Mike Jiang
| Snapshot Date: 2023-03-28 14:00:22 -0400 (Tue, 28 Mar 2023) |
| git_url: https://git.bioconductor.org/packages/CytoML |
| git_branch: devel |
| git_last_commit: c252d18 |
| git_last_commit_date: 2022-11-01 11:14:00 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-29 11:06:09 -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 CytoML package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CytoML.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 478/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CytoML 2.11.0 (landing page) Mike Jiang
| 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: CytoML |
| Version: 2.11.0 |
| Command: rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CytoML_2.11.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CytoML.buildbin-libdir |
| StartedAt: 2023-03-29 07:06:08 -0400 (Wed, 29 Mar 2023) |
| EndedAt: 2023-03-29 07:09:28 -0400 (Wed, 29 Mar 2023) |
| EllapsedTime: 199.7 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: CytoML_2.11.0.tgz |
| PackageFileSize: 8.85 MiB |
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### Running command:
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### rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CytoML_2.11.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CytoML.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CytoML.buildbin-libdir CytoML_2.11.0.tar.gz'
>>>>>>>
* installing *source* package ‘CytoML’ ...
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++11 accepts -g... yes
checking for gcc... clang -mmacosx-version-min=10.13
checking whether we are using the GNU C compiler... yes
checking whether clang -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
configure: setting xml2 flags...
configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.
checking for xml2-config... /usr/bin/xml2-config
configure: setting cytolib-ml commandline tool path...
configure: Using the following compilation and linking flags
configure: PKG_CPPFLAGS=-I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/libxml2 -ftemplate-depth=900
configure: PKG_LIBS=-L/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm
configure: CYTOLIBML_BIN=/usr/local/bin
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/cytolibml_bin_path.R
** 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/ -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/libxml2 -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR -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'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/flowWorkspace/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 ./CytoML_types.h:5:
In file included from ../inst/include/CytoML/openWorkspace.hpp:11:
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10:
In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11:
In file included from ../inst/include/CytoML/workspace.hpp:10:
../inst/include/CytoML/workspace_type.hpp:67:44: warning: 'recursive_directory_iterator' is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations]
for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse))
^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include/boost/filesystem/directory.hpp:576:5: note: 'recursive_directory_iterator' has been explicitly marked deprecated here
BOOST_FILESYSTEM_DETAIL_DEPRECATED("Use directory_options instead of symlink_option")
^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include/boost/filesystem/config.hpp:85:64: note: expanded from macro 'BOOST_FILESYSTEM_DETAIL_DEPRECATED'
#define BOOST_FILESYSTEM_DETAIL_DEPRECATED(msg) __attribute__((deprecated(msg)))
^
In file included from cpp11.cpp:4:
In file included from ./CytoML_types.h:5:
In file included from ../inst/include/CytoML/openWorkspace.hpp:11:
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10:
In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11:
In file included from ../inst/include/CytoML/workspace.hpp:10:
../inst/include/CytoML/workspace_type.hpp:67:44: warning: 'recursive_directory_iterator' is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations]
for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse))
^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include/boost/filesystem/directory.hpp:576:5: note: 'recursive_directory_iterator' has been explicitly marked deprecated here
BOOST_FILESYSTEM_DETAIL_DEPRECATED("Use directory_options instead of symlink_option")
^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include/boost/filesystem/config.hpp:85:64: note: expanded from macro 'BOOST_FILESYSTEM_DETAIL_DEPRECATED'
#define BOOST_FILESYSTEM_DETAIL_DEPRECATED(msg) __attribute__((deprecated(msg)))
^
In file included from cpp11.cpp:4:
In file included from ./CytoML_types.h:5:
In file included from ../inst/include/CytoML/openWorkspace.hpp:12:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: '/*' within block comment [-Wcomment]
* "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/libxml2 -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR -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'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/flowWorkspace/include' -I/usr/local/include -fPIC -Wall -g -O2 -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from parseFlowJoWorkspace.cpp:10:
In file included from ../inst/include/CytoML/openWorkspace.hpp:11:
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10:
In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11:
In file included from ../inst/include/CytoML/workspace.hpp:10:
../inst/include/CytoML/workspace_type.hpp:67:44: warning: 'recursive_directory_iterator' is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations]
for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse))
^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include/boost/filesystem/directory.hpp:576:5: note: 'recursive_directory_iterator' has been explicitly marked deprecated here
BOOST_FILESYSTEM_DETAIL_DEPRECATED("Use directory_options instead of symlink_option")
^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include/boost/filesystem/config.hpp:85:64: note: expanded from macro 'BOOST_FILESYSTEM_DETAIL_DEPRECATED'
#define BOOST_FILESYSTEM_DETAIL_DEPRECATED(msg) __attribute__((deprecated(msg)))
^
In file included from parseFlowJoWorkspace.cpp:10:
In file included from ../inst/include/CytoML/openWorkspace.hpp:11:
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10:
In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11:
In file included from ../inst/include/CytoML/workspace.hpp:10:
../inst/include/CytoML/workspace_type.hpp:67:44: warning: 'recursive_directory_iterator' is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations]
for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse))
^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include/boost/filesystem/directory.hpp:576:5: note: 'recursive_directory_iterator' has been explicitly marked deprecated here
BOOST_FILESYSTEM_DETAIL_DEPRECATED("Use directory_options instead of symlink_option")
^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include/boost/filesystem/config.hpp:85:64: note: expanded from macro 'BOOST_FILESYSTEM_DETAIL_DEPRECATED'
#define BOOST_FILESYSTEM_DETAIL_DEPRECATED(msg) __attribute__((deprecated(msg)))
^
In file included from parseFlowJoWorkspace.cpp:10:
In file included from ../inst/include/CytoML/openWorkspace.hpp:12:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: '/*' within block comment [-Wcomment]
* "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
^
3 warnings generated.
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 CytoML.so cpp11.o parseFlowJoWorkspace.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 -L/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/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 (CytoML)
>>>>>>>
>>>>>>> FIXING LINKS FOR CytoML.buildbin-libdir/CytoML/libs/CytoML.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" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgfortran.5.dylib" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libquadmath.0.dylib" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so"