| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:24 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 Rsamtools package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rsamtools.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 1732/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rsamtools 2.14.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: Rsamtools |
| Version: 2.14.0 |
| Command: rm -rf Rsamtools.buildbin-libdir && mkdir Rsamtools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rsamtools_2.14.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rsamtools.buildbin-libdir |
| StartedAt: 2023-04-11 00:02:10 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 00:03:15 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 64.6 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: Rsamtools_2.14.0.tgz |
| PackageFileSize: 3.944 MiB |
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### Running command:
###
### rm -rf Rsamtools.buildbin-libdir && mkdir Rsamtools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rsamtools_2.14.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rsamtools.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rsamtools.buildbin-libdir Rsamtools_2.14.0.tar.gz'
>>>>>>>
* installing *source* package ‘Rsamtools’ ...
** using staged installation
** libs
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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PileupBuffer.cpp -o PileupBuffer.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PosCacheColl.cpp -o PosCacheColl.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_Rsamtools.c -o R_init_Rsamtools.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ResultManager.cpp -o ResultManager.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/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 -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c as_bam.c -o as_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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bam_data.c -o bam_data.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bam_mate_iter.cpp -o bam_mate_iter.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bam_sort.c -o bam_sort.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bambuffer.c -o bambuffer.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bamfile.c -o bamfile.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bcffile.c -o bcffile.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bedidx.c -o bedidx.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c encode.c -o encode.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fafile.c -o fafile.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c idxstats.c -o idxstats.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c io_sam.c -o io_sam.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c pbuffer_wrapper.cpp -o pbuffer_wrapper.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c pileup.cpp -o pileup.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c pileupbam.c -o pileupbam.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c samtools_patch.c -o samtools_patch.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c scan_bam_data.c -o scan_bam_data.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c tabixfile.c -o tabixfile.o
tabixfile.c:190:9: warning: 'bgzf_is_bgzf' is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
if (bgzf_is_bgzf(fn) != 1)
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/bgzf.h:270:38: note: 'bgzf_is_bgzf' has been explicitly marked deprecated here
int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/hts_defs.h:75:49: note: expanded from macro 'HTS_DEPRECATED'
#define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message)))
^
1 warning generated.
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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c tagfilter.c -o tagfilter.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utilities.c -o utilities.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/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I/usr/local/include -fPIC -Wall -g -O2 -c zip_compression.c -o zip_compression.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 Rsamtools.so Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o bedidx.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.16-bioc/meat/Rsamtools.buildbin-libdir/00LOCK-Rsamtools/00new/Rsamtools/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 (Rsamtools)
>>>>>>>
>>>>>>> FIXING LINKS FOR Rsamtools.buildbin-libdir/Rsamtools/libs/Rsamtools.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "Rsamtools.buildbin-libdir/Rsamtools/libs/Rsamtools.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "Rsamtools.buildbin-libdir/Rsamtools/libs/Rsamtools.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "Rsamtools.buildbin-libdir/Rsamtools/libs/Rsamtools.so"