nd$nobs - res_2nd$nparams)
  > 
  > sum_2nd = summary(res_2nd, .vcov = res_2nd$cov.iid / res_2nd$sigma2 * sigma2_iv)
  > 
  > # We only check that on Windows => avoids super odd bug in fedora devel
  > # The worst is that I just can't debug it.... so that's the way it's done.
  > if(Sys.info()["sysname"] == "Windows"){
  +   test(se(sum_2nd), se(est_iv))
  + }
  > 
  > # check no bug when all exogenous vars are removed bc of collinearity
  > df = data.frame(x = rnorm(8), y = rnorm(8),
  +                 z = rnorm(8), fe = rep(0:1, each = 4))
  > 
  > est_iv = feols(y ~ fe | fe | x ~ z, df)
  > est_iv = feols(y ~ sw(fe, fe) | fe | x ~ z, df)
  > 
  > # check no bug
  > etable(summary(est_iv, stage = 1:2))
                  summary(est_..1 summary(es..2 summary(est_..3 summary(es..4
  Dependent Var.:               x             y               x             y
                                                                             
  z               0.1127 (0.5532)               0.1127 (0.5532)              
  x                               1.110 (6.499)                 1.110 (6.499)
  Fixed-Effects:  --------------- ------------- --------------- -------------
  fe                          Yes           Yes             Yes           Yes
  _______________ _______________ _____________ _______________ _____________
  S.E. type                   IID           IID             IID           IID
  Observations                  8             8               8             8
  R2                      0.35875      -0.08261         0.35875      -0.08261
  Within R2               0.00823      -0.33354         0.00823      -0.33354
  ---
  Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  > 
  > setFixest_vcov(reset = TRUE)
  > 
  > ####
  > #### ... VCOV at estimation ####
  > ####
  > 
  > chunk("vcov at estimation")
  VCOV AT ESTIMATION
  
  > 
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > base$clu = sample(6, 150, TRUE)
  > base$clu[1:5] = NA
  > 
  > est = feols(y ~ x1 | species, base, cluster = ~clu, ssc = ssc(adj = FALSE))
  > 
  > # The three should be identical
  > v1 = est$cov.scaled
  > v1b = vcov(est)
  > v1c = summary(est)$cov.scaled
  > 
  > test(v1, v1b)
  > test(v1, v1c)
  > 
  > # Only ssc change
  > v2 = summary(est, ssc = ssc())$cov.scaled
  > v2b = vcov(est, ssc = ssc())
  > 
  > test(v2, v2b)
  > test(max(abs(v1 - v2)) == 0, FALSE)
  > 
  > # vcov change only
  > v3 = summary(est, se = "hetero")$cov.scaled
  > v3b = vcov(est, se = "hetero")
  > 
  > test(v3, v3b)
  > test(max(abs(v1 - v3)) == 0, FALSE)
  > test(max(abs(v2 - v3)) == 0, FALSE)
  > 
  > # feols.fit
  > 
  > ymat = base$y
  > xmat = base[, 2:3]
  > fe = base$species
  > 
  > for(use_fe in c(TRUE, FALSE)){
  +   all_vcov = stvec("iid, hetero")
  +   if(use_fe){
  +     setFixest_fml(..fe = ~ 1 | species)
  +     all_vcov = c(all_vcov, "cluster")
  +   } else {
  +     setFixest_fml(..fe = ~ 1)
  +   }
  + 
  +   for(v in all_vcov){
  + 
  +     if(use_fe){
  +       est_fit = feols.fit(ymat, xmat, fe, vcov = v)
  +     } else {
  +       est_fit = feols.fit(ymat, cbind(1, xmat), vcov = v)
  +     }
  + 
  +     est = feols(y ~ x1 + x2 + ..fe, base, vcov = v)
  + 
  +     test(vcov(est), vcov(est_fit))
  +   }
  + }
  > 
  > 
  > 
  > 
  > ####
  > #### ... Argument sliding ####
  > ####
  > 
  > chunk("argument sliding")
  ARGUMENT SLIDING
  
  > 
  > base = setNames(iris, c("y", "x1", "x2", "x3", "species"))
  > 
  > setFixest_estimation(data = base)
  > 
  > raw = feols(y ~ x1 + x2, base, ~species)
  > slided = feols(y ~ x1 + x2, ~species)
  > 
  > test(coef(raw), coef(slided))
  > 
  > # Error, with error msg relative to 'data'
  > test(feols(y ~ x1 + x2, 1:5), "err")
  > 
  > # should be another estimation
  > other_est = feols(y ~ x1 + x2, head(base, 50))
  > test(nobs(other_est), 50)
  > 
  > setFixest_estimation(reset = TRUE)
  > 
  > ####
  > #### ... Offset ####
  > ####
  > 
  > chunk("offset")
  OFFSET
  
  > 
  > # we test the different ways to set an offset
  > 
  > base = setNames(iris, c("y", "x1", "x2", "x3", "species"))
  > 
  > o1 = feols(y ~ x1 + offset(x2) + offset(x3^2 + 3), base)
  > o2 = feols(y ~ x1, base, offset = ~x2 + x3^2 + 3)
  > test(coef(o1), coef(o2))
  > 
  > test(predict(o1, newdata = head(base)), 
  +      predict(o2, newdata = head(base)))
  > 
  > # error
  > test(feols(y ~ x1 + offset(x2), base, offset = ~x3), "err")
  > 
  > 
  > ####
  > #### ... Only Coef ####
  > ####
  > 
  > chunk("only.coef")
  ONLY.COEF
  
