Entering edit mode
7.5 years ago
saj98
▴
140
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’
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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.
Happy to help. I have moved my comment to an answer, so you can accept it to mark this question as solved.