Mock Version: 1.4.9 Mock Version: 1.4.9 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R-GenomicAlignments.spec'], chrootPath='/var/lib/mock/f29-build-18493-9734/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', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'}shell=Falselogger=timeout=345600uid=995gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R-GenomicAlignments.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', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'} and shell False Building target platforms: riscv64 Building for target riscv64 Wrote: /builddir/build/SRPMS/R-GenomicAlignments-1.16.0-2.fc29.src.rpm Child return code was: 0 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-GenomicAlignments.spec'], chrootPath='/var/lib/mock/f29-build-18493-9734/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', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'}shell=Falselogger=timeout=345600uid=995gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-GenomicAlignments.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', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'} and shell False Building target platforms: riscv64 Building for target riscv64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.s4Z1N8 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf GenomicAlignments + /usr/bin/mkdir -p GenomicAlignments + cd GenomicAlignments + /usr/bin/gzip -dc /builddir/build/SOURCES/GenomicAlignments_1.16.0.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.xcCDlf + umask 022 + cd /builddir/build/BUILD + cd GenomicAlignments + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.iumy9k + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-GenomicAlignments-1.16.0-2.fc29.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-GenomicAlignments-1.16.0-2.fc29.riscv64 BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/R-GenomicAlignments-1.16.0-2.fc29.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-GenomicAlignments-1.16.0-2.fc29.riscv64 + cd GenomicAlignments + mkdir -p /builddir/build/BUILDROOT/R-GenomicAlignments-1.16.0-2.fc29.riscv64/usr/lib64/R/library + R CMD INSTALL GenomicAlignments -l /builddir/build/BUILDROOT/R-GenomicAlignments-1.16.0-2.fc29.riscv64/usr/lib64/R/library BUILDSTDERR: * installing *source* package 'GenomicAlignments' ... BUILDSTDERR: ** libs gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/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 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/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_GenomicAlignments.c -o R_init_GenomicAlignments.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/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 -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/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 cigar_utils.c -o cigar_utils.o BUILDSTDERR: cigar_utils.c: In function 'cigar_ranges': BUILDSTDERR: cigar_utils.c:658:27: warning: 'range_buf2' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: range_buf1 = range_buf2->elts[*f_elt - 1]; BUILDSTDERR: ~~~~~~~~~~^~~~~~ BUILDSTDERR: In file included from /usr/include/R/Rdefines.h:40, BUILDSTDERR: from GenomicAlignments.h:1, BUILDSTDERR: from cigar_utils.c:1: BUILDSTDERR: /usr/include/R/Rinternals.h:1352:20: warning: 'f_levels' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: #define duplicate Rf_duplicate BUILDSTDERR: ^~~~~~~~~~~~ BUILDSTDERR: cigar_utils.c:587:29: note: 'f_levels' was declared here BUILDSTDERR: SEXP ans, ans_breakpoints, f_levels, cigar_elt; BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: cigar_utils.c:542:4: warning: 'ans_breakpoints' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: new_PartitioningByEnd("PartitioningByEnd", BUILDSTDERR: ^~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: cigar_utils.c:587:12: note: 'ans_breakpoints' was declared here BUILDSTDERR: SEXP ans, ans_breakpoints, f_levels, cigar_elt; BUILDSTDERR: ^~~~~~~~~~~~~~~ BUILDSTDERR: cigar_utils.c:676:9: warning: 'f_elt' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: f_elt++; BUILDSTDERR: ~~~~~^~ BUILDSTDERR: cigar_utils.c:674:22: warning: 'range_buf1' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: *(breakpoint++) = IntPairAE_get_nelt(range_buf1); BUILDSTDERR: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: *(breakpoint++) = IntPairAE_get_nelt(range_buf1); BUILDSTDERR: ~~~~~~~~~~~^~~ BUILDSTDERR: cigar_utils.c:626:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: if (*flag_elt == NA_INTEGER) { BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: cigar_utils.c: In function 'cigar_width': BUILDSTDERR: cigar_utils.c:708:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: if (*flag_elt == NA_INTEGER) { BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: cigar_utils.c: In function 'cigar_narrow': BUILDSTDERR: cigar_utils.c:880:6: warning: 'Roffset' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: if (offset == Roffset) BUILDSTDERR: ^ BUILDSTDERR: cigar_utils.c:852:15: note: 'Roffset' was declared here BUILDSTDERR: int Loffset, Roffset, buf_offset; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: cigar_utils.c:878:6: warning: 'Loffset' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: if (offset == Loffset) BUILDSTDERR: ^ BUILDSTDERR: cigar_utils.c:852:6: note: 'Loffset' was declared here BUILDSTDERR: int Loffset, Roffset, buf_offset; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: cigar_utils.c: In function 'cigar_qnarrow': BUILDSTDERR: cigar_utils.c:1064:6: warning: 'Roffset' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: if (offset == Roffset) BUILDSTDERR: ^ BUILDSTDERR: cigar_utils.c:1036:15: note: 'Roffset' was declared here BUILDSTDERR: int Loffset, Roffset, buf_offset; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: cigar_utils.c:1062:6: warning: 'Loffset' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: if (offset == Loffset) BUILDSTDERR: ^ BUILDSTDERR: cigar_utils.c:1036:6: note: 'Loffset' was declared here BUILDSTDERR: int Loffset, Roffset, buf_offset; BUILDSTDERR: ^~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/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 coordinate_mapping_methods.c -o coordinate_mapping_methods.