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This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 170/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biobase 2.64.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/Biobase
git_branch: RELEASE_3_19
git_last_commit: a3b75b7
git_last_commit_date: 2024-04-30 10:10:44 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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  UNNEEDED, same version is already published

BUILD BIN results for Biobase on kjohnson3

To the developers/maintainers of the Biobase package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Biobase.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: Biobase
Version: 2.64.0
Command: rm -rf Biobase.buildbin-libdir && mkdir Biobase.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Biobase_2.64.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Biobase.buildbin-libdir
StartedAt: 2024-06-11 10:17:54 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 10:18:22 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 27.8 seconds
RetCode: 0
Status:   OK  
PackageFile: Biobase_2.64.0.tgz
PackageFileSize: 2.503 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Biobase.buildbin-libdir && mkdir Biobase.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Biobase_2.64.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Biobase.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Biobase.buildbin-libdir Biobase_2.64.0.tar.gz'
>>>>>>> 

* installing *source* package ‘Biobase’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Rinit.c -o Rinit.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c anyMissing.c -o anyMissing.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c envir.c -o envir.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c matchpt.c -o matchpt.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rowMedians.c -o rowMedians.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sublist_extract.c -o sublist_extract.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-bioc/meat/Biobase.buildbin-libdir/00LOCK-Biobase/00new/Biobase/libs
** R
** data
** 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 (Biobase)


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

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

>>>>>>> Paths after fix:
Biobase.buildbin-libdir/Biobase/libs/Biobase.so:
	Biobase.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/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)