| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:23:39 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 rtracklayer package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rtracklayer.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 1722/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rtracklayer 1.56.1 (landing page) Michael Lawrence
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: rtracklayer |
| Version: 1.56.1 |
| Command: rm -rf rtracklayer.buildbin-libdir && mkdir rtracklayer.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rtracklayer_1.56.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R rtracklayer.buildbin-libdir |
| StartedAt: 2022-10-19 11:06:14 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 11:08:00 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 106.1 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: rtracklayer_1.56.1.tgz |
| PackageFileSize: 6.701 MiB |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf rtracklayer.buildbin-libdir && mkdir rtracklayer.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rtracklayer_1.56.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R rtracklayer.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rtracklayer.buildbin-libdir rtracklayer_1.56.1.tar.gz'
>>>>>>>
* installing *source* package ‘rtracklayer’ ...
** using staged installation
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENSSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/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/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/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/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/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 -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c R_init_rtracklayer.c -o R_init_rtracklayer.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c readGFF.c -o readGFF.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c bbiHelper.c -o bbiHelper.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c bigWig.c -o bigWig.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c bigBedHelper.c -o bigBedHelper.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c bigBed.c -o bigBed.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c chain_io.c -o chain_io.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c twoBit.c -o twoBit.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c handlers.c -o handlers.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c utils.c -o utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/memgfx.c -o ucsc/memgfx.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/aliType.c -o ucsc/aliType.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/binRange.c -o ucsc/binRange.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/htmlColor.c -o ucsc/htmlColor.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/sqlList.c -o ucsc/sqlList.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/tokenizer.c -o ucsc/tokenizer.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/asParse.c -o ucsc/asParse.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/basicBed.c -o ucsc/basicBed.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bigBed.c -o ucsc/bigBed.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bbiRead.c -o ucsc/bbiRead.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/cirTree.c -o ucsc/cirTree.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/common.c -o ucsc/common.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/dnautil.c -o ucsc/dnautil.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/errAbort.c -o ucsc/errAbort.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/hash.c -o ucsc/hash.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/linefile.c -o ucsc/linefile.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/localmem.c -o ucsc/localmem.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/zlibFace.c -o ucsc/zlibFace.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/dystring.c -o ucsc/dystring.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/hmmstats.c -o ucsc/hmmstats.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/obscure.c -o ucsc/obscure.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/pipeline.c -o ucsc/pipeline.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/rangeTree.c -o ucsc/rangeTree.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/rbTree.c -o ucsc/rbTree.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/memalloc.c -o ucsc/memalloc.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/dlist.c -o ucsc/dlist.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/hex.c -o ucsc/hex.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/filePath.c -o ucsc/filePath.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/htmlPage.c -o ucsc/htmlPage.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/udc.c -o ucsc/udc.o
In file included from ucsc/udc.c:41:
ucsc/net.h:178:1: warning: '/*' within block comment [-Wcomment]
/* Use byteRange as a work-around alternate method to get file size (content-length).
^
ucsc/udc.c:1088:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while (c = *str++)
~~^~~~~~~~
ucsc/udc.c:1088:14: note: place parentheses around the assignment to silence this warning
while (c = *str++)
^
( )
ucsc/udc.c:1088:14: note: use '==' to turn this assignment into an equality comparison
while (c = *str++)
^
==
ucsc/udc.c:1101:60: warning: taking the absolute value of unsigned type 'unsigned long' has no effect [-Wabsolute-value]
int total_size = url_size + floor(1.0 + log10((double) llabs(hash_id))) + 1;
^
ucsc/udc.c:1101:60: note: remove the call to 'llabs' since unsigned values cannot be negative
int total_size = url_size + floor(1.0 + log10((double) llabs(hash_id))) + 1;
^~~~~
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/net.c -o ucsc/net.o
In file included from ucsc/net.c:19:
ucsc/net.h:178:1: warning: '/*' within block comment [-Wcomment]
/* Use byteRange as a work-around alternate method to get file size (content-length).
^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bits.c -o ucsc/bits.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/twoBit.c -o ucsc/twoBit.o
In file included from ucsc/twoBit.c:15:
ucsc/net.h:178:1: warning: '/*' within block comment [-Wcomment]
/* Use byteRange as a work-around alternate method to get file size (content-length).
^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/internet.c -o ucsc/internet.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/https.c -o ucsc/https.o
In file included from ucsc/https.c:17:
ucsc/net.h:178:1: warning: '/*' within block comment [-Wcomment]
/* Use byteRange as a work-around alternate method to get file size (content-length).
^
ucsc/https.c:22:22: warning: unused function 'openssl_id_callback' [-Wunused-function]
static unsigned long openssl_id_callback(void)
^
ucsc/https.c:27:13: warning: unused function 'openssl_locking_callback' [-Wunused-function]
static void openssl_locking_callback(int mode, int n, const char * file, int line)
^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/base64.c -o ucsc/base64.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/verbose.c -o ucsc/verbose.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/os.c -o ucsc/os.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/openssl@1.1/1.1.1k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -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/usr/local/include -fPIC -Wall -g -O2 -c ucsc/_portimpl.c -o ucsc/_portimpl.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 rtracklayer.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bbiHelper.o bigWig.o bigBedHelper.o bigBed.o chain_io.o twoBit.o handlers.o utils.o ucsc/memgfx.o ucsc/aliType.o ucsc/binRange.o ucsc/htmlColor.o ucsc/sqlList.o ucsc/tokenizer.o ucsc/asParse.o ucsc/basicBed.o ucsc/bigBed.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/hex.o ucsc/filePath.o ucsc/htmlPage.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread /usr/local/opt/openssl@1.1/lib/libssl.a /usr/local/opt/openssl@1.1/lib/libcrypto.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.15-bioc/meat/rtracklayer.buildbin-libdir/00LOCK-rtracklayer/00new/rtracklayer/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’
** 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 (rtracklayer)
>>>>>>>
>>>>>>> FIXING LINKS FOR rtracklayer.buildbin-libdir/rtracklayer/libs/rtracklayer.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" "rtracklayer.buildbin-libdir/rtracklayer/libs/rtracklayer.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "rtracklayer.buildbin-libdir/rtracklayer/libs/rtracklayer.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "rtracklayer.buildbin-libdir/rtracklayer/libs/rtracklayer.so"