undefined symbol: glp_error_hook

User_1NH09

Hi guys,

We're trying to install Rglpk package however an error is raised and we don't have ideas how to solve it.

This is an Oracle R installation on top of Oracle Linux 6.9 (x86_64).

Appreciate your support.

Thanks

During startup - Warning message:Setting LC_CTYPE failed, using "C" * installing *source* package 'Rglpk' ...** package 'Rglpk' successfully unpacked and MD5 sums checkedDuring startup - Warning message:Setting LC_CTYPE failed, using "C" ** libsgcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Rglpk_error.c -o Rglpk_error.ogcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Rglpk_initialize.c -o Rglpk_initialize.ogcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Rglpk_read_file.c -o Rglpk_read_file.ogcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Rglpk_solve.c -o Rglpk_solve.ogcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.ogcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o Rglpk.so Rglpk_error.o Rglpk_initialize.o Rglpk_read_file.o Rglpk_solve.o init.o -lglpk -L/usr/lib64/R/lib -lRinstalling to /usr/lib64/R/library/Rglpk/libs** R** inst** preparing package for lazy loading** help*** installing help indices  converting help for package 'Rglpk'    finding HTML links ... done    Rglpk_read_file                         html  Rd warning: /tmp/RtmpBCIgSW/R.INSTALLcf53f4f47e8/Rglpk/man/Rglpk_read_file.Rd:43: missing file link 'simple_triplet_matrix'Rd warning: /tmp/RtmpBCIgSW/R.INSTALLcf53f4f47e8/Rglpk/man/Rglpk_read_file.Rd:45: missing file link 'simple_triplet_matrix'    Rglpk_solve                             html  ** building package indices** testing if installed package can be loadedDuring startup - Warning message:Setting LC_CTYPE failed, using "C" Error in dyn.load(file, DLLpath = DLLpath, ...) :   unable to load shared object '/usr/lib64/R/library/Rglpk/libs/Rglpk.so':  /usr/lib64/R/library/Rglpk/libs/Rglpk.so: undefined symbol: glp_error_hookError: loading failedExecution haltedERROR: loading failed* removing '/usr/lib64/R/library/Rglpk'The downloaded source packages are in  '/tmp/RtmpTg2Pdn/downloaded_packages'Updating HTML index of packages in '.Library'Making 'packages.html' ... doneWarning message:In install.packages("Rglpk") :  installation of package 'Rglpk' had non-zero exit status

rtiran

Hello,

I could reproduce your issue on an ol6.9 system as well.

In order for the install to complete, I had to use an older version of Rglpk - i.e. version 6.0:

[[email protected]**-**-*** ec2-user]# wget https://cran.r-project.org/src/contrib/Archive/Rglpk/Rglpk_0.6-0.tar.gz

--2017-06-07 11:35:51--  https://cran.r-project.org/src/contrib/Archive/Rglpk/Rglpk_0.6-0.tar.gz

Resolving cran.r-project.org... 137.208.57.37

Connecting to cran.r-project.org|137.208.57.37|:443... connected.

HTTP request sent, awaiting response... 200 OK

Length: 18284 (18K) [application/x-gzip]

Saving to: “Rglpk_0.6-0.tar.gz”

100%[======================================================================================================================================================================>] 18,284      --.-K/s  in 0.04s

2017-06-07 11:35:52 (461 KB/s) - “Rglpk_0.6-0.tar.gz” saved [18284/18284]

[[email protected]**-**-*** ec2-user]#  R CMD INSTALL Rglpk_0.6-0.tar.gz

* installing to library ‘/usr/lib64/R/library’

* installing *source* package ‘Rglpk’ ...

** package ‘Rglpk’ successfully unpacked and MD5 sums checked

** libs

gcc -m64 -std=gnu99 -I/usr/lib64/R/../../include/R -DNDEBUG  -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/zlib -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/xz -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/bzip2 -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include    -fpic  -g -O2  -c Rglpk_initialize.c -o Rglpk_initialize.o

gcc -m64 -std=gnu99 -I/usr/lib64/R/../../include/R -DNDEBUG  -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/zlib -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/xz -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/bzip2 -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include    -fpic  -g -O2  -c Rglpk_read_file.c -o Rglpk_read_file.o

gcc -m64 -std=gnu99 -I/usr/lib64/R/../../include/R -DNDEBUG  -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/zlib -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/xz -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/bzip2 -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include    -fpic  -g -O2  -c Rglpk_solve.c -o Rglpk_solve.o

gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -L/builddir/build/BUILD/R-3.3.0/port/Linux-X64/lib -o Rglpk.so Rglpk_initialize.o Rglpk_read_file.o Rglpk_solve.o -lglpk -L/usr/lib64/R/lib -lR

installing to /usr/lib64/R/library/Rglpk/libs

** R

** inst

** preparing package for lazy loading

** help

*** installing help indices

  converting help for package ‘Rglpk’

    finding HTML links ... done

    Rglpk_read_file                        html

Rd warning: /tmp/Rtmpn3I7Nc/R.INSTALL65f27bb91e78/Rglpk/man/Rglpk_read_file.Rd:43: missing file link ‘simple_triplet_matrix’

Rd warning: /tmp/Rtmpn3I7Nc/R.INSTALL65f27bb91e78/Rglpk/man/Rglpk_read_file.Rd:45: missing file link ‘simple_triplet_matrix’

    Rglpk_solve                            html

** building package indices

** testing if installed package can be loaded

* DONE (Rglpk)

Making 'packages.html' ... done

[[email protected]**-**-*** ec2-user]#

Install failed for me with all versions more recent than 6.0.

That said, I could not reproduce that issue on an ol7.3 system and it works fine with the current version.

Hope this helps.

