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-Biostrings.spec'], chrootPath='/var/lib/mock/f29-build-18486-9722/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', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x2001fd7710>timeout=345600uid=998gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R-Biostrings.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', '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-Biostrings-2.48.0-2.fc29.src.rpm
Child return code was: 0
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-Biostrings.spec'], chrootPath='/var/lib/mock/f29-build-18486-9722/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', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x2001fd7710>timeout=345600uid=998gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-Biostrings.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', '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.JnCSac
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf Biostrings
+ /usr/bin/mkdir -p Biostrings
+ cd Biostrings
+ /usr/bin/gzip -dc /builddir/build/SOURCES/Biostrings_2.48.0.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.WtXzDd
+ umask 022
+ cd /builddir/build/BUILD
+ cd Biostrings
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.TDMZ4t
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/R-Biostrings-2.48.0-2.fc29.riscv64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.48.0-2.fc29.riscv64
BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/R-Biostrings-2.48.0-2.fc29.riscv64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/R-Biostrings-2.48.0-2.fc29.riscv64
+ cd Biostrings
+ rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.48.0-2.fc29.riscv64
+ mkdir -p /builddir/build/BUILDROOT/R-Biostrings-2.48.0-2.fc29.riscv64/usr/lib64/R/library
+ R CMD INSTALL Biostrings -l /builddir/build/BUILDROOT/R-Biostrings-2.48.0-2.fc29.riscv64/usr/lib64/R/library
BUILDSTDERR: * installing *source* package 'Biostrings' ...
BUILDSTDERR: ** libs
gcc -I"/usr/include/R" -DNDEBUG  -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 BAB_class.c -o BAB_class.o
gcc -I"/usr/include/R" -DNDEBUG  -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 BitMatrix.c -o BitMatrix.o
BUILDSTDERR: BitMatrix.c:299:13: warning: 'BitMatrix_print' defined but not used [-Wunused-function]
BUILDSTDERR:  static void BitMatrix_print(BitMatrix *bitmat)
BUILDSTDERR:              ^~~~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -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  -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 MIndex_class.c -o MIndex_class.o
BUILDSTDERR: MIndex_class.c: In function 'SparseMIndex_endIndex':
BUILDSTDERR: MIndex_class.c:184:20: warning: unused variable 'poffsets_order' [-Wunused-variable]
BUILDSTDERR:   IntAE *poffsets, *poffsets_order;
BUILDSTDERR:                     ^~~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -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 PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I"/usr/include/R" -DNDEBUG  -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_Biostrings.c -o R_init_Biostrings.o
gcc -I"/usr/include/R" -DNDEBUG  -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 RoSeqs_utils.c -o RoSeqs_utils.o
gcc -I"/usr/include/R" -DNDEBUG  -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  -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 SparseList_utils.c -o SparseList_utils.o
gcc -I"/usr/include/R" -DNDEBUG  -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 XStringSetList_class.c -o XStringSetList_class.o
gcc -I"/usr/include/R" -DNDEBUG  -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 XStringSet_class.c -o XStringSet_class.o
BUILDSTDERR: XStringSet_class.c: In function 'new_XStringSet_from_CHARACTER':
BUILDSTDERR: XStringSet_class.c:124:3: warning: 'lkup_len' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:    _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
BUILDSTDERR:    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR:      INTEGER(start)[i], lkup0, lkup_len);
BUILDSTDERR:      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -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 XStringSet_io.c -o XStringSet_io.o
BUILDSTDERR: XStringSet_io.c: In function 'parse_FASTQ_file':
BUILDSTDERR: XStringSet_io.c:832:8: warning: 'seq_len' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:      if (data.length != seq_len) {
BUILDSTDERR:         ^
BUILDSTDERR: XStringSet_io.c:831:7: warning: 'load_rec' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:     if (load_rec) {
BUILDSTDERR:        ^
gcc -I"/usr/include/R" -DNDEBUG  -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 XString_class.c -o XString_class.o
gcc -I"/usr/include/R" -DNDEBUG  -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  -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 align_needwunsQS.c -o align_needwunsQS.o
BUILDSTDERR: align_needwunsQS.c: In function 'align_needwunsQS':