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/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 encodeOverlaps_methods.c -o encodeOverlaps_methods.o BUILDSTDERR: encodeOverlaps_methods.c: In function 'overlap_encoding': BUILDSTDERR: encodeOverlaps_methods.c:180:33: warning: 'out_nelt0' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: CharAE_set_nelt(out, out_nelt0 + j2 * nrow); BUILDSTDERR: ~~~~~~~~~~^~~~~~~~~~~ BUILDSTDERR: encodeOverlaps_methods.c:99:6: note: 'out_nelt0' was declared here BUILDSTDERR: int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej, BUILDSTDERR: ^~~~~~~~~ gcc -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -L/usr/lib64/R/lib -lR BUILDSTDERR: installing to /builddir/build/BUILDROOT/R-GenomicAlignments-1.16.0-2.fc29.riscv64/usr/lib64/R/library/GenomicAlignments/libs BUILDSTDERR: ** R BUILDSTDERR: ** inst BUILDSTDERR: ** byte-compile and prepare package for lazy loading BUILDSTDERR: ** help BUILDSTDERR: *** installing help indices converting help for package 'GenomicAlignments' BUILDSTDERR: finding HTML links ... done BUILDSTDERR: GAlignmentPairs-class html BUILDSTDERR: finding level-2 HTML links ... done Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignmentPairs-class.Rd:168: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignmentPairs-class.Rd:191: file link 'Seqinfo' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignmentPairs-class.Rd:278: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignmentPairs-class.Rd:355: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignmentPairs-class.Rd:357: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignmentPairs-class.Rd:357: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignmentPairs-class.Rd:389: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignmentPairs-class.Rd:390: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic GAlignments-class html Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignments-class.Rd:173: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignments-class.Rd:185: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignments-class.Rd:227: file link 'Seqinfo' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignments-class.Rd:279: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignments-class.Rd:295: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignments-class.Rd:300: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignments-class.Rd:301: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignments-class.Rd:343: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignments-class.Rd:349: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignments-class.Rd:375: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignments-class.Rd:394: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignments-class.Rd:394: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignments-class.Rd:427: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignments-class.Rd:428: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignments-class.Rd:431: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic GAlignmentsList-class html Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignmentsList-class.Rd:133: file link 'Seqinfo' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignmentsList-class.Rd:174: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignmentsList-class.Rd:192: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignmentsList-class.Rd:260: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignmentsList-class.Rd:291: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GAlignmentsList-class.Rd:292: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic GappedReads-class html Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/GappedReads-class.Rd:43: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic OverlapEncodings-class html Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/OverlapEncodings-class.Rd:112: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/OverlapEncodings-class.Rd:273: file link 'pcompare' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/OverlapEncodings-class.Rd:277: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic cigar-utils html Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/cigar-utils.Rd:133: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/cigar-utils.Rd:135: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/cigar-utils.Rd:139: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/cigar-utils.Rd:189: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/cigar-utils.Rd:221: file link 