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This page was generated on 2023-04-12 11:06:03 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 clusterExperiment on lconway


To the developers/maintainers of the clusterExperiment package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/clusterExperiment.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 349/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clusterExperiment 2.18.2  (landing page)
Elizabeth Purdom
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/clusterExperiment
git_branch: RELEASE_3_16
git_last_commit: eae8335
git_last_commit_date: 2023-01-19 11:15:47 -0400 (Thu, 19 Jan 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: clusterExperiment
Version: 2.18.2
Command: rm -rf clusterExperiment.buildbin-libdir && mkdir clusterExperiment.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh clusterExperiment_2.18.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R clusterExperiment.buildbin-libdir
StartedAt: 2023-04-10 23:37:23 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 23:38:44 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 80.2 seconds
RetCode: 0
Status:   OK  
PackageFile: clusterExperiment_2.18.2.tgz
PackageFileSize: 11.09 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf clusterExperiment.buildbin-libdir && mkdir clusterExperiment.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh clusterExperiment_2.18.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R clusterExperiment.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=clusterExperiment.buildbin-libdir clusterExperiment_2.18.2.tar.gz'
>>>>>>> 

* installing *source* package ‘clusterExperiment’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c search_pairs.cpp -o search_pairs.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c subsampleLoop.cpp -o subsampleLoop.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o clusterExperiment.so RcppExports.o search_pairs.o subsampleLoop.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: dylib (/usr/local/gfortran/lib/libgfortran.dylib) was built for newer macOS version (10.14) than being linked (10.13)
ld: warning: dylib (/usr/local/gfortran/lib/libquadmath.dylib) was built for newer macOS version (10.14) than being linked (10.13)
installing to /Users/biocbuild/bbs-3.16-bioc/meat/clusterExperiment.buildbin-libdir/00LOCK-clusterExperiment/00new/clusterExperiment/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
** 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 (clusterExperiment)


>>>>>>> 
>>>>>>> FIXING LINKS FOR clusterExperiment.buildbin-libdir/clusterExperiment/libs/clusterExperiment.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "clusterExperiment.buildbin-libdir/clusterExperiment/libs/clusterExperiment.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "clusterExperiment.buildbin-libdir/clusterExperiment/libs/clusterExperiment.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "clusterExperiment.buildbin-libdir/clusterExperiment/libs/clusterExperiment.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "clusterExperiment.buildbin-libdir/clusterExperiment/libs/clusterExperiment.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "clusterExperiment.buildbin-libdir/clusterExperiment/libs/clusterExperiment.so"