  > 
  > 
  > base = setNames(iris, c("y", "x1", "x2", "x3", "species"))
  > base$x4 = base$x1 + 5
  > 
  > m = feols(y ~ x1 + x2 + x4, base, only.coef = TRUE)
  > test(length(m), 4)
  > test(sum(is.na(m)), 1)
  > 
  > m = fepois(y ~ x1 + x2 + x4, base, only.coef = TRUE)
  > test(length(m), 4)
  > test(sum(is.na(m)), 1)
  > 
  > m = femlm(y ~ x1 + x2, base, only.coef = TRUE)
  > test(length(m), 3)
  > test(sum(is.na(m)), 0)
  > 
  > test(feols(y ~ sw(x1, x2), base, only.coef = TRUE), "err")
  > 
  > 
  > ####
  > #### Standard-errors ####
  > ####
  > 
  > chunk("STANDARD ERRORS")
  STANDARD ERRORS
  
  > 
  > #
  > # Fixed-effects corrections
  > #
  > 
  > # We create "irregular" FEs
  > set.seed(0)
  > base = data.frame(x = rnorm(20))
  > base$y = base$x + rnorm(20)
  > base$fe1 = rep(rep(1:3, c(4, 3, 3)), 2)
  > base$fe2 = rep(rep(1:5, each = 2), 2)
  > est = feols(y ~ x | fe1 + fe2, base)
  > 
  > # fe1: 3 FEs
  > # fe2: 5 FEs
  > 
  > #
  > # Clustered standard-errors: by fe1
  > #
  > 
  > # Default: fixef.K = "nested"
  > #  => adjustment K = 1 + 5 (i.e. x + fe2)
  > test(attr(vcov(est, ssc = ssc(fixef.K = "nested"), attr = TRUE), "dof.K"), 6)
  > 
  > # fixef.K = FALSE
  > #  => adjustment K = 1 (i.e. only x)
  > test(attr(vcov(est, ssc = ssc(fixef.K = "none"), attr = TRUE), "dof.K"), 1)
  > 
  > # fixef.K = TRUE
  > #  => adjustment K = 1 + 3 + 5 - 1 (i.e. x + fe1 + fe2 - 1 restriction)
  > test(attr(vcov(est, ssc = ssc(fixef.K = "full"), attr = TRUE), "dof.K"), 8)
  > 
  > # fixef.K = TRUE & fixef.exact = TRUE
  > #  => adjustment K = 1 + 3 + 5 - 2 (i.e. x + fe1 + fe2 - 2 restrictions)
  > test(attr(vcov(est, ssc = ssc(fixef.K = "full", fixef.force_exact = TRUE), attr = TRUE), "dof.K"), 7)
  > 
  > #
  > # Manual checks of the SEs
  > #
  > 
  > n = est$nobs
  > VCOV_raw = est$cov.iid / ((n - 1) / (n - est$nparams))
  > 
  > # standard
  > for(k_val in c("none", "nested", "full")){
  +   for(adj in c(FALSE, TRUE)){
  + 
  +     K = switch(k_val, none = 1, nested = 8, full = 8)
  +     my_adj = ifelse(adj, (n - 1) / (n - K), 1)
  + 
  +     test(vcov(est, se = "standard", ssc = ssc(adj = adj, fixef.K = k_val)), VCOV_raw * my_adj)
  + 
  +     # cat("adj = ", adj, " ; fixef.K = ", k_val, "\n", sep = "")
  +   }
  + }
  > 
  > # Clustered, fe1
  > VCOV_raw = est$cov.iid / est$sigma2
  > H = vcovClust(est$fixef_id$fe1, VCOV_raw, scores = est$scores, adj = FALSE)
  > n = nobs(est)
  > 
  > for(tdf in c("conventional", "min")){
  +   for(k_val in c("none", "nested", "full")){
  +     for(c_adj in c(FALSE, TRUE)){
  +       for(adj in c(FALSE, TRUE)){
  + 
  +         K = switch(k_val, none = 1, nested = 6, full = 8)
  +         cluster_factor = ifelse(c_adj, 3/2, 1)
  +         df = ifelse(tdf == "min", 2, 20 - K)
  +         my_adj = ifelse(adj, (n - 1) / (n - K), 1)
  + 
  +         V = H * cluster_factor
  + 
  +         # test SE
  +         test(vcov(est, se = "cluster", ssc = ssc(adj = adj, fixef.K = k_val, cluster.adj = c_adj)), V * my_adj)
  + 
  +         # test pvalue
  +         my_tstat = tstat(est, se = "cluster", ssc = ssc(adj = adj, fixef.K = k_val, cluster.adj = c_adj))
  +         test(pvalue(est, se = "cluster", ssc = ssc(adj = adj, fixef.K = k_val, cluster.adj = c_adj, t.df = tdf)), 2*pt(-abs(my_tstat), df))
  + 
  +         # cat("adj = ", adj, " ; fixef.K = ", k_val, " ; cluster.adj = ", c_adj, " t.df = ", tdf, "\n", sep = "")
  +       }
  +     }
  +   }
  + }
  > 
  > 
  > # 2-way Clustered, fe1 fe2
  > VCOV_raw = est$cov.iid / est$sigma2
  > M_i  = vcovClust(est$fixef_id$fe1, VCOV_raw, scores = est$scores, adj = FALSE)
  > M_t  = vcovClust(est$fixef_id$fe2, VCOV_raw, scores = est$scores, adj = FALSE)
  > M_it = vcovClust(paste(base$fe1, base$fe2), VCOV_raw, scores = est$scores, adj = FALSE, do.unclass = TRUE)
  > 
  > M_i + M_t - M_it
              [,1]
  [1,] 0.005391594
  > vcov(est, se = "two", ssc = ssc(adj = FALSE, cluster.adj = FALSE))
              x
  x 0.005391594
  > 
  > for(cdf in c("conventional", "min")){
  +   for(tdf in c("conventional", "min")){
  +     for(k_val in c("none", "nested", "full")){
  +       for(c_adj in c(FALSE, TRUE)){
  +         for(adj in c(FALSE, TRUE)){
  + 
  +           K = switch(k_val, none = 1, nested = 2, full = 8)
  + 
  +           if(c_adj){
  +             if(cdf == "min"){
  +               V = (M_i + M_t - M_it) * 3/2
  +             } else {
  +               V = M_i  * 3/2 + M_t * 5/4 - M_it * 6/5
  +             }
  +           } else {
  +             V = M_i + M_t - M_it
  +           }
  + 
  +           df = ifelse(tdf == "min", 2, 20 - K)
  +           my_adj = ifelse(adj, (n - 1) / (n - K), 1)
  + 
  +           # test SE
  +           test(vcov(est, se = "two", ssc = ssc(adj = adj, fixef.K = k_val, cluster.adj = c_adj, cluster.df = cdf)),
  +              V * my_adj)
  + 
  +           # test pvalue
  +           my_tstat = tstat(est, se = "two", ssc = ssc(adj = adj, fixef.K = k_val, cluster.adj = c_adj, cluster.df = cdf))
  +           test(pvalue(est, se = "two", ssc = ssc(adj = adj, fixef.K = k_val, cluster.adj = c_adj, cluster.df = cdf, t.df = tdf)),
  +              2*pt(-abs(my_tstat), df))
  + 
  +           # cat("adj = ", adj, " ; fixef.K = ", k_val, " ; cluster.adj = ", c_adj, " t.df = ", tdf, "\n", sep = "")
  +         }
  +       }
  +     }
  +   }
  + }
  > 
  > 
  > #
  > # Comparison with sandwich and plm
  > #
  > 
  > library(sandwich)
  