Regards,

Raphaël

rtiran

Hello,

I could reproduce your issue on an ol6.9 system as well.

In order for the install to complete, I had to use an older version of Rglpk - i.e. version 6.0:

[[email protected]**-**-*** ec2-user]# wget https://cran.r-project.org/src/contrib/Archive/Rglpk/Rglpk_0.6-0.tar.gz

--2017-06-07 11:35:51--  https://cran.r-project.org/src/contrib/Archive/Rglpk/Rglpk_0.6-0.tar.gz

Resolving cran.r-project.org... 137.208.57.37

Connecting to cran.r-project.org|137.208.57.37|:443... connected.

HTTP request sent, awaiting response... 200 OK

Length: 18284 (18K) [application/x-gzip]

Saving to: “Rglpk_0.6-0.tar.gz”

100%[======================================================================================================================================================================>] 18,284      --.-K/s  in 0.04s

2017-06-07 11:35:52 (461 KB/s) - “Rglpk_0.6-0.tar.gz” saved [18284/18284]

[[email protected]**-**-*** ec2-user]#  R CMD INSTALL Rglpk_0.6-0.tar.gz

* installing to library ‘/usr/lib64/R/library’

* installing *source* package ‘Rglpk’ ...

** package ‘Rglpk’ successfully unpacked and MD5 sums checked

** libs

gcc -m64 -std=gnu99 -I/usr/lib64/R/../../include/R -DNDEBUG  -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/zlib -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/xz -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/bzip2 -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include    -fpic  -g -O2  -c Rglpk_initialize.c -o Rglpk_initialize.o

gcc -m64 -std=gnu99 -I/usr/lib64/R/../../include/R -DNDEBUG  -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/zlib -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/xz -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/bzip2 -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include    -fpic  -g -O2  -c Rglpk_read_file.c -o Rglpk_read_file.o

gcc -m64 -std=gnu99 -I/usr/lib64/R/../../include/R -DNDEBUG  -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/zlib -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/xz -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include/bzip2 -I/builddir/build/BUILD/R-3.3.0/port/Linux-X64/include    -fpic  -g -O2  -c Rglpk_solve.c -o Rglpk_solve.o

gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -L/builddir/build/BUILD/R-3.3.0/port/Linux-X64/lib -o Rglpk.so Rglpk_initialize.o Rglpk_read_file.o Rglpk_solve.o -lglpk -L/usr/lib64/R/lib -lR

installing to /usr/lib64/R/library/Rglpk/libs

** R

** inst

** preparing package for lazy loading

** help

*** installing help indices

  converting help for package ‘Rglpk’

    finding HTML links ... done

    Rglpk_read_file                        html

Rd warning: /tmp/Rtmpn3I7Nc/R.INSTALL65f27bb91e78/Rglpk/man/Rglpk_read_file.Rd:43: missing file link ‘simple_triplet_matrix’

Rd warning: /tmp/Rtmpn3I7Nc/R.INSTALL65f27bb91e78/Rglpk/man/Rglpk_read_file.Rd:45: missing file link ‘simple_triplet_matrix’

    Rglpk_solve                            html

** building package indices

** testing if installed package can be loaded

* DONE (Rglpk)

Making 'packages.html' ... done

[[email protected]**-**-*** ec2-user]#

Install failed for me with all versions more recent than 6.0.

That said, I could not reproduce that issue on an ol7.3 system and it works fine with the current version.

Hope this helps.

Regards,

Raphaël

Christos Iraklis Tsatsoulis

Nice catch Raphaël.

Nevertheless, for me (in OL6.9) it would still not work, unless I set the CPATH environment variable.

So, here are the steps that worked for me:

1) Install glpk package:

sudo yum install glpk glpk-devel

2) Download & install an older version of the slam package (the latest one needs R >= 3.3.1):

wget https://cran.r-project.org/src/contrib/Archive/slam/slam_0.1-32.tar.gz

su root

R CMD INSTALL slam_0.1-32.tar.gz

3) Set the environment variable CPATH:

export CPATH=/usr/include/glpk

4) Download & install Rglpk 0.6-0:

wget https://cran.r-project.org/src/contrib/Archive/Rglpk/Rglpk_0.6-0.tar.gz

R CMD INSTALL Rglpk_0.6-0.tar.gz

installing to library ‘/u01/app/oracle/product/12.1.0.2/dbhome_1/R/library’

* installing *source* package ‘Rglpk’ ...

** package ‘Rglpk’ successfully unpacked and MD5 sums checked

** libs

gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Rglpk_initialize.c -o Rglpk_initialize.o

gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Rglpk_read_file.c -o Rglpk_read_file.o

gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Rglpk_solve.c -o Rglpk_solve.o

gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o Rglpk.so Rglpk_initialize.o Rglpk_read_file.o Rglpk_solve.o -lglpk -L/usr/lib64/R/lib -lR

installing to /u01/app/oracle/product/12.1.0.2/dbhome_1/R/library/Rglpk/libs

** R

** inst

** preparing package for lazy loading

** help

*** installing help indices

  converting help for package ‘Rglpk’

    finding HTML links ... done

    Rglpk_read_file                         html 

Rd warning: /tmp/RtmpXVb3rd/R.INSTALL3454276682c/Rglpk/man/Rglpk_read_file.Rd:43: missing file link ‘simple_triplet_matrix’

Rd warning: /tmp/RtmpXVb3rd/R.INSTALL3454276682c/Rglpk/man/Rglpk_read_file.Rd:45: missing file link ‘simple_triplet_matrix’

    Rglpk_solve                             html 

** building package indices

** testing if installed package can be loaded

* DONE (Rglpk)

In R:

> library(Rglpk)

Loading required package: slam

Using the GLPK callable library version 4.40

Christos

User_1NH09

Thank you so much.