'CompressedRleList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/cigar-utils.Rd:229: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/cigar-utils.Rd:230: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/cigar-utils.Rd:233: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/cigar-utils.Rd:233: file link 'SimpleIRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/cigar-utils.Rd:234: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/cigar-utils.Rd:289: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/cigar-utils.Rd:289: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/cigar-utils.Rd:290: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/cigar-utils.Rd:292: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic coordinate-mapping-methods html coverage-methods html Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/coverage-methods.Rd:15: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/coverage-methods.Rd:17: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/coverage-methods.Rd:19: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/coverage-methods.Rd:20: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/coverage-methods.Rd:20: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/coverage-methods.Rd:22: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/coverage-methods.Rd:23: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/coverage-methods.Rd:46: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/coverage-methods.Rd:49: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/coverage-methods.Rd:53: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/coverage-methods.Rd:65: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/coverage-methods.Rd:70: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/coverage-methods.Rd:84: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/coverage-methods.Rd:92: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: 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a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/summarizeOverlaps-methods.Rd:251: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/summarizeOverlaps-methods.Rd:252: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/summarizeOverlaps-methods.Rd:254: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/summarizeOverlaps-methods.Rd:259: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/summarizeOverlaps-methods.Rd:261: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/summarizeOverlaps-methods.Rd:284: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/summarizeOverlaps-methods.Rd:315: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/summarizeOverlaps-methods.Rd:320: file link 'BamFileList' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicAlignments/GenomicAlignments/man/summarizeOverlaps-methods.Rd:320: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic BUILDSTDERR: ** building package indices BUILDSTDERR: ** installing vignettes BUILDSTDERR: ** testing if installed package can be loaded BUILDSTDERR: * DONE (GenomicAlignments) + test -d GenomicAlignments/src + cd GenomicAlignments/src + rm -f IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o GenomicAlignments.so + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-GenomicAlignments-1.16.0-2.fc29.riscv64/usr/lib64/R/library/R.css + /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 1.16.0-2.fc29 --unique-debug-suffix -1.16.0-2.fc29.riscv64 --unique-debug-src-base R-GenomicAlignments-1.16.0-2.fc29.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/GenomicAlignments extracting debug info from /builddir/build/BUILDROOT/R-GenomicAlignments-1.16.0-2.fc29.riscv64/usr/lib64/R/library/GenomicAlignments/libs/GenomicAlignments.so /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. BUILDSTDERR: 120 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig BUILDSTDERR: /sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory + /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 1 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.sqYK7U + umask 022 + cd /builddir/build/BUILD + cd GenomicAlignments + exit 0 Processing files: R-GenomicAlignments-1.16.0-2.fc29.riscv64 Provides: R-GenomicAlignments = 1.16.0-2.fc29 R-GenomicAlignments(riscv-64) = 1.16.0-2.fc29 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: 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) rtld(GNU_HASH) Processing files: R-GenomicAlignments-debugsource-1.16.0-2.fc29.riscv64 Provides: R-GenomicAlignments-debugsource = 1.16.0-2.fc29 R-GenomicAlignments-debugsource(riscv-64) = 1.16.0-2.fc29 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-GenomicAlignments-debuginfo-1.16.0-2.fc29.riscv64 Provides: R-GenomicAlignments-debuginfo = 1.16.0-2.fc29 R-GenomicAlignments-debuginfo(riscv-64) = 1.16.0-2.fc29 debuginfo(build-id) = d7d58f48a27d019bb85d705e47863b9808758385 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-GenomicAlignments-debugsource(riscv-64) = 1.16.0-2.fc29 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-GenomicAlignments-1.16.0-2.fc29.riscv64 Wrote: /builddir/build/RPMS/R-GenomicAlignments-1.16.0-2.fc29.riscv64.rpm Wrote: /builddir/build/RPMS/R-GenomicAlignments-debugsource-1.16.0-2.fc29.riscv64.rpm Wrote: /builddir/build/RPMS/R-GenomicAlignments-debuginfo-1.16.0-2.fc29.riscv64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.WS7deW + umask 022 + cd /builddir/build/BUILD + cd GenomicAlignments + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-GenomicAlignments-1.16.0-2.fc29.riscv64 + exit 0 Child return code was: 0