Well, it was surprising when I install again the second day it fixed and the .bashrc is
export R_LD_LIBRARY_PATH=" /mnt/disk1/qiaowei/pepatac_tutorial/tools/pepatac/tools/R-3.6.1/lib:/usr/local/lib" but just as some people say don't change LD_LIBRARY_PATH easily because it will causing dynamic library conflicts.And for me now I am not root,so maybe it is the only way I can do. Any advice welcome! On Wed, Oct 2, 2019 at 9:55 PM Wei QIAO <[email protected]> wrote: > Hi > after some trying,I have install gsl-2.6 in my account, and I found there > are two GSL : > > [qiaowei@clust1 ~]$ /usr/local/bin/gsl-config --version > > 2.4 > > [qiaowei@clust1 ~]$ ~/configure/gsl/bin/gsl-config --version > > 2.6 > so I know that it is not the problem of version>=1.6,maybe the problem of > LD_LIBRARY_PATH, > so I add this > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib > to my .bashrc after source ~/.bashrc ,install MotIV it still the same > error.then I also tried > export R_LD_LIBRARY_PATH=" > /mnt/disk1/qiaowei/pepatac_tutorial/tools/pepatac/tools/R-3.6.1/lib:/usr/local/lib > " > still same error.Could you please give me some advice how to fix this > problem?Thank you so much in advance. > > Best regards > Wei > > > On Wed, Oct 2, 2019 at 1:22 PM Wei QIAO <[email protected]> wrote: > >> Hi dear gsl developers, >> Thank you for developing gsl. But now I came across a problem I think it >> is something about install gsl then modify LD_LOBRARY_PATH. >> When I install ATACseqQC Rpackage in centos by OS Bioconductor version >> 3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05)I found these warnings: >> >> Warning messages: >> >> 1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : >> >> installation of package ‘MotIV’ had non-zero exit status >> >> 2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : >> >> installation of package ‘motifStack’ had non-zero exit status >> >> 3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : >> >> installation of package ‘ATACseqQC’ had non-zero exit status >> then I looked its history: >> >> ERROR: dependency ‘rGADEM’ is not available for package ‘MotIV’ >> >> ERROR: dependency ‘MotIV’ is not available for package ‘motifStack’ >> >> ERROR: dependency ‘motifStack’ is not available for package ‘ATACseqQC’ >> so I decided to install one by one: >> BiocManager::install("rGADEM") >> >> BiocManager::install("MotIV") >> >> BiocManager::install("motifStack") >> >> BiocManager::install("ATACseqQC") >> but unfortunately only rGADEM successed. >> >> DONE (rGADEM) >> and the error when install MotIV is: >> >> * installing *source* package ‘MotIV’ ... >> >> ** using staged installation >> >> checking for gcc... gcc -std=gnu99 >> >> checking for C compiler default output file name... a.out >> >> checking whether the C compiler works... yes >> >> checking whether we are cross compiling... no >> >> checking for suffix of executables... >> >> checking for suffix of object files... o >> >> checking whether we are using the GNU C compiler... yes >> >> checking whether gcc -std=gnu99 accepts -g... yes >> >> checking for gcc -std=gnu99 option to accept ISO C89... none needed >> >> checking for gsl-config... /usr/local/bin/gsl-config >> >> checking for GSL - version >= 1.6... no >> >> *** Could not run GSL test program, checking why... >> >> *** The test program compiled, but did not run. This usually means >> >> *** that the run-time linker is not finding GSL or finding the wrong >> >> *** version of GSL. If it is not finding GSL, you'll need to set your >> >> *** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point >> >> *** to the installed location Also, make sure you have run ldconfig if >> that >> >> *** is required on your system >> >> *** >> >> *** If you have an old version installed, it is best to remove it, >> although >> >> *** you may also be able to get things to work by modifying >> LD_LIBRARY_PATH >> >> configure: error: Cannot find Gnu Scientific Library >=1.6 >> >> ERROR: configuration failed for package ‘MotIV’ >> >> * removing >> ‘/mnt/disk1/qiaowei/pepatac_tutorial/tools/pepatac/tools/R-3.6.1/library/MotIV’ >> >> >> The downloaded source packages are in >> >> ‘/tmp/RtmpkYgayg/downloaded_packages’ >> >> Updating HTML index of packages in '.Library' >> >> Making 'packages.html' ... done >> >> Warning message: >> >> In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : >> >> installation of package ‘MotIV’ had non-zero exit status >> so I guess there is something wrong with my gsl and its configure.then I >> decided to install gsl by myself, but not like others, I am not root and I >> cannot use >> >> sudo apt-get install libgsl0ldbl >> so I get the three file from http://mirrors.nju.edu.cn/gnu/gsl/ >> >> -rw-r--r--. 1 qiaowei qiaowei 1.7K Oct 2 12:39 gsl_key.txt >> >> -rwxrwxr-x. 1 qiaowei qiaowei 287 Oct 2 12:27 gsl-2.6.tar.gz.sig >> >> -rwxrwxr-x. 1 qiaowei qiaowei 7.1M Oct 2 12:27 gsl-2.6.tar.gz >> but the question is I don't know how to do the next steps and I also >> didn't find README and INSTALL files.And another thing is how can I well >> configure in order to install MotIV Rpackage successfully. >> Thank you so much in advance! >> >> Regards, >> Wei >> >
