R dependency problems with readline libraries
Hi, installation of deseq2 1.10.0 causes next problem: /home/galaxy/galaxy/tools/dependencies/R/3.2.1/iuc/package_r_3_2_1/d9f7d84125b7/lib/R/bin/exec/R: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory Installed tool dependencies: deseq2 R 3.2.1 installed without problems readline 6.3 installed too why does it happen? Is something missing? The same readline dependency problem from R happen also during installation of packages bioconductor_limma & bioconductor_edger Meanwhile dseq2 1.2.10 depended on R 3.0.3 has installed but shown warnings and also related to R: /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: warning: libgfortran.so.1, needed by /home/galaxy/galaxy/tools/dependencies/R/3.0.3/iuc/package_r_3_0_3/afc48696ee5c/lib/R/lib/libR.so, not found (try using -rpath or -rpath-link) /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: warning: libreadline.so.6, needed by /home/galaxy/galaxy/tools/dependencies/R/3.0.3/iuc/package_r_3_0_3/afc48696ee5c/lib/R/lib/libR.so, not found (try using -rpath or -rpath-link) Thanx, Nikolaos
I suppose this is the same as https://github.com/galaxyproject/tools-devteam/issues/100 , just for a different R version. Cheers, Nicola On 03/10/16 20:10, Nikolaos Tur wrote:
Hi,
installation of deseq2 1.10.0 causes next problem:
/home/galaxy/galaxy/tools/dependencies/R/3.2.1/iuc/package_r_3_2_1/d9f7d84125b7/lib/R/bin/exec/R: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory Installed tool dependencies: deseq2
R 3.2.1 installed without problems readline 6.3 installed too
why does it happen? Is something missing?
The same readline dependency problem from R happen also during installation of packages bioconductor_limma & bioconductor_edger
Meanwhile dseq2 1.2.10 depended on R 3.0.3 has installed but shown warnings and also related to R:
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: warning: libgfortran.so.1, needed by /home/galaxy/galaxy/tools/dependencies/R/3.0.3/iuc/package_r_3_0_3/afc48696ee5c/lib/R/lib/libR.so, not found (try using -rpath or -rpath-link) /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: warning: libreadline.so.6, needed by /home/galaxy/galaxy/tools/dependencies/R/3.0.3/iuc/package_r_3_0_3/afc48696ee5c/lib/R/lib/libR.so, not found (try using -rpath or -rpath-link)
Thanx, Nikolaos
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Is there any part of conda here? This reminds me of the exact same problems that I had with a few libs (readline for example) and conda linkage. On 2016-10-03 13:37, Nicola Soranzo wrote:
I suppose this is the same as https://github.com/galaxyproject/tools-devteam/issues/100 , just for a different R version.
Cheers, Nicola
On 03/10/16 20:10, Nikolaos Tur wrote:
Hi,
installation of deseq2 1.10.0 causes next problem:
/home/galaxy/galaxy/tools/dependencies/R/3.2.1/iuc/package_r_3_2_1/d9f7d84125b7/lib/R/bin/exec/R:
error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory Installed tool dependencies: deseq2
R 3.2.1 installed without problems readline 6.3 installed too
why does it happen? Is something missing?
The same readline dependency problem from R happen also during installation of packages bioconductor_limma & bioconductor_edger
Meanwhile dseq2 1.2.10 depended on R 3.0.3 has installed but shown warnings and also related to R:
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld:
warning: libgfortran.so.1, needed by
/home/galaxy/galaxy/tools/dependencies/R/3.0.3/iuc/package_r_3_0_3/afc48696ee5c/lib/R/lib/libR.so,
not found (try using -rpath or -rpath-link)
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld:
warning: libreadline.so.6, needed by
/home/galaxy/galaxy/tools/dependencies/R/3.0.3/iuc/package_r_3_0_3/afc48696ee5c/lib/R/lib/libR.so,
not found (try using -rpath or -rpath-link)
Thanx, Nikolaos
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So... it seems there is not solution of this. And for the long time. Or I am wrong? And it is somehow related to ncurses. But ncrurses as well as readline are in the list of linked libraries. At least what I see in tool_dependencies.xml to Tiago Antao there is no conda there. Cheers, NIkolaos On Mon, Oct 3, 2016 at 9:37 PM, Nicola Soranzo <nsoranzo@tiscali.it> wrote:
I suppose this is the same as https://github.com/ galaxyproject/tools-devteam/issues/100 , just for a different R version.
Cheers, Nicola
On 03/10/16 20:10, Nikolaos Tur wrote:
Hi,
installation of deseq2 1.10.0 causes next problem:
/home/galaxy/galaxy/tools/dependencies/R/3.2.1/iuc/ package_r_3_2_1/d9f7d84125b7/lib/R/bin/exec/R: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory Installed tool dependencies: deseq2
R 3.2.1 installed without problems readline 6.3 installed too
why does it happen? Is something missing?
The same readline dependency problem from R happen also during installation of packages bioconductor_limma & bioconductor_edger
Meanwhile dseq2 1.2.10 depended on R 3.0.3 has installed but shown warnings and also related to R:
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: warning: libgfortran.so.1, needed by /home/galaxy/galaxy/tools/ dependencies/R/3.0.3/iuc/package_r_3_0_3/afc48696ee5c/lib/R/lib/libR.so, not found (try using -rpath or -rpath-link) /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: warning: libreadline.so.6, needed by /home/galaxy/galaxy/tools/ dependencies/R/3.0.3/iuc/package_r_3_0_3/afc48696ee5c/lib/R/lib/libR.so, not found (try using -rpath or -rpath-link)
Thanx, Nikolaos
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participants (3)
-
Nicola Soranzo -
Nikolaos Tur -
Tiago Antao