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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 1488/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PCAtools 2.17.0  (landing page)
Kevin Blighe
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/PCAtools
git_branch: devel
git_last_commit: f7b5819
git_last_commit_date: 2024-04-30 11:11:50 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


BUILD BIN results for PCAtools on kjohnson1

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: 2.17.0
Command: rm -rf PCAtools.buildbin-libdir && mkdir PCAtools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PCAtools_2.17.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R PCAtools.buildbin-libdir
StartedAt: 2024-06-11 14:26:54 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 14:27:41 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 46.6 seconds
RetCode: 0
Status:   OK  
PackageFile: PCAtools_2.17.0.tgz
PackageFileSize: 5.909 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf PCAtools.buildbin-libdir && mkdir PCAtools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PCAtools_2.17.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R PCAtools.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=PCAtools.buildbin-libdir PCAtools_2.17.0.tar.gz'
>>>>>>> 

* installing *source* package ‘PCAtools’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -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/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/dqrng/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -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/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/dqrng/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c shuffle_matrix.cpp -o shuffle_matrix.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o PCAtools.so RcppExports.o shuffle_matrix.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/PCAtools.buildbin-libdir/00LOCK-PCAtools/00new/PCAtools/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 (PCAtools)


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

>>>>>>> Paths before fix:
PCAtools.buildbin-libdir/PCAtools/libs/PCAtools.so:
	PCAtools.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 4.4.0)
	/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" "PCAtools.buildbin-libdir/PCAtools/libs/PCAtools.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "PCAtools.buildbin-libdir/PCAtools/libs/PCAtools.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "PCAtools.buildbin-libdir/PCAtools/libs/PCAtools.so"

>>>>>>> Paths after fix:
PCAtools.buildbin-libdir/PCAtools/libs/PCAtools.so:
	PCAtools.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 4.4.0)
	/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)