Mock Version: 1.4.21 Mock Version: 1.4.21 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R-rtracklayer.spec'], chrootPath='/var/lib/mock/f33-build-194291-47088/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=432000uid=987gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R-rtracklayer.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1580169600 Wrote: /builddir/build/SRPMS/R-rtracklayer-1.46.0-3.fc33.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-rtracklayer.spec'], chrootPath='/var/lib/mock/f33-build-194291-47088/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=432000uid=987gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-rtracklayer.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1580169600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.x5Ufyc + 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_1.46.0.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 . + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.AK9are + umask 022 + cd /builddir/build/BUILD + cd rtracklayer + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.8ZhGge + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-rtracklayer-1.46.0-3.fc33.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-rtracklayer-1.46.0-3.fc33.riscv64 ++ dirname /builddir/build/BUILDROOT/R-rtracklayer-1.46.0-3.fc33.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-rtracklayer-1.46.0-3.fc33.riscv64 + cd rtracklayer + mkdir -p /builddir/build/BUILDROOT/R-rtracklayer-1.46.0-3.fc33.riscv64/usr/lib64/R/library + /usr/bin/R CMD INSTALL rtracklayer -l /builddir/build/BUILDROOT/R-rtracklayer-1.46.0-3.fc33.riscv64/usr/lib64/R/library * installing *source* package 'rtracklayer' ... ** using staged installation checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for OPENSSL... yes configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c XVector_stubs.c -o XVector_stubs.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c R_init_rtracklayer.c -o R_init_rtracklayer.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c readGFF.c -o readGFF.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c bigWig.c -o bigWig.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c chain_io.c -o chain_io.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c twoBit.c -o twoBit.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c handlers.c -o handlers.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c utils.c -o utils.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o In function 'writeIndexLevel', inlined from 'bptFileBulkIndexToOpenFile' at ucsc/bPlusTree.c:567:29: ucsc/bPlusTree.c:461:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 461 | keyBuf[keySize] = 0; | ~~~~~~~~~~~~~~~~^~~ ucsc/bPlusTree.c: In function 'bptFileBulkIndexToOpenFile': ucsc/bPlusTree.c:460:6: note: at offset [-9223372036854775808, 9223372036854775807] to an object with size at most 4294967295 declared here 460 | char keyBuf[keySize+1]; | ^~~~~~ In function 'writeLeafLevel', inlined from 'bptFileBulkIndexToOpenFile' at ucsc/bPlusTree.c:575:1: ucsc/bPlusTree.c:513:17: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 513 | keyBuf[keySize] = 0; | ~~~~~~~~~~~~~~~~^~~ ucsc/bPlusTree.c: In function 'bptFileBulkIndexToOpenFile': ucsc/bPlusTree.c:512:6: note: at offset [-9223372036854775808, 9223372036854775807] to an object with size at most 4294967295 declared here 512 | char keyBuf[keySize+1]; | ^~~~~~ gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/bbiRead.c -o ucsc/bbiRead.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 187 | char *blockPt, *blockEnd; | ^~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/cirTree.c -o ucsc/cirTree.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/common.c -o ucsc/common.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/dnaseq.c -o ucsc/dnaseq.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/dnautil.c -o ucsc/dnautil.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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] 331 | write(STDERR_FILENO, errMsg, strlen(errMsg)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/hash.c -o ucsc/hash.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/linefile.c -o ucsc/linefile.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/localmem.c -o ucsc/localmem.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/sqlNum.c -o ucsc/sqlNum.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/zlibFace.c -o ucsc/zlibFace.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/dystring.c -o ucsc/dystring.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/hmmstats.c -o ucsc/hmmstats.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/obscure.c -o ucsc/obscure.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/pipeline.c -o ucsc/pipeline.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/rangeTree.c -o ucsc/rangeTree.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/rbTree.c -o ucsc/rbTree.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/memalloc.c -o ucsc/memalloc.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/dlist.c -o ucsc/dlist.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/udc.c -o ucsc/udc.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/net.c -o ucsc/net.o ucsc/net.c: In function 'netConnectWithTimeout': ucsc/net.c:148:31: warning: passing argument 3 to 'restrict'-qualified parameter aliases with argument 4 [-Wrestrict] 148 | res = select(sd+1, NULL, &mySet, &mySet, &tempTime); | ^~~~~~ ~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/bits.c -o ucsc/bits.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/twoBit.c -o ucsc/twoBit.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/internet.c -o ucsc/internet.