Mock Version: 1.3.4 Mock Version: 1.3.4 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target i686 --nodeps /builddir/build/SPECS/R-rtracklayer.spec'], logger=chrootPath='/var/lib/mock/f24-build-8760756-758251/root'user='mockbuild'timeout=172800printOutput=Falsegid=425nspawn_args=[]env={'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'TERM': 'vt100', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir'}shell=Falseuid=1000) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target i686 --nodeps /builddir/build/SPECS/R-rtracklayer.spec'] with env {'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'TERM': 'vt100', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir'} and shell False Building target platforms: i686 Building for target i686 Wrote: /builddir/build/SRPMS/R-rtracklayer-1.36.3-1.fc24.src.rpm Child return code was: 0 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target i686 --nodeps /builddir/build/SPECS/R-rtracklayer.spec'], logger=chrootPath='/var/lib/mock/f24-build-8760756-758251/root'user='mockbuild'timeout=172800printOutput=Falsegid=425nspawn_args=[]env={'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'TERM': 'vt100', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir'}shell=Falseuid=1000) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target i686 --nodeps /builddir/build/SPECS/R-rtracklayer.spec'] with env {'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'TERM': 'vt100', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir'} and shell False Building target platforms: i686 Building for target i686 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.B7QHCZ + 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_1.36.3.tar.gz + /usr/bin/tar -xof - + 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.U3OZfT + umask 022 + cd /builddir/build/BUILD + cd rtracklayer + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.Hx9HTM + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-rtracklayer-1.36.3-1.fc24.i386 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-rtracklayer-1.36.3-1.fc24.i386 ++ dirname /builddir/build/BUILDROOT/R-rtracklayer-1.36.3-1.fc24.i386 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-rtracklayer-1.36.3-1.fc24.i386 + cd rtracklayer + mkdir -p /builddir/build/BUILDROOT/R-rtracklayer-1.36.3-1.fc24.i386/usr/lib/R/library + /usr/bin/R CMD INSTALL rtracklayer -l /builddir/build/BUILDROOT/R-rtracklayer-1.36.3-1.fc24.i386/usr/lib/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... no configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c IRanges_stubs.c -o IRanges_stubs.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c XVector_stubs.c -o XVector_stubs.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c R_init_rtracklayer.c -o R_init_rtracklayer.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c readGFF.c -o readGFF.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -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, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ new_DataFrame("DataFrame", ans_score_l, R_NilValue, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ScalarInteger(nhits))); ~~~~~~~~~~~~~~~~~~~~~~ bigWig.c:319:7: warning: 'rangesListEls' may be used uninitialized in this function [-Wmaybe-uninitialized] SET_VECTOR_ELT(rangesListEls, i, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ new_IRanges("IRanges", ans_start, ans_width, R_NilValue)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -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), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ line-header_line); ~~~~~~~~~~~~~~~~~ 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 -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c twoBit.c -o twoBit.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c handlers.c -o handlers.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -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 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -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 -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -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: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 -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -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:187:18: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable] char *blockPt, *blockEnd; ^~~~~~~~ gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/cirTree.c -o ucsc/cirTree.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/common.c -o ucsc/common.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/dnaseq.c -o ucsc/dnaseq.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -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 -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -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 -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/hash.c -o ucsc/hash.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/linefile.c -o ucsc/linefile.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/localmem.c -o ucsc/localmem.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/sqlNum.c -o ucsc/sqlNum.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/zlibFace.c -o ucsc/zlibFace.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/dystring.c -o ucsc/dystring.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/hmmstats.c -o ucsc/hmmstats.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/obscure.c -o ucsc/obscure.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/pipeline.c -o ucsc/pipeline.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/rangeTree.c -o ucsc/rangeTree.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/rbTree.c -o ucsc/rbTree.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/memalloc.c -o ucsc/memalloc.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/dlist.c -o ucsc/dlist.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -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 -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -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:1448:8: warning: variable 'version' set but not used [-Wunused-but-set-variable] char *version, *code; ^~~~~~~ gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/bits.c -o ucsc/bits.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/twoBit.c -o ucsc/twoBit.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/internet.c -o ucsc/internet.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/https.c -o ucsc/https.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/base64.c -o ucsc/base64.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/verbose.c -o ucsc/verbose.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/os.c -o ucsc/os.