Xiuwen Zheng
| Snapshot Date: 2026-04-17 13:40 -0400 (Fri, 17 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/HIBAG |
| git_branch: devel |
| git_last_commit: dd2c9ff |
| git_last_commit_date: 2026-04-16 01:07:39 -0400 (Thu, 16 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-18 11:36 -0400 (Sat, 18 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4957 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4686 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 991/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HIBAG 1.47.2 (landing page) Xiuwen Zheng
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
| See other builds for HIBAG in R Universe. | ||||||||||||||
|
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: 1.47.2 |
| Command: rm -rf HIBAG.buildbin-libdir && mkdir HIBAG.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HIBAG_1.47.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R HIBAG.buildbin-libdir |
| StartedAt: 2026-04-17 23:16:20 -0400 (Fri, 17 Apr 2026) |
| EndedAt: 2026-04-17 23:16:31 -0400 (Fri, 17 Apr 2026) |
| EllapsedTime: 11.2 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: HIBAG_1.47.2.tgz |
| PackageFileSize: 2.176 MiB |
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### Running command:
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### rm -rf HIBAG.buildbin-libdir && mkdir HIBAG.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HIBAG_1.47.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R HIBAG.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=HIBAG.buildbin-libdir HIBAG_1.47.2.tar.gz'
>>>>>>>
* installing *source* package ‘HIBAG’ ...
** this is package ‘HIBAG’ version ‘1.47.2’
** using staged installation
** libs
specified C++11
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c HIBAG.cpp -o HIBAG.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibHLA.cpp -o LibHLA.o
LibHLA.cpp:724:22: warning: unused variable 'UTYPE_BIT_NUM' [-Wunused-const-variable]
724 | static const ssize_t UTYPE_BIT_NUM = sizeof(UTYPE)*8;
| ^~~~~~~~~~~~~
LibHLA.cpp:730:27: warning: unused function 'u_popcount' [-Wunused-function]
730 | static ALWAYS_INLINE int u_popcount(uint64_t v)
| ^~~~~~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibHLA_ext_avx.cpp -o LibHLA_ext_avx.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibHLA_ext_avx2.cpp -o LibHLA_ext_avx2.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibHLA_ext_avx512bw.cpp -o LibHLA_ext_avx512bw.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibHLA_ext_avx512f.cpp -o LibHLA_ext_avx512f.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibHLA_ext_avx512vpopcnt.cpp -o LibHLA_ext_avx512vpopcnt.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibHLA_ext_sse2.cpp -o LibHLA_ext_sse2.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibHLA_ext_sse4_2.cpp -o LibHLA_ext_sse4_2.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c samtools_ext.c -o samtools_ext.o
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o HIBAG.so 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 -L/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/lib -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/HIBAG.buildbin-libdir/00LOCK-HIBAG/00new/HIBAG/libs
** 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
** 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 (HIBAG)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR HIBAG.buildbin-libdir/HIBAG/libs/HIBAG.so
>>>>>>>
>>>>>>> Paths before fix:
HIBAG.buildbin-libdir/HIBAG/libs/HIBAG.so:
HIBAG.so (compatibility version 0.0.0, current version 0.0.0)
@rpath/libtbb.dylib (compatibility version 0.0.0, current version 0.0.0)
@rpath/libtbbmalloc.dylib (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 2000.67.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libgcc_s.1.1.dylib" "HIBAG.buildbin-libdir/HIBAG/libs/HIBAG.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libgfortran.5.dylib" "HIBAG.buildbin-libdir/HIBAG/libs/HIBAG.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libquadmath.0.dylib" "HIBAG.buildbin-libdir/HIBAG/libs/HIBAG.so"
>>>>>>> Paths after fix:
HIBAG.buildbin-libdir/HIBAG/libs/HIBAG.so:
HIBAG.so (compatibility version 0.0.0, current version 0.0.0)
@rpath/libtbb.dylib (compatibility version 0.0.0, current version 0.0.0)
@rpath/libtbbmalloc.dylib (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 2000.67.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)