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/https.c -o ucsc/https.o ucsc/https.c:27:13: warning: 'openssl_locking_callback' defined but not used [-Wunused-function] 27 | static void openssl_locking_callback(int mode, int n, const char * file, int line) | ^~~~~~~~~~~~~~~~~~~~~~~~ ucsc/https.c:22:22: warning: 'openssl_id_callback' defined but not used [-Wunused-function] 22 | static unsigned long openssl_id_callback(void) | ^~~~~~~~~~~~~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/base64.c -o ucsc/base64.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/verbose.c -o ucsc/verbose.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/os.c -o ucsc/os.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/wildcmp.c -o ucsc/wildcmp.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ucsc/_portimpl.c -o ucsc/_portimpl.o gcc -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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 -lssl -lcrypto -L/usr/lib64/R/lib -lR installing to /builddir/build/BUILDROOT/R-rtracklayer-1.46.0-3.fc33.riscv64/usr/lib64/R/library/00LOCK-rtracklayer/00new/rtracklayer/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading Warning: no function found corresponding to methods exports from 'GenomicAlignments' for: 'concatenateObjects' 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:136: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BEDFile-class.Rd:210: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic BamFile-methods html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BamFile-methods.Rd:11: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BamFile-methods.Rd:12: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BamFile-methods.Rd:13: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BamFile-methods.Rd:33: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BamFile-methods.Rd:46: file link 'filterBam' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BamFile-methods.Rd:51: file link 'readGAlignmentPairs' in package 'GenomicAlignments' 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:139: file link 'Seqinfo' in package 'GenomeInfoDb' does not exist and so has been treated as a topic BigWigSelection-class html finding level-2 HTML links ... done Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BigWigSelection-class.Rd:15: file link 'RangedSelection' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BigWigSelection-class.Rd:37: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BigWigSelection-class.Rd:38: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic BrowserViewList-class html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/BrowserViewList-class.Rd:13: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic Chain-class html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/Chain-class.Rd:51: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic FastaFile-class html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/FastaFile-class.Rd:50: file link 'writeXStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/FastaFile-class.Rd:51: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/FastaFile-class.Rd:58: file link 'writeXStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/FastaFile-class.Rd:59: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic GFFFile-class html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GFFFile-class.Rd:125: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GFFFile-class.Rd:190: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic GRangesForUCSCGenome html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GRangesForUCSCGenome.Rd:12: file link 'Seqinfo' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GRangesForUCSCGenome.Rd:31: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GRangesForUCSCGenome.Rd:35: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GRangesForUCSCGenome.Rd:54: file link 'seqlengths' in package 'GenomeInfoDb' does not exist and so has been treated as a topic GenomicData html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GenomicData.Rd:45: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic GenomicSelection html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GenomicSelection.Rd:7: file link 'RangedSelection' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GenomicSelection.Rd:26: file link 'RangedSelection' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/GenomicSelection.Rd:33: file link 'RangedSelection' in package 'IRanges' does not exist and so has been treated as a topic IntegerRangesList-methods html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/IntegerRangesList-methods.Rd:29: missing file link 'names' Quickload-class html QuickloadGenome-class html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/QuickloadGenome-class.Rd:61: file link 'GenomeDescription' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/QuickloadGenome-class.Rd:83: file link 'Seqinfo' in package 'GenomeInfoDb' does not exist and so has been treated as a topic RTLFile-class html TabixFile-methods html TrackDb-class html TwoBitFile-class html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/TwoBitFile-class.Rd:107: file link 'Seqinfo' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/TwoBitFile-class.Rd:92: file link 'replaceAmbiguities' in package 'Biostrings' does not exist and so has been treated as a topic UCSCData-class html UCSCFile-class html UCSCSchema-class html UCSCTableQuery-class html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/UCSCTableQuery-class.Rd:70: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/UCSCTableQuery-class.Rd:71: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic 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: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic browseGenome html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/browseGenome.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/browseGenome.Rd:19: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/browseGenome.Rd:20: file link 'GenomicRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/browseGenome.