Mock Version: 1.4.14 Mock Version: 1.4.14 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/bfast.spec'], chrootPath='/var/lib/mock/f31-build-75397-31249/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=345600uid=986gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/bfast.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1563926400 Wrote: /builddir/build/SRPMS/bfast-0.7.0a-22.fc31.src.rpm Child return code was: 0 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/bfast.spec'], chrootPath='/var/lib/mock/f31-build-75397-31249/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=345600uid=986gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/bfast.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1563926400 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.NBZ7qo + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf bfast-0.7.0a + /usr/bin/gzip -dc /builddir/build/SOURCES/bfast-0.7.0a.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd bfast-0.7.0a + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (bfast-pthread-new.patch):' + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 + sed -i -e 's,^\(CFLAGS="${default_CFLAGS} ${extended_CFLAGS}"\),# \1,' configure.ac + autoreconf -fi BUILDSTDERR: parallel-tests: installing 'config/test-driver' + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 Patch #0 (bfast-pthread-new.patch): patching file bfast/Makefile.am patching file bfast/Makefile.in patching file butil/Makefile.am patching file butil/Makefile.in patching file scripts/Makefile.am patching file scripts/Makefile.in patching file tests/Makefile.in Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.aS9vYm + umask 022 + cd /builddir/build/BUILD + cd bfast-0.7.0a + CFLAGS='-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' + export CFLAGS + CXXFLAGS='-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' + export CXXFLAGS + FFLAGS='-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 -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-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 -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + export LDFLAGS + '[' 1 = 1 ']' BUILDSTDERR: +++ dirname ./configure BUILDSTDERR: ++ find . -name config.guess -o -name config.sub + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) BUILDSTDERR: ++ basename ./config/config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./config/config.guess BUILDSTDERR: ++ basename ./config/config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config/config.guess + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) BUILDSTDERR: ++ basename ./config/config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./config/config.sub BUILDSTDERR: ++ basename ./config/config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config/config.sub + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' BUILDSTDERR: ++ find . -name ltmain.sh + ./configure --build=riscv64-koji-linux-gnu --host=riscv64-koji-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-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 -fgnu89-inline' BUILDSTDERR: ./configure: line 4530: git: command not found + make -j4 '/usr/lib/rpm/redhat/config.guess' -> './config/config.guess' '/usr/lib/rpm/redhat/config.sub' -> './config/config.sub' checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... riscv64-koji-linux-gnu checking for riscv64-koji-linux-gnu-gcc... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for an ANSI C-conforming const... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for pow in -lm... yes checking for gzread in -lz... yes checking for floor... yes checking for pow... yes checking for sqrt... yes checking for strchr... yes checking for strdup... yes checking for strpbrk... yes checking for strstr... yes checking for strtok_r... yes checking for _LARGEFILE_SOURCE value needed for large files... no checking for int8_t... yes checking for int32_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint32_t... yes checking for uint64_t... yes checking size of short int... 2 checking size of int... 4 checking size of long int... 8 checking for ANSI C header files... (cached) yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking for inline... inline checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating bfast/Makefile config.status: creating butil/Makefile config.status: creating scripts/Makefile config.status: creating tests/Makefile config.status: creating config.h config.status: executing depfiles commands make all-recursive make[1]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a' Making all in bfast make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' BUILDSTDERR: gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=formatRGBinary.c: In function 'RGBinaryReadBinaryHeader': BUILDSTDERR: RGBinary.c:260:10: warning: variable 'numCharsPerByte' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 260 | int32_t numCharsPerByte; BUILDSTDERR: | ^~~~~~~~~~~~~~~ BUILDSTDERR: RGBinary.c: In function 'RGBinaryWriteBinaryHeader': BUILDSTDERR: RGBinary.c:387:10: warning: variable 'numCharsPerByte' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 387 | int32_t numCharsPerByte; BUILDSTDERR: | ^~~~~~~~~~~~~~~ BUILDSTDERR: RGBinary.c: In function 'RGBinaryWriteBinary': BUILDSTDERR: RGBinary.c:421:10: warning: variable 'numCharsPerByte' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 421 | int32_t numCharsPerByte; BUILDSTDERR: | ^~~~~~~~~~~~~~~ BUILDSTDERR: RGBinary.c: In function 'RGBinaryGetFourBit': BUILDSTDERR: RGBinary.c:820:7: warning: variable 'curChar' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 820 | char curChar; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: RGIndex.c: In function 'RGIndexCreateHelper': BUILDSTDERR: RGIndex.c:463:24: warning: variable 'keyEndPos' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 463 | uint32_t keyStartPos, keyEndPos; BUILDSTDERR: | ^~~~~~~~~ BUILDSTDERR: RGIndex.c: In function 'RGIndexCompareContigPos': BUILDSTDERR: RGIndex.c:2428:11: warning: variable 'length' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 2428 | int32_t length; BUILDSTDERR: | ^~~~~~ -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 -fgnu89-inline -c -o AlignedEnd.o AlignedEnd.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o AlignedEntry.o AlignedEntry.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o AlignedRead.o AlignedRead.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o AlignedReadConvert.o AlignedReadConvert.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o BError.o BError.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o BLib.o BLib.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o RGBinary.o RGBinary.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o RGIndex.o RGIndex.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o RGIndexAccuracy.o RGIndexAccuracy.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o RGIndexExons.o RGIndexExons.c BUILDSTDERR: gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o RGRGMatch.c: In function 'RGMatchRead': BUILDSTDERR: RGMatch.c:23:11: warning: passing argument 1 of 'feof' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: 23 | if(feof(fp) != 0) { BUILDSTDERR: | ^~ BUILDSTDERR: | | BUILDSTDERR: | gzFile {aka struct gzFile_s *} BUILDSTDERR: In file included from RGMatch.c:2: BUILDSTDERR: /usr/include/stdio.h:759:24: note: expected 'FILE *' {aka 'struct _IO_FILE *'} but argument is of type 'gzFile' {aka 'struct gzFile_s *'} BUILDSTDERR: 759 | extern int feof (FILE *__stream) __THROW __wur; BUILDSTDERR: | ~~~~~~^~~~~~~~ BUILDSTDERR: AlignNTSpace.c: In function 'AlignNTSpaceRecoverAlignmentFromMatrix': BUILDSTDERR: AlignNTSpace.c:225:7: warning: variable 'curReadBase' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 225 | char curReadBase; BUILDSTDERR: | ^~~~~~~~~~~ BUILDSTDERR: Align.c: In function 'AlignExact': BUILDSTDERR: Align.c:499:8: warning: variable 'colorErrorAligned' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 499 | char colorErrorAligned[SEQUENCE_LENGTH]="\0"; BUILDSTDERR: | ^~~~~~~~~~~~~~~~~ BUILDSTDERR: AlignColorSpace.c: In function 'AlignColorSpaceGappedConstrained': BUILDSTDERR: AlignColorSpace.c:379:40: warning: operation on '(*(matrix->cells + ((sizetype)i + 1) * 8) + ((sizetype)j + 1) * 180)->s.score[k]' may be undefined [-Wsequence-point] BUILDSTDERR: 379 | matrix->cells[i+1][j+1].s.score[k] = LOWERBOUNDSCORE(matrix->cells[i+1][j+1].s.score[k]); BUILDSTDERR: AlignColorSpace.c:384:10: warning: variable 'max' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 384 | char max = GAP; BUILDSTDERR: | ^~~ BUILDSTDERR: AlignColorSpace.c: In function 'AlignColorSpaceFillInCell': BUILDSTDERR: AlignColorSpace.c:848:9: warning: variable 'max' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 848 | char max = GAP; BUILDSTDERR: | ^~~ BUILDSTDERR: AlignColorSpace.c:899:8: warning: variable 'max' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 899 | char max = GAP; BUILDSTDERR: | ^~~ BUILDSTDERR: AlignColorSpace.c:986:9: warning: variable 'max' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 986 | char max = GAP; BUILDSTDERR: | ^~~ BUILDSTDERR: AlignMatrix.c: In function 'AlignMatrixReallocate': BUILDSTDERR: AlignMatrix.c:12:23: warning: variable 'prevNCol' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 12 | int32_t i, prevNRow, prevNCol; BUILDSTDERR: | ^~~~~~~~ IndexLayout.o RGIndexLayout.