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This page was generated on 2023-06-09 11:06:51 -0400 (Fri, 09 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.0 RC (2023-04-13 r84269) -- "Already Tomorrow" 4628
palomino3Windows Server 2022 Datacenterx644.3.0 RC (2023-04-13 r84269 ucrt) -- "Already Tomorrow" 4379
merida1macOS 12.6.4 Montereyx86_644.3.0 RC (2023-04-13 r84257) -- "Already Tomorrow" 4385
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

BUILD BIN results for flagme on merida1


To the developers/maintainers of the flagme package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flagme.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

Package 703/2229HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flagme 1.56.0  (landing page)
Mark Robinson , Riccardo Romoli
Snapshot Date: 2023-06-08 14:00:15 -0400 (Thu, 08 Jun 2023)
git_url: https://git.bioconductor.org/packages/flagme
git_branch: RELEASE_3_17
git_last_commit: b6ecc43
git_last_commit_date: 2023-04-25 09:48:03 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: flagme
Version: 1.56.0
Command: rm -rf flagme.buildbin-libdir && mkdir flagme.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flagme_1.56.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R flagme.buildbin-libdir
StartedAt: 2023-06-09 09:30:10 -0400 (Fri, 09 Jun 2023)
EndedAt: 2023-06-09 09:32:28 -0400 (Fri, 09 Jun 2023)
EllapsedTime: 137.8 seconds
RetCode: 0
Status:   OK  
PackageFile: flagme_1.56.0.tgz
PackageFileSize: 1.174 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf flagme.buildbin-libdir && mkdir flagme.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flagme_1.56.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R flagme.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flagme.buildbin-libdir flagme_1.56.0.tar.gz'
>>>>>>> 

* installing *source* package ‘flagme’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c dp.c -o dp.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pearson.c -o pearson.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o flagme.so dp.o init.o pearson.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc/meat/flagme.buildbin-libdir/00LOCK-flagme/00new/flagme/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 (flagme)


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

>>>>>>> Paths before fix:
flagme.buildbin-libdir/flagme/libs/flagme.so:
	flagme.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.0)
	/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/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "flagme.buildbin-libdir/flagme/libs/flagme.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "flagme.buildbin-libdir/flagme/libs/flagme.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "flagme.buildbin-libdir/flagme/libs/flagme.so"

>>>>>>> Paths after fix:
flagme.buildbin-libdir/flagme/libs/flagme.so:
	flagme.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.0)
	/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)