  Attaching package: 'sandwich'
  
  The following object is masked _by_ '.GlobalEnv':
  
      estfun
  
  > 
  > # Data generation
  > set.seed(0)
  > N = 20; G = N/5; T = N/G
  > d = data.frame( y=rnorm(N), x=rnorm(N), grp=rep(1:G,T), tm=rep(1:T,each=G) )
  > 
  > # Estimations
  > est_lm    = lm(y ~ x + as.factor(grp) + as.factor(tm), data=d)
  > est_feols = feols(y ~ x | grp + tm, data=d)
  > 
  > #
  > # Standard
  > #
  > 
  > test(se(est_feols, se = "st")["x"], se(est_lm)["x"])
  > 
  > #
  > # Clustered
  > #
  > 
  > # Clustered by grp
  > se_CL_grp_lm_HC1 = sqrt(vcovCL(est_lm, cluster = d$grp, type = "HC1")["x", "x"])
  > se_CL_grp_lm_HC0 = sqrt(vcovCL(est_lm, cluster = d$grp, type = "HC0")["x", "x"])
  > 
  > # How to get the lm
  > test(se(est_feols, ssc = ssc(fixef.K = "full")), se_CL_grp_lm_HC1)
  > test(se(est_feols, ssc = ssc(adj = FALSE, fixef.K = "full")), se_CL_grp_lm_HC0)
  > 
  > #
  > # Heteroskedasticity-robust
  > #
  > 
  > se_white_lm_HC1 = sqrt(vcovHC(est_lm, type = "HC1")["x", "x"])
  > se_white_lm_HC0 = sqrt(vcovHC(est_lm, type = "HC0")["x", "x"])
  > 
  > test(se(est_feols, se = "hetero"), se_white_lm_HC1)
  > test(se(est_feols, se = "hetero", ssc = ssc(adj = FALSE, cluster.adj = FALSE)), se_white_lm_HC0)
  > 
  > #
  > # Two way
  > #
  > 
  > # Clustered by grp & tm
  > se_CL_2w_lm    = sqrt(vcovCL(est_lm, cluster = ~ grp + tm, type = "HC1")["x", "x"])
  > se_CL_2w_feols = se(est_feols, se = "twoway")
  > 
  > test(se(est_feols, se = "twoway", ssc = ssc(fixef.K = "full", cluster.df = "conv")), se_CL_2w_lm)
  > 
  > #
  > # Checking the calls work properly
  > #
  > 
  > data(trade)
  > 
  > est_pois = femlm(Euros ~ log(dist_km)|Origin+Destination, trade)
  > 
  > se_clust = se(est_pois, se = "cluster", cluster = "Product")
  > test(se(est_pois, cluster = trade$Product), se_clust)
  > test(se(est_pois, cluster = ~Product), se_clust)
  > 
  > se_two = se(est_pois, se = "twoway", cluster = trade[, c("Product", "Destination")])
  > test(se_two, se(est_pois, cluster = c("Product", "Destination")))
  > test(se_two, se(est_pois, cluster = ~Product+Destination))
  > 
  > se_clu_comb = se(est_pois, cluster = "Product^Destination")
  > test(se_clu_comb, se(est_pois, cluster = paste(trade$Product, trade$Destination)))
  > test(se_clu_comb, se(est_pois, cluster = ~Product^Destination))
  > 
  > se_two_comb = se(est_pois, cluster = c("Origin^Destination", "Product"))
  > test(se_two_comb, se(est_pois, cluster = list(paste(trade$Origin, trade$Destination), trade$Product)))
  > test(se_two_comb, se(est_pois, cluster = ~Origin^Destination + Product))
  > 
  > # With cluster removed
  > base = trade
  > base$Euros[base$Origin == "FR"] = 0
  > est_pois = femlm(Euros ~ log(dist_km)|Origin+Destination, base)
  > 
  > se_clust = se(est_pois, se = "cluster", cluster = "Product")
  > test(se(est_pois, cluster = base$Product), se_clust)
  > test(se(est_pois, cluster = ~Product), se_clust)
  > 
  > se_two = se(est_pois, se = "twoway", cluster = base[, c("Product", "Destination")])
  > test(se_two, se(est_pois, cluster = c("Product", "Destination")))
  > test(se_two, se(est_pois, cluster = ~Product+Destination))
  > 
  > se_clu_comb = se(est_pois, cluster = "Product^Destination")
  > test(se_clu_comb, se(est_pois, cluster = paste(base$Product, base$Destination)))
  > test(se_clu_comb, se(est_pois, cluster = ~Product^Destination))
  > 
  > se_two_comb = se(est_pois, cluster = c("Origin^Destination", "Product"))
  > test(se_two_comb, se(est_pois, cluster = list(paste(base$Origin, base$Destination), base$Product)))
  > test(se_two_comb, se(est_pois, cluster = ~Origin^Destination + Product))
  > 
  > # With cluster removed and NAs
  > base = trade
  > base$Euros[base$Origin == "FR"] = 0
  > base$Euros_na = base$Euros ; base$Euros_na[sample(nrow(base), 50)] = NA
  > base$Destination_na = base$Destination ; base$Destination_na[sample(nrow(base), 50)] = NA
  > base$Origin_na = base$Origin ; base$Origin_na[sample(nrow(base), 50)] = NA
  > base$Product_na = base$Product ; base$Product_na[sample(nrow(base), 50)] = NA
  > 
  > est_pois = femlm(Euros ~ log(dist_km)|Origin+Destination_na, base)
  > 
  > se_clust = se(est_pois, se = "cluster", cluster = "Product")
  > test(se(est_pois, cluster = base$Product), se_clust)
  > test(se(est_pois, cluster = ~Product), se_clust)
  > 
  > se_two = se(est_pois, se = "twoway", cluster = base[, c("Product", "Destination")])
  > test(se_two, se(est_pois, cluster = c("Product", "Destination")))
  > test(se_two, se(est_pois, cluster = ~Product+Destination))
  > 
  > se_clu_comb = se(est_pois, cluster = "Product^Destination")
  > test(se_clu_comb, se(est_pois, cluster = paste(base$Product, base$Destination)))