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/wildcmp.c -o ucsc/wildcmp.o gcc -m32 -I/usr/include/R -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I/usr/local/include -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 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ucsc/_portimpl.c -o ucsc/_portimpl.o gcc -m32 -shared -L/usr/lib/R/lib -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -L/usr/lib/R/lib -lR installing to /builddir/build/BUILDROOT/R-rtracklayer-1.36.3-1.fc24.i386/usr/lib/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 converting help for package 'rtracklayer' finding HTML links ... done BEDFile-class html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BEDFile-class.Rd:117: missing file link 'findOverlaps' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BEDFile-class.Rd:183: missing file link 'BamFile' BamFile-methods html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BamFile-methods.Rd:11: missing file link 'GAlignments' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BamFile-methods.Rd:12: missing file link 'GAlignmentPairs' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BamFile-methods.Rd:13: missing file link 'BamFile' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BamFile-methods.Rd:33: missing file link 'ScanBamParam' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BamFile-methods.Rd:46: missing file link 'filterBam' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BamFile-methods.Rd:51: missing file link 'readGAlignmentPairs' Bed15TrackLine-class html BigWigFile html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BigWigFile.Rd:138: missing file link 'Seqinfo' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BigWigFile.Rd:153: 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 Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BrowserViewList-class.Rd:13: missing file link 'Vector' Chain-class html FastaFile-class html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/FastaFile-class.Rd:50: missing file link 'writeXStringSet' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/FastaFile-class.Rd:51: missing file link 'readDNAStringSet' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/FastaFile-class.Rd:58: missing file link 'writeXStringSet' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/FastaFile-class.Rd:59: missing file link 'readDNAStringSet' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/FastaFile-class.Rd:62: file link 'export-methods' in package 'BSgenome' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/FastaFile-class.Rd:63: missing file link 'BSgenome' GFFFile-class html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GFFFile-class.Rd:125: missing file link 'findOverlaps' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GFFFile-class.Rd:190: missing file link 'BamFile' GRangesForUCSCGenome html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GRangesForUCSCGenome.Rd:12: missing file link 'Seqinfo' 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' GenomicData html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GenomicData.Rd:46: missing file link 'GRanges' 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 Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/QuickloadGenome-class.Rd:60: missing file link 'BSgenome' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/QuickloadGenome-class.Rd:61: missing file link 'GenomeDescription' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/QuickloadGenome-class.Rd:83: missing file link 'Seqinfo' RTLFile-class html RangesList-methods html TabixFile-methods html TrackDb-class html TwoBitFile-class html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/TwoBitFile-class.Rd:99: missing file link 'Seqinfo' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/TwoBitFile-class.Rd:107: file link 'export-methods' in package 'BSgenome' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/TwoBitFile-class.Rd:108: missing file link 'BSgenome' 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 Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/blocks-methods.Rd:9: missing file link 'GRanges' browseGenome html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/browseGenome.Rd:19: missing file link 'GRanges' 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 'GenomicRangesList' 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:138: missing file link 'BamFile' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/export.Rd:148: missing file link 'FaFile' genomeBrowsers html laySequence-methods html layTrack-methods html liftOver html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/liftOver.Rd:23: missing file link 'GRanges' readGFF html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/readGFF.Rd:11: missing file link 'DataFrame' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/readGFF.Rd:64: missing file link 'GRanges' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/readGFF.Rd:68: missing file link 'GRanges' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/readGFF.Rd:69: missing file link 'DataFrame' Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/readGFF.Rd:75: missing file link 'DataFrame' 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 ** installing vignettes ** testing if installed package can be loaded * DONE (rtracklayer) + test -d rtracklayer/src + cd rtracklayer/src + rm -f IRanges_stubs.o R_init_rtracklayer.o S4Vectors_stubs.o XVector_stubs.o bigWig.o chain_io.o handlers.o readGFF.o twoBit.o utils.o rtracklayer.so + rm -rf /builddir/build/BUILDROOT/R-rtracklayer-1.36.3-1.fc24.i386/usr/lib/R/library/R.css + rm -rf /builddir/build/BUILDROOT/R-rtracklayer-1.36.3-1.fc24.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-1.36.3-1.fc24.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. 1760 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.JMPI9J + umask 022 + cd /builddir/build/BUILD + cd rtracklayer Processing files: R-rtracklayer-1.36.3-1.fc24.i686 + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.Anm8pH + umask 022 + cd /builddir/build/BUILD + cd rtracklayer + LICENSEDIR=/builddir/build/BUILDROOT/R-rtracklayer-1.36.3-1.fc24.i386/usr/share/licenses/R-rtracklayer + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/R-rtracklayer-1.36.3-1.fc24.i386/usr/share/licenses/R-rtracklayer + cp -pr rtracklayer_jimkent_license.txt /builddir/build/BUILDROOT/R-rtracklayer-1.36.3-1.fc24.i386/usr/share/licenses/R-rtracklayer + exit 0 Provides: R-rtracklayer = 1.36.3-1.fc24 R-rtracklayer(x86-32) = 1.36.3-1.fc24 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) 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-1.36.3-1.fc24.i686 Provides: R-rtracklayer-debuginfo = 1.36.3-1.fc24 R-rtracklayer-debuginfo(x86-32) = 1.36.3-1.fc24 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-rtracklayer-1.36.3-1.fc24.i386 Wrote: /builddir/build/RPMS/R-rtracklayer-1.36.3-1.fc24.i686.rpm Wrote: /builddir/build/RPMS/R-rtracklayer-debuginfo-1.36.3-1.fc24.i686.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.5WhhyI + umask 022 + cd /builddir/build/BUILD + cd rtracklayer + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-rtracklayer-1.36.3-1.fc24.i386 + exit 0 Child return code was: 0