BUILDSTDERR: align_needwunsQS.c:155:22: warning: 'sc' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   INTEGER(ans_elt)[0] = score;
BUILDSTDERR:   ~~~~~~~~~~~~~~~~~~~~^~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -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 align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -I"/usr/include/R" -DNDEBUG  -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 align_utils.c -o align_utils.o
BUILDSTDERR: align_utils.c: In function 'PairwiseAlignmentsSingleSubject_align_aligned':
BUILDSTDERR: align_utils.c:254:14: warning: 'indelWidthSubject' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:      jPattern += indelWidthSubject;
BUILDSTDERR:      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: align_utils.c:235:36: warning: 'indelStartSubject' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:     if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
BUILDSTDERR:         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: align_utils.c:225:26: warning: 'indelWidthPattern' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:    int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
BUILDSTDERR:                           ^~~~~~~~~~~~~~~~~
BUILDSTDERR: align_utils.c:236:37: warning: 'indelStartPattern' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:      if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
BUILDSTDERR:          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -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 find_palindromes.c -o find_palindromes.o
gcc -I"/usr/include/R" -DNDEBUG  -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 gtestsim.c -o gtestsim.o
gcc -I"/usr/include/R" -DNDEBUG  -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 inject_code.c -o inject_code.o
gcc -I"/usr/include/R" -DNDEBUG  -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 letter_frequency.c -o letter_frequency.o
BUILDSTDERR: letter_frequency.c: In function 'XStringSet_two_way_letter_frequency':
BUILDSTDERR: letter_frequency.c:957:48: warning: unused variable 'x_pos' [-Wunused-variable]
BUILDSTDERR:    int x_width, y_width, x_length, *ans_mat, i, x_pos;
BUILDSTDERR:                                                 ^~~~~
BUILDSTDERR: letter_frequency.c:956:13: warning: unused variable 'ans_dimnames' [-Wunused-variable]
BUILDSTDERR:    SEXP ans, ans_dimnames;
BUILDSTDERR:              ^~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -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 lowlevel_matching.c -o lowlevel_matching.o
gcc -I"/usr/include/R" -DNDEBUG  -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 match_PWM.c -o match_PWM.o
gcc -I"/usr/include/R" -DNDEBUG  -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 match_pattern.c -o match_pattern.o
gcc -I"/usr/include/R" -DNDEBUG  -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 match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -I"/usr/include/R" -DNDEBUG  -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 match_pattern_indels.c -o match_pattern_indels.o
BUILDSTDERR: match_pattern_indels.c:7:13: warning: 'test_match_pattern_indels' defined but not used [-Wunused-function]
BUILDSTDERR:  static void test_match_pattern_indels(const char *p, const char *s,
BUILDSTDERR:              ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -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 match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -I"/usr/include/R" -DNDEBUG  -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 match_pdict.c -o match_pdict.o
BUILDSTDERR: match_pdict.c: In function 'vmatch_PDict3Parts_XStringSet':
BUILDSTDERR: match_pdict.c:419:12: warning: 'ans_col' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:     ans_col += tb_length;
BUILDSTDERR:     ~~~~~~~~^~~~~~~~~~~~
BUILDSTDERR: match_pdict.c:392:58: note: 'ans_col' was declared here
BUILDSTDERR:   int tb_length, S_length, collapse0, i, j, match_count, *ans_col;
BUILDSTDERR:                                                           ^~~~~~~
BUILDSTDERR: match_pdict.c: In function 'vmatch_XStringSet_XStringSet':
BUILDSTDERR: match_pdict.c:470:13: warning: 'ans_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:      ans_elt += P_length;
BUILDSTDERR:      ~~~~~~~~^~~~~~~~~~~
BUILDSTDERR: match_pdict.c:441:57: note: 'ans_elt' was declared here
BUILDSTDERR:   int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
BUILDSTDERR:                                                          ^~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -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 match_pdict_ACtree2.c -o match_pdict_ACtree2.o
BUILDSTDERR: match_pdict_ACtree2.c: In function 'split_and_move_pointers':
BUILDSTDERR: match_pdict_ACtree2.c:1031:10: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   ACnode *node0, *node1, *node2;
BUILDSTDERR:           ^~~~~
BUILDSTDERR: match_pdict_ACtree2.c: In function 'merge_pointers':
