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ElToro1966
Asked: 2021-05-21 10:39:58 +0800 CST

Installing specific version of R pgmm library fails

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I am trying to install a specific version fo the pgmm library in R, and it fails:

> library(fs)
> old_lib <- path_home_r("R/x86_64-pc-linux-gnu-library/old-versions/")
> library(remotes)
> install_version("pgmm", version = "1.1", lib = old_lib, build = TRUE)
Downloading package from url: https://cloud.r-project.org/src/contrib/Archive/pgmm/pgmm_1.1.tar.gz
Running `R CMD build`...
* checking for file ‘/tmp/Rtmp6Jj3B0/remotes3b5e8d11b5fe/pgmm/DESCRIPTION’ ... OK
* preparing ‘pgmm’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘pgmm_1.1.tar.gz’
* installing *source* package ‘pgmm’ ...
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-PsrVor/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c aecm.c -o aecm.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-PsrVor/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gaussj.c -o gaussj.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-PsrVor/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c myalloc.c -o myalloc.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-PsrVor/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pgmm.c -o pgmm.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-PsrVor/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c updates.c -o updates.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o pgmm.so aecm.o gaussj.o myalloc.o pgmm.o updates.o -L/usr/lib/R/lib -lR
/usr/bin/ld: gaussj.o:/tmp/RtmpGlEBF9/R.INSTALL3b70d1f18017d/pgmm/src/functions.h:4: multiple definition of `testfunc2'; aecm.o:/tmp/RtmpGlEBF9/R.INSTALL3b70d1f18017d/pgmm/src/functions.h:4: first defined here
/usr/bin/ld: gaussj.o:/tmp/RtmpGlEBF9/R.INSTALL3b70d1f18017d/pgmm/src/functions.h:1: multiple definition of `testfunc'; aecm.o:/tmp/RtmpGlEBF9/R.INSTALL3b70d1f18017d/pgmm/src/functions.h:1: first defined here
/usr/bin/ld: myalloc.o:/tmp/RtmpGlEBF9/R.INSTALL3b70d1f18017d/pgmm/src/functions.h:4: multiple definition of `testfunc2'; aecm.o:/tmp/RtmpGlEBF9/R.INSTALL3b70d1f18017d/pgmm/src/functions.h:4: first defined here
/usr/bin/ld: myalloc.o:/tmp/RtmpGlEBF9/R.INSTALL3b70d1f18017d/pgmm/src/functions.h:1: multiple definition of `testfunc'; aecm.o:/tmp/RtmpGlEBF9/R.INSTALL3b70d1f18017d/pgmm/src/functions.h:1: first defined here
/usr/bin/ld: pgmm.o:/tmp/RtmpGlEBF9/R.INSTALL3b70d1f18017d/pgmm/src/functions.h:4: multiple definition of `testfunc2'; aecm.o:/tmp/RtmpGlEBF9/R.INSTALL3b70d1f18017d/pgmm/src/functions.h:4: first defined here
/usr/bin/ld: pgmm.o:/tmp/RtmpGlEBF9/R.INSTALL3b70d1f18017d/pgmm/src/functions.h:1: multiple definition of `testfunc'; aecm.o:/tmp/RtmpGlEBF9/R.INSTALL3b70d1f18017d/pgmm/src/functions.h:1: first defined here
/usr/bin/ld: updates.o:/tmp/RtmpGlEBF9/R.INSTALL3b70d1f18017d/pgmm/src/functions.h:4: multiple definition of `testfunc2'; aecm.o:/tmp/RtmpGlEBF9/R.INSTALL3b70d1f18017d/pgmm/src/functions.h:4: first defined here
/usr/bin/ld: updates.o:/tmp/RtmpGlEBF9/R.INSTALL3b70d1f18017d/pgmm/src/functions.h:1: multiple definition of `testfunc'; aecm.o:/tmp/RtmpGlEBF9/R.INSTALL3b70d1f18017d/pgmm/src/functions.h:1: first defined here
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:6: pgmm.so] Error 1
ERROR: compilation failed for package ‘pgmm’
* removing ‘/home/eric/R/x86_64-pc-linux-gnu-library/old-versions/pgmm’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/Rtmp6Jj3B0/file3b5e87e350a98/pgmm_1.1.tar.gz’ had non-zero exit status

The "R/x86_64-pc-linux-gnu-library/old-versions/"-directory exists and the 1.1 version of the pgmm package also exists. Any suggestion for fix greatly appreciated.

package-management

2 Answers

  1. Best Answer

    On Ubuntu 20.10 it is possible to install pgmm 1.1 using gcc-9:

    sudo apt-get install gcc-9
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-9 9

    and then compile R package.

    To revert the gcc version to default use command below:

    sudo update-alternatives --remove-all gcc
    • 2

  2. The issue is not related to the specific version of R pgmm, but to any R extension that fails to comply with the guidelines Writing R Extensions: 1.6.4.1 Common symbols when building using GCC 10 and above.

    We can demonstrate using a minimal functions.h copied from pgmm/src, plus a couple of minimal C source files that both include it:

    $ head functions.h A.c B.c
==> functions.h <==
double (*testfunc)(double **, double **, int *,int,int,int,int,double *,double *,double);
typedef typeof(testfunc) funcType;

double (*testfunc2)(double **, double **,int,int,int,int,double *,double *,double);
typedef typeof(testfunc2) funcType2;

==> A.c <==
#include "functions.h"

==> B.c <==
#include "functions.h"

    Then with GCC 10, using the default -fno-common:

    $ make CC=gcc-10 A.o B.o
gcc-10    -c -o A.o A.c
gcc-10    -c -o B.o B.c
$ gcc -shared A.o B.o && echo "OK" || echo "FAILED"
/usr/bin/ld: B.o:(.bss+0x0): multiple definition of `testfunc'; A.o:(.bss+0x0): first defined here
/usr/bin/ld: B.o:(.bss+0x8): multiple definition of `testfunc2'; A.o:(.bss+0x8): first defined here
collect2: error: ld returned 1 exit status
FAILED

    whereas with -fcommon

    $ rm *.o
$ make CC=gcc-10 CFLAGS=-fcommon A.o B.o
gcc-10 -fcommon   -c -o A.o A.c
gcc-10 -fcommon   -c -o B.o B.c
$ gcc -shared A.o B.o && echo "OK" || echo "FAILED"
OK
$

    The solution is either to build using an older version of GCC, or to customize your R build process as explained in R Installation and Administration: 6.3.3 Customizing package compilation to pass option -fcommon via the CFLAGS variable.

    See also:

    • 1