  > test(se_clu_comb, se(est_pois, cluster = ~Product^Destination))
  > 
  > se_two_comb = se(est_pois, cluster = c("Origin^Destination", "Product"))
  > test(se_two_comb, se(est_pois, cluster = list(paste(base$Origin, base$Destination), base$Product)))
  > test(se_two_comb, se(est_pois, cluster = ~Origin^Destination + Product))
  > 
  > #
  > # Checking errors
  > #
  > 
  > # Should report error
  > test(se(est_pois, cluster = "Origin_na"), "err")
  > test(se(est_pois, cluster = base$Origin_na), "err")
  > test(se(est_pois, cluster = list(base$Origin_na)), "err")
  > test(se(est_pois, cluster = ~Origin_na^Destination), "err")
  > 
  > test(se(est_pois, se = "cluster", cluster = ~Origin_na^not_there), "err")
  > 
  > #
  > # Checking that the aliases work fine
  > #
  > 
  > se_hetero = se(est_pois, se = "hetero")
  > se_hc1    = se(est_pois, se = "hc1")
  > se_white  = se(est_pois, se = "white")
  > 
  > test(se_hetero, se_hc1)
  > test(se_hetero, se_white)
  > 
  > #
  > # New argument vcov
  > #
  > 
  > # We mostly check the absence of errors
  > data(base_did)
  > 
  > est_panel = feols(y ~ x1, base_did, panel.id = ~id + period, subset = 1:500)
  > 
  > se_est = se(est_panel)
  > test(se(est_panel, ~id), se_est)
  > 
  > # changing ssc argument
  > test(se(est_panel, ssc = ssc(adj = FALSE)), se(est_panel, ~id + ssc(adj = FALSE)))
  > 
  > # using vcov_cluster
  > test(se_est, se(est_panel, vcov_cluster("id")))
  > test(se_est, se(vcov_cluster(est_panel, "id")))
  > 
  > # NW
  > se_NW = se(est_panel, "NW")
  > test(se_NW, se(est_panel, NW ~ id + period))
  > test(se_NW, se(est_panel, newey ~ id + period))
  > test(se_NW, se(est_panel, vcov_NW("id", "period")))
  > test(se_NW, se(est_panel, vcov_NW(time = "period"))) # here unit is deduced
  > 
  > se_NW2 = se(est_panel, NW(2))
  > test(se_NW2, se(est_panel, NW(2) ~ id + period))
  > test(se_NW2, se(est_panel, vcov_NW(lag = 2)))
  > 
  > # errors
  > est = feols(y ~ x1, base_did)
  > test(se(est, NW ~ period), "err")
  > 
  > # DK
  > se_DK = se(est_panel, "DK")
  > test(se_DK, se(est_panel, DK ~ period))
  > test(se_DK, se(est_panel, dris ~ period))
  > test(se_DK, se(est_panel, vcov_DK("period")))
  > 
  > se_DK2 = se(est_panel, DK(2))
  > test(se_DK2, se(est_panel, DK(2) ~ period))
  > test(se_DK2, se(est_panel, vcov_DK(lag = 2)))
  > 
  > 
  > # Conley
  > data(quakes)
  > 
  > est = feols(depth ~ mag, quakes, "conley")
  > 
  > se_conley = se(est)
  > test(se_conley, se(est, conley(90) ~ 1))
  > test(se_conley, se(est, conley(90) ~ lat + long))
  > 
  > se_conley200 = se(est, conley(200) ~ lat + long)
  > test(se_conley200, se(est, vcov_conley(cutoff = 200)))
  > test(se_conley200, se(est, vcov_conley("lat", "long", cutoff = 200)))
  > 
  > se_conleyExtra = se(est, conley(pixel = 20, distance = "spherical"))
  > test(se_conleyExtra, se(vcov_conley(est, pixel = 20, distance = "spherical")))
  > 
  > 
  > # Checking the value of Conley SEs with equivalences
  > # we generate data that leads to simple values
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > 
  > # scattered along 111km
  > base$lat = rep(seq(-0.5, 0.5, length.out = 50), 3)
  > 
  > # scattered across very long distances
  > base$lon = rep(c(0, 80, 160), each = 50)
  > 
  > est = feols(y ~ x1, base)
  > 
  > # Equivalence 1 -- clustered SEs
  > se_clu = se(est, ~lon + ssc(adj = FALSE, cluster.adj = FALSE))
  > test(se_clu, se(est, conley(200) ~ ssc(adj = FALSE)))
  > 
  > # Equivalence 2 -- White SEs
  > se_hc1 = se(est, hetero ~ ssc(adj = FALSE, cluster.adj = FALSE))
  > test(se_hc1, se(est, conley(1) ~ ssc(adj = FALSE)))
  > 
  > 
  > #
  > # ssc with custom t.df values
  > #
  > 
  > est = feols(y ~ x1 + x2, base)
  > 
  > m = summary(est, ssc = ssc(t.df = 5))
  > 
  > test(m$coeftable[, 4], 2*pt(-abs(m$coeftable[, 3]), 5))
  > 
  > #
  > # feols.fit
  > #
  > 
  > 
  > base = setNames(iris, c("y", "x1", "x2", "x3", "species"))
  > 
  > est = feols(y ~ x1 | species, base, vcov = "hete")
  > est_fit = feols.fit(base$y, base$x1, base$species, vcov = "hete")
  > 
  > test(se(est), se(est_fit))
  > 
  > est = feols(y ~ x1 | species, base, cluster = base$species)
  > est_fit = feols.fit(base$y, base$x1, base$species, cluster = base$species)
  > 
  > test(se(est), se(est_fit))
  > 
  > est = feols(y ~ x1 | species, base, vcov = "cluster")
  > est_fit = feols.fit(base$y, base$x1, base$species, vcov = "cluster")
  > 
  > test(se(est), se(est_fit))
  > 
  > 
  > # error for the other VCOVs
  > test(feols.fit(base$y, base$x1, base$species, vcov = "hac"), "err")
  > test(feols.fit(base$y, base$x1, base$species, vcov = "conley"), "err")
  > 
  > ####
  > #### Residuals ####
  > ####
  > 
  > chunk("RESIDUALS")
  RESIDUALS
  
