| Back to Multiple platform build/check report for BioC 3.23: simplified long |
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This page was generated on 2026-03-21 11:35 -0400 (Sat, 21 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4866 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" | 4545 |
| 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 1984/2368 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SeqArray 1.51.3 (landing page) Xiuwen Zheng
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| See other builds for SeqArray in R Universe. | ||||||||||||||
|
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. |
| Package: SeqArray |
| Version: 1.51.3 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SeqArray |
| StartedAt: 2026-03-20 17:55:05 -0400 (Fri, 20 Mar 2026) |
| EndedAt: 2026-03-20 17:55:21 -0400 (Fri, 20 Mar 2026) |
| EllapsedTime: 16.1 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SeqArray
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘SeqArray’ ...
** this is package ‘SeqArray’ version ‘1.51.3’
** 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 /Library/Frameworks/R.framework/Versions/4.6/Resources/library/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)