Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-19 11:42 -0400 (Wed, 19 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4742 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
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 1481/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
oposSOM 2.25.0 (landing page) Henry Loeffler-Wirth
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the oposSOM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/oposSOM.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: oposSOM |
Version: 2.25.0 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL oposSOM |
StartedAt: 2025-03-18 16:10:02 -0400 (Tue, 18 Mar 2025) |
EndedAt: 2025-03-18 16:11:09 -0400 (Tue, 18 Mar 2025) |
EllapsedTime: 66.4 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL oposSOM ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'oposSOM' ... ** this is package 'oposSOM' version '2.25.0' ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 14.2.0' using C++11 g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DeltaMatrix.cpp -o DeltaMatrix.o In file included from E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/tbb.h:32, from E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/RcppParallel/TBB.h:10, from E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/RcppParallel.h:24, from DeltaMatrix.cpp:2: E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]': E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here 251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id); | ~~~~~~~~~^~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined] 544 | return (atomic<T>&)t; | ^~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]': E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here 291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined] 544 | return (atomic<T>&)t; | ^~~~~~~~~~~~~ g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DistanceCalculator.cpp -o DistanceCalculator.o In file included from E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/tbb.h:32, from E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/RcppParallel/TBB.h:10, from E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/RcppParallel.h:24, from DistanceCalculator.cpp:2: E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]': E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here 251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id); | ~~~~~~~~~^~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined] 544 | return (atomic<T>&)t; | ^~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]': E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here 291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined] 544 | return (atomic<T>&)t; | ^~~~~~~~~~~~~ g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NeighborhoodMatrix.cpp -o NeighborhoodMatrix.o In file included from E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/tbb.h:32, from E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/RcppParallel/TBB.h:10, from E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/RcppParallel.h:24, from NeighborhoodMatrix.cpp:2: E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]': E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here 251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id); | ~~~~~~~~~^~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined] 544 | return (atomic<T>&)t; | ^~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]': E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here 291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined] 544 | return (atomic<T>&)t; | ^~~~~~~~~~~~~ g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -shared -s -static-libgcc -o oposSOM.dll tmp.def DeltaMatrix.o DistanceCalculator.o NeighborhoodMatrix.o RcppExports.o -LE:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/libs/x64 -lRcppParallel -LE:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-oposSOM/00new/oposSOM/libs/x64 ** R ** data ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (oposSOM)