Rapid builds (Linux only) of a subset of BioC 3.22<BR>Report updated every 6 hours

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	886
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 SingleR on teran2

To the developers/maintainers of the SingleR package:
- 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: SingleR

Version: 2.11.2

Command: /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD INSTALL SingleR

StartedAt: 2025-06-17 18:19:32 -0400 (Tue, 17 Jun 2025)

EndedAt: 2025-06-17 18:20:30 -0400 (Tue, 17 Jun 2025)

EllapsedTime: 57.1 seconds

RetCode: 0

Status: OK

Command output

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### Running command:
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###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD INSTALL SingleR
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library’
* installing *source* package ‘SingleR’ ...
** this is package ‘SingleR’ version ‘2.11.2’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c classify_integrated.cpp -o classify_integrated.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c classify_single.cpp -o classify_single.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c find_classic_markers.cpp -o find_classic_markers.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c grouped_medians.cpp -o grouped_medians.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c set_executor.cpp -o set_executor.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c train_integrated.cpp -o train_integrated.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c train_single.cpp -o train_single.o
train_single.cpp: In function ‘SEXPREC* train_single(Rcpp::IntegerVector, Rcpp::RObject, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::List, Rcpp::RObject, int)’:
train_single.cpp:19:9: warning: unused variable ‘NR’ [-Wunused-variable]
   19 |     int NR = parsed->ptr->nrow();
      |         ^~
g++ -std=gnu++17 -shared -L/usr/local/lib -o SingleR.so RcppExports.o classify_integrated.o classify_single.o find_classic_markers.o grouped_medians.o set_executor.o train_integrated.o train_single.o
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/00LOCK-SingleR/00new/SingleR/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 (SingleR)