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This page was generated on 2023-04-12 11:06:07 -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 flowWorkspace on lconway


To the developers/maintainers of the flowWorkspace package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowWorkspace.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 712/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowWorkspace 4.10.1  (landing page)
Greg Finak , Mike Jiang
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/flowWorkspace
git_branch: RELEASE_3_16
git_last_commit: af121c6
git_last_commit_date: 2022-12-28 21:02:10 -0400 (Wed, 28 Dec 2022)
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: flowWorkspace
Version: 4.10.1
Command: rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowWorkspace_4.10.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R flowWorkspace.buildbin-libdir
StartedAt: 2023-04-10 23:44:06 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 23:46:51 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 165.3 seconds
RetCode: 0
Status:   OK  
PackageFile: flowWorkspace_4.10.1.tgz
PackageFileSize: 4.847 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowWorkspace_4.10.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R flowWorkspace.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flowWorkspace.buildbin-libdir flowWorkspace_4.10.1.tar.gz'
>>>>>>> 

* installing *source* package ‘flowWorkspace’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_API.cpp -o R_API.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_GatingSet.cpp -o R_GatingSet.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cpp11.cpp -o cpp11.o
In file included from cpp11.cpp:4:
In file included from ./flowWorkspace_types.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include/cpp11/declarations.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include/cpp11.hpp:10:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include/cpp11/external_pointer.hpp:17:3: warning: delete called on non-final 'cytolib::CytoFrameView' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
  delete obj;
  ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include/cpp11/external_pointer.hpp:20:42: note: in instantiation of function template specialization 'cpp11::default_deleter<cytolib::CytoFrameView>' requested here
template <typename T, void Deleter(T*) = default_deleter<T>>
                                         ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cytoframeAPI.cpp -o cytoframeAPI.o
In file included from cytoframeAPI.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include/cpp11.hpp:10:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include/cpp11/external_pointer.hpp:17:3: warning: delete called on non-final 'cytolib::CytoFrameView' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
  delete obj;
  ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include/cpp11/external_pointer.hpp:20:42: note: in instantiation of function template specialization 'cpp11::default_deleter<cytolib::CytoFrameView>' requested here
template <typename T, void Deleter(T*) = default_deleter<T>>
                                         ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cytosetAPI.cpp -o cytosetAPI.o
In file included from cytosetAPI.cpp:2:
In file included from ../inst/include/flowWorkspace/pairVectorCpp11Convert.h:10:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include/cpp11.hpp:10:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include/cpp11/external_pointer.hpp:17:3: warning: delete called on non-final 'cytolib::CytoFrameView' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
  delete obj;
  ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include/cpp11/external_pointer.hpp:20:42: note: in instantiation of function template specialization 'cpp11::default_deleter<cytolib::CytoFrameView>' requested here
template <typename T, void Deleter(T*) = default_deleter<T>>
                                         ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c getDescendants.cpp -o getDescendants.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c getPopStats.cpp -o getPopStats.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c getSingleCellExpression.cpp -o getSingleCellExpression.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c h5_error_r_handler.cpp -o h5_error_r_handler.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c setCounts.cpp -o setCounts.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 flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o cpp11.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o /Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/lib -lsz -laec -lz -ldl -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.16-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/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 (flowWorkspace)


>>>>>>> 
>>>>>>> FIXING LINKS FOR flowWorkspace.buildbin-libdir/flowWorkspace/libs/flowWorkspace.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" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/flowWorkspace.so"