rtracklayer 1.36.4
Michael Lawrence
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/rtracklayer | | Last Changed Rev: 131118 / Revision: 131943 | | Last Changed Date: 2017-07-11 14:48:38 -0400 (Tue, 11 Jul 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:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD INSTALL rtracklayer
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* installing to library ‘/home/biocbuild/bbs-3.5-bioc/R/library’
* installing *source* package ‘rtracklayer’ ...
checking for pkg-config... /usr/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
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c readGFF.c -o readGFF.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c bigWig.c -o bigWig.o
bigWig.c: In function ‘BWGFile_query’:
bigWig.c:289:9: warning: ‘numericListEls’ may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(numericListEls, elt_len, ans_numeric);
^
bigWig.c:321:7: warning: ‘dataFrameListEls’ may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(dataFrameListEls, i,
^
bigWig.c:319:7: warning: ‘rangesListEls’ may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(rangesListEls, i,
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c chain_io.c -o chain_io.o
chain_io.c: In function ‘read_chain_file’:
chain_io.c:119:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(linebuf, LINEBUF_SIZE, stream); /* skip empty line */
^
chain_io.c:116:9: warning: ‘header_line’ may be used uninitialized in this function [-Wmaybe-uninitialized]
IntAE_insert_at(block->length, IntAE_get_nelt(block->length),
^
chain_io.c:116:60: warning: ‘block’ may be used uninitialized in this function [-Wmaybe-uninitialized]
IntAE_insert_at(block->length, IntAE_get_nelt(block->length),
^
chain_io.c:110:12: warning: ‘qrc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (qrc)
^
chain_io.c:106:12: warning: ‘trc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (trc) /* width already subtracted above */
^
chain_io.c:98:14: warning: ‘qstart’ may be used uninitialized in this function [-Wmaybe-uninitialized]
qstart -= (qrc ? width : 0);
^
chain_io.c:97:14: warning: ‘tstart’ may be used uninitialized in this function [-Wmaybe-uninitialized]
tstart -= (trc ? width : 0);
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c twoBit.c -o twoBit.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c handlers.c -o handlers.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o
utils.c: In function ‘_STRSXP_collapse’:
utils.c:4:8: warning: unused variable ‘ans’ [-Wunused-variable]
SEXP ans;
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c: In function ‘bptDataStart’:
ucsc/bPlusTree.c:286:12: warning: variable ‘childCount’ set but not used [-Wunused-but-set-variable]
bits16 childCount;
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function ‘bbiTotalSummary’:
ucsc/bbiRead.c:748:34: warning: variable ‘chromEnd’ set but not used [-Wunused-but-set-variable]
bits32 chromId, chromStart, chromEnd;
^
ucsc/bbiRead.c:748:22: warning: variable ‘chromStart’ set but not used [-Wunused-but-set-variable]
bits32 chromId, chromStart, chromEnd;
^
ucsc/bbiRead.c:748:13: warning: variable ‘chromId’ set but not used [-Wunused-but-set-variable]
bits32 chromId, chromStart, chromEnd;
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function ‘bigWigIntervalQuery’:
ucsc/bwgQuery.c:187:18: warning: variable ‘blockEnd’ set but not used [-Wunused-but-set-variable]
char *blockPt, *blockEnd;
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/common.c -o ucsc/common.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function ‘reverseComplementSlashSeparated’:
ucsc/dnautil.c:496:9: warning: implicit declaration of function ‘isAllNt’ [-Wimplicit-function-declaration]
if (isAllNt(allele, alLen))
^
ucsc/dnautil.c: In function ‘findHeadPolyTMaybeMask’:
ucsc/dnautil.c:977:5: warning: variable ‘pastPoly’ set but not used [-Wunused-but-set-variable]
int pastPoly = 0;
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function ‘getThreadVars’:
ucsc/errAbort.c:331:5: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
write(STDERR_FILENO, errMsg, strlen(errMsg));
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/hash.c -o ucsc/hash.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/linefile.c -o ucsc/linefile.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/localmem.c -o ucsc/localmem.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/zlibFace.c -o ucsc/zlibFace.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/dystring.c -o ucsc/dystring.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/obscure.c -o ucsc/obscure.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/dlist.c -o ucsc/dlist.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function ‘udcBitmapOpen’:
ucsc/udc.c:570:8: warning: variable ‘reserved64’ set but not used [-Wunused-but-set-variable]
bits64 reserved64;
^
ucsc/udc.c:569:8: warning: variable ‘reserved32’ set but not used [-Wunused-but-set-variable]
bits32 reserved32;
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/net.c -o ucsc/net.o
ucsc/net.c: In function ‘netSkipHttpHeaderLinesWithRedirect’:
ucsc/net.c:1448:8: warning: variable ‘version’ set but not used [-Wunused-but-set-variable]
char *version, *code;
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/bits.c -o ucsc/bits.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/internet.c -o ucsc/internet.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/https.c -o ucsc/https.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/base64.c -o ucsc/base64.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/verbose.c -o ucsc/verbose.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/os.c -o ucsc/os.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I/usr/local/include -fpic -g -O2 -Wall -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/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 -lssl -lcrypto -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/R/library/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)