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/browseGenome.Rd:24: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic browserSession-class html browserSession-methods html browserView-class html browserView-methods html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/browserView-methods.Rd:15: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/browserView-methods.Rd:16: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic browserViews-methods html cpneTrack html export html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/export.Rd:137: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/export.Rd:147: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic genomeBrowsers html laySequence-methods html layTrack-methods html liftOver html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/liftOver.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic readGFF html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/readGFF.Rd:11: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/readGFF.Rd:64: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/readGFF.Rd:68: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/readGFF.Rd:69: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/readGFF.Rd:75: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic targets html tracks-methods html ucscGenomes html ucscSession-class html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/ucscSession-class.Rd:62: file link 'Seqinfo' in package 'GenomeInfoDb' does not exist and so has been treated as a topic ucscTrackLine-class html ucscTrackModes-class html ucscTrackModes-methods html ucscView-class html Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/ucscView-class.Rd:46: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/rtracklayer/rtracklayer/man/ucscView-class.Rd:47: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic wigToBigWig html wigTrackLine-class html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: no function found corresponding to methods exports from 'GenomicAlignments' for: 'concatenateObjects' ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: no function found corresponding to methods exports from 'GenomicAlignments' for: 'concatenateObjects' ** testing if installed package keeps a record of temporary installation path * 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-1.46.0-3.fc33.riscv64/usr/lib64/R/library/R.css + rm -rf /builddir/build/BUILDROOT/R-rtracklayer-1.46.0-3.fc33.riscv64/usr/lib64/R/library/rtracklayer/tests/quickload/T_species_Oct_2011/bedGraphData.bw + /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 1.46.0-3.fc33 --unique-debug-suffix -1.46.0-3.fc33.riscv64 --unique-debug-src-base R-rtracklayer-1.46.0-3.fc33.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/rtracklayer explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-rtracklayer-1.46.0-3.fc33.riscv64/usr/lib64/R/library/rtracklayer/libs/rtracklayer.so extracting debug info from /builddir/build/BUILDROOT/R-rtracklayer-1.46.0-3.fc33.riscv64/usr/lib64/R/library/rtracklayer/libs/rtracklayer.so original debug info size: 1652kB, size after compression: 1568kB /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. 1752 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/redhat/brp-python-bytecompile /usr/bin/python 1 0 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.yanGAf + umask 022 + cd /builddir/build/BUILD + cd rtracklayer + RPM_EC=0 ++ jobs -p + exit 0 Processing files: R-rtracklayer-1.46.0-3.fc33.riscv64 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.KsAy8c + umask 022 + cd /builddir/build/BUILD + cd rtracklayer + LICENSEDIR=/builddir/build/BUILDROOT/R-rtracklayer-1.46.0-3.fc33.riscv64/usr/share/licenses/R-rtracklayer + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/R-rtracklayer-1.46.0-3.fc33.riscv64/usr/share/licenses/R-rtracklayer + cp -pr rtracklayer_jimkent_license.txt /builddir/build/BUILDROOT/R-rtracklayer-1.46.0-3.fc33.riscv64/usr/share/licenses/R-rtracklayer + RPM_EC=0 ++ jobs -p + exit 0 Provides: R(rtracklayer) = 1.46.0 R-rtracklayer = 1.46.0-3.fc33 R-rtracklayer(riscv-64) = 1.46.0-3.fc33 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: R(BiocGenerics) >= 0.25.1 R(Biostrings) >= 2.47.6 R(GenomeInfoDb) >= 1.15.2 R(GenomicAlignments) >= 1.15.6 R(GenomicRanges) >= 1.37.2 R(IRanges) >= 2.13.13 R(RCurl) >= 1.4-2 R(Rsamtools) >= 1.31.2 R(S4Vectors) >= 0.23.18 R(XML) >= 1.98-0 R(XVector) >= 0.19.7 R(methods) R(tools) R-core >= 3.3 ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libc.so.6(GLIBC_2.28)(64bit) libcrypto.so.1.1()(64bit) libcrypto.so.1.1(OPENSSL_1_1_0)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.27)(64bit) libssl.so.1.1()(64bit) libssl.so.1.1(OPENSSL_1_1_0)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Suggests: R(BSgenome) >= 1.33.4 R(RUnit) Processing files: R-rtracklayer-debugsource-1.46.0-3.fc33.riscv64 Provides: R-rtracklayer-debugsource = 1.46.0-3.fc33 R-rtracklayer-debugsource(riscv-64) = 1.46.0-3.fc33 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-rtracklayer-debuginfo-1.46.0-3.fc33.riscv64 Provides: R-rtracklayer-debuginfo = 1.46.0-3.fc33 R-rtracklayer-debuginfo(riscv-64) = 1.46.0-3.fc33 debuginfo(build-id) = 66e5999525c770d26aefacbfa2187a8d84604700 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-rtracklayer-debugsource(riscv-64) = 1.46.0-3.fc33 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-rtracklayer-1.46.0-3.fc33.riscv64 Wrote: /builddir/build/RPMS/R-rtracklayer-debugsource-1.46.0-3.fc33.riscv64.rpm Wrote: /builddir/build/RPMS/R-rtracklayer-debuginfo-1.46.0-3.fc33.riscv64.rpm Wrote: /builddir/build/RPMS/R-rtracklayer-1.46.0-3.fc33.riscv64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.N67Zud + umask 022 + cd /builddir/build/BUILD + cd rtracklayer + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-rtracklayer-1.46.0-3.fc33.riscv64 + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0