RNA-seq: problems with edgeR installation
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alam • 0
@0d44d54a
Last seen 12 weeks 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 • 494 views
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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().

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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

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