1.12.0 compilation error on Red Hat Linux / Trisquel

[iembry]

Hi, I tried unsuccessfully to install the v1.12.0 (13 Jan 2019) data.table package in Trisquel GNU/Linux system. I have the sessionInfo information at the bottom of this issue.

Please see the installation log below:

> install.packages("data.table")
Installing package into ‘/x86_64-pc-linux-gnu-library/library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/data.table_1.12.0.tar.gz'
Content type 'application/x-gzip' length 3311096 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

* installing *source* package ‘data.table’ ...
** package ‘data.table’ successfully unpacked and MD5 sums checked
** libs
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c assign.c -o assign.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c between.c -o between.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c bmerge.c -o bmerge.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c chmatch.c -o chmatch.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c dogroups.c -o dogroups.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c fastmean.c -o fastmean.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c fcast.c -o fcast.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c fmelt.c -o fmelt.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c forder.c -o forder.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c frank.c -o frank.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c fread.c -o fread.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c freadR.c -o freadR.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c froll.c -o froll.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c frollR.c -o frollR.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c frolladaptive.c -o frolladaptive.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c fsort.c -o fsort.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c fwrite.c -o fwrite.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c fwriteR.c -o fwriteR.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c gsumm.c -o gsumm.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c ijoin.c -o ijoin.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c init.c -o init.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c inrange.c -o inrange.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c nqrecreateindices.c -o nqrecreateindices.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c openmp-utils.c -o openmp-utils.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c quickselect.c -o quickselect.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c rbindlist.c -o rbindlist.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c reorder.c -o reorder.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c shift.c -o shift.o
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fopenmp -fpic  -std=gnu99 -c subset.c -o subset.o
subset.c: In function ‘subsetVectorRaw’:
subset.c:36:105: error: stray ‘#’ in program
     PARLOOP(NA_INTEGER)
                                                                                                         ^
subset.c:36:106: error: unknown type name ‘pragma’
     PARLOOP(NA_INTEGER)
                                                                                                          ^
subset.c:36:117: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘parallel’
     PARLOOP(NA_INTEGER)
                                                                                                                     ^
subset.c:36:16: error: ‘i’ undeclared (first use in this function)
     PARLOOP(NA_INTEGER)
                ^
subset.c:36:16: note: each undeclared identifier is reported only once for each function it appears in
subset.c:36:24: error: expected ‘;’ before ‘)’ token
     PARLOOP(NA_INTEGER)
                        ^
subset.c:36:24: error: expected statement before ‘)’ token
subset.c:42:124: error: stray ‘#’ in program
       PARLOOP(INT64_MIN)
                                                                                                                            ^
subset.c:42:125: error: unknown type name ‘pragma’
       PARLOOP(INT64_MIN)
                                                                                                                             ^
subset.c:42:136: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘parallel’
       PARLOOP(INT64_MIN)
                                                                                                                                        ^
subset.c:42:24: error: expected ‘;’ before ‘)’ token
       PARLOOP(INT64_MIN)
                        ^
subset.c:42:24: error: expected statement before ‘)’ token
subset.c:46:106: error: stray ‘#’ in program
       PARLOOP(NA_REAL)
                                                                                                          ^
subset.c:46:107: error: unknown type name ‘pragma’
       PARLOOP(NA_REAL)
                                                                                                           ^
subset.c:46:118: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘parallel’
       PARLOOP(NA_REAL)
                                                                                                                      ^
subset.c:46:24: error: expected ‘;’ before ‘)’ token
       PARLOOP(NA_REAL)
                        ^
subset.c:46:24: error: expected statement before ‘)’ token
subset.c:76:105: error: stray ‘#’ in program
     PARLOOP(NA_CPLX)
                                                                                                         ^
subset.c:76:106: error: unknown type name ‘pragma’
     PARLOOP(NA_CPLX)
                                                                                                          ^
subset.c:76:117: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘parallel’
     PARLOOP(NA_CPLX)
                                                                                                                     ^
subset.c:76:24: error: expected ‘;’ before ‘)’ token
     PARLOOP(NA_CPLX)
                        ^
subset.c:76:24: error: expected statement before ‘)’ token
subset.c:81:99: error: stray ‘#’ in program
     PARLOOP(0)
                                                                                                   ^
subset.c:81:100: error: unknown type name ‘pragma’
     PARLOOP(0)
                                                                                                    ^
subset.c:81:111: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘parallel’
     PARLOOP(0)
                                                                                                               ^
subset.c:81:24: error: expected ‘;’ before ‘)’ token
     PARLOOP(0)
                        ^
subset.c:81:24: error: expected statement before ‘)’ token
make: *** [subset.o] Error 1
ERROR: compilation failed for package ‘data.table’

