Help!
I'm trying to install DEseq2 to perform differential gene expression analysis R Studio. I'm using the free R Studio on Posit Cloud. R Sudio version is 4.3.2, BiocManager is 3.1.8.
This is my issue with the error:
library(BiocManager)
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
BiocManager::install("DESeq2")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package
= "BiocManager")' for details.
Replacement repositories:
CRAN: http://rspm/default/__linux__/focal/latest
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
Installing package(s) 'DESeq2'
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/DESeq2_1.42.0.tar.gz'
Content type 'application/x-gzip' length 2097442 bytes (2.0 MB)
==================================================
downloaded 2.0 MB
- installing source package ‘DESeq2’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’
g++ -std=gnu++17 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.3/Rcpp/include' -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.3/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c DESeq2.cpp -o DESeq2.o
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make: *** [/opt/R/4.3.2/lib/R/etc/Makeconf:200: DESeq2.o] Error 1
ERROR: compilation failed for package ‘DESeq2’ - removing ‘/cloud/lib/x86_64-pc-linux-gnu-library/4.3/DESeq2’
The downloaded source packages are in
‘/tmp/RtmpeSsu8g/downloaded_packages’
Installation paths not writeable, unable to update packages
path: /opt/R/4.3.2/lib/R/library
packages:
lattice, Matrix
Warning message:
In install.packages(...) :
installation of package ‘DESeq2’ had non-zero exit status