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o RGMatch.o RGMatch.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o RGMatches.o RGMatches.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o RGRanges.o RGRanges.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o RGReads.o RGReads.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ScoringMatrix.o ScoringMatrix.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o Align.o Align.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o AlignNTSpace.o AlignNTSpace.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o AlignColorSpace.o AlignColorSpace.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o AlignMatrix.o AlignMatrix.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o MatchesReadInputFiles.o MatchesReadInputFiles.c BUILDSTDERR: gcc -DHAVE_CONFIG_H -I. -I.. -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/rRunPostProcess.c: In function 'FilterAlignedRead': BUILDSTDERR: RunPostProcess.c:685:16: warning: variable 'bestIndex' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 685 | int32_t best, bestIndex, numBest; BUILDSTDERR: | ^~~~~~~~~ BUILDSTDERR: RunPostProcess.c: In function 'GetPEDBins': BUILDSTDERR: RunPostProcess.c:850:10: warning: variable 'alignQueueLength' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 850 | int32_t alignQueueLength; BUILDSTDERR: | ^~~~~~~~~~~~~~~~ pm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fgnu89-inline -c -o RunMatch.o RunMatch.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o RunLocalAlign.o RunLocalAlign.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o RunPostProcess.o RunPostProcess.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o RunAlign.o RunAlign.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o BfastFasta2BRG.o BfastFasta2BRG.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o BfastIndex.o BfastIndex.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o BfastMatch.o BfastMatch.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o BfastLocalAlign.o BfastLocalAlign.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o BfastPostProcess.o BfastPostProcess.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o BfastBAFConvert.o BfastBAFConvert.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o BfastHeader.o BfastHeader.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o BfastBMFConvert.o BfastBMFConvert.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o BfastBRG2Fasta.o BfastBRG2Fasta.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o BfastAlign.o BfastAlign.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o aflib.o aflib.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o Main.o Main.c gcc -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 -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o bfast AlignedEnd.o AlignedEntry.o AlignedRead.o AlignedReadConvert.o BError.o BLib.o RGBinary.o RGIndex.o RGIndexAccuracy.o RGIndexExons.o RGIndexLayout.o RGMatch.o RGMatches.o RGRanges.o RGReads.o ScoringMatrix.o Align.o AlignNTSpace.o AlignColorSpace.o AlignMatrix.o MatchesReadInputFiles.o RunMatch.o RunLocalAlign.o RunPostProcess.o RunAlign.o BfastFasta2BRG.o BfastIndex.o BfastMatch.o BfastLocalAlign.o BfastPostProcess.o BfastBAFConvert.o BfastHeader.o BfastBMFConvert.o BfastBRG2Fasta.o BfastAlign.o aflib.o Main.o -lpthread -lm -lbz2 -lz make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' Making all in butil make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o balignmentscoredistribution.o balignmentscoredistribution.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o SimRead.o SimRead.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o balignsim.o balignsim.c BUILDSTDERR: gcc -DHAVE_CONFIG_H -I. -I.. balignsim.c: In function 'Run': BUILDSTDERR: balignsim.c:174:9: warning: variable 'mismatchScore' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 174 | double mismatchScore; BUILDSTDERR: | ^~~~~~~~~~~~~ BUILDSTDERR: bindexdist.c: In function 'PrintDistribution': BUILDSTDERR: bindexdist.c:128:10: warning: variable 'numDifferent' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 128 | int64_t numDifferent = 0; BUILDSTDERR: | ^~~~~~~~~~~~ BUILDSTDERR: bindexhist.c: In function 'PrintHistogramThread': BUILDSTDERR: bindexhist.c:372:6: warning: variable 'skip' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 372 | int skip; BUILDSTDERR: | ^~~~ -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 -fgnu89-inline -c -o bevalsim.o bevalsim.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o bgeneratereads.o bgeneratereads.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/RGReads.o ../bfast/RGReads.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o bindexdist.o bindexdist.