BUILDSTDERR: match_pdict_ACtree2.c:1076:10: warning: variable 'node0' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   ACnode *node0, *node1, *node2;
BUILDSTDERR:           ^~~~~
BUILDSTDERR: At top level:
BUILDSTDERR: match_pdict_ACtree2.c:602:21: warning: 'a_nice_max_nodeextbuf_nelt' defined but not used [-Wunused-function]
BUILDSTDERR:  static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
BUILDSTDERR:                      ^~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: match_pdict_ACtree2.c:139:13: warning: 'debug_node_counting_functions' defined but not used [-Wunused-function]
BUILDSTDERR:  static void debug_node_counting_functions(int maxdepth)
BUILDSTDERR:              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -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 match_pdict_Twobit.c -o match_pdict_Twobit.o
BUILDSTDERR: match_pdict_Twobit.c: In function 'build_Twobit':
BUILDSTDERR: match_pdict_Twobit.c:75:20: warning: 'twobit_sign2pos' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos));
BUILDSTDERR:                     ^~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: match_pdict_Twobit.c:110:12: note: 'twobit_sign2pos' was declared here
BUILDSTDERR:   SEXP ans, twobit_sign2pos;
BUILDSTDERR:             ^~~~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -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 match_pdict_utils.c -o match_pdict_utils.o
BUILDSTDERR: match_pdict_utils.c: In function 'match_ppheadtail0':
BUILDSTDERR: match_pdict_utils.c:652:49: warning: unused variable 'ncol' [-Wunused-variable]
BUILDSTDERR:   int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
BUILDSTDERR:                                                  ^~~~
BUILDSTDERR: match_pdict_utils.c: In function 'match_ppheadtail':
BUILDSTDERR: match_pdict_utils.c:712:6: warning: unused variable 'nelt' [-Wunused-variable]
BUILDSTDERR:   int nelt, nkey0, nkey1, nkey2, i, key;
BUILDSTDERR:       ^~~~
BUILDSTDERR: match_pdict_utils.c: In function '_match_pdict_all_flanks':
BUILDSTDERR: match_pdict_utils.c:819:44: warning: unused variable 'subtotal_NFC' [-Wunused-variable]
BUILDSTDERR:   static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
BUILDSTDERR:                                             ^~~~~~~~~~~~
BUILDSTDERR: match_pdict_utils.c:819:27: warning: unused variable 'total_NFC' [-Wunused-variable]
BUILDSTDERR:   static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
BUILDSTDERR:                            ^~~~~~~~~
BUILDSTDERR: match_pdict_utils.c:818:33: warning: unused variable 'NFC' [-Wunused-variable]
BUILDSTDERR:   unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
BUILDSTDERR:                                  ^~~
BUILDSTDERR: match_pdict_utils.c:818:26: warning: unused variable 'nloci' [-Wunused-variable]
BUILDSTDERR:   unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
BUILDSTDERR:                           ^~~~~
BUILDSTDERR: match_pdict_utils.c:818:20: warning: unused variable 'ndup' [-Wunused-variable]
BUILDSTDERR:   unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
BUILDSTDERR:                     ^~~~
BUILDSTDERR: At top level:
BUILDSTDERR: match_pdict_utils.c:819:27: warning: 'total_NFC' defined but not used [-Wunused-variable]
BUILDSTDERR:   static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
BUILDSTDERR:                            ^~~~~~~~~
BUILDSTDERR: match_pdict_utils.c:819:44: warning: 'subtotal_NFC' defined but not used [-Wunused-variable]
BUILDSTDERR:   static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
BUILDSTDERR:                                             ^~~~~~~~~~~~
BUILDSTDERR: match_pdict_utils.c:260:13: warning: 'match_headtail_by_loc' defined but not used [-Wunused-function]
BUILDSTDERR:  static void match_headtail_by_loc(const HeadTail *headtail,
BUILDSTDERR:              ^~~~~~~~~~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -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 match_reporting.c -o match_reporting.o
gcc -I"/usr/include/R" -DNDEBUG  -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 matchprobes.c -o matchprobes.o
gcc -I"/usr/include/R" -DNDEBUG  -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 pmatchPattern.c -o pmatchPattern.o
gcc -I"/usr/include/R" -DNDEBUG  -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 replaceAt.c -o replaceAt.o
gcc -I"/usr/include/R" -DNDEBUG  -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 replace_letter_at.c -o replace_letter_at.o
gcc -I"/usr/include/R" -DNDEBUG  -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 strutils.c -o strutils.o
gcc -I"/usr/include/R" -DNDEBUG  -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 translate.c -o translate.o
BUILDSTDERR: translate.c: In function 'DNAStringSet_translate':
BUILDSTDERR: translate.c:110:8: warning: 'if_ambig0' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:      if (if_ambig == TRANSLATE_ERROR) {
BUILDSTDERR:         ^
BUILDSTDERR: translate.c:136:29: note: 'if_ambig0' was declared here
