Mock Version: 1.1.41 Mock Version: 1.1.41 ENTER do(['bash', '--login', '-c', 'rpmbuild -bs --target i686 --nodeps builddir/build/SPECS/R-rtracklayer.spec'], False, '/var/lib/mock/f21-build-2215223-406599/root/', None, 86400, True, False, 1000, 425, None, False, {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'echo -n ""', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'}, logger=) Executing command: ['bash', '--login', '-c', 'rpmbuild -bs --target i686 --nodeps builddir/build/SPECS/R-rtracklayer.spec'] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'echo -n ""', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'} warning: Could not canonicalize hostname: buildhw-05.phx2.fedoraproject.org Building target platforms: i686 Building for target i686 Wrote: /builddir/build/SRPMS/R-rtracklayer-1.22.3-4.fc21.src.rpm Child return code was: 0 LEAVE do --> ENTER do(['bash', '--login', '-c', 'rpmbuild -bb --target i686 --nodeps builddir/build/SPECS/R-rtracklayer.spec'], False, '/var/lib/mock/f21-build-2215223-406599/root/', None, 86400, True, False, 1000, 425, None, False, {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'echo -n ""', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'}, logger=) Executing command: ['bash', '--login', '-c', 'rpmbuild -bb --target i686 --nodeps builddir/build/SPECS/R-rtracklayer.spec'] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'echo -n ""', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'} Building target platforms: i686 Building for target i686 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.pyWDN6 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf rtracklayer + /usr/bin/mkdir -p rtracklayer + cd rtracklayer + /usr/bin/gzip -dc /builddir/build/SOURCES/rtracklayer_1.22.3.tar.gz + /usr/bin/tar -xf - + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + sed -i -e 's|zlibbioc,||' rtracklayer/DESCRIPTION + sed -i -e 's|import(zlibbioc)||' rtracklayer/NAMESPACE + cp /builddir/build/SOURCES/rtracklayer_jimkent_license.txt . + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.2W6rsD + umask 022 + cd /builddir/build/BUILD + cd rtracklayer + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.xEeL79 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-rtracklayer-1.22.3-4.fc21.i386 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-rtracklayer-1.22.3-4.fc21.i386 ++ dirname /builddir/build/BUILDROOT/R-rtracklayer-1.22.3-4.fc21.i386 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-rtracklayer-1.22.3-4.fc21.i386 + cd rtracklayer + mkdir -p /builddir/build/BUILDROOT/R-rtracklayer-1.22.3-4.fc21.i386/usr/lib/R/library + /usr/bin/R CMD INSTALL rtracklayer -l /builddir/build/BUILDROOT/R-rtracklayer-1.22.3-4.fc21.i386/usr/lib/R/library * installing *source* package 'rtracklayer' ... ** libs gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c IRanges_stubs.c -o IRanges_stubs.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c XVector_stubs.c -o XVector_stubs.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c R_init_rtracklayer.c -o R_init_rtracklayer.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c bigWig.c -o bigWig.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -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:101:54: warning: 'block' may be used uninitialized in this function [-Wmaybe-uninitialized] IntAE_insert_at(&block->offset, IntAE_get_nelt(&block->offset), ^ 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 -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c twoBit.c -o twoBit.o twoBit.c: In function 'TwoBitFile_read': twoBit.c:108:7: warning: pointer targets in passing argument 3 of 'Ocopy_bytes_to_i1i2_with_lkup' differ in signedness [-Wpointer-sign] Ocopy_bytes_to_i1i2_with_lkup(offset, offset + frag->size - 1, ^ In file included from rtracklayer.h:7:0, from twoBit.h:4, from twoBit.c:5: /usr/lib/R/library/XVector/include/XVector_interface.h:81:6: note: expected 'char *' but argument is of type 'Rbyte *' void Ocopy_bytes_to_i1i2_with_lkup( ^ gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c handlers.c -o handlers.