Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-02-07 11:07:10 -0500 (Tue, 07 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4483 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" | 4249 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4272 |
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 |
To the developers/maintainers of the QuasR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/QuasR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1565/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
QuasR 1.39.2 (landing page) Michael Stadler
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
Package: QuasR |
Version: 1.39.2 |
Command: rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh QuasR_1.39.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R QuasR.buildbin-libdir |
StartedAt: 2023-02-07 09:40:43 -0500 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 09:44:09 -0500 (Tue, 07 Feb 2023) |
EllapsedTime: 206.4 seconds |
RetCode: 0 |
Status: OK |
PackageFile: QuasR_1.39.2.tgz |
PackageFileSize: 3.141 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh QuasR_1.39.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R QuasR.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=QuasR.buildbin-libdir QuasR_1.39.2.tar.gz' >>>>>>> * installing *source* package ‘QuasR’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’ using C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’ using SDK: ‘’ clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_QuasR.cpp -o R_init_QuasR.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bam_cat.c -o bam_cat.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cat_bam.c -o cat_bam.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c count_alignments.c -o count_alignments.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c count_alignments_subregions.c -o count_alignments_subregions.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c count_junctions.cpp -o count_junctions.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c export_wig.c -o export_wig.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c extract_unmapped_reads.c -o extract_unmapped_reads.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c filter_hisat2.c -o filter_hisat2.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c idxstats_bam.c -o idxstats_bam.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c merge_reorder_sam.cpp -o merge_reorder_sam.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c profile_alignments.c -o profile_alignments.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c quantify_methylation.cpp -o quantify_methylation.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c sam_opts.c -o sam_opts.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c sam_utils.c -o sam_utils.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c split_sam_chr.c -o split_sam_chr.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utilities.c -o utilities.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 QuasR.so R_init_QuasR.o bam_cat.o bam_plbuf.o cat_bam.o convert_reads_id_bis_rc.o count_alignments.o count_alignments_subregions.o count_junctions.o export_wig.o extract_unmapped_reads.o filter_hisat2.o idxstats_bam.o merge_reorder_sam.o nucleotide_alignment_frequencies.o profile_alignments.o quantify_methylation.o remove_unmapped_from_sam.o sam_opts.o sam_utils.o split_sam_chr.o utilities.o /Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.17-bioc/meat/QuasR.buildbin-libdir/00LOCK-QuasR/00new/QuasR/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 (QuasR) >>>>>>> >>>>>>> FIXING LINKS FOR QuasR.buildbin-libdir/QuasR/libs/QuasR.so >>>>>>> install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgcc_s.1.dylib" "QuasR.buildbin-libdir/QuasR/libs/QuasR.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgfortran.5.dylib" "QuasR.buildbin-libdir/QuasR/libs/QuasR.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libquadmath.0.dylib" "QuasR.buildbin-libdir/QuasR/libs/QuasR.so"