hello everyone, Whenever i am trying to install cummeRbund i am getting same error. I am using R3.2.0. Can anyone give me any suggestions for fixing this problem. thankx Megha

> biocLite("cummeRbund")
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.19.5), R 3.2.0 (2015-04-16).
Installing package(s) ‘cummeRbund’
also installing the dependencies ‘stringi’, ‘Hmisc’, ‘stringr’, ‘biovizBase’, ‘ggplot2’, ‘reshape2’, ‘Gviz’

trying URL 'http://cran.fhcrc.org/src/contrib/stringi_0.4-1.tar.gz'
Error in download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'http://cran.fhcrc.org/src/contrib/stringi_0.4-1.tar.gz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open: HTTP status was '0 (null)'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘stringi’ failed
trying URL 'http://cran.fhcrc.org/src/contrib/Hmisc_3.16-0.tar.gz'
Content type 'application/x-gzip' length 629536 bytes (614 KB)
==================================================
downloaded 614 KB

trying URL 'http://cran.fhcrc.org/src/contrib/stringr_1.0.0.tar.gz'
Content type 'application/x-gzip' length 34880 bytes (34 KB)
==================================================
downloaded 34 KB

trying URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/biovizBase_1.17.1.tar.gz'
Content type 'application/x-gzip' length 2429502 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'http://cran.fhcrc.org/src/contrib/ggplot2_1.0.1.tar.gz'
Error in download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'http://cran.fhcrc.org/src/contrib/ggplot2_1.0.1.tar.gz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open: HTTP status was '0 (null)'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘ggplot2’ failed
trying URL 'http://cran.fhcrc.org/src/contrib/reshape2_1.4.1.tar.gz'
Content type 'application/x-gzip' length 34693 bytes (33 KB)
==================================================
downloaded 33 KB

trying URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/Gviz_1.13.0.tar.gz'
Content type 'application/x-gzip' length 3379445 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

trying URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/cummeRbund_2.11.1.tar.gz'
Content type 'application/x-gzip' length 2309059 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

ERROR: dependency ‘ggplot2’ is not available for package ‘Hmisc’
* removing ‘/usr/local/lib64/R/library/Hmisc’
ERROR: dependency ‘stringi’ is not available for package ‘stringr’
* removing ‘/usr/local/lib64/R/library/stringr’
ERROR: dependency ‘Hmisc’ is not available for package ‘biovizBase’
* removing ‘/usr/local/lib64/R/library/biovizBase’
ERROR: dependency ‘stringr’ is not available for package ‘reshape2’
* removing ‘/usr/local/lib64/R/library/reshape2’
ERROR: dependency ‘biovizBase’ is not available for package ‘Gviz’
* removing ‘/usr/local/lib64/R/library/Gviz’
ERROR: dependencies ‘ggplot2’, ‘reshape2’, ‘Gviz’ are not available for package ‘cummeRbund’
* removing ‘/usr/local/lib64/R/library/cummeRbund’

The downloaded source packages are in
    ‘/tmp/Rtmp0lVxSj/downloaded_packages’
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Hmisc’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘stringr’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘biovizBase’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘reshape2’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Gviz’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘cummeRbund’ had non-zero exit status
7: In file.createf.tg) :
  cannot create file '/usr/local/lib64/R/doc/html/packages.html', reason 'Permission denied'
8: In make.packages.html(.Library) : cannot update HTML package index

When you see things like this:

trying URL 'http://cran.fhcrc.org/src/contrib/stringi_0.4-1.tar.gz'
Error in download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'http://cran.fhcrc.org/src/contrib/stringi_0.4-1.tar.gz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open: HTTP status was '0 (null)'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘stringi’ failed

It implies that you had some internet problems while installing, and were not able to download some of the packages you need. Usually you can just try again and it will work.