BUILDSTDERR:   int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
BUILDSTDERR:                              ^~~~~~~~~
BUILDSTDERR: translate.c:106:8: warning: 'if_non_ambig0' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:      if (if_non_ambig == TRANSLATE_TO_X)
BUILDSTDERR:         ^
BUILDSTDERR: translate.c:136:14: note: 'if_non_ambig0' was declared here
BUILDSTDERR:   int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
BUILDSTDERR:               ^~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -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 unstrsplit_methods.c -o unstrsplit_methods.o
gcc -I"/usr/include/R" -DNDEBUG  -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
BUILDSTDERR: utils.c: In function '_get_twobit_signature':
BUILDSTDERR: utils.c:157:9: warning: 'twobit_sign' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   return twobit_sign;
BUILDSTDERR:          ^~~~~~~~~~~
BUILDSTDERR: utils.c: In function '_get_twobit_signature_at':
BUILDSTDERR: utils.c:164:12: warning: 'twobit_sign' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   int i, j, twobit_sign;
BUILDSTDERR:             ^~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG  -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 xscat.c -o xscat.o
BUILDSTDERR: In file included from /usr/lib64/R/library/S4Vectors/include/S4Vectors_defines.h:18,
BUILDSTDERR:                  from /usr/lib64/R/library/IRanges/include/IRanges_defines.h:18,
BUILDSTDERR:                  from ../inst/include/Biostrings_defines.h:18,
BUILDSTDERR:                  from Biostrings.h:1,
BUILDSTDERR:                  from xscat.c:1:
BUILDSTDERR: xscat.c: In function 'XString_xscat':
BUILDSTDERR: /usr/include/R/Rdefines.h:98:21: warning: 'ans_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:  #define NEW_RAW(n)  Rf_allocVector(RAWSXP,n)
BUILDSTDERR:                      ^~~~~~~~~~~~~~
BUILDSTDERR: xscat.c:18:13: note: 'ans_length' was declared here
BUILDSTDERR:   int nargs, ans_length, tag_offset, j;
BUILDSTDERR:              ^~~~~~~~~~
BUILDSTDERR: xscat.c:52:16: warning: 'ans_classname' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag));
BUILDSTDERR:                 ^~~~~~~~~~~~~~~~~
BUILDSTDERR: In file included from /usr/lib64/R/library/S4Vectors/include/S4Vectors_defines.h:18,
BUILDSTDERR:                  from /usr/lib64/R/library/IRanges/include/IRanges_defines.h:18,
BUILDSTDERR:                  from ../inst/include/Biostrings_defines.h:18,
BUILDSTDERR:                  from Biostrings.h:1,
BUILDSTDERR:                  from xscat.c:1:
BUILDSTDERR: xscat.c: In function 'XStringSet_xscat':
BUILDSTDERR: /usr/include/R/Rdefines.h:92:25: warning: 'ans_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:  #define NEW_INTEGER(n)  Rf_allocVector(INTSXP,n)
BUILDSTDERR:                          ^~~~~~~~~~~~~~
BUILDSTDERR: xscat.c:66:32: note: 'ans_length' was declared here
BUILDSTDERR:   int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
BUILDSTDERR:                                 ^~~~~~~~~~
BUILDSTDERR: xscat.c:108:16: warning: 'ans_element_type' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width));
BUILDSTDERR:                 ^~~~~~~~~~~~~~~~~
gcc -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XStringSet_io.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/usr/lib64/R/lib -lR
BUILDSTDERR: installing to /builddir/build/BUILDROOT/R-Biostrings-2.48.0-2.fc29.riscv64/usr/lib64/R/library/Biostrings/libs
BUILDSTDERR: ** R
BUILDSTDERR: ** data
BUILDSTDERR: ** inst
BUILDSTDERR: ** byte-compile and prepare package for lazy loading
BUILDSTDERR: Creating a new generic function for 'strsplit' in package 'Biostrings'
BUILDSTDERR: Creating a generic function for 'ls' from package 'base' in package 'Biostrings'
BUILDSTDERR: Creating a new generic function for 'offset' in package 'Biostrings'
BUILDSTDERR: ** help
BUILDSTDERR: *** installing help indices
  converting help for package 'Biostrings'
BUILDSTDERR:     finding HTML links ... done
    AAString-class                          html  
    AMINO_ACID_CODE                         html  
    AlignedXStringSet-class                 html  
    Biostrings-internals                    html  
    DNAString-class                         html  
    GENETIC_CODE                            html  
    HNF4alpha                               html  
    IUPAC_CODE_MAP                          html  
    InDel-class                             html  
    MIndex-class                            html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/MIndex-class.Rd:94: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/MIndex-class.Rd:96: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/MIndex-class.Rd:98: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
    MaskedXString-class                     html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/MaskedXString-class.Rd:182: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
