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This page was generated on 2023-02-06 11:06:37 -0500 (Mon, 06 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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 flowCore on merida1


To the developers/maintainers of the flowCore package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowCore.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 682/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowCore 2.11.0  (landing page)
Mike Jiang
Snapshot Date: 2023-02-05 14:00:11 -0500 (Sun, 05 Feb 2023)
git_url: https://git.bioconductor.org/packages/flowCore
git_branch: master
git_last_commit: 351ad59
git_last_commit_date: 2022-11-01 10:42:20 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: flowCore
Version: 2.11.0
Command: rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowCore_2.11.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R flowCore.buildbin-libdir
StartedAt: 2023-02-06 08:42:19 -0500 (Mon, 06 Feb 2023)
EndedAt: 2023-02-06 08:44:47 -0500 (Mon, 06 Feb 2023)
EllapsedTime: 148.0 seconds
RetCode: 0
Status:   OK  
PackageFile: flowCore_2.11.0.tgz
PackageFileSize: 8.114 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowCore_2.11.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R flowCore.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flowCore.buildbin-libdir flowCore_2.11.0.tar.gz'
>>>>>>> 

* installing *source* package ‘flowCore’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
using C++11
using SDK: ‘’
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c FastLogicle.cpp -o FastLogicle.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c Hyperlog.cpp -o Hyperlog.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c Logicle.cpp -o Logicle.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c biexponential.cpp -o biexponential.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c convertRawBytes.cpp -o convertRawBytes.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c cpp11.cpp -o cpp11.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c fcsTextParse.cpp -o fcsTextParse.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c hyperlogTransform.cpp -o hyperlogTransform.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c inPolygon.cpp -o inPolygon.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c inPolytope.cpp -o inPolytope.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c logicleTransform.cpp -o logicleTransform.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c poly_centroid.cpp -o poly_centroid.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c sortBytes.cpp -o sortBytes.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c uint2double.cpp -o uint2double.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RProtoBufLib/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c zeroin.cpp -o zeroin.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 flowCore.so FastLogicle.o Hyperlog.o Logicle.o biexponential.o convertRawBytes.o cpp11.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o poly_centroid.o sortBytes.o uint2double.o zeroin.o /Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/lib/libcytolib.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.so; fi
installing to /Users/biocbuild/bbs-3.17-bioc/meat/flowCore.buildbin-libdir/00LOCK-flowCore/00new/flowCore/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 (flowCore)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgcc_s.1.dylib" "flowCore.buildbin-libdir/flowCore/libs/flowCore.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgfortran.5.dylib" "flowCore.buildbin-libdir/flowCore/libs/flowCore.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libquadmath.0.dylib" "flowCore.buildbin-libdir/flowCore/libs/flowCore.so"