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -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 -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -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] bits32 chromId, chromStart, chromEnd; ^ ucsc/bbiRead.c:703:22: warning: variable 'chromStart' set but not used [-Wunused-but-set-variable] bits32 chromId, chromStart, chromEnd; ^ ucsc/bbiRead.c:703:13: warning: variable 'chromId' set but not used [-Wunused-but-set-variable] bits32 chromId, chromStart, chromEnd; ^ gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -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] char *blockPt, *blockEnd; ^ gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/cirTree.c -o ucsc/cirTree.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -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] v.bytes[0] = u.bytes[7]; ^ ucsc/common.c:2766:21: warning: array subscript is above array bounds [-Warray-bounds] v.bytes[1] = u.bytes[6]; ^ ucsc/common.c:2767:21: warning: array subscript is above array bounds [-Warray-bounds] v.bytes[2] = u.bytes[5]; ^ ucsc/common.c:2768:21: warning: array subscript is above array bounds [-Warray-bounds] v.bytes[3] = u.bytes[4]; ^ ucsc/common.c:2769:8: warning: array subscript is above array bounds [-Warray-bounds] v.bytes[4] = u.bytes[3]; ^ ucsc/common.c:2770:8: warning: array subscript is above array bounds [-Warray-bounds] v.bytes[5] = u.bytes[2]; ^ ucsc/common.c:2771:8: warning: array subscript is above array bounds [-Warray-bounds] v.bytes[6] = u.bytes[1]; ^ ucsc/common.c:2772:8: warning: array subscript is above array bounds [-Warray-bounds] v.bytes[7] = u.bytes[0]; ^ ucsc/common.c: In function 'byteSwapDouble': ucsc/common.c:2899:21: warning: array subscript is above array bounds [-Warray-bounds] v.bytes[0] = u.bytes[7]; ^ ucsc/common.c:2900:21: warning: array subscript is above array bounds [-Warray-bounds] v.bytes[1] = u.bytes[6]; ^ ucsc/common.c:2901:21: warning: array subscript is above array bounds [-Warray-bounds] v.bytes[2] = u.bytes[5]; ^ ucsc/common.c:2902:21: warning: array subscript is above array bounds [-Warray-bounds] v.bytes[3] = u.bytes[4]; ^ ucsc/common.c:2903:8: warning: array subscript is above array bounds [-Warray-bounds] v.bytes[4] = u.bytes[3]; ^ ucsc/common.c:2904:8: warning: array subscript is above array bounds [-Warray-bounds] v.bytes[5] = u.bytes[2]; ^ ucsc/common.c:2905:8: warning: array subscript is above array bounds [-Warray-bounds] v.bytes[6] = u.bytes[1]; ^ ucsc/common.c:2906:8: warning: array subscript is above array bounds [-Warray-bounds] v.bytes[7] = u.bytes[0]; ^ gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/dnaseq.c -o ucsc/dnaseq.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -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] int pastPoly = 0; ^ gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/errabort.c -o ucsc/errabort.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/hash.c -o ucsc/hash.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/linefile.c -o ucsc/linefile.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/localmem.c -o ucsc/localmem.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/sqlNum.c -o ucsc/sqlNum.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/zlibFace.c -o ucsc/zlibFace.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/dystring.c -o ucsc/dystring.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/hmmstats.c -o ucsc/hmmstats.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/obscure.c -o ucsc/obscure.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/pipeline.c -o ucsc/pipeline.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/rangeTree.c -o ucsc/rangeTree.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/rbTree.c -o ucsc/rbTree.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/memalloc.c -o ucsc/memalloc.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/dlist.c -o ucsc/dlist.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/udc.c -o ucsc/udc.o ucsc/udc.c: In function 'udcInfoViaHttp': ucsc/udc.c:405:1: warning: implicit declaration of function 'strptime' [-Wimplicit-function-declaration] if (strptime(lastModString, "%a, %d %b %Y %H:%M:%S %Z", &tm) == NULL) ^ ucsc/udc.c:405:62: warning: comparison between pointer and integer if (strptime(lastModString, "%a, %d %b %Y %H:%M:%S %Z", &tm) == NULL) ^ ucsc/udc.c: In function 'udcBitmapOpen': ucsc/udc.c:544:8: warning: variable 'reserved64' set but not used [-Wunused-but-set-variable] bits64 reserved64; ^ ucsc/udc.c:543:8: warning: variable 'reserved32' set but not used [-Wunused-but-set-variable] bits32 reserved32; ^ gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -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] char *version, *code; ^ gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/bits.c -o ucsc/bits.