installation of package ‘DESeq2’ had non-zero exit status

Question

[Sarita]

if (!requireNamespace("BiocManager", quietly = TRUE))
+   install.packages("BiocManager")
> BiocManager::install("DESeq2", force = TRUE, Ncpus = 1)
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.21 (BiocManager 1.30.26), R 4.5.1 (2025-06-13)
Installing package(s) 'DESeq2'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/DESeq2_1.48.2.tar.gz'
Content type 'application/x-gzip' length 2683636 bytes (2.6 MB)
==================================================
downloaded 2.6 MB

* installing *source* package ‘DESeq2’ ...
** this is package ‘DESeq2’ version ‘1.48.2’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04.2) 11.4.0’
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/RcppArmadillo/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-0RQCNp/r-base-4.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -c DESeq2.cpp -o DESeq2.o
In file included from /usr/lib/R/site-library/Rcpp/include/Rcpp/routines.h:26,
                 from /usr/lib/R/site-library/Rcpp/include/RcppCommon.h:127,
                 from /usr/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
                 from /usr/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from DESeq2.cpp:16:
/usr/lib/R/site-library/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function ‘std::streamsize Rcpp::Rstreambuf<OUTPUT>::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long int]’:
/usr/lib/R/site-library/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
   53 |         Rprintf("%.*s", num, s);
      |                  ~~^~   ~~~
      |                    |    |
      |                    int  std::streamsize {aka long int}
/usr/lib/R/site-library/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function ‘std::streamsize Rcpp::Rstreambuf<OUTPUT>::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long int]’:
/usr/lib/R/site-library/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
   57 |         REprintf("%.*s", num, s);
      |                   ~~^~   ~~~
      |                     |    |
      |                     int  std::streamsize {aka long int}
In file included from /usr/lib/R/site-library/Rcpp/include/RcppCommon.h:180,
                 from /usr/lib/R/site-library/RcppArmadillo/include/RcppArmadilloForward.h:25,
                 from /usr/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from DESeq2.cpp:16:
/usr/lib/R/site-library/Rcpp/include/Rcpp/print.h: In function ‘void Rcpp::warningcall(SEXP, const string&)’:
/usr/lib/R/site-library/Rcpp/include/Rcpp/print.h:30:19: error: format not a string literal and no format arguments [-Werror=format-security]
   30 |     Rf_warningcall(call, s.c_str());
      |     ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
cc1plus: some warnings being treated as errors
make: *** [/usr/lib/R/etc/Makeconf:211: DESeq2.o] Error 1
ERROR: compilation failed for package ‘DESeq2’
* removing ‘/home/user/R/x86_64-pc-linux-gnu-library/4.5/DESeq2’
The downloaded source packages are in
    ‘/tmp/RtmphORcmS/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    codetools, lattice, mgcv, spatial
  path: /usr/lib/R/site-library
  packages:
    abind, acepack, askpass, backports, bench, BH, bit, bit64, bitops, blob, brio, broom, cachem, callr, caret, caTools, cba, checkmate,
    chron, classInt, cli, cliapp, colorspace, commonmark, conquer, covr, cpp11, crayon, crosstalk, curl, CVST, data.table, DBI, DBItest,
    dbplyr, ddalpha, decor, deldir, DEoptimR, desc, diffobj, digest, dimRed, dplyr, DT, e1071, earth, evaluate, fansi, farver, fastICA,
    fastmap, fastmatch, filehash, FNN, Formula, fs, furrr, future, future.apply, gdata, generics, geometry, geosphere, ggplot2, gh, gitcreds,
    globals, glue, gower, gplots, gtable, gtools, hexbin, highr, Hmisc, hms, htmlTable, htmltools, htmlwidgets, httpuv, httr, igraph, interp,
    ipred, isoband, jpeg, jsonlite, kernlab, knitr, ks, labeling, later, latticeExtra, lava, lifecycle, linprog, listenv, lme4, lobstr,
    logcondens, lpSolve, lubridate, magic, magrittr, mapproj, maps, markdown, MatrixModels, matrixStats, mclust, mda, mets, mime, minqa,
    mlbench, MLmetrics, mockery, mockr, modeldata, multcomp, multicool, munsell, mvtnorm, nloptr, openssl, palmerpenguins, parallelly, pillar,
    pkgbuild, pkgKitten, pkgload, plot3D, plotmo, plotrix, pls, plyr, png, polyclip, pracma, prettyunits, pROC, processx, prodlim, profmem,
    progress, progressr, promises, proxy, ps, purrr, quantmod, quantreg, R6, ragg, RANN, RColorBrewer, Rcpp, RcppArmadillo, RcppEigen,
    RcppRoll, recipes, rgl, rlang, rmarkdown, robustbase, RPostgreSQL, rprojroot, rsample, RSpectra, RSQLite, rstudioapi, RUnit, s2, sandwich,
    sass, scales, setRNG, sfsmisc, shiny, slider, sodium, sourcetools, sp, SparseM, spatstat, spatstat.data, spatstat.geom, spatstat.linnet,
    spatstat.sparse, spatstat.utils, statmod, stringi, stringr, svglite, sys, systemfonts, TeachingDemos, tensor, testthat, textshaping,
    TH.data, tibble, tidyr, tidyselect, tikzDevice, timeDate, timereg, timeSeries, tinytex, tseries, TTR, units, utf8, vctrs, vdiffr, viridis,
    viridisLite, waldo, warp, webutils, withr, wk, xfun, XML, xml2, xts, yaml, zoo
Warning message:
In install.packages(...) :
  installation of package ‘DESeq2’ had non-zero exit status

[lieven.sterck]

Hi Sarita

welcome to the forum.

Quite an extensive post but I can't seem to find a real question?

Please don't simply dump tool output/warnings without any question tied to it. Do show what you did try already for instance ...

[GenoMax]

Installation paths not writeable, unable to update packages

Are you a normal user on a system administered by other admins?