Greg Finak
| Snapshot Date: 2023-03-28 14:00:22 -0400 (Tue, 28 Mar 2023) |
| git_url: https://git.bioconductor.org/packages/flowWorkspace |
| git_branch: devel |
| git_last_commit: 3f5adab |
| git_last_commit_date: 2022-12-28 20:58:18 -0400 (Wed, 28 Dec 2022) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-29 11:06:13 -0400 (Wed, 29 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" | 4547 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" | 4308 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" | 4301 |
| 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 | ||||
|
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. |
| Package 720/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flowWorkspace 4.11.1 (landing page) Greg Finak
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: flowWorkspace |
| Version: 4.11.1 |
| Command: rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowWorkspace_4.11.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R flowWorkspace.buildbin-libdir |
| StartedAt: 2023-03-29 07:14:50 -0400 (Wed, 29 Mar 2023) |
| EndedAt: 2023-03-29 07:21:53 -0400 (Wed, 29 Mar 2023) |
| EllapsedTime: 423.0 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: flowWorkspace_4.11.1.tgz |
| PackageFileSize: 4.847 MiB |
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### Running command:
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### rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowWorkspace_4.11.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R flowWorkspace.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flowWorkspace.buildbin-libdir flowWorkspace_4.11.1.tar.gz'
>>>>>>>
* installing *source* package ‘flowWorkspace’ ...
** 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 -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -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/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/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/4.3/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/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/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/4.3/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/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/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/4.3/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/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/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/4.3/Resources/library/cpp11/include/cpp11/declarations.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/cpp11/include/cpp11.hpp:10:
/Library/Frameworks/R.framework/Versions/4.3/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/4.3/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/4.3/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/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/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/4.3/Resources/library/cpp11/include/cpp11.hpp:10:
/Library/Frameworks/R.framework/Versions/4.3/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/4.3/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/4.3/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/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/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/4.3/Resources/library/cpp11/include/cpp11.hpp:10:
/Library/Frameworks/R.framework/Versions/4.3/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/4.3/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/4.3/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/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/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/4.3/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/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/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/4.3/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/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/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/4.3/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/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/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/4.3/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/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/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/4.3/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.3/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-3.17-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/4.3/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/4.3/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/4.3/Resources/lib/libquadmath.0.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/flowWorkspace.so"