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This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 2191/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantAnnotation 1.51.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/VariantAnnotation
git_branch: devel
git_last_commit: 6d549f2
git_last_commit_date: 2024-04-30 10:25:08 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino6Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  


BUILD BIN results for VariantAnnotation on palomino6

To the developers/maintainers of the VariantAnnotation package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VariantAnnotation.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: VariantAnnotation
Version: 1.51.0
Command: rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL --build --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.51.0.tar.gz
StartedAt: 2024-07-16 06:53:16 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 06:55:05 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 109.2 seconds
RetCode: 0
Status:   OK  
PackageFile: VariantAnnotation_1.51.0.zip
PackageFileSize: 8.33 MiB

Command output

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###
### Running command:
###
###   rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL --build --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.51.0.tar.gz
###
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##############################################################################


* installing *source* package 'VariantAnnotation' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XVector_stubs.c -o XVector_stubs.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dna_hash.c -o dna_hash.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rle.c -o rle.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c strhash.c -o strhash.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utilities.c -o utilities.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c vcffile.c -o vcffile.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c vcftype.c -o vcftype.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c writevcf.c -o writevcf.o
gcc -shared -s -static-libgcc -o VariantAnnotation.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/meat/VariantAnnotation.buildbin-libdir/00LOCK-VariantAnnotation/00new/VariantAnnotation/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'tabulate' in package 'VariantAnnotation'
** 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
* MD5 sums
packaged installation of 'VariantAnnotation' as VariantAnnotation_1.51.0.zip
* DONE (VariantAnnotation)