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o bindexhist.o bindexhist.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/MatchesReadInputFiles.o ../bfast/MatchesReadInputFiles.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/aflib.o ../bfast/aflib.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o bmfmerge.o bmfmerge.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o brepeat.o brepeat.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o btestindexes.o btestindexes.c BUILDSTDERR: gcc -DHAVE_CONFIG_H -I. -I.. -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-ann../bfast/RGIndex.c: In function 'RGIndexCreateHelper': BUILDSTDERR: ../bfast/RGIndex.c:463:24: warning: variable 'keyEndPos' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 463 | uint32_t keyStartPos, keyEndPos; BUILDSTDERR: | ^~~~~~~~~ BUILDSTDERR: ../bfast/RGIndex.c: In function 'RGIndexCompareContigPos': BUILDSTDERR: ../bfast/RGIndex.c:2428:11: warning: variable 'length' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 2428 | int32_t length; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: ../bfast/RGBinary.c: In function 'RGBinaryReadBinaryHeader': BUILDSTDERR: ../bfast/RGBinary.c:260:10: warning: variable 'numCharsPerByte' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 260 | int32_t numCharsPerByte; BUILDSTDERR: | ^~~~~~~~~~~~~~~ BUILDSTDERR: ../bfast/RGBinary.c: In function 'RGBinaryWriteBinaryHeader': BUILDSTDERR: ../bfast/RGBinary.c:387:10: warning: variable 'numCharsPerByte' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 387 | int32_t numCharsPerByte; BUILDSTDERR: | ^~~~~~~~~~~~~~~ BUILDSTDERR: ../bfast/RGBinary.c: In function 'RGBinaryWriteBinary': BUILDSTDERR: ../bfast/RGBinary.c:421:10: warning: variable 'numCharsPerByte' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 421 | int32_t numCharsPerByte; BUILDSTDERR: | ^~~~~~~~~~~~~~~ BUILDSTDERR: ../bfast/RGBinary.c: In function 'RGBinaryGetFourBit': BUILDSTDERR: ../bfast/RGBinary.c:820:7: warning: variable 'curChar' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 820 | char curChar; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: ../bfast/RGMatch.c: In function 'RGMatchRead': BUILDSTDERR: ../bfast/RGMatch.c:23:11: warning: passing argument 1 of 'feof' from incompatible pointer type [-Wincompatible-pointer-types] BUILDSTDERR: 23 | if(feof(fp) != 0) { BUILDSTDERR: | ^~ BUILDSTDERR: | | BUILDSTDERR: | gzFile {aka struct gzFile_s *} BUILDSTDERR: In file included from ../bfast/RGMatch.c:2: BUILDSTDERR: /usr/include/stdio.h:759:24: note: expected 'FILE *' {aka 'struct _IO_FILE *'} but argument is of type 'gzFile' {aka 'struct gzFile_s *'} BUILDSTDERR: 759 | extern int feof (FILE *__stream) __THROW __wur; BUILDSTDERR: | ~~~~~~^~~~~~~~ obin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fgnu89-inline -c -o ../bfast/BError.o ../bfast/BError.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/RGIndex.o ../bfast/RGIndex.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/BLib.o ../bfast/BLib.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/RGBinary.o ../bfast/RGBinary.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/RGRanges.o ../bfast/RGRanges.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/RGMatch.o ../bfast/RGMatch.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/AlignedRead.o ../bfast/AlignedRead.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/AlignedReadConvert.o ../bfast/AlignedReadConvert.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/AlignedEnd.o ../bfast/AlignedEnd.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/AlignedEntry.o ../bfast/AlignedEntry.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/RGIndexExons.o ../bfast/RGIndexExons.c BUILDSTDERR: gc../bfast/Align.c: In function 'AlignExact': BUILDSTDERR: ../bfast/Align.c:499:8: warning: variable 'colorErrorAligned' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 499 | char colorErrorAligned[SEQUENCE_LENGTH]="\0"; BUILDSTDERR: | ^~~~~~~~~~~~~~~~~ BUILDSTDERR: ../bfast/AlignColorSpace.c: In function 'AlignColorSpaceGappedConstrained': BUILDSTDERR: ../bfast/AlignColorSpace.c:379:40: warning: operation on '(*(matrix->cells + ((sizetype)i + 1) * 8) + ((sizetype)j + 1) * 180)->s.score[k]' may be undefined [-Wsequence-point] BUILDSTDERR: 379 | matrix->cells[i+1][j+1].s.score[k] = LOWERBOUNDSCORE(matrix->cells[i+1][j+1].s.score[k]); BUILDSTDERR: ../bfast/AlignColorSpace.c:384:10: warning: variable 'max' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 384 | char max = GAP; BUILDSTDERR: | ^~~ BUILDSTDERR: ../bfast/AlignColorSpace.c: In function 'AlignColorSpaceFillInCell': BUILDSTDERR: ../bfast/AlignColorSpace.c:848:9: warning: variable 'max' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 848 | char max = GAP; BUILDSTDERR: | ^~~ BUILDSTDERR: ../bfast/AlignColorSpace.c:899:8: warning: variable 'max' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 899 | char max = GAP; BUILDSTDERR: | ^~~ BUILDSTDERR: ../bfast/AlignColorSpace.c:986:9: warning: variable 'max' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 986 | char max = GAP; BUILDSTDERR: | ^~~ BUILDSTDERR: ../bfast/AlignNTSpace.c: In function 'AlignNTSpaceRecoverAlignmentFromMatrix': BUILDSTDERR: ../bfast/AlignNTSpace.c:225:7: warning: variable 'curReadBase' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 225 | char curReadBase; BUILDSTDERR: | ^~~~~~~~~~~ BUILDSTDERR: ../bfast/AlignMatrix.c: In function 'AlignMatrixReallocate': BUILDSTDERR: ../bfast/AlignMatrix.c:12:23: warning: variable 'prevNCol' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 12 | int32_t i, prevNRow, prevNCol; BUILDSTDERR: | ^~~~~~~~ c -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/RGMatches.o ../bfast/RGMatches.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/RGIndexAccuracy.o ../bfast/RGIndexAccuracy.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/RunLocalAlign.o ../bfast/RunLocalAlign.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/ScoringMatrix.o ../bfast/ScoringMatrix.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/Align.o ../bfast/Align.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/AlignColorSpace.o ../bfast/AlignColorSpace.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/AlignNTSpace.o ../bfast/AlignNTSpace.c gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o ../bfast/AlignMatrix.o ../bfast/AlignMatrix.c gcc -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 -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o bevalsim ../bfast/BError.o ../bfast/RGIndexExons.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGRanges.o ../bfast/RGMatches.o ../bfast/RGMatch.o ../bfast/AlignedRead.o ../bfast/AlignedEnd.o ../bfast/AlignedEntry.o bevalsim.o -lpthread -lm -lbz2 -lz gcc -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 -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o bgeneratereads ../bfast/BError.o ../bfast/RGIndexExons.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGMatch.o ../bfast/RGRanges.o SimRead.o bgeneratereads.o -lpthread -lm -lbz2 -lz gcc -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 -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o bindexdist ../bfast/BError.o ../bfast/RGIndexExons.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGMatch.o ../bfast/RGRanges.o ../bfast/RGReads.o bindexdist.o -lpthread -lm -lbz2 -lz gcc -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 -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o bindexhist ../bfast/BError.o ../bfast/RGIndexExons.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGMatch.o ../bfast/RGRanges.o ../bfast/RGReads.o bindexhist.o -lpthread -lm -lbz2 -lz gcc -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 -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o bmfmerge ../bfast/BError.o ../bfast/RGIndexExons.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGRanges.o ../bfast/RGReads.o ../bfast/RGMatch.o ../bfast/RGMatches.o ../bfast/MatchesReadInputFiles.o ../bfast/aflib.o bmfmerge.o -lpthread -lm -lbz2 -lz gcc -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 -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o brepeat ../bfast/BError.o ../bfast/RGIndexExons.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGMatch.o ../bfast/RGRanges.o brepeat.o -lpthread -lm -lbz2 -lz gcc -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 -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o btestindexes ../bfast/RGMatch.o ../bfast/RGRanges.o ../bfast/RGBinary.o ../bfast/RGIndex.o ../bfast/RGIndexAccuracy.o ../bfast/BError.o ../bfast/BLib.o btestindexes.o -lpthread -lm -lbz2 -lz BUILDSTDERR: gcc -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 -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o balignmentscoredistribution ../bfast/BError.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGRanges.o ../bfast/RGMatch.o ../bfast/AlignedRead.o ../bfas+ RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 t/AlignedReadConvert.o ../bfast/AlignedEnd.o ../bfast/AlignedEntry.o balignmentscoredistribution.o -lpthread -lm -lbz2 -lz gcc -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 -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o balignsim SimRead.o ../bfast/BError.o ../bfast/RGIndexExons.