Mock Version: 2.6 Mock Version: 2.6 Mock Version: 2.6 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target i686 --nodeps /builddir/build/SPECS/bfast.spec'], chrootPath='/var/lib/mock/f34-build-24894566-2695019/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': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target i686 --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': 'C.UTF-8'} and shell False Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1609459200 Wrote: /builddir/build/SRPMS/bfast-0.7.0a-26.fc34.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target i686 --nodeps /builddir/build/SPECS/bfast.spec'], chrootPath='/var/lib/mock/f34-build-24894566-2695019/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': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target i686 --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': 'C.UTF-8'} and shell False Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1609459200 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.cQ6DTL + 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):' Patch #0 (bfast-pthread-new.patch): + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 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 + sed -i -e 's,^\(CFLAGS="${default_CFLAGS} ${extended_CFLAGS}"\),# \1,' configure.ac + autoreconf -fi parallel-tests: installing 'config/test-driver' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.MXQgdL + umask 022 + cd /builddir/build/BUILD + cd bfast-0.7.0a + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']' ++ find . -type f -name configure -print + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure + diff -u ./configure.backup ./configure --- ./configure.backup 2021-01-01 06:18:11.440885784 +0000 +++ ./configure 2021-01-01 06:18:12.439973325 +0000 @@ -1778,7 +1778,7 @@ #ifdef __cplusplus extern "C" #endif -char $2 (); +__attribute__ ((used)) char $2 (); /* The GNU C library defines this for functions which it implements to always fail with ENOSYS. Some functions are actually named something starting with __ and the normal name is an alias. */ + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config/config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./config/config.guess ++ basename ./config/config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config/config.guess '/usr/lib/rpm/redhat/config.guess' -> './config/config.guess' + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config/config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./config/config.sub ++ basename ./config/config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config/config.sub '/usr/lib/rpm/redhat/config.sub' -> './config/config.sub' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh + ./configure --build=i686-redhat-linux-gnu --host=i686-redhat-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/lib --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline' 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... i686-redhat-linux-gnu checking for i686-redhat-linux-gnu-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 ./configure: line 4530: git: command not found 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... 64 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... 4 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 + /usr/bin/make -O -j6 V=1 VERBOSE=1 /usr/bin/make all-recursive Making all in bfast make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o BError.o BError.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o AlignedRead.o AlignedRead.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o AlignedEntry.o AlignedEntry.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o AlignedEnd.o AlignedEnd.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o RGIndexExons.o RGIndexExons.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o RGBinary.o RGBinary.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' RGBinary.c: In function 'RGBinaryReadBinaryHeader': RGBinary.c:260:17: warning: variable 'numCharsPerByte' set but not used [-Wunused-but-set-variable] 260 | int32_t numCharsPerByte; | ^~~~~~~~~~~~~~~ RGBinary.c: In function 'RGBinaryWriteBinaryHeader': RGBinary.c:387:17: warning: variable 'numCharsPerByte' set but not used [-Wunused-but-set-variable] 387 | int32_t numCharsPerByte; | ^~~~~~~~~~~~~~~ RGBinary.c: In function 'RGBinaryWriteBinary': RGBinary.c:421:17: warning: variable 'numCharsPerByte' set but not used [-Wunused-but-set-variable] 421 | int32_t numCharsPerByte; | ^~~~~~~~~~~~~~~ RGBinary.c: In function 'RGBinaryGetFourBit': RGBinary.c:820:14: warning: variable 'curChar' set but not used [-Wunused-but-set-variable] 820 | char curChar; | ^~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o RGIndexLayout.o RGIndexLayout.