Xiuwen Zheng
| Snapshot Date: 2025-07-21 13:25 -0400 (Mon, 21 Jul 2025) |
| git_url: https://git.bioconductor.org/packages/SeqArray |
| git_branch: devel |
| git_last_commit: 309bc23 |
| git_last_commit_date: 2025-07-05 01:00:02 -0400 (Sat, 05 Jul 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-07-22 12:06 -0400 (Tue, 22 Jul 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4791 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4527 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4572 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4513 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4510 |
| 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 1938/2311 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SeqArray 1.49.3 (landing page) Xiuwen Zheng
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | TIMEOUT | skipped | ||||||||||
|
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: 1.49.3 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SeqArray |
| StartedAt: 2025-07-21 15:22:37 -0400 (Mon, 21 Jul 2025) |
| EndedAt: 2025-07-21 15:23:17 -0400 (Mon, 21 Jul 2025) |
| EllapsedTime: 40.1 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SeqArray
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘SeqArray’ ...
** this is package ‘SeqArray’ version ‘1.49.3’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ConvToGDS.cpp -o ConvToGDS.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FileMerge.cpp -o FileMerge.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c GetData.cpp -o GetData.o
GetData.cpp:159:17: warning: ‘LANG_NEW_RLE’ initialized and declared ‘extern’
159 | extern "C" SEXP LANG_NEW_RLE = NULL;
| ^~~~~~~~~~~~
GetData.cpp:871:17: warning: ‘OBJ_CompressedList’ initialized and declared ‘extern’
871 | extern "C" SEXP OBJ_CompressedList = NULL;
| ^~~~~~~~~~~~~~~~~~
GetData.cpp:873:17: warning: ‘LANG_AS_LIST’ initialized and declared ‘extern’
873 | extern "C" SEXP LANG_AS_LIST = NULL;
| ^~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c Index.cpp -o Index.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c LinkSNPRelate.cpp -o LinkSNPRelate.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c Methods.cpp -o Methods.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c R_SeqArray.c -o R_SeqArray.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ReadBySample.cpp -o ReadBySample.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ReadByUnit.cpp -o ReadByUnit.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ReadByVariant.cpp -o ReadByVariant.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c SeqArray.cpp -o SeqArray.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c pkg_test.cpp -o pkg_test.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c samtools_ext.c -o samtools_ext.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/gdsfmt/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c vectorization.cpp -o vectorization.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/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 -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-SeqArray/00new/SeqArray/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘GenomeInfoDb’ for requests: ‘seqnames’, ‘seqlevels’ when loading ‘SeqArray’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘GenomeInfoDb’ for requests: ‘seqnames’, ‘seqlevels’ when loading ‘SeqArray’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
No methods found in package ‘GenomeInfoDb’ for requests: ‘seqnames’, ‘seqlevels’ when loading ‘SeqArray’
** testing if installed package keeps a record of temporary installation path
* DONE (SeqArray)