Entering edit mode
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
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().
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