Mike Jiang
| Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/CytoML |
| git_branch: RELEASE_3_18 |
| git_last_commit: 4710056 |
| git_last_commit_date: 2023-10-24 10:51:13 -0400 (Tue, 24 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:08 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 | ||||
| Package 491/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CytoML 2.14.0 (landing page) Mike Jiang
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the CytoML package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: CytoML |
| Version: 2.14.0 |
| Command: rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CytoML_2.14.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CytoML.buildbin-libdir |
| StartedAt: 2024-04-18 08:54:29 -0400 (Thu, 18 Apr 2024) |
| EndedAt: 2024-04-18 08:56:00 -0400 (Thu, 18 Apr 2024) |
| EllapsedTime: 90.7 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: CytoML_2.14.0.tgz |
| PackageFileSize: 9.173 MiB |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CytoML_2.14.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CytoML.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CytoML.buildbin-libdir CytoML_2.14.0.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++ -arch arm64 -std=gnu++11 accepts -g... yes
checking for gcc... clang -arch arm64
checking whether we are using the GNU C compiler... yes
checking whether clang -arch arm64 accepts -g... yes
checking for clang -arch arm64 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/MacOSX11.sdk/usr/include -ftemplate-depth=900
configure: PKG_LIBS=-L/Library/Developer/CommandLineTools/SDKs/MacOSX11.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 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/flowWorkspace/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cpp11.cpp -o cpp11.o
In file included from cpp11.cpp:4:
In file included from ./CytoML_types.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/flowWorkspace/include/flowWorkspace.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct]
for (const pb::Range range : gate_pb.mrg().ranges()) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying
for (const pb::Range range : gate_pb.mrg().ranges()) {
^~~~~~~~~~~~~~~~~~~~~~~
&
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-arm64/Resources/library/BH/include/boost/filesystem/directory.hpp:922:5: 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-arm64/Resources/library/BH/include/boost/filesystem/config.hpp:73:49: note: expanded from macro 'BOOST_FILESYSTEM_DETAIL_DEPRECATED'
#define BOOST_FILESYSTEM_DETAIL_DEPRECATED(msg) BOOST_DEPRECATED(msg)
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/config/compiler/clang.hpp:342:46: note: expanded from macro 'BOOST_DEPRECATED'
#define BOOST_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-arm64/Resources/library/BH/include/boost/filesystem/directory.hpp:922:5: 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-arm64/Resources/library/BH/include/boost/filesystem/config.hpp:73:49: note: expanded from macro 'BOOST_FILESYSTEM_DETAIL_DEPRECATED'
#define BOOST_FILESYSTEM_DETAIL_DEPRECATED(msg) BOOST_DEPRECATED(msg)
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/config/compiler/clang.hpp:342:46: note: expanded from macro 'BOOST_DEPRECATED'
#define BOOST_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
^
4 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/flowWorkspace/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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:
In file included from ../inst/include/CytoML/workspace_type.hpp:4:
In file included from ../inst/include/CytoML/wsNode.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct]
for (const pb::Range range : gate_pb.mrg().ranges()) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying
for (const pb::Range range : gate_pb.mrg().ranges()) {
^~~~~~~~~~~~~~~~~~~~~~~
&
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-arm64/Resources/library/BH/include/boost/filesystem/directory.hpp:922:5: 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-arm64/Resources/library/BH/include/boost/filesystem/config.hpp:73:49: note: expanded from macro 'BOOST_FILESYSTEM_DETAIL_DEPRECATED'
#define BOOST_FILESYSTEM_DETAIL_DEPRECATED(msg) BOOST_DEPRECATED(msg)
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/config/compiler/clang.hpp:342:46: note: expanded from macro 'BOOST_DEPRECATED'
#define BOOST_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-arm64/Resources/library/BH/include/boost/filesystem/directory.hpp:922:5: 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-arm64/Resources/library/BH/include/boost/filesystem/config.hpp:73:49: note: expanded from macro 'BOOST_FILESYSTEM_DETAIL_DEPRECATED'
#define BOOST_FILESYSTEM_DETAIL_DEPRECATED(msg) BOOST_DEPRECATED(msg)
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/config/compiler/clang.hpp:342:46: note: expanded from macro 'BOOST_DEPRECATED'
#define BOOST_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
^
4 warnings generated.
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o CytoML.so cpp11.o parseFlowJoWorkspace.o /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -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/MacOSX11.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: ignoring duplicate libraries: '-lm', '-lz'
installing to /Users/biocbuild/bbs-3.18-bioc-mac-arm64/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 PATHS TO DYNAMIC LIBRARIES FOR CytoML.buildbin-libdir/CytoML/libs/CytoML.so
>>>>>>>
>>>>>>> Paths before fix:
CytoML.buildbin-libdir/CytoML/libs/CytoML.so:
CytoML.so (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.3)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libxml2.2.dylib (compatibility version 10.0.0, current version 10.9.0)
/usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 66.1.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.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-arm64/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-arm64/Resources/lib/libquadmath.0.dylib" "CytoML.buildbin-libdir/CytoML/libs/CytoML.so"
>>>>>>> Paths after fix:
CytoML.buildbin-libdir/CytoML/libs/CytoML.so:
CytoML.so (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.3)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libxml2.2.dylib (compatibility version 10.0.0, current version 10.9.0)
/usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 66.1.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)