RNA-seq: problems with edgeR installation
0
0
Entering edit mode
alam • 0
@0d44d54a
Last seen 2.6 years ago
Mexico

Thank you for attention I'm running a RNA-seq analysis so tried to install differents pkgs. Unfortunately I'm not able to install "edgeR", I've looking for any possible solution but i hasn't success, I would be really thankful for any kind of help. Thank you!!

these are one of the errors I found:

 if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> BiocManager::install("edgeR")
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10)
Installing package(s) 'edgeR'
also installing the dependencies ‘limma’, ‘locfit’

probando la URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/limma_3.50.1.tar.gz'
Content type 'application/x-gzip' length 1559241 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

probando la URL 'https://cloud.r-project.org/src/contrib/locfit_1.5-9.5.tar.gz'
Content type 'application/x-gzip' length 201031 bytes (196 KB)
==================================================
downloaded 196 KB

probando la URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/edgeR_3.36.0.tar.gz'
Content type 'application/x-gzip' length 1738194 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

* installing *source* package ‘limma’ ...
** using staged installation
** libs
sh: 1: make: not found
Warning in system(cmd) : error in running command
**ERROR**: compilation failed for package ‘limma’
* removing ‘/home/bio/R/x86_64-pc-linux-gnu-library/4.1/limma’
* installing *source* package ‘locfit’ ...
** package ‘locfit’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: 1: make: not found
Warning in system(cmd) : error in running command
**ERROR**: compilation failed for package ‘locfit’
* removing ‘/home/bio/R/x86_64-pc-linux-gnu-library/4.1/locfit’
**ERROR**: dependencies ‘limma’, ‘locfit’ are not available for package ‘edgeR’
* removing ‘/home/bio/R/x86_64-pc-linux-gnu-library/4.1/edgeR’

The downloaded source packages are in
    ‘/tmp/Rtmp7XgBUS/downloaded_packages’
Installation paths not **writeable**, unable to update packages
  path: /usr/lib/R/library
  packages:
    spatial, survival
  path: /usr/lib/R/site-library
  packages:
    qvalue, RColorBrewer
Warning messages:
1: In .inet_warning(msg) :
  installation of package ‘limma’ had non-zero exit status
2: In .inet_warning(msg) :
  installation of package ‘locfit’ had non-zero exit status
3: In .inet_warning(msg) :
  installation of package ‘edgeR’ had non-zero exit status

gretings!

my session info is

> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=es_MX.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=es_MX.UTF-8        LC_COLLATE=es_MX.UTF-8    
 [5] LC_MONETARY=es_MX.UTF-8    LC_MESSAGES=es_MX.UTF-8   
 [7] LC_PAPER=es_MX.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=es_MX.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.1.3
BiocManager edgeR • 2.5k views
ADD COMMENT
0
Entering edit mode

Installation works fine for other people using all versions of R and Bioconductor, so the problem is specific to your R setup. It looks like you can't install any packages. Does installation fail for all packages or only for packages than contain C or Fortran source code?

The posting guide asks you to specify your setup, for example by showing the output of sessionInfo().

ADD REPLY
0
Entering edit mode

You seem to be on a pretty "blank" Linux installation lacking the build-essentials such as make. Try https://askubuntu.com/questions/192645/make-command-not-found

ADD REPLY

Login before adding your answer.

Traffic: 635 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6