Installation failed on CentOS7 with R 3.5.3 #8
Comments
|
It seems like there's a problem with the boost libraries. Either they're not installed, or they're not loaded. I don't remember how you install a package in centos (`yum`? ). If it's installed maybe you use `module` to load and unload packages? In that case you should load boost prior to running R.
You might get similar problems with other libraries. Check the readme for the list of package dependencies.
…________________________________
From: ehenrion <[email protected]>
Sent: Thursday, May 2, 2019 10:50:44 PM
To: 3DGenomes/binless
Cc: Subscribed
Subject: [3DGenomes/binless] Installation failed on CentOS7 with R 3.5.3 (#8)
Hi there,
I am having trouble installing binless....
I am working on CentOS7 with R3.5.3 and tried the following command :
devtools::install_github("3DGenomes/binless/binless")
Everything seems to go quite smoothly during compilation, then....
Here is the end of the output :
`...
g++ -std=gnu++11 -shared -Linstall_path_of_R/lib64/R/lib -L/usr/local/lib64 -o binless.so AnalyticalGAMLibrary.o FastData.o GFLLibraryTrapezeImpl.o GFLLibraryTriangleImpl.o QuadProg++.o QuadProgGAMLibrary.o candidate_generation.o csnorm_cpp.o cts_core.o cts_to_mat.o fast_binless.o fast_dataframe.o gam.o gfl_csparse.o gfl_graph_fl.o gfl_tf.o gfl_utils.o graph_helpers.o minimum_UB.o perf_iteration_diff.o perf_iteration_signal.o spline.o util.o -lgsl -lgslcblas -lboost_iostreams -Linstall_path_of_R/lib64/R/lib -lR
installing to install_path_of_R/lib64/R/library/binless/libs
** R
** byte-compile and prepare package for lazy loading
** help
No man pages found in package ‘binless’
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error: package or namespace load failed for ‘binless’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object 'install_path_of_R/lib64/R/library/binless/libs/binless.so':
install_path_of_R/lib64/R/library/binless/libs/binless.so: undefined symbol: _ZN5boost9iostreams20file_descriptor_sinkC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt13_Ios_Openmode
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘install_path_of_R/lib64/R/library/binless’
Error in i.p(...) :
(converted from warning) installation of package ‘/gs/scratch/ehenrion/RtmpqcSM3H/filed9f577dd233/binless_0.15.0.tar.gz’ had non-zero exit status
`
Any help would be greatly appreciated !
Thanks so much,
Edouard
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub<#8>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AA455NPFFO53O4RFIGAHCZDPTNH2JANCNFSM4HKHXNLA>.
|
|
Hi, |
|
So... |
|
Let's try a manual installation. Could you please open a fresh terminal, unpack the latest release source file, and type |
|
Hi, There seems to be a problem linking to the boost libraries. You can check that the boost libraries are in their place by doing:
Verify also that the installed boost libraries are the 64bit libraries if your system is 64bits. Try to install
Regards David |
|
Hi there ! First to answer your questions : On my side, I tried to go the rough way by hunting for the undefined symbol The boost libraries being installed in This unfortunately gave me no result... On CentOS 7, the version of the boost libraries being 1.53.0 I decided to install a newer version (1.66.0) as a module and went hunting again : Great !!! isn't it ? Here is what my module file does : Do you see anything missing ? I feel like I am almost there. Regards, |
|
Hi, Maybe the LD_LIBRARY_PATH is not properly passed to R. You should see the path where the library is Regards David |
|
Hi, This is also what I thought but LD_LIBRARY_PATH is updated : the boost libraries folder is appended to LD_LIBRARY_PATH. Here it the output of the command : Regards, |
|
Hi, I'm also running out of ideas |
|
Another question: how do you load R? Through rstudio, or in a shell, plain R ? |
|
@yannickspill You should now be able to see the LD_LIBRARY_PATH value, the last entry being I use plain R, not Rstudio... Haha ! you are running out of idea too ! :) What version of Boost are you guys using ? If I ever succeed to make it work on CentOS 7 (with or without the use of modules) I will let you guys know for sure. Thanks a lot for you help ! Regards, |
|
Yes, let us know! This is indeed weird and I suspect this is related to |
|
I'm also on centos 7. My boost libraries are 1.53.0 but I'm pretty sure the version of boost is not the problem. Regards David |
|
@yannickspill @david-castillo Thanks again for your help and for your time ! Regards, |
|
Here are a couple of things I could think of out of the top of my head. I don't use I think you don't need R to be aware of the location of boost libraries and headers. What matters, is that the C++ compiler does. and the end of the compile process for binless |
|
Thanks for all this ! My installation on Ubuntu did work ! So if you had no problem with I'll run the same commands as yours and post the output there. The bright part, at least there is one now, is that binless is working and available for the people who need it ! Ed |
|
Yes, keep us posted, and don't hesitate to open other issues if your users find other problems |
|
Hi, I'm also having the same problem as @ehenrion. I'm working in a CentOS server. CentOS Linux release 7.6.1810 (Core) And I tried to install either using R with devtools and manually, but both return the same error: x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -shared -L/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib -Wl,-rpath-link,/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib -L/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib -Wl,-rpath-link,/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib -o binless.so AnalyticalGAMLibrary.o FastData.o GFLLibraryTrapezeImpl.o GFLLibraryTriangleImpl.o QuadProg++.o QuadProgGAMLibrary.o candidate_generation.o csnorm_cpp.o cts_core.o cts_to_mat.o fast_binless.o fast_dataframe.o gam.o gfl_csparse.o gfl_graph_fl.o gfl_tf.o gfl_utils.o graph_helpers.o minimum_UB.o perf_iteration_diff.o perf_iteration_signal.o spline.o util.o -lgsl -lgslcblas -lboost_iostreams -L/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib/R/lib -lR
I appreciate if you could help me. Thanks so much, |
|
I supposed you tried |
|
Dear @yannickspill , Thank you very much for your reply. Sorry, I was a bit busy with other things, now I'm back again to set binless in the server.
