Aaron Lun
| Snapshot Date: 2025-11-02 13:45 -0500 (Sun, 02 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/SingleR |
| git_branch: RELEASE_3_22 |
| git_last_commit: 39ca8d4 |
| git_last_commit_date: 2025-10-29 10:54:00 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-03 12:04 -0500 (Mon, 03 Nov 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" | 4902 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4692 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| 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 2035/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SingleR 2.12.0 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the SingleR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SingleR.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. |
| Package: SingleR |
| Version: 2.12.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SingleR |
| StartedAt: 2025-11-02 15:28:27 -0500 (Sun, 02 Nov 2025) |
| EndedAt: 2025-11-02 15:29:41 -0500 (Sun, 02 Nov 2025) |
| EllapsedTime: 73.6 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SingleR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SingleR’ ...
** this is package ‘SingleR’ version ‘2.12.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++17
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c classify_integrated.cpp -o classify_integrated.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c classify_single.cpp -o classify_single.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_classic_markers.cpp -o find_classic_markers.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c grouped_medians.cpp -o grouped_medians.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c set_executor.cpp -o set_executor.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c train_integrated.cpp -o train_integrated.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c train_single.cpp -o train_single.o
train_single.cpp:19:9: warning: unused variable 'NR' [-Wunused-variable]
int NR = parsed->ptr->nrow();
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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)