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

[Wei QIAO]

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 <address@hidden> 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 <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
>>
>