Entering edit mode
9.4 years ago
eem0306
•
0
I try to install "R package; DiffBind"
I think other depends package was installed well..
but I got a problem like this;
(I tried to do this in a various versions of R, such as R 3.1.1 or R 2.15.0)
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'Rsamtools-Overview.Rnw'
'Rsamtools-UsingCLibraries.Rnw'
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/data/eem0306/R-2.15.0/library/Rsamtools/libs/Rsamtools.so':
/data/eem0306/R-2.15.0/library/Rsamtools/libs/Rsamtools.so: undefined symbol: gzopen64
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/data/eem0306/R-2.15.0/library/Rsamtools'
ERROR: dependency 'RSQLite' is not available for package 'AnnotationDbi'
* removing '/data/eem0306/R-2.15.0/library/AnnotationDbi'
ERROR: dependency 'AnnotationDbi' is not available for package 'annotate'
* removing '/data/eem0306/R-2.15.0/library/annotate'
ERROR: dependencies 'AnnotationDbi', 'annotate' are not available for package 'genefilter'
* removing '/data/eem0306/R-2.15.0/library/genefilter'
ERROR: dependencies 'annotate', 'AnnotationDbi' are not available for package 'geneplotter'
* removing '/data/eem0306/R-2.15.0/library/geneplotter'
ERROR: dependencies 'genefilter', 'geneplotter' are not available for package 'DESeq'
* removing '/data/eem0306/R-2.15.0/library/DESeq'
ERROR: dependencies 'gplots', 'DESeq' are not available for package 'DiffBind'
* removing '/data/eem0306/R-2.15.0/library/DiffBind'
The downloaded source packages are in
'/tmp/RtmpzoA8Si/downloaded_packages'
Updating HTML index of packages in '.Library'
Making packages.html ... done
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package 'RSQLite' had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package 'Rsamtools' had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package 'AnnotationDbi' had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package 'annotate' had non-zero exit status
5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package 'genefilter' had non-zero exit status
6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package 'geneplotter' had non-zero exit status
7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package 'DESeq' had non-zero exit status
8: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package 'DiffBind' had non-zero exit status
>
Do you not have zlib installed?
Do you mean zlibbioc?
No, the base zlib on your system, completely independent from R/Bioconductor. The root of the problem you reported is this line:
/data/eem0306/R-2.15.0/library/Rsamtools/libs/Rsamtools.so: undefined symbol: gzopen64
The function gzopen64() is defined in zlib, so either (A) you don't have that installed (highly unlikely), (B) somehow R isn't finding it, or (C) somehow you have a version of zlib without gzopen64(). In any case, have a look through this thread on the bioconductor site for help.
I tried to install all of zlib...
and it showed a list of installed zlib like this
Am I wrong? T.T..
Right, so follow the instructions in the link I posted previously to try and determine the root of the problem.
OK!! I Will try!!
Thx So much!