Back to Multiple platform build/check report for BioC 3.23:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2026-04-04 11:35 -0400 (Sat, 04 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.6.0 alpha (2026-03-30 r89742) 4900
kjohnson3macOS 13.7.7 Venturaarm644.6.0 alpha (2026-03-28 r89739) 4634
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 1994/2381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqArray 1.51.5  (landing page)
Xiuwen Zheng
Snapshot Date: 2026-04-03 13:40 -0400 (Fri, 03 Apr 2026)
git_url: https://git.bioconductor.org/packages/SeqArray
git_branch: devel
git_last_commit: 5b30be4
git_last_commit_date: 2026-04-03 02:11:30 -0400 (Fri, 03 Apr 2026)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  YES
See other builds for SeqArray in R Universe.

BUILD BIN results for SeqArray on kjohnson3

To the developers/maintainers of the SeqArray package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SeqArray.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.

raw results


Summary

Package: SeqArray
Version: 1.51.5
Command: rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SeqArray_1.51.5.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SeqArray.buildbin-libdir
StartedAt: 2026-04-03 23:28:55 -0400 (Fri, 03 Apr 2026)
EndedAt: 2026-04-03 23:29:15 -0400 (Fri, 03 Apr 2026)
EllapsedTime: 19.4 seconds
RetCode: 0
Status:   OK  
PackageFile: SeqArray_1.51.5.tgz
PackageFileSize: 4.148 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SeqArray_1.51.5.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SeqArray.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SeqArray.buildbin-libdir SeqArray_1.51.5.tar.gz'
>>>>>>> 

* installing *source* package ‘SeqArray’ ...
** this is package ‘SeqArray’ version ‘1.51.5’
** using staged installation
** libs
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 -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/gdsfmt/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/gdsfmt/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ConvToGDS.cpp -o ConvToGDS.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/gdsfmt/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/gdsfmt/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FileMerge.cpp -o FileMerge.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/gdsfmt/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c GetData.cpp -o GetData.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/gdsfmt/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Index.cpp -o Index.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/gdsfmt/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c LinkSNPRelate.cpp -o LinkSNPRelate.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/gdsfmt/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Methods.cpp -o Methods.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/gdsfmt/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_SeqArray.c -o R_SeqArray.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/gdsfmt/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ReadBySample.cpp -o ReadBySample.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/gdsfmt/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ReadByUnit.cpp -o ReadByUnit.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/gdsfmt/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ReadByVariant.cpp -o ReadByVariant.o
ReadByVariant.cpp:33:21: warning: unused variable 'VAR_SAMP_ID' [-Wunused-const-variable]
   33 | static const string VAR_SAMP_ID("sample.id");
      |                     ^~~~~~~~~~~
ReadByVariant.cpp:48:21: warning: unused variable 'VAR_DOSAGE_SP' [-Wunused-const-variable]
   48 | static const string VAR_DOSAGE_SP("$dosage_sp");
      |                     ^~~~~~~~~~~~~
ReadByVariant.cpp:49:21: warning: unused variable 'VAR_DOSAGE_SP2' [-Wunused-const-variable]
   49 | static const string VAR_DOSAGE_SP2("$dosage_sp2");
      |                     ^~~~~~~~~~~~~~
ReadByVariant.cpp:51:21: warning: unused variable 'VAR_REF_ALLELE' [-Wunused-const-variable]
   51 | static const string VAR_REF_ALLELE("$ref");
      |                     ^~~~~~~~~~~~~~
ReadByVariant.cpp:52:21: warning: unused variable 'VAR_ALT_ALLELE' [-Wunused-const-variable]
   52 | static const string VAR_ALT_ALLELE("$alt");
      |                     ^~~~~~~~~~~~~~
ReadByVariant.cpp:53:21: warning: unused variable 'VAR_CHROM_POS' [-Wunused-const-variable]
   53 | static const string VAR_CHROM_POS("$chrom_pos");
      |                     ^~~~~~~~~~~~~
ReadByVariant.cpp:54:21: warning: unused variable 'VAR_CHROM_POS2' [-Wunused-const-variable]
   54 | static const string VAR_CHROM_POS2("$chrom_pos2");
      |                     ^~~~~~~~~~~~~~
ReadByVariant.cpp:55:21: warning: unused variable 'VAR_CHROM_POS_ALLELE' [-Wunused-const-variable]
   55 | static const string VAR_CHROM_POS_ALLELE("$chrom_pos_allele");
      |                     ^~~~~~~~~~~~~~~~~~~~
ReadByVariant.cpp:56:21: warning: unused variable 'VAR_SAMPLE_INDEX' [-Wunused-const-variable]
   56 | static const string VAR_SAMPLE_INDEX("$sample_index");
      |                     ^~~~~~~~~~~~~~~~
ReadByVariant.cpp:57:21: warning: unused variable 'VAR_VARIANT_INDEX' [-Wunused-const-variable]
   57 | static const string VAR_VARIANT_INDEX("$variant_index");
      |                     ^~~~~~~~~~~~~~~~~
10 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/gdsfmt/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c SeqArray.cpp -o SeqArray.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/gdsfmt/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c pkg_test.cpp -o pkg_test.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/gdsfmt/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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/gdsfmt/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c vectorization.cpp -o vectorization.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 SeqArray.so ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByUnit.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/SeqArray.buildbin-libdir/00LOCK-SeqArray/00new/SeqArray/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 (SeqArray)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR SeqArray.buildbin-libdir/SeqArray/libs/SeqArray.so
>>>>>>> 

>>>>>>> Paths before fix:
SeqArray.buildbin-libdir/SeqArray/libs/SeqArray.so:
	SeqArray.so (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" "SeqArray.buildbin-libdir/SeqArray/libs/SeqArray.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libgfortran.5.dylib" "SeqArray.buildbin-libdir/SeqArray/libs/SeqArray.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libquadmath.0.dylib" "SeqArray.buildbin-libdir/SeqArray/libs/SeqArray.so"

>>>>>>> Paths after fix:
SeqArray.buildbin-libdir/SeqArray/libs/SeqArray.so:
	SeqArray.so (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)