rtracklayer 1.36.6
Michael Lawrence
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/rtracklayer | | Branch: RELEASE_3_5 | | Last Commit: 8c0ac72 | | Last Changed Date: 2017-10-11 14:57:24 -0400 (Wed, 11 Oct 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | [ OK ] | |
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###
### Running command:
###
### rm -rf rtracklayer.buildbin-libdir && mkdir rtracklayer.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rtracklayer_1.36.6.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R rtracklayer.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rtracklayer.buildbin-libdir rtracklayer_1.36.6.tar.gz'
>>>>>>>
* installing *source* package ‘rtracklayer’ ...
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 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_rtracklayer.c -o R_init_rtracklayer.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c readGFF.c -o readGFF.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c bigWig.c -o bigWig.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c chain_io.c -o chain_io.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c twoBit.c -o twoBit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c handlers.c -o handlers.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c utils.c -o utils.o
utils.c:4:8: warning: unused variable 'ans' [-Wunused-variable]
SEXP ans;
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bbiRead.c -o ucsc/bbiRead.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/cirTree.c -o ucsc/cirTree.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/common.c -o ucsc/common.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/dnaseq.c -o ucsc/dnaseq.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c:496:9: warning: implicit declaration of function 'isAllNt' is invalid in C99 [-Wimplicit-function-declaration]
if (isAllNt(allele, alLen))
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/errAbort.c -o ucsc/errAbort.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/hash.c -o ucsc/hash.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/linefile.c -o ucsc/linefile.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/localmem.c -o ucsc/localmem.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/zlibFace.c -o ucsc/zlibFace.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/dystring.c -o ucsc/dystring.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/hmmstats.c -o ucsc/hmmstats.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/obscure.c -o ucsc/obscure.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/pipeline.c -o ucsc/pipeline.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/rangeTree.c -o ucsc/rangeTree.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/rbTree.c -o ucsc/rbTree.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/memalloc.c -o ucsc/memalloc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/dlist.c -o ucsc/dlist.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/udc.c -o ucsc/udc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/net.c -o ucsc/net.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/bits.c -o ucsc/bits.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/twoBit.c -o ucsc/twoBit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/internet.c -o ucsc/internet.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/https.c -o ucsc/https.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/base64.c -o ucsc/base64.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/verbose.c -o ucsc/verbose.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/os.c -o ucsc/os.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/openssl/1.0.2k/include -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
clang -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 bigWig.o chain_io.o twoBit.o handlers.o utils.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/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/Cellar/openssl/1.0.2k/lib/libssl.a /usr/local/Cellar/openssl/1.0.2k/lib/libcrypto.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
installing to /Users/biocbuild/bbs-3.5-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’
Creating a generic function from function ‘uri’ in package ‘rtracklayer’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* 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/3.4/Resources/lib/libgcc_s.1.dylib" "rtracklayer.buildbin-libdir/rtracklayer/libs//rtracklayer.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "rtracklayer.buildbin-libdir/rtracklayer/libs//rtracklayer.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "rtracklayer.buildbin-libdir/rtracklayer/libs//rtracklayer.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "rtracklayer.buildbin-libdir/rtracklayer/libs//rtracklayer.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "rtracklayer.buildbin-libdir/rtracklayer/libs//rtracklayer.so"