I didn't have the "BH" package installed. However, even after installing the problem still the same. Then neither exporting to my bash_rc the library path nor making a symbolic link toa directory listed before made it work. I'm still having the same error: x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -shared -L/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib -Wl,-rpath-link,/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib -L/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib -Wl,-rpath-link,/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib -o binless.so AnalyticalGAMLibrary.o FastData.o GFLLibraryTrapezeImpl.o GFLLibraryTriangleImpl.o QuadProg++.o QuadProgGAMLibrary.o candidate_generation.o csnorm_cpp.o cts_core.o cts_to_mat.o fast_binless.o fast_dataframe.o gam.o gfl_csparse.o gfl_graph_fl.o gfl_tf.o gfl_utils.o graph_helpers.o minimum_UB.o perf_iteration_diff.o perf_iteration_signal.o spline.o util.o -lgsl -lgslcblas -lboost_iostreams -L/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib/R/lib -lR
|
|
Could you type |
|
Hi, Thanks for the help. /usr/lib64/libboost_iostreams.so.1.53.0 |
|
well it looks like you did not include that path in your library. (That being said, all paths and your compiler is something I haven't seen, but maybe @david-castillo knows what this is). To add alibrary to your search path, write |
|
Thank you very much for your patience to my naive issue. SO, what I did is to run as following:
Actually it worked, but gave another error: x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -shared -L/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib -Wl,-rpath-link,/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib -L/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib -Wl,-rpath-link,/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib -o binless.so AnalyticalGAMLibrary.o FastData.o GFLLibraryTrapezeImpl.o GFLLibraryTriangleImpl.o QuadProg++.o QuadProgGAMLibrary.o candidate_generation.o csnorm_cpp.o cts_core.o cts_to_mat.o fast_binless.o fast_dataframe.o gam.o gfl_csparse.o gfl_graph_fl.o gfl_tf.o gfl_utils.o graph_helpers.o minimum_UB.o perf_iteration_diff.o perf_iteration_signal.o spline.o util.o -lgsl -lgslcblas -lboost_iostreams -L/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib/R/lib -lR
besides the Japanese messages, the problem seems to be the /yshare3/home/nagailae/local/share/bcbio/anaconda/envs/R01/lib/R/library/00LOCK-binless/00new/binless/libs/binless.so |
|
@david-castillo any clue? I developed it in centos just fine, and here it doesn't even compile... |
|
This is my environment This is a working installation under conda 4.6.14. The clue here is to install boost and any existing package within conda: |
Hi there,
I am having trouble installing binless....
I am working on CentOS7 with R3.5.3 and tried the following command :
devtools::install_github("3DGenomes/binless/binless")Everything seems to go quite smoothly during compilation, then....
Here is the end of the output :
`g++ -std=gnu++11 -shared -Linstall_path_of_R/lib64/R/lib -L/usr/local/lib64 -o binless.so AnalyticalGAMLibrary.o FastData.o GFLLibraryTrapezeImpl.o GFLLibraryTriangleImpl.o QuadProg++.o QuadProgGAMLibrary.o candidate_generation.o csnorm_cpp.o cts_core.o cts_to_mat.o fast_binless.o fast_dataframe.o gam.o gfl_csparse.o gfl_graph_fl.o gfl_tf.o gfl_utils.o graph_helpers.o minimum_UB.o perf_iteration_diff.o perf_iteration_signal.o spline.o util.o -lgsl -lgslcblas -lboost_iostreams -Linstall_path_of_R/lib64/R/lib -lR
installing to install_path_of_R/lib64/R/library/binless/libs
** R
** byte-compile and prepare package for lazy loading
** help
No man pages found in package ‘binless’
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error: package or namespace load failed for ‘binless’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object 'install_path_of_R/lib64/R/library/binless/libs/binless.so':
install_path_of_R/lib64/R/library/binless/libs/binless.so: undefined symbol: _ZN5boost9iostreams20file_descriptor_sinkC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt13_Ios_Openmode
Error: loading failed
Execution halted
ERROR: loading failed
Error in i.p(...) :
(converted from warning) installation of package ‘/gs/scratch/ehenrion/RtmpqcSM3H/filed9f577dd233/binless_0.15.0.tar.gz’ had non-zero exit status
`
Any help would be greatly appreciated !
Thanks so much,
Edouard
The text was updated successfully, but these errors were encountered: