Multiple platform build/check report for BioC 3.23 - BUILD results for PCAtools on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences"	4848
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4627
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*

BUILD results for PCAtools on nebbiolo1

To the developers/maintainers of the PCAtools package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PCAtools.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: PCAtools

Version: 2.23.1

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data PCAtools

StartedAt: 2026-01-13 19:21:21 -0500 (Tue, 13 Jan 2026)

EndedAt: 2026-01-13 19:21:25 -0500 (Tue, 13 Jan 2026)

EllapsedTime: 4.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data PCAtools
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* checking for file ‘PCAtools/DESCRIPTION’ ... OK
* preparing ‘PCAtools’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
      -----------------------------------
Warning: SystemRequirements specified C++11: support will be removed soon
* installing *source* package ‘PCAtools’ ...
** this is package ‘PCAtools’ version ‘2.23.1’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/dqrng/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/dqrng/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c shuffle_matrix.cpp -o shuffle_matrix.o
In file included from shuffle_matrix.cpp:1:
/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/Rtatami.h:6:10: fatal error: tatami_r/parallelize.hpp: No such file or directory
    6 | #include "tatami_r/parallelize.hpp"
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [/home/biocbuild/bbs-3.23-bioc/R/etc/Makeconf:209: shuffle_matrix.o] Error 1
ERROR: compilation failed for package ‘PCAtools’
* removing ‘/tmp/RtmpDwWOjC/Rinst1907e15284eb1c/PCAtools’
      -----------------------------------
ERROR: package installation failed