rtracklayer 1.26.3
Michael Lawrence
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/rtracklayer | | Last Changed Rev: 101258 / Revision: 102249 | | Last Changed Date: 2015-03-26 16:45:11 -0700 (Thu, 26 Mar 2015) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | [ OK ] | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK |
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD INSTALL rtracklayer
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* installing to library ‘/home/biocbuild/bbs-3.0-bioc/R/library’
* installing *source* package ‘rtracklayer’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c bigWig.c -o bigWig.o
bigWig.c: In function ‘BWGFile_query’:
bigWig.c:330:9: warning: ‘numericListEls’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c chain_io.c -o chain_io.o
chain_io.c: In function ‘read_chain_file’:
chain_io.c:119:14: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
chain_io.c:116:24: warning: ‘header_line’ may be used uninitialized in this function [-Wuninitialized]
chain_io.c:101:54: warning: ‘block’ may be used uninitialized in this function [-Wuninitialized]
chain_io.c:110:12: warning: ‘qrc’ may be used uninitialized in this function [-Wuninitialized]
chain_io.c:106:12: warning: ‘trc’ may be used uninitialized in this function [-Wuninitialized]
chain_io.c:98:14: warning: ‘qstart’ may be used uninitialized in this function [-Wuninitialized]
chain_io.c:97:14: warning: ‘tstart’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c twoBit.c -o twoBit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c handlers.c -o handlers.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -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]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function ‘bbiTotalSummary’:
ucsc/bbiRead.c:703:34: warning: variable ‘chromEnd’ set but not used [-Wunused-but-set-variable]
ucsc/bbiRead.c:703:22: warning: variable ‘chromStart’ set but not used [-Wunused-but-set-variable]
ucsc/bbiRead.c:703:13: warning: variable ‘chromId’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
ucsc/bwgCreate.c: In function ‘bwgCreate’:
ucsc/bwgCreate.c:837:6: warning: unused variable ‘minRes’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function ‘bigWigIntervalQuery’:
ucsc/bwgQuery.c:186:18: warning: variable ‘blockEnd’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function ‘byteSwap64’:
ucsc/common.c:2765:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2766:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2767:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2768:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2769:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2770:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2771:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2772:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c: In function ‘byteSwapDouble’:
ucsc/common.c:2899:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2900:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2901:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2902:21: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2903:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2904:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2905:8: warning: array subscript is above array bounds [-Warray-bounds]
ucsc/common.c:2906:8: warning: array subscript is above array bounds [-Warray-bounds]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function ‘findHeadPolyTMaybeMask’:
ucsc/dnautil.c:943:5: warning: variable ‘pastPoly’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/errabort.c -o ucsc/errabort.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/hash.c -o ucsc/hash.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/linefile.c -o ucsc/linefile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/localmem.c -o ucsc/localmem.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/zlibFace.c -o ucsc/zlibFace.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/dystring.c -o ucsc/dystring.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/obscure.c -o ucsc/obscure.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/dlist.c -o ucsc/dlist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function ‘udcBitmapOpen’:
ucsc/udc.c:550:8: warning: variable ‘reserved64’ set but not used [-Wunused-but-set-variable]
ucsc/udc.c:549:8: warning: variable ‘reserved32’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/net.c -o ucsc/net.o
ucsc/net.c: In function ‘netSkipHttpHeaderLinesWithRedirect’:
ucsc/net.c:1332:8: warning: variable ‘version’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/bits.c -o ucsc/bits.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/internet.c -o ucsc/internet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/https.c -o ucsc/https.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/base64.c -o ucsc/base64.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/verbose.c -o ucsc/verbose.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/os.c -o ucsc/os.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/XVector/include" -g -fpic -g -O2 -Wall -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o rtracklayer.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.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 -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-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)