Michael Love
| Snapshot Date: 2025-09-26 13:45 -0400 (Fri, 26 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/DESeq2 |
| git_branch: devel |
| git_last_commit: 5f5e305 |
| git_last_commit_date: 2025-08-18 13:30:36 -0400 (Mon, 18 Aug 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-27 12:07 -0400 (Sat, 27 Sep 2025).
| 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" | 4832 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4620 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4565 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
| 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 | ||||
| Package 566/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DESeq2 1.49.4 (landing page) Michael Love
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: DESeq2 |
| Version: 1.49.4 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL DESeq2 |
| StartedAt: 2025-09-25 20:32:43 -0000 (Thu, 25 Sep 2025) |
| EndedAt: 2025-09-25 20:33:52 -0000 (Thu, 25 Sep 2025) |
| EllapsedTime: 68.6 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL DESeq2
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘DESeq2’ ...
** this is package ‘DESeq2’ version ‘1.49.4’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/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/R/R-4.5.0/site-library/RcppArmadillo/include/current/armadillo:201,
from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:32,
from DESeq2.cpp:16:
/home/biocbuild/R/R-4.5.0/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/R/R-4.5.0/site-library/RcppArmadillo/include/current/armadillo:692:
/home/biocbuild/R/R-4.5.0/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
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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)