CummeRbund installation error

Question

[saj98]

Hello everyone

I am trying to call cummeRbund library but I got the following error Error in library(cummeRbund) : there is no package called ‘cummeRbund’ I am pasting some of the installation messages that I got. Does anybody have an idea to help me resolve the issue?

Thanks for help

> library(cummeRbund)
Error in library(cummeRbund) : there is no package called ‘cummeRbund’
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
installation path not writeable, unable to update packages: foreign
Old packages: 'AnnotationDbi', 'backports', 'Biobase', 'biomaRt', 'Biostrings', 'DelayedArray',
  'GenomeInfoDb', 'GenomicAlignments', 'GenomicFeatures', 'GenomicRanges', 'hunspell', 'IRanges', 'irlba',
  'jsonlite', 'knitr', 'R6', 'Rcpp', 'readr', 'rmarkdown', 'rtracklayer', 'S4Vectors', 'SummarizedExperiment',
  'tibble', 'VariantAnnotation', 'XML'
Update all/some/none? [a/s/n]: 
a
also installing the dependency ‘rlang’

trying URL 'https://cran.rstudio.com/src/contrib/rlang_0.1.1.tar.gz'
Content type 'application/x-gzip' length 201419 bytes (196 KB)
==================================================
downloaded 196 KB

Then at the end of the installation, I got

The downloaded source packages are in
    ‘/tmp/RtmpEKXzAr/downloaded_packages’
> biocLite("cummeRbund")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘cummeRbund’
also installing the dependencies ‘openssl’, ‘httr’, ‘AnnotationHub’, ‘ensembldb’, ‘biovizBase’, ‘Gviz’

trying URL 'https://cran.rstudio.com/src/contrib/openssl_0.9.6.tar.gz'
Content type 'application/x-gzip' length 1239339 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/src/contrib/httr_1.2.1.tar.gz'
Content type 'application/x-gzip' length 133398 bytes (130 KB)
==================================================
downloaded 130 KB

Then

1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘openssl’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘httr’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘AnnotationHub’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘ensembldb’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘biovizBase’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Gviz’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘cummeRbund’ had non-zero exit status
> library(cummeRbund)
Error in library(cummeRbund) : there is no package called ‘cummeRbund’
> library(cummeRbund)
Error in library(cummeRbund) : there is no package called ‘cummeRbund’

[WouterDeCoster]

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

[saj98]

Thank you so much I did install sudo apt-get install libssl-dev on linux terminal and I reinstall cummeRbund. Now it is running perfectly and smoothly.

[WouterDeCoster]

Happy to help. I have moved my comment to an answer, so you can accept it to mark this question as solved.

Answer 1

[WouterDeCoster]

Looks like the cullprit here is the openssl package, you can confirm this by installing just that one. The failure of installation of this one caused all the rest to fail, too.

You probably need something like sudo apt-get install libssl-dev, depending on your operating system (which you didn't mention...)

[saj98]

Hello Thanks for answering, I installed libssl, shall I reinstall cummeRbund?