Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:43 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 490/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CytoML 2.17.0 (landing page) Mike Jiang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the CytoML package: - 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 Troubleshooting Build Report for more information. - 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: 2.17.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CytoML |
StartedAt: 2024-08-26 15:21:47 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 15:23:02 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 75.8 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CytoML ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * 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 x86_64 -std=gnu++11 accepts -g... yes checking for gcc... clang -arch x86_64 checking whether we are using the GNU C compiler... yes checking whether clang -arch x86_64 accepts -g... yes checking for clang -arch x86_64 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 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -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/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/flowWorkspace/include' -I/opt/R/x86_64/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/4.4-x86_64/Resources/library/flowWorkspace/include/flowWorkspace.h:5: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: /Library/Frameworks/R.framework/Versions/4.4-x86_64/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/4.4-x86_64/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: In file included from ../inst/include/CytoML/workspace_type.hpp:4: ../inst/include/CytoML/wsNode.hpp:27:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] Rprintf("%.*s", n, s); ~~^~ ~ 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/4.4-x86_64/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/4.4-x86_64/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/4.4-x86_64/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/4.4-x86_64/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/4.4-x86_64/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/4.4-x86_64/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 ^ 5 warnings generated. clang++ -arch x86_64 -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/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/flowWorkspace/include' -I/opt/R/x86_64/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/4.4-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: /Library/Frameworks/R.framework/Versions/4.4-x86_64/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/4.4-x86_64/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: In file included from ../inst/include/CytoML/workspace_type.hpp:4: ../inst/include/CytoML/wsNode.hpp:27:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] Rprintf("%.*s", n, s); ~~^~ ~ 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/4.4-x86_64/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/4.4-x86_64/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/4.4-x86_64/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/4.4-x86_64/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/4.4-x86_64/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/4.4-x86_64/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 ^ 5 warnings generated. clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o CytoML.so cpp11.o parseFlowJoWorkspace.o /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/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)