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-GenomicAlignments.spec'], chrootPath='/var/lib/mock/f33-build-193664-46967/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x3fb7c8e700>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-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;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: riscv64
Building for target riscv64
setting SOURCE_DATE_EPOCH=1580515200
Wrote: /builddir/build/SRPMS/R-GenomicAlignments-1.22.1-1.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-GenomicAlignments.spec'], chrootPath='/var/lib/mock/f33-build-193664-46967/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x3fb7c8e700>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-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;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: riscv64
Building for target riscv64
setting SOURCE_DATE_EPOCH=1580515200
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.BnScqx
+ 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_1.22.1.tar.gz
+ /usr/bin/tar -xof -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.bDnVLu
+ umask 022
+ cd /builddir/build/BUILD
+ cd GenomicAlignments
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.v7H7py
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/R-GenomicAlignments-1.22.1-1.fc33.riscv64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/R-GenomicAlignments-1.22.1-1.fc33.riscv64
++ dirname /builddir/build/BUILDROOT/R-GenomicAlignments-1.22.1-1.fc33.riscv64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/R-GenomicAlignments-1.22.1-1.fc33.riscv64
+ cd GenomicAlignments
+ mkdir -p /builddir/build/BUILDROOT/R-GenomicAlignments-1.22.1-1.fc33.riscv64/usr/lib64/R/library
+ R CMD INSTALL GenomicAlignments -l /builddir/build/BUILDROOT/R-GenomicAlignments-1.22.1-1.fc33.riscv64/usr/lib64/R/library
* installing *source* package 'GenomicAlignments' ...
** using staged installation
** 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
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:676:9: warning: 'f_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
  676 |    f_elt++;
      |    ~~~~~^~
cigar_utils.c:658:27: warning: 'range_buf2' may be used uninitialized in this function [-Wmaybe-uninitialized]
  658 |    range_buf1 = range_buf2->elts[*f_elt - 1];
      |                 ~~~~~~~~~~^~~~~~
cigar_utils.c:674:22: warning: 'range_buf1' may be used uninitialized in this function [-Wmaybe-uninitialized]
  674 |    *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
      |                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this function [-Wmaybe-uninitialized]
  674 |    *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
      |     ~~~~~~~~~~~^~~
cigar_utils.c:626:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
  626 |    if (*flag_elt == NA_INTEGER) {
      |        ^~~~~~~~~
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:708:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
  708 |    if (*flag_elt == NA_INTEGER) {
      |        ^~~~~~~~~
cigar_utils.c: In function 'cigar_narrow':
cigar_utils.c:876:2: warning: 'Roffset' may be used uninitialized in this function [-Wmaybe-uninitialized]
  876 |  for (offset = Loffset; offset <= Roffset; offset += n) {
      |  ^~~
cigar_utils.c:852:15: note: 'Roffset' was declared here
  852 |  int Loffset, Roffset, buf_offset;
      |               ^~~~~~~
cigar_utils.c:878:6: warning: 'Loffset' may be used uninitialized in this function [-Wmaybe-uninitialized]
  878 |   if (offset == Loffset)
      |      ^
cigar_utils.c:852:6: note: 'Loffset' was declared here
  852 |  int Loffset, Roffset, buf_offset;
      |      ^~~~~~~
cigar_utils.c: In function 'cigar_qnarrow':
cigar_utils.c:1064:6: warning: 'Roffset' may be used uninitialized in this function [-Wmaybe-uninitialized]
 1064 |   if (offset == Roffset)
      |      ^
cigar_utils.c:1036:15: note: 'Roffset' was declared here
 1036 |  int Loffset, Roffset, buf_offset;
      |               ^~~~~~~
cigar_utils.c:1062:6: warning: 'Loffset' may be used uninitialized in this function [-Wmaybe-uninitialized]
 1062 |   if (offset == Loffset)
      |      ^
cigar_utils.c:1036:6: note: 'Loffset' was declared here
 1036 |  int Loffset, Roffset, buf_offset;
      |      ^~~~~~~
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
encodeOverlaps_methods.c: In function 'overlap_encoding':
encodeOverlaps_methods.c:182:2: warning: 'out_nelt0' may be used uninitialized in this function [-Wmaybe-uninitialized]
  182 |  CharAE_delete_at(out, out_nelt0, j1 * nrow);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
encodeOverlaps_methods.c:99:6: note: 'out_nelt0' was declared here
   99 |  int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
      |      ^~~~~~~~~
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 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
installing to /builddir/build/BUILDROOT/R-GenomicAlignments-1.22.1-1.fc33.riscv64/usr/lib64/R/library/00LOCK-GenomicAlignments/00new/GenomicAlignments/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicAlignments'
