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This page was generated on 2021-09-24 15:06:42 -0400 (Fri, 24 Sep 2021).

BUILD BIN results for GenomicAlignments on machv2

To the developers/maintainers of the GenomicAlignments package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicAlignments.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 739/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicAlignments 1.28.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/GenomicAlignments
git_branch: RELEASE_3_13
git_last_commit: e755dc1
git_last_commit_date: 2021-05-19 12:01:53 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GenomicAlignments
Version: 1.28.0
Command: rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GenomicAlignments_1.28.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R GenomicAlignments.buildbin-libdir
StartedAt: 2021-09-24 02:13:20 -0400 (Fri, 24 Sep 2021)
EndedAt: 2021-09-24 02:14:31 -0400 (Fri, 24 Sep 2021)
EllapsedTime: 71.1 seconds
RetCode: 0
Status:   OK  
PackageFile: GenomicAlignments_1.28.0.tgz
PackageFileSize: 2.301 MiB

Command output

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###
### Running command:
###
###   rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GenomicAlignments_1.28.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R GenomicAlignments.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.28.0.tar.gz'
>>>>>>> 

* installing *source* package ‘GenomicAlignments’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cigar_utils.c -o cigar_utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.13-bioc/meat/GenomicAlignments.buildbin-libdir/00LOCK-GenomicAlignments/00new/GenomicAlignments/libs
** R
** 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 (GenomicAlignments)


>>>>>>> 
>>>>>>> FIXING LINKS FOR GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/GenomicAlignments.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgcc_s.1.dylib" "GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/GenomicAlignments.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/GenomicAlignments.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/GenomicAlignments.so"