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/twoBit.c -o ucsc/twoBit.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/internet.c -o ucsc/internet.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/https.c -o ucsc/https.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/base64.c -o ucsc/base64.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/verbose.c -o ucsc/verbose.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/os.c -o ucsc/os.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/wildcmp.c -o ucsc/wildcmp.o gcc -m32 -std=gnu99 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -g -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/_portimpl.c -o ucsc/_portimpl.o gcc -m32 -std=gnu99 -shared -Wl,-z,relro -o rtracklayer.so 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/usr/lib/R/lib -lR installing to /builddir/build/BUILDROOT/R-rtracklayer-1.22.3-4.fc21.i386/usr/lib/R/library/rtracklayer/libs ** R ** data ** demo ** inst ** preparing package for lazy loading No methods found in "Rsamtools" for requests: readGAlignmentsFromBam Creating a generic function for 'offset' from package 'stats' in package 'rtracklayer' Creating a generic function from function 'uri' in package 'rtracklayer' Creating a generic function for 'toString' from package 'base' in package 'rtracklayer' in method for 'export' with signature '"GAlignments","BamFile"': no definition for class "GAlignments" ** help *** installing help indices converting help for package 'rtracklayer' finding HTML links ... done BEDFile-class html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BEDFile-class.Rd:167: missing file link 'BamFile' BamFile-methods html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BamFile-methods.Rd:10: file link 'GAlignments' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BamFile-methods.Rd:11: missing file link 'BamFile' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BamFile-methods.Rd:27: missing file link 'ScanBamParam' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BamFile-methods.Rd:39: missing file link 'filterBam' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BamFile-methods.Rd:43: file link 'readGAlignments' in package 'GenomicRanges' does not exist and so has been treated as a topic Bed15TrackLine-class html BigWigFile html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BigWigFile.Rd:134: missing file link 'RleList-class' BigWigSelection-class html finding level-2 HTML links ... done Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BigWigSelection-class.Rd:15: missing file link 'RangedSelection' BrowserViewList-class html Chain-class html FastaFile-class html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/FastaFile-class.Rd:53: missing file link 'writeXStringSet' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/FastaFile-class.Rd:54: missing file link 'readDNAStringSet' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/FastaFile-class.Rd:61: missing file link 'writeXStringSet' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/FastaFile-class.Rd:62: missing file link 'readDNAStringSet' GFFFile-class html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GFFFile-class.Rd:191: missing file link 'BamFile' GRangesForUCSCGenome html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GRangesForUCSCGenome.Rd:35: missing file link 'GRanges' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GRangesForUCSCGenome.Rd:54: missing file link 'seqlengths' GenomicSelection html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GenomicSelection.Rd:7: missing file link 'RangedSelection' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GenomicSelection.Rd:26: missing file link 'RangedSelection' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GenomicSelection.Rd:33: missing file link 'RangedSelection' Quickload-class html QuickloadGenome-class html RTLFile-class html RangedData-methods html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/RangedData-methods.Rd:71: missing file link 'GRanges' RangesList-methods