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Re: [Help-gsl] how to install gsl then install MotIV Rpackage


From: Wei QIAO
Subject: Re: [Help-gsl] how to install gsl then install MotIV Rpackage
Date: Wed, 2 Oct 2019 21:55:42 +0800

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 <address@hidden> 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
>


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