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o AlignedReadConvert.o AlignedReadConvert.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o RGRanges.o RGRanges.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o BLib.o BLib.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ScoringMatrix.o ScoringMatrix.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o RGIndexAccuracy.o RGIndexAccuracy.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o RGMatch.o RGMatch.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' RGMatch.c: In function 'RGMatchRead': RGMatch.c:23:25: warning: passing argument 1 of 'feof' from incompatible pointer type [-Wincompatible-pointer-types] 23 | if(feof(fp) != 0) { | ^~ | | | gzFile {aka struct gzFile_s *} In file included from RGMatch.c:2: /usr/include/stdio.h:764:24: note: expected 'FILE *' but argument is of type 'gzFile' {aka 'struct gzFile_s *'} 764 | extern int feof (FILE *__stream) __THROW __wur; | ~~~~~~^~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o RGReads.o RGReads.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o AlignMatrix.o AlignMatrix.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' AlignMatrix.c: In function 'AlignMatrixReallocate': AlignMatrix.c:12:30: warning: variable 'prevNCol' set but not used [-Wunused-but-set-variable] 12 | int32_t i, prevNRow, prevNCol; | ^~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o RGMatches.o RGMatches.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o RGIndex.o RGIndex.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' RGIndex.c: In function 'RGIndexCreateHelper': RGIndex.c:463:31: warning: variable 'keyEndPos' set but not used [-Wunused-but-set-variable] 463 | uint32_t keyStartPos, keyEndPos; | ^~~~~~~~~ RGIndex.c: In function 'RGIndexCompareContigPos': RGIndex.c:2428:25: warning: variable 'length' set but not used [-Wunused-but-set-variable] 2428 | int32_t length; | ^~~~~~ make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o Align.o Align.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' Align.c: In function 'AlignExact': Align.c:499:22: warning: variable 'colorErrorAligned' set but not used [-Wunused-but-set-variable] 499 | char colorErrorAligned[SEQUENCE_LENGTH]="\0"; | ^~~~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o AlignNTSpace.o AlignNTSpace.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' AlignNTSpace.c: In function 'AlignNTSpaceRecoverAlignmentFromMatrix': AlignNTSpace.c:225:14: warning: variable 'curReadBase' set but not used [-Wunused-but-set-variable] 225 | char curReadBase; | ^~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o RunAlign.o RunAlign.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o RunLocalAlign.o RunLocalAlign.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o BfastFasta2BRG.o BfastFasta2BRG.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o MatchesReadInputFiles.o MatchesReadInputFiles.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o AlignColorSpace.o AlignColorSpace.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' AlignColorSpace.c: In function 'AlignColorSpaceGappedConstrained': AlignColorSpace.c:379:68: warning: operation on '(*(matrix->cells + ((sizetype)i + 1) * 4) + ((sizetype)j + 1) * 180)->s.score[k]' may be undefined [-Wsequence-point] 379 | matrix->cells[i+1][j+1].s.score[k] = LOWERBOUNDSCORE(matrix->cells[i+1][j+1].s.score[k]); AlignColorSpace.c:384:38: warning: variable 'max' set but not used [-Wunused-but-set-variable] 384 | char max = GAP; | ^~~ AlignColorSpace.c: In function 'AlignColorSpaceFillInCell': AlignColorSpace.c:848:30: warning: variable 'max' set but not used [-Wunused-but-set-variable] 848 | char max = GAP; | ^~~ AlignColorSpace.c:899:22: warning: variable 'max' set but not used [-Wunused-but-set-variable] 899 | char max = GAP; | ^~~ AlignColorSpace.c:986:30: warning: variable 'max' set but not used [-Wunused-but-set-variable] 986 | char max = GAP; | ^~~ make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o BfastIndex.o BfastIndex.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o BfastLocalAlign.o BfastLocalAlign.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o RunMatch.o RunMatch.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o BfastHeader.o BfastHeader.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o BfastBAFConvert.o BfastBAFConvert.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o RunPostProcess.o RunPostProcess.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' RunPostProcess.c: In function 'FilterAlignedRead': RunPostProcess.c:685:23: warning: variable 'bestIndex' set but not used [-Wunused-but-set-variable] 685 | int32_t best, bestIndex, numBest; | ^~~~~~~~~ RunPostProcess.c: In function 'GetPEDBins': RunPