Multiple platform build/check report for BioC 3.22 - INSTALL results for DESeq2 on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4814
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4603
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4547
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4553
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

INSTALL results for DESeq2 on nebbiolo2

To the developers/maintainers of the DESeq2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DESeq2.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: DESeq2

Version: 1.49.4

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL DESeq2

StartedAt: 2025-09-21 15:22:05 -0400 (Sun, 21 Sep 2025)

EndedAt: 2025-09-21 15:22:53 -0400 (Sun, 21 Sep 2025)

EllapsedTime: 47.5 seconds

RetCode: 0

Status: OK

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL DESeq2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘DESeq2’ ...
** this is package ‘DESeq2’ version ‘1.49.4’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c DESeq2.cpp -o DESeq2.o
DESeq2.cpp: In function ‘Rcpp::List fitDispGrid(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
DESeq2.cpp:501:19: warning: ‘eT arma::Mat<eT>::max(arma::uword&) const [with eT = double; arma::uword = unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations]
  501 |     logpostvec.max(idxmax);
      |     ~~~~~~~~~~~~~~^~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/current/armadillo:201,
                 from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:32,
                 from DESeq2.cpp:16:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/current/armadillo_bits/Mat_bones.hpp:545:56: note: declared here
  545 |   [[deprecated("use .index_max() instead")]] inline eT max(uword& index_of_max_val) const;
      |                                                        ^~~
DESeq2.cpp:508:19: warning: ‘eT arma::Mat<eT>::max(arma::uword&) const [with eT = double; arma::uword = unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations]
  508 |     logpostvec.max(idxmax);
      |     ~~~~~~~~~~~~~~^~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/current/armadillo:692:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:7850:1: note: declared here
 7850 | Mat<eT>::max(uword& index_of_max_val) const
      | ^~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -llapack -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-DESeq2/00new/DESeq2/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DESeq2)