Xiuwen Zheng
| Snapshot Date: 2025-03-23 13:40 -0400 (Sun, 23 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/HIBAG |
| git_branch: devel |
| git_last_commit: 4d1767d |
| git_last_commit_date: 2024-11-19 22:12:43 -0400 (Tue, 19 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-24 11:42 -0400 (Mon, 24 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4779 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4550 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4578 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4530 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4461 |
| 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 960/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HIBAG 1.43.1 (landing page) Xiuwen Zheng
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the HIBAG package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HIBAG.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: HIBAG |
| Version: 1.43.1 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL HIBAG |
| StartedAt: 2025-03-23 15:23:54 -0400 (Sun, 23 Mar 2025) |
| EndedAt: 2025-03-23 15:25:51 -0400 (Sun, 23 Mar 2025) |
| EllapsedTime: 117.2 seconds |
| RetCode: 0 |
| Status: OK |
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###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL HIBAG
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'HIBAG' ...
** this is package 'HIBAG' version '1.43.1'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
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"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c HIBAG.cpp -o HIBAG.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 HIBAG.cpp:32:
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"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LibHLA.cpp -o LibHLA.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 LibHLA.cpp:49:
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"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LibHLA_ext_avx.cpp -o LibHLA_ext_avx.o
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"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LibHLA_ext_avx2.cpp -o LibHLA_ext_avx2.o
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"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -ffixed-xmm16 -ffixed-xmm17 -ffixed-xmm18 -ffixed-xmm19 -ffixed-xmm20 -ffixed-xmm21 -ffixed-xmm22 -ffixed-xmm23 -ffixed-xmm24 -ffixed-xmm25 -ffixed-xmm26 -ffixed-xmm27 -ffixed-xmm28 -ffixed-xmm29 -ffixed-xmm30 -ffixed-xmm31 LibHLA_ext_avx512bw.cpp -c -o LibHLA_ext_avx512bw.o
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"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -ffixed-xmm16 -ffixed-xmm17 -ffixed-xmm18 -ffixed-xmm19 -ffixed-xmm20 -ffixed-xmm21 -ffixed-xmm22 -ffixed-xmm23 -ffixed-xmm24 -ffixed-xmm25 -ffixed-xmm26 -ffixed-xmm27 -ffixed-xmm28 -ffixed-xmm29 -ffixed-xmm30 -ffixed-xmm31 LibHLA_ext_avx512f.cpp -c -o LibHLA_ext_avx512f.o
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"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -ffixed-xmm16 -ffixed-xmm17 -ffixed-xmm18 -ffixed-xmm19 -ffixed-xmm20 -ffixed-xmm21 -ffixed-xmm22 -ffixed-xmm23 -ffixed-xmm24 -ffixed-xmm25 -ffixed-xmm26 -ffixed-xmm27 -ffixed-xmm28 -ffixed-xmm29 -ffixed-xmm30 -ffixed-xmm31 LibHLA_ext_avx512vpopcnt.cpp -c -o LibHLA_ext_avx512vpopcnt.o
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"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LibHLA_ext_sse2.cpp -o LibHLA_ext_sse2.o
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"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LibHLA_ext_sse4_2.cpp -o LibHLA_ext_sse4_2.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppParallel/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c samtools_ext.c -o samtools_ext.o
g++ -shared -s -static-libgcc -o HIBAG.dll tmp.def HIBAG.o LibHLA.o LibHLA_ext_avx.o LibHLA_ext_avx2.o LibHLA_ext_avx512bw.o LibHLA_ext_avx512f.o LibHLA_ext_avx512vpopcnt.o LibHLA_ext_sse2.o LibHLA_ext_sse4_2.o samtools_ext.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-HIBAG/00new/HIBAG/libs/x64
** R
** data
*** moving datasets to lazyload DB
** 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 (HIBAG)