  > 
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > base$y_int = as.integer(base$y) + 1
  > 
  > # OLS + GLM + FENMLM
  > 
  > for(method in c("ols", "feglm", "femlm", "fenegbin")){
  +   cat("Method: ", format(method, width = 8))
  +   for(do_weight in c(FALSE, TRUE)){
  +     cat(".")
  + 
  +     if(do_weight){
  +       w = unclass(as.factor(base$species))
  +     } else {
  +       w = NULL
  +     }
  + 
  +     if(method == "ols"){
  +       m = feols(y_int ~ x1 | species, base, weights = w)
  +       mm = lm(y_int ~ x1 + species, base, weights = w)
  + 
  +     } else if(method == "feglm"){
  +       m = feglm(y_int ~ x1 | species, base, weights = w, family = "poisson")
  +       mm = glm(y_int ~ x1 + species, base, weights = w, family = poisson())
  + 
  +     } else if(method == "femlm"){
  +       if(!is.null(w)) next
  +       m = femlm(y_int ~ x1 | species, base)
  +       mm = glm(y_int ~ x1 + species, base, family = poisson())
  + 
  +     } else if(method == "fenegbin"){
  +       if(!is.null(w)) next
  +       m = fenegbin(y_int ~ x1 | species, base, notes = FALSE)
  +       mm = MASS::glm.nb(y_int ~ x1 + species, base)
  +     }
  + 
  +     tol = ifelse(method == "fenegbin", 1e-2, 1e-6)
  + 
  +     test(resid(m, "r"), resid(mm, "resp"), "~", tol = tol)
  +     test(resid(m, "d"), resid(mm, "d"), "~", tol = tol)
  +     test(resid(m, "p"), resid(mm, "pearson"), "~", tol = tol)
  + 
  +     test(deviance(m), deviance(mm), "~", tol = tol)
  +   }
  +   cat("\n")
  + }
  Method:  ols     ..
  Method:  feglm   ..
  Method:  femlm   ..
  Method:  fenegbin..
  Warning messages:
  1: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
    iteration limit reached
  2: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
    iteration limit reached
  > cat("\n")
  