BUILDSTDERR:     MultipleAlignment-class                 html  
BUILDSTDERR:     finding level-2 HTML links ... done
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/MultipleAlignment-class.Rd:122: file link 'narrow' in package 'IRanges' does not exist and so has been treated as a topic
    PDict-class                             html  
    PairwiseAlignments-class                html  
    PairwiseAlignments-io                   html  
    QualityScaledXStringSet-class           html  
    RNAString-class                         html  
    XString-class                           html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XString-class.Rd:180: file link 'subseq' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XString-class.Rd:188: file link 'compact' in package 'XVector' does not exist and so has been treated as a topic
    XStringPartialMatches-class             html  
    XStringQuality-class                    html  
    XStringSet-class                        html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:92: file link 'narrow' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:179: file link 'subseq' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:199: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:201: file link 'XVector' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:207: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:213: file link 'threebands' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:218: file link 'subseq<-' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:219: file link 'XVector' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:220: file link 'subseq<-' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:331: file link 'subseq' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:331: file link 'narrow' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:334: file link 'compact' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSet-class.Rd:336: file link 'XVectorList' in package 'XVector' does not exist and so has been treated as a topic
    XStringSet-comparison                   html  
    XStringSet-io                           html  
    XStringSetList-class                    html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSetList-class.Rd:70: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSetList-class.Rd:77: file link 'elementNROWS' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringSetList-class.Rd:78: file link 'PartitioningByEnd' in package 'IRanges' does not exist and so has been treated as a topic
    XStringViews-class                      html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/XStringViews-class.Rd:155: file link 'gaps' in package 'IRanges' does not exist and so has been treated as a topic
    align-utils                             html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/align-utils.Rd:87: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
    chartr                                  html  
    detail                                  html  
    dinucleotideFrequencyTest               html  
    findPalindromes                         html  
    getSeq                                  html  
    gregexpr2                               html  
    injectHardMask                          html  
    letter                                  html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/letter.Rd:49: file link 'subseq' in package 'XVector' does not exist and so has been treated as a topic
    letterFrequency                         html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/letterFrequency.Rd:290: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
    longestConsecutive                      html  
    lowlevel-matching                       html  
    maskMotif                               html  
    match-utils                             html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/match-utils.Rd:42: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/match-utils.Rd:48: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/match-utils.Rd:72: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/match-utils.Rd:74: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/match-utils.Rd:87: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
    matchLRPatterns                         html  
    matchPDict-exact                        html  
    matchPDict-inexact                      html  
    matchPWM                                html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/matchPWM.Rd:84: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
    matchPattern                            html  
    matchProbePair                          html  
    matchprobes                             html  
    misc                                    html  
    needwunsQS                              html  
    nucleotideFrequency                     html  