    finding HTML links ... done
    GAlignmentPairs-class                   html  
    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:177: 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:189: 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:231: 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:283: 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:299: 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:304: 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:305: 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:347: 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:353: 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:379: 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:398: 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:398: 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:431: 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:432: 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:435: 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
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    encodeOverlaps-methods                  html  
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    findCompatibleOverlaps-methods          html  
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    findMateAlignment                       html  
    findOverlaps-methods                    html  
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    findSpliceOverlaps-methods              html  
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    intra-range-methods                     html  
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    junctions-methods                       html  
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    pileLettersAt                           html  
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    readGAlignments                         html  
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    sequenceLayer                           html  
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    setops-methods                          html  
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    stackStringsFromGAlignments             html  
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    summarizeOverlaps-methods               html  
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** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* 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-1.22.1-1.fc33.riscv64/usr/lib64/R/library/R.css
+ /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 1.22.1-1.fc33 --unique-debug-suffix -1.22.1-1.fc33.riscv64 --unique-debug-src-base R-GenomicAlignments-1.22.1-1.fc33.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/GenomicAlignments
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-GenomicAlignments-1.22.1-1.fc33.riscv64/usr/lib64/R/library/GenomicAlignments/libs/GenomicAlignments.so
extracting debug info from /builddir/build/BUILDROOT/R-GenomicAlignments-1.22.1-1.fc33.riscv64/usr/lib64/R/library/GenomicAlignments/libs/GenomicAlignments.so
original debug info size: 280kB, size after compression: 276kB
/usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
120 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.ggYUgx
+ umask 022
+ cd /builddir/build/BUILD
+ cd GenomicAlignments
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: R-GenomicAlignments-1.22.1-1.fc33.riscv64
Provides: R(GenomicAlignments) = 1.22.1 R-GenomicAlignments = 1.22.1-1.fc33 R-GenomicAlignments(riscv-64) = 1.22.1-1.fc33
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: R(BiocGenerics) >= 0.15.3 R(BiocParallel) R(Biostrings) >= 2.47.6 R(GenomeInfoDb) >= 1.13.1 R(GenomicRanges) >= 1.37.2 R(IRanges) >= 2.15.12 R(Rsamtools) >= 1.31.2 R(S4Vectors) >= 0.23.19 R(SummarizedExperiment) >= 1.9.13 R(methods) R(stats) R(utils) R-core >= 3.5.0 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)
Suggests: R(BSgenome) R(RUnit) R(rtracklayer)
Processing files: R-GenomicAlignments-debugsource-1.22.1-1.fc33.riscv64
Provides: R-GenomicAlignments-debugsource = 1.22.1-1.fc33 R-GenomicAlignments-debugsource(riscv-64) = 1.22.1-1.fc33
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-GenomicAlignments-debuginfo-1.22.1-1.fc33.riscv64
Provides: R-GenomicAlignments-debuginfo = 1.22.1-1.fc33 R-GenomicAlignments-debuginfo(riscv-64) = 1.22.1-1.fc33 debuginfo(build-id) = d0bdfa1c3cda6df5de175885cd2b17b15b4ffa30
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) = 1.22.1-1.fc33
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-GenomicAlignments-1.22.1-1.fc33.riscv64
Wrote: /builddir/build/RPMS/R-GenomicAlignments-debugsource-1.22.1-1.fc33.riscv64.rpm
Wrote: /builddir/build/RPMS/R-GenomicAlignments-debuginfo-1.22.1-1.fc33.riscv64.rpm
Wrote: /builddir/build/RPMS/R-GenomicAlignments-1.22.1-1.fc33.riscv64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.MGaxGx
+ umask 022
+ cd /builddir/build/BUILD
+ cd GenomicAlignments
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/R-GenomicAlignments-1.22.1-1.fc33.riscv64
+ RPM_EC=0
++ jobs -p
+ exit 0
Child return code was: 0