  > 
  > 
  > ####
  > #### fixef ####
  > ####
  > 
  > chunk("FIXEF")
  FIXEF
  
  > 
  > set.seed(0)
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > base$x4 = rnorm(150) + 0.25*base$y
  > base$fe_bis = sample(10, 150, TRUE)
  > base$fe_ter = sample(15, 150, TRUE)
  > 
  > get_coef = function(all_coef, x){
  +   res = all_coef[grepl(x, names(all_coef), perl = TRUE)]
  +   names(res) = gsub(x, "", names(res), perl = TRUE)
  +   res
  + }
  > 
  > #
  > # With 2 x 1 FE
  > #
  > 
  > m = feols(y ~ x1 + x2 | species + fe_bis, base)
  > all_coef = coef(feols(y ~ -1 + x1 + x2 + species + factor(fe_bis), base))
  > 
  > m_fe = fixef(m)
  > c1  = get_coef(all_coef, "species")
  > test(var(c1 - m_fe$species[names(c1)]), 0)
  > 
  > c2  = get_coef(all_coef, "factor\\(fe_bis\\)")
  > test(var(c2 - m_fe$fe_bis[names(c2)]), 0)
  > 
  > 
  > #
  > # With 1 FE + 1 FE 1 VS
  > #
  > 
  > m = feols(y ~ x1 + x2 | species + fe_bis[x3], base)
  > all_coef = coef(feols(y ~ -1 + x1 + x2 + species + factor(fe_bis) + i(fe_bis, x3), base))
  > 
  > m_fe = fixef(m)
  > c1  = get_coef(all_coef, "species")
  > test(var(c1 - m_fe$species[names(c1)]), 0, "~")
  > 
  > c2  = get_coef(all_coef, "factor\\(fe_bis\\)")
  > test(var(c2 - m_fe$fe_bis[names(c2)]), 0, "~")
  > 
  > c3  = get_coef(all_coef, "fe_bis::|:x3")
  > test(c3, m_fe[["fe_bis[[x3]]"]][names(c3)], "~", tol = 1e-5)
  > # This test does not pass in R 3.5.0.... why?
  > # diff: 6.56851425546723e-05
  > 
  > #
  > # With 2 x (1 FE + 1 VS) + 1 FE
  > #
  > 
  > m = feols(y ~ x1 | species[x2] + fe_bis[x3] + fe_ter, base)
  > all_coef = coef(feols(y ~ -1 + x1 + species + i(species, x2) + factor(fe_bis) + i(fe_bis, x3) + factor(fe_ter), base))
  > 
  > m_fe = fixef(m)
  > c1  = get_coef(all_coef, "^species(?=[^:])")
  > test(var(c1 - m_fe$species[names(c1)]), 0, "~")
  > 
  > c2  = get_coef(all_coef, "^factor\\(fe_bis\\)")
  > test(var(c2 - m_fe$fe_bis[names(c2)]), 0, "~")
  > 
  > c3  = get_coef(all_coef, "fe_bis::|:x3")
  > test(c3, m_fe[["fe_bis[[x3]]"]][names(c3)], "~", tol = 2e-4)
  > 
  > c4  = get_coef(all_coef, "species::|:x2")
  > test(c4, m_fe[["species[[x2]]"]][names(c4)], "~", tol = 2e-4)
  > 
  > #
  > # With 2 x (1 FE) + 1 FE 2 VS
  > #
  > 
  > m = feols(y ~ x1 | species + fe_bis[x2,x3] + fe_ter, base)
  > all_coef = coef(feols(y ~ x1 + species + factor(fe_bis) + i(fe_bis, x2) + i(fe_bis, x3) + factor(fe_ter), base))
  > 
  > m_fe = fixef(m)
  > c1  = get_coef(all_coef, "^species")
  > test(var(c1 - m_fe$species[names(c1)]), 0, "~")
  > 
  > c2  = get_coef(all_coef, "^factor\\(fe_bis\\)")
  > test(var(c2 - m_fe$fe_bis[names(c2)]), 0, "~")
  > 
  > c3  = get_coef(all_coef, "fe_bis::(?=.+x2)|:x2")
  > test(c3, m_fe[["fe_bis[[x2]]"]][names(c3)], "~", tol = 2e-4)
  > 
  > c4  = get_coef(all_coef, "fe_bis::(?=.+x3)|:x3")
  > test(c4, m_fe[["fe_bis[[x3]]"]][names(c4)], "~", tol = 2e-4)
  > # This test does not pass in R 3.5.0.... why?
  > # diff: 0.000239702137861342
  > 
  > #
  > # With weights
  > #
  > 
  > w = 3 * (as.integer(base$species) - 0.95)
  > m = feols(y ~ x1 | species + fe_bis[x2,x3] + fe_ter, base, weights = w)
  > all_coef = coef(feols(y ~ x1 + species + factor(fe_bis) + i(fe_bis, x2) + i(fe_bis, x3) + factor(fe_ter), base, weights = w))
  > 
  > m_fe = fixef(m)
  > c1  = get_coef(all_coef, "^species")
  > test(var(c1 - m_fe$species[names(c1)]), 0, "~")
  > 
  > c2  = get_coef(all_coef, "^factor\\(fe_bis\\)")
  > test(var(c2 - m_fe$fe_bis[names(c2)]), 0, "~")
  > 
  > c3  = get_coef(all_coef, "fe_bis::(?=.+x2)|:x2")
  > test(c3, m_fe[["fe_bis[[x2]]"]][names(c3)], "~", tol = 2e-4)
  > 
  > c4  = get_coef(all_coef, "fe_bis::(?=.+x3)|:x3")
  > test(c4, m_fe[["fe_bis[[x3]]"]][names(c4)], "~", tol = 2e-4)
  > 
  > 
  > ####
  > #### To Integer ####
  > ####
  > 
  > chunk("TO_INTEGER")
  TO_INTEGER
  
