installation error in CI test jobs

[jangorecki]

reported in: https://rdatatable.gitlab.io/data.table/web/checks/check_results_data.table.html
lin-dev-gcc-strict-cran
win-dev

* checking whether package ‘data.table’ can be installed ... [21s/14s] ERROR
Installation failed.
See ‘/builds/Rdatatable/data.table/data.table.Rcheck/00install.out’ for details.

* installing *source* package ‘data.table’ ...
** using staged installation
gcc 13.2.0
zlib 1.3 is available ok
R CMD SHLIB supports OpenMP without any extra hint
** libs
using C compiler: ‘gcc (Debian 13.2.0-13) 13.2.0’
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c assign.c -o assign.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c between.c -o between.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c bmerge.c -o bmerge.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c chmatch.c -o chmatch.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c cj.c -o cj.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c coalesce.c -o coalesce.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c dogroups.c -o dogroups.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c fastmean.c -o fastmean.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c fcast.c -o fcast.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c fifelse.c -o fifelse.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c fmelt.c -o fmelt.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c forder.c -o forder.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c frank.c -o frank.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c fread.c -o fread.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c freadR.c -o freadR.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c froll.c -o froll.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c frollR.c -o frollR.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c frolladaptive.c -o frolladaptive.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c fsort.c -o fsort.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c fwrite.c -o fwrite.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c fwriteR.c -o fwriteR.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c gsumm.c -o gsumm.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c idatetime.c -o idatetime.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c ijoin.c -o ijoin.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c init.c -o init.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c inrange.c -o inrange.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c nafill.c -o nafill.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c negate.c -o negate.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c nqrecreateindices.c -o nqrecreateindices.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c openmp-utils.c -o openmp-utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c programming.c -o programming.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c quickselect.c -o quickselect.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c rbindlist.c -o rbindlist.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c reorder.c -o reorder.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c shift.c -o shift.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c snprintf.c -o snprintf.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c subset.c -o subset.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c transpose.c -o transpose.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c types.c -o types.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c uniqlist.c -o uniqlist.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c vecseq.c -o vecseq.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c wrappers.c -o wrappers.o
gcc -shared -L/usr/local/lib -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 -lz
PKG_CFLAGS = -fopenmp
PKG_LIBS = -fopenmp -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 /builds/Rdatatable/data.table/data.table.Rcheck/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error in paste(gettext("Error: compilation failed - "), msg, "\n") : 
  inserting non-tracking CDR in tracking cell
Calls: <Anonymous> ... tryCatchOne -> <Anonymous> -> notifyCompilerError -> cat
Execution halted
ERROR: lazy loading failed for package ‘data.table’
* removing ‘/builds/Rdatatable/data.table/data.table.Rcheck/data.table’

[jangorecki]

Could be regression in rdevel as well

[MichaelChirico]

Error is coming from here:

https://github.com/r-devel/r-svn/blob/1a700217eec8d1b20cce240601571ab32efba3af/src/main/memory.c#L4363-L4376

There are no changes to this region lately so it'd have to be somewhere calling this code that's changed.

I am not able to reproduce locally with

PKG_CFLAGS='-fopenmp  -fpic  -g -O2 -flto=auto -fno-common -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2'  R CMD INSTALL . --preclean

Nor with adding -DTESTING_WRITE_BARRIER to the PKG_CFLAGS.