Output of sessionInfo()

R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Trisquel GNU/Linux Belenos (7.0)

Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] graphics  grDevices datasets  stats     utils     methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.5.2 tools_3.5.2   

[s-yazar]

Hello,

I am also having trouble installing data.table in Linux with the following error:

gcc -std=gnu99 -I"/share/ClusterShare/software/contrib/seyyaz/R-v3.5.1/lib64/R/include" -DNDEBUG   -I/share/ClusterShare/software/contrib/seyyaz/zlib-1.2.11/include -I/share/ClusterShare/software/contrib/seyyaz/bzip2-1.0.6/include -I/share/ClusterShare/software/contrib/seyyaz/xz-5.2.4/include -I/share/ClusterShare/software/contrib/seyyaz/pcre-8.42/include -I//share/ClusterShare/software/contrib/seyyaz/curl-7.63.0/include  -fopenmp -fpic  -g -O2  -c forder.c -o forder.o
forder.c: In function 'range_str':
forder.c:296: error: expected end of line before 'update'
make: *** [forder.o] Error 1
ERROR: compilation failed for package 'data.table'
* removing '/share/ClusterShare/software/contrib/seyyaz/R_libs/data.table'
* restoring previous '/share/ClusterShare/software/contrib/seyyaz/R_libs/data.table'

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.8 (Final)

Matrix products: default
BLAS: /share/ClusterShare/software/contrib/seyyaz/R-v3.5.1/lib64/R/lib/libRblas.so
LAPACK: /share/ClusterShare/software/contrib/seyyaz/R-v3.5.1/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
 [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
 [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
 [7] LC_PAPER=en_US.iso885915       LC_NAME=C
 [9] LC_ADDRESS=C                   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] usethis_1.4.0  devtools_2.0.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0         ps_1.3.0           prettyunits_1.0.2  rprojroot_1.3-2
 [5] withr_2.1.2        digest_0.6.18      crayon_1.3.4       assertthat_0.2.0
 [9] R6_2.3.0           backports_1.1.3    magrittr_1.5       rlang_0.3.1
[13] cli_1.0.1          curl_3.3           fs_1.2.6           remotes_2.0.2
[17] callr_3.1.1        desc_1.2.0         tools_3.5.1        glue_1.3.0
[21] pkgload_1.0.2      compiler_3.5.1     processx_3.2.1     pkgbuild_1.0.2
[25] BiocManager_1.30.4 sessioninfo_1.1.1  memoise_1.1.0

[jangorecki]

please report also version of your compilers, something like gcc --version

[s-yazar]

Mine was gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-17). I have also compiled one version with gcc-7.3.0 and it gives an error too

[CharlesBordet]

It seems to be related to CentOS. I had the same issue as s-yazar on a brand new R install.

The problem was solved by upgrading gcc to 4.9.0.

[jangorecki]

@Huitziii thanks for feedback. Still it is strange that @s-yazar is getting error on gcc-7.3 while for you upgrade to gcc-4.9 resolved the problem. We don't have environment on hand to reproduce that issue at the moment.

[s-yazar]

Hi @jangorecki,
I went back and recompiled R 3.5.1 with gcc-7.3 again. This time installed data.table without a problem. Not sure what has caused the earlier error.

[jangorecki]

@s-yazar thanks for feedback.
So as of now @s-yazar and @Huitziii compilation error has been solved by upgrading compiler.
@iembry are you able to upgrade your compiler?

[jangorecki]

@iembry please lets us know if upgrading compiler resolved the problem, if not I will re-open this issue.

[philippbayer]

I ran into the same issue on a RedHat system running gcc v4.4.7 - I installed devtoolset-2 as described here: https://unix.stackexchange.com/a/125621 since the 'standard' RedHat gcc on this distro is still v4.4.7, so yum update didn't do anything (I also had to download and install the GPG key as listed in this comment)

devtoolset-2 contains a bunch of stuff, including a newer gcc v4.8.2, enable that environment:

source scl_source enable devtoolset-2

and then you have gcc v4.8.2, and then the installation of data.table v1.1.2.0 worked.