  > 
  > base = iris
  > names(base) = c("y", "x1", "x2", "x3", "species")
  > base$z = sample(5, 150, TRUE)
  > 
  > # Normal
  > m = to_integer(base$species)
  > test(length(unique(m)), 3)
  > 
  > m = to_integer(base$species, base$z)
  > test(length(unique(m)), 15)
  > 
  > # with NA
  > base$species_na = base$species
  > base$species_na[base$species == "setosa"] = NA
  > 
  > m = to_integer(base$species_na, base$z)
  > test(length(unique(m)), 11)
  > 
  > m = to_integer(base$species_na, base$z, add_items = TRUE, items.list = TRUE)
  > test(length(m$items), 10)
  > 
  > 
  > 
  > ####
  > #### Interact ####
  > ####
  > 
  > 
  > chunk("Interact")
  INTERACT
  
  > 
  > base = setNames(iris, c("y", "x1", "x2", "x3", "species"))
  > base$fe_2 = round(seq(-5, 5, length.out = 150))
  > 
  > #
  > # We just ensure it works without error
  > #
  > 
  > m = feols(y ~ x1 + i(fe_2), base)
  > coefplot(m)
  > etable(m, dict = c("0" = "zero"))
                                   m
  Dependent Var.:                  y
                                    
  Constant         2.367*** (0.4683)
  x1              0.7513*** (0.1275)
  fe_2 = -4          0.0679 (0.2247)
  fe_2 = -3          0.1381 (0.2239)
  fe_2 = -2         0.4083. (0.2242)
  fe_2 = -1        1.406*** (0.2389)
  fe_2 = zero      1.693*** (0.2423)
  fe_2 = 1         1.319*** (0.2366)
  fe_2 = 2         1.827*** (0.2323)
  fe_2 = 3         2.047*** (0.2314)
  fe_2 = 4         2.072*** (0.2285)
  fe_2 = 5         1.732*** (0.2601)
  _______________ __________________
  S.E. type                      IID
  Observations                   150
  R2                         0.64694
  Adj. R2                    0.61880
  ---
  Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  > 
  > m = feols(y ~ x1 + i(fe_2) + i(fe_2, x2), base)
  > coefplot(m)
  > etable(m, dict = c("0" = "zero"))
                                    m
  Dependent Var.:                   y
                                     
  Constant              2.290 (1.400)
  x1               0.4049*** (0.0835)
  fe_2 = -4            0.1078 (1.520)
  fe_2 = -3             2.222 (1.594)
  fe_2 = -2            0.3446 (1.414)
  fe_2 = -1           -0.7139 (1.587)
  fe_2 = zero          0.3448 (1.587)
  fe_2 = 1             0.1762 (1.630)
  fe_2 = 2            -0.3183 (1.467)
  fe_2 = 3             -1.715 (1.538)
  fe_2 = 4             -2.226 (1.721)
  fe_2 = 5             0.1711 (2.374)
  x2 x fe_2 = -5      0.8629 (0.9673)
  x2 x fe_2 = -4     0.8919* (0.4045)
  x2 x fe_2 = -3     -0.5411 (0.4828)
  x2 x fe_2 = -2   0.6065*** (0.0600)
  x2 x fe_2 = -1   0.7534*** (0.1848)
  x2 x fe_2 = zero  0.5449** (0.1746)
  x2 x fe_2 = 1      0.5115* (0.1984)
  x2 x fe_2 = 2    0.6090*** (0.0846)
  x2 x fe_2 = 3    0.8699*** (0.1164)
  x2 x fe_2 = 4    0.9780*** (0.1816)
  x2 x fe_2 = 5       0.5037 (0.3634)
  ________________ __________________
  S.E. type                       IID
  Observations                    150
  R2                          0.88552
  Adj. R2                     0.86569
  ---
  Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  > 
  > a = i(base$fe_2)
  > b = i(base$fe_2, ref = 0:1)
  > d = i(base$fe_2, keep = 0:1)
  > 
  > test(ncol(a), ncol(b) + 2)
  > test(ncol(d), 2)
  > 
  > #
  > # binning
  > #
  > 
  > m = feols(y ~ x1 + i(fe_2, bin = list("0" = -1:1)), base)
  > test(length(coef(m)), 12 - 2)
  > 
  > # SA
  > data(base_stagg)
  > res_sunab = feols(y ~ x1 + sunab(year_treated, year, bin = "bin::2"), base_stagg)
  > iplot(res_sunab)
  > test(length(coef(res_sunab)), 15)
  > 
  > res_sunab = feols(y ~ x1 + sunab(year_treated, year, bin.rel = "bin::2"), base_stagg)
  > iplot(res_sunab)
  > test(length(coef(res_sunab)), 12)
  > 
  > 
  > ####
  > #### bin ####
  > ####
  > 
  > chunk("BIN")
  BIN
  