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGMatch.o ../bfast/RGMatches.o ../bfast/RGRanges.o ../bfast/AlignedRead.o ../bfast/AlignedEnd.o ../bfast/RGIndexAccuracy.o ../bfast/AlignedEntry.o ../bfast/RunLocalAlign.o ../bfast/ScoringMatrix.o ../bfast/Align.o ../bfast/AlignColorSpace.o ../bfast/AlignNTSpace.o ../bfast/AlignMatrix.o balignsim.o -lpthread -lm -lbz2 -lz make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' Making all in scripts make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/scripts' gcc -DHAVE_CONFIG_H -I. -I.. -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 -fgnu89-inline -c -o solid2fastq.o solid2fastq.c gcc -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 -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o solid2fastq ../bfast/BError.o ../bfast/RGIndex.o ../bfast/BLib.o ../bfast/RGBinary.o ../bfast/RGRanges.o ../bfast/RGMatch.o ../bfast/aflib.o solid2fastq.o -lpthread -lm -lbz2 -lz make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/scripts' Making all in tests make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/tests' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/tests' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a' make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a' make[1]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a' Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.UtVnap + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64 BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64 + cd bfast-0.7.0a + make install DESTDIR=/builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64 + rm /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64//usr/share/doc/bfast/LICENSE + rm /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64//usr/share/doc/bfast/bfast-book.pdf + /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 0.7.0a-22.fc31 --unique-debug-suffix -0.7.0a-22.fc31.riscv64 --unique-debug-src-base bfast-0.7.0a-22.fc31.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/bfast-0.7.0a Making install in bfast make[1]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -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 -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o bfast AlignedEnd.o AlignedEntry.o AlignedRead.o AlignedReadConvert.o BError.o BLib.o RGBinary.o RGIndex.o RGIndexAccuracy.o RGIndexExons.o RGIndexLayout.o RGMatch.o RGMatches.o RGRanges.o RGReads.o ScoringMatrix.o Align.o AlignNTSpace.o AlignColorSpace.o AlignMatrix.o MatchesReadInputFiles.o RunMatch.o RunLocalAlign.o RunPostProcess.o RunAlign.o BfastFasta2BRG.o BfastIndex.o BfastMatch.o BfastLocalAlign.o BfastPostProcess.o BfastBAFConvert.o BfastHeader.o BfastBMFConvert.o BfastBRG2Fasta.o BfastAlign.o aflib.o Main.o -lpthread -lm -lbz2 -lz make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin' /usr/bin/install -c bfast '/builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[1]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' Making install in butil make[1]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin' /usr/bin/install -c balignmentscoredistribution balignsim bevalsim bgeneratereads bindexdist bindexhist bmfmerge brepeat btestindexes '/builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[1]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' Making install in scripts make[1]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/scripts' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/scripts' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin' /usr/bin/install -c solid2fastq '/builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin' /usr/bin/install -c bfast.resubmit.pl bfast.submit.pl ill2fastq.pl '/builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/scripts' make[1]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/scripts' Making install in tests make[1]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/tests' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/tests' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/tests' make[1]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/tests' make[1]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a' make[2]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/share/doc/bfast' /usr/bin/install -c -m 644 LICENSE manual/bfast-book.pdf '/builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/share/doc/bfast' make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a' make[1]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a' explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/balignsim explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/balignmentscoredistribution BUILDSTDERR: explicitly deco1563 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /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 0 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs mpress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/bfast explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/bevalsim extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/balignmentscoredistribution extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/balignsim extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/bevalsim extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/bfast explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/bgeneratereads extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/bgeneratereads explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/bindexdist extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/bindexdist explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/bindexhist extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/bindexhist explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/bmfmerge extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/bmfmerge explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/brepeat extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/brepeat explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/btestindexes extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/btestindexes explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/solid2fastq extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/bin/solid2fastq original debug info size: 6048kB, size after compression: 5568kB /usr/lib/rpm/sepdebugcrcfix: Updated 11 CRC32s, 0 CRC32s did match. Processing files: bfast-0.7.0a-22.fc31.riscv64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.VcDj9o + umask 022 + cd /builddir/build/BUILD + cd bfast-0.7.0a + DOCDIR=/builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/share/doc/bfast + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/share/doc/bfast + cp -pr AUTHORS /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/share/doc/bfast + cp -pr ChangeLog /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/share/doc/bfast + cp -pr NEWS /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/share/doc/bfast + cp -pr README /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/share/doc/bfast + cp -pr manual/bfast-book.pdf /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/share/doc/bfast + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.7VbZXo + umask 022 + cd /builddir/build/BUILD + cd bfast-0.7.0a + LICENSEDIR=/builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/share/licenses/bfast + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/share/licenses/bfast + cp -pr LICENSE /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64/usr/share/licenses/bfast + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 Provides: bfast = 0.7.0a-22.fc31 bfast(riscv-64) = 0.7.0a-22.fc31 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/perl ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.27)(64bit) libz.so.1()(64bit) perl(Cwd) perl(Data::Dumper) perl(File::Path) perl(Getopt::Long) perl(Getopt::Std) perl(Pod::Usage) perl(XML::Simple) perl(constant) perl(strict) perl(warnings) rtld(GNU_HASH) Processing files: bfast-debugsource-0.7.0a-22.fc31.riscv64 Provides: bfast-debugsource = 0.7.0a-22.fc31 bfast-debugsource(riscv-64) = 0.7.0a-22.fc31 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: bfast-debuginfo-0.7.0a-22.fc31.riscv64 Provides: bfast-debuginfo = 0.7.0a-22.fc31 bfast-debuginfo(riscv-64) = 0.7.0a-22.fc31 debuginfo(build-id) = 0bfae9393965eef6360786cbd8d403137cf4b95c debuginfo(build-id) = 336ea7ab3b09939fa1c9bb84970179653cc8929d debuginfo(build-id) = 471555dbd6d79d4c6feece8ffe26b7bfdf5136d0 debuginfo(build-id) = 513c6ad5e315b7da5e5a9523de93ae666da103ab debuginfo(build-id) = 6b1fdab11cb030345cdcdab32f229ae866be60ec debuginfo(build-id) = 6c96397c09a627de8e2cee8b4da7a7225f035236 debuginfo(build-id) = 6d1855d06c70146ea3134ee2bea55fc7a9c28653 debuginfo(build-id) = 7ec51bf82d9b78d95f6e50d6cc6dd3de4b6cf8e2 debuginfo(build-id) = ac9c3b682fa93905807a8a63e3cc9b2140d29055 debuginfo(build-id) = b9c7b126878576090bba50f9aeb2554c22511092 debuginfo(build-id) = d6c427d1b6d576555be0d55132c785acc240d742 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bfast-debugsource(riscv-64) = 0.7.0a-22.fc31 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64 Wrote: /builddir/build/RPMS/bfast-debugsource-0.7.0a-22.fc31.riscv64.rpm Wrote: /builddir/build/RPMS/bfast-0.7.0a-22.fc31.riscv64.rpm Wrote: /builddir/build/RPMS/bfast-debuginfo-0.7.0a-22.fc31.riscv64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.p7O1go + umask 022 + cd /builddir/build/BUILD + cd bfast-0.7.0a + /usr/bin/rm -rf /builddir/build/BUILDROOT/bfast-0.7.0a-22.fc31.riscv64 + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 Child return code was: 0