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 <weiqiao1...@gmail.com> 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 >