  > 
  > plen = iris$Petal.Length
  > years = round(rnorm(1000, 2000, 5))
  > 
  > my_cuts = c("cut::3", "cut::2]5]", "cut::q1]q2]q3]", "cut::p20]p50]p70]p90]", "cut::2[q2]p90]")
  > 
  > for(type in 1:2){
  + 
  +   x = switch(type, "1" = plen, "2" = years)
  + 
  +   for(cut in my_cuts){
  + 
  +     my_bin = bin(x, cut)
  +     bin_char = as.character(my_bin)
  + 
  +     if(grepl("[", bin_char[1], fixed = TRUE)){
  +       all_min = as.numeric(gsub("(^\\[)|(;.+)", "", bin_char))
  +       all_max = as.numeric(gsub(".+; |\\]", "", bin_char))
  +     } else {
  +       all_min = as.numeric(gsub("-.+", "", bin_char))
  +       all_max = as.numeric(gsub(".+-", "", bin_char))
  +     }
  + 
  +     test(all(x >= all_min), TRUE)
  +     test(all(x <= all_max), TRUE)
  +   }
  + }
  > 
  > 
  > 
  > 
  > 
  > 
  > 
  > ####
  > #### demean ####
  > ####
  > 
  > chunk("DEMEAN")
  DEMEAN
  
  > 
  > data(trade)
  > 
  > base = trade
  > base$ln_euros = log(base$Euros)
  > base$ln_dist = log(base$dist_km)
  > 
  > X = base[, c("ln_euros", "ln_dist")]
  > fe = base[, c("Origin", "Destination")]
  > 
  > base_new = demean(X, fe)
  > 
  > a = feols(ln_euros ~ ln_dist, base_new)
  > b = feols(ln_euros ~ ln_dist | Origin + Destination, base, demeaned = TRUE)
  > 
  > test(coef(a)[-1], coef(b), "~", 1e-12)
  > 
  > test(base_new$ln_euros, b$y_demeaned)
  > test(base_new$ln_dist, b$X_demeaned)
  > 
  > # Now we just check there's no error
  > 
  > # NAs
  > X_NA = X
  > fe_NA = fe
  > X_NA[1:5, 1] = NA
  > fe_NA[6:10, 1] = NA
  > X_demean = demean(X_NA, fe_NA, na.rm = FALSE)
  > test(nrow(X_demean), nrow(X))
  > 
  > # integer
  > X_int = X
  > X_int[[1]] = as.integer(X_int[[1]])
  > X_demean = demean(X_int, fe)
  > 
  > # matrix/DF
  > X_demean = demean(X_int, fe, as.matrix = TRUE)
  > test(is.matrix(X_demean), TRUE)
  > 
  > X_demean = demean(as.matrix(X_int), fe, as.matrix = FALSE)
  > test(is.matrix(X_demean), FALSE)
  > 
  > # slopes
  > X_dm_slopes = demean(ln_dist ~ Origin + Destination[ln_euros], data = base)
  > X_dm_slopes_bis = demean(base$ln_dist, fe, slope.vars = base$ln_euros, slope.flag = c(0, 1))
  > 
  > test(X_dm_slopes[[1]], X_dm_slopes_bis)
  > 
  > # with data table + formula call
  > trade_dt = as.data.table(trade)
  > trade_dt$ln_dist = log(trade_dt$dist_km)
  > 
  > dist_dm_dt = demean(ln_dist ~ Origin + Destination, data = trade_dt)
  > dist_dm_df = demean(ln_dist ~ Origin + Destination, data = base)
  > 
  > ####
  > #### hatvalues ####
  > ####
  > 
  > 
  > chunk("HATVALUES")
  HATVALUES
  
  > 
  > base = setNames(iris, c("y", "x1", "x2", "x3", "species"))
  > base$y_int = as.integer(base$y)
  > base$y_bin = 1 * (base$y > mean(base$y))
  > 
  > fm  = lm(y ~ x1 + x2, base)
  > ffm = feols(y ~ x1 + x2, base)
  > test(hatvalues(ffm), hatvalues(fm))
  > 
  > glm_poi  = glm(y_int ~ x1 + x2, family = poisson(), base)
  > feglm_poi = fepois(y_int ~ x1 + x2, base)
  > test(hatvalues(feglm_poi), hatvalues(glm_poi))
  > 
  > 
  > glm_logit  = glm(y_bin ~ x1 + x2, family = binomial(), base)
  > feglm_logit = feglm(y_bin ~ x1 + x2, base, binomial())
  > test(hatvalues(feglm_logit), hatvalues(glm_logit))
  > 
  > glm_probit  = glm(y_bin ~ x1 + x2, family = binomial("probit"), base)
  > feglm_probit = feglm(y_bin ~ x1 + x2, base, binomial("probit"))
  > test(hatvalues(feglm_probit), hatvalues(glm_probit))
  > 
  > 
  > ####
  > #### sandwich ####
  > ####
  > 
  > chunk("SANDWICH")
  SANDWICH
  
  > 
  > # Compatibility with sandwich
  > 
  > library(sandwich)
  > 
  > data(base_did)
  > est = feols(y ~ x1 + I(x1**2) + factor(id), base_did)
  > 
  > test(vcov(est, cluster = ~id), vcovCL(est, cluster = ~id, type = "HC1"))
  > 
  > est_pois = fepois(as.integer(y) + 20 ~ x1 + I(x1**2) + factor(id), base_did)
  > 
  > test(vcov(est_pois, cluster = ~id), vcovCL(est_pois, cluster = ~id, type = "HC1"))
  > 
  > # With FEs
  > 
  > est = feols(y ~ x1 + I(x1**2) | id, base_did)
  > 
  > test(vcov(est, cluster = ~id, ssc = ssc(adj = FALSE)), vcovCL(est, cluster = ~id))
  Error in test(vcov(est, cluster = ~id, ssc = ssc(adj = FALSE)), vcovCL(est,  : 
    Difference > tol: Max abs. diff: 2.13414988018377e-06 (in position 1)
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  '/tmp/th798/16189510/R-release/474/fixest.Rcheck/00check.log'
for details.

[1] "2025-03-30 01:28:01 MST"
> 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)
+ }
>