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This page was generated on 2024-11-09 21:31 -0500 (Sat, 09 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4505
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4486
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1979/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SingleR 2.8.0  (landing page)
Aaron Lun
Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024)
git_url: https://git.bioconductor.org/packages/SingleR
git_branch: RELEASE_3_20
git_last_commit: 0035541
git_last_commit_date: 2024-10-29 10:39:43 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


BUILD BIN results for SingleR on kjohnson3

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.

raw results


Summary

Package: SingleR
Version: 2.8.0
Command: rm -rf SingleR.buildbin-libdir && mkdir SingleR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SingleR_2.8.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SingleR.buildbin-libdir
StartedAt: 2024-11-09 17:12:46 -0500 (Sat, 09 Nov 2024)
EndedAt: 2024-11-09 17:13:07 -0500 (Sat, 09 Nov 2024)
EllapsedTime: 20.3 seconds
RetCode: 0
Status:   OK  
PackageFile: SingleR_2.8.0.tgz
PackageFileSize: 966.2 KiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf SingleR.buildbin-libdir && mkdir SingleR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SingleR_2.8.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SingleR.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SingleR.buildbin-libdir SingleR_2.8.0.tar.gz'
>>>>>>> 

* installing *source* package ‘SingleR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c classify_integrated.cpp -o classify_integrated.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c classify_single.cpp -o classify_single.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c find_classic_markers.cpp -o find_classic_markers.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c grouped_medians.cpp -o grouped_medians.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c train_integrated.cpp -o train_integrated.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o SingleR.so RcppExports.o classify_integrated.o classify_single.o find_classic_markers.o grouped_medians.o train_integrated.o train_single.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/SingleR.buildbin-libdir/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)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR SingleR.buildbin-libdir/SingleR/libs/SingleR.so
>>>>>>> 

>>>>>>> Paths before fix:
SingleR.buildbin-libdir/SingleR/libs/SingleR.so:
	SingleR.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "SingleR.buildbin-libdir/SingleR/libs/SingleR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "SingleR.buildbin-libdir/SingleR/libs/SingleR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "SingleR.buildbin-libdir/SingleR/libs/SingleR.so"

>>>>>>> Paths after fix:
SingleR.buildbin-libdir/SingleR/libs/SingleR.so:
	SingleR.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)