html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/RangesList-methods.Rd:46: missing file link 'universe' TabixFile-methods html TrackDb-class html TwoBitFile-class html UCSCData-class html UCSCFile-class html UCSCSchema-class html UCSCTableQuery-class html WIGFile-class html activeView-methods html asBED html asGFF html basicTrackLine-class html blocks-methods html browseGenome html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/browseGenome.Rd:20: missing file link 'GRanges' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/browseGenome.Rd:21: missing file link 'RangedData' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/browseGenome.Rd:22: missing file link 'RangedData' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/browseGenome.Rd:23: missing file link 'RangedDataList' browserSession-class html browserSession-methods html browserView-class html browserView-methods html browserViews-methods html cpneTrack html export html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/export.Rd:132: missing file link 'BamFile' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/export.Rd:142: missing file link 'FaFile' genomeBrowsers html laySequence-methods html layTrack-methods html liftOver html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/liftOver.Rd:22: missing file link 'GRanges' targets html tracks-methods html ucscGenomes html ucscSession-class html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/ucscSession-class.Rd:62: missing file link 'Seqinfo' ucscTrackLine-class html ucscTrackModes-class html ucscTrackModes-methods html ucscView-class html wigToBigWig html wigTrackLine-class html ** building package indices ** testing if installed package can be loaded No methods found in "Rsamtools" for requests: readGAlignmentsFromBam * DONE (rtracklayer) + test -d rtracklayer/src + cd rtracklayer/src + rm -f IRanges_stubs.o R_init_rtracklayer.o XVector_stubs.o bigWig.o chain_io.o handlers.o twoBit.o utils.o rtracklayer.so + rm -rf /builddir/build/BUILDROOT/R-rtracklayer-1.22.3-4.fc21.i386/usr/lib/R/library/R.css + rm -rf /builddir/build/BUILDROOT/R-rtracklayer-1.22.3-4.fc21.i386/usr/lib/R/library/rtracklayer/tests/quickload/T_species_Oct_2011/bedGraphData.bw + /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 /builddir/build/BUILD/rtracklayer extracting debug info from /builddir/build/BUILDROOT/R-rtracklayer-1.22.3-4.fc21.i386/usr/lib/R/library/rtracklayer/libs/rtracklayer.so dwz: Too few files for multifile optimization /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. 1555 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-java-repack-jars Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.aojF8Y + umask 022 + cd /builddir/build/BUILD + cd rtracklayer Processing files: R-rtracklayer-1.22.3-4.fc21.i686 + exit 0 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.GgDjaO + umask 022 + cd /builddir/build/BUILD + cd rtracklayer + DOCDIR=/builddir/build/BUILDROOT/R-rtracklayer-1.22.3-4.fc21.i386/usr/share/doc/R-rtracklayer + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/R-rtracklayer-1.22.3-4.fc21.i386/usr/share/doc/R-rtracklayer + cp -pr rtracklayer_jimkent_license.txt /builddir/build/BUILDROOT/R-rtracklayer-1.22.3-4.fc21.i386/usr/share/doc/R-rtracklayer + exit 0 Provides: R-rtracklayer = 1.22.3-4.fc21 R-rtracklayer(x86-32) = 1.22.3-4.fc21 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libR.so libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.15) libc.so.6(GLIBC_2.2) libc.so.6(GLIBC_2.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.4) libc.so.6(GLIBC_2.7) libpthread.so.0 libpthread.so.0(GLIBC_2.0) libpthread.so.0(GLIBC_2.1) libpthread.so.0(GLIBC_2.2) libz.so.1 rtld(GNU_HASH) Processing files: R-rtracklayer-debuginfo-1.22.3-4.fc21.i686 Provides: R-rtracklayer-debuginfo = 1.22.3-4.fc21 R-rtracklayer-debuginfo(x86-32) = 1.22.3-4.fc21 Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-rtracklayer-1.22.3-4.fc21.i386 Wrote: /builddir/build/RPMS/R-rtracklayer-1.22.3-4.fc21.i686.rpm Wrote: /builddir/build/RPMS/R-rtracklayer-debuginfo-1.22.3-4.fc21.i686.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.m5W1RG + umask 022 + cd /builddir/build/BUILD + cd rtracklayer + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-rtracklayer-1.22.3-4.fc21.i386 + exit 0 Child return code was: 0 LEAVE do -->