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;\\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=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;\\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-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;\\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=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;\\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.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