trouble with installing DiffBind R package

Question

[eem0306]

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
>

[Devon Ryan]

Do you not have zlib installed?

[eem0306]

Do you mean zlibbioc?

[Devon Ryan]

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.

[eem0306]

I tried to install all of zlib...

and it showed a list of installed zlib like this

Setting up Install Process
Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest version
Package jzlib-javadoc-1.0.7-7.5.el6.x86_64 already installed and latest version
Package zlib-1.2.3-29.el6.x86_64 already installed and latest version
Package jzlib-demo-1.0.7-7.5.el6.x86_64 already installed and latest version
Package zlib-static-1.2.3-29.el6.x86_64 already installed and latest version
Package jzlib-1.0.7-7.5.el6.x86_64 already installed and latest version
Nothing to do

Am I wrong? T.T..

[Devon Ryan]

Right, so follow the instructions in the link I posted previously to try and determine the root of the problem.

[eem0306]

OK!! I Will try!!

Thx So much!