    padAndClip                              html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/padAndClip.Rd:33: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/padAndClip.Rd:109: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
    pairwiseAlignment                       html  
    phiX174Phage                            html  
    pid                                     html  
    pmatchPattern                           html  
    replaceAt                               html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:36: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:37: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:43: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:51: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:52: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:53: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:72: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:98: file link 'subseq' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:103: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:110: file link 'subseq' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:110: file link 'subseq<-' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:115: file link 'unstrsplit' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:127: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:127: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:128: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceAt.Rd:128: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
    replaceLetterAt                         html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/replaceLetterAt.Rd:43: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
    reverseComplement                       html  
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/reverseComplement.Rd:48: file link 'reverse' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /builddir/build/BUILD/Biostrings/Biostrings/man/reverseComplement.Rd:71: file link 'reverse' in package 'IRanges' does not exist and so has been treated as a topic
    stringDist                              html  
    substitution_matrices                   html  
    toComplex                               html  
    translate                               html  
    trimLRPatterns                          html  
    xscat                                   html  
    yeastSEQCHR1                            html  
BUILDSTDERR: ** building package indices
BUILDSTDERR: ** installing vignettes
BUILDSTDERR: ** testing if installed package can be loaded
BUILDSTDERR: * DONE (Biostrings)
+ test -d Biostrings/src
+ cd Biostrings/src
+ rm -f BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XStringSet_io.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o Biostrings.so
+ rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.48.0-2.fc29.riscv64/usr/lib64/R/library/R.css
+ rm -f /builddir/build/BUILDROOT/R-Biostrings-2.48.0-2.fc29.riscv64/usr/lib64/R/library/Biostrings/doc/GenomeSearching.R
+ /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 2.48.0-2.fc29 --unique-debug-suffix -2.48.0-2.fc29.riscv64 --unique-debug-src-base R-Biostrings-2.48.0-2.fc29.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/Biostrings
extracting debug info from /builddir/build/BUILDROOT/R-Biostrings-2.48.0-2.fc29.riscv64/usr/lib64/R/library/Biostrings/libs/Biostrings.so
/usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
BUILDSTDERR: 785 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.4iqooo
+ umask 022
+ cd /builddir/build/BUILD
+ cd Biostrings
+ exit 0
Processing files: R-Biostrings-2.48.0-2.fc29.riscv64
Provides: R-Biostrings = 2.48.0-2.fc29 R-Biostrings(riscv-64) = 2.48.0-2.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-Biostrings-devel-2.48.0-2.fc29.riscv64
Provides: R-Biostrings-devel = 2.48.0-2.fc29 R-Biostrings-devel(riscv-64) = 2.48.0-2.fc29
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-Biostrings-debugsource-2.48.0-2.fc29.riscv64
Provides: R-Biostrings-debugsource = 2.48.0-2.fc29 R-Biostrings-debugsource(riscv-64) = 2.48.0-2.fc29
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-Biostrings-debuginfo-2.48.0-2.fc29.riscv64
Provides: R-Biostrings-debuginfo = 2.48.0-2.fc29 R-Biostrings-debuginfo(riscv-64) = 2.48.0-2.fc29 debuginfo(build-id) = 572b173e286c64a8e5ca05a64f61a6ae1aa0a3ce
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: R-Biostrings-debugsource(riscv-64) = 2.48.0-2.fc29
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-Biostrings-2.48.0-2.fc29.riscv64
Wrote: /builddir/build/RPMS/R-Biostrings-2.48.0-2.fc29.riscv64.rpm
Wrote: /builddir/build/RPMS/R-Biostrings-devel-2.48.0-2.fc29.riscv64.rpm
Wrote: /builddir/build/RPMS/R-Biostrings-debugsource-2.48.0-2.fc29.riscv64.rpm
Wrote: /builddir/build/RPMS/R-Biostrings-debuginfo-2.48.0-2.fc29.riscv64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.Gawa6L
+ umask 022
+ cd /builddir/build/BUILD
+ cd Biostrings
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/R-Biostrings-2.48.0-2.fc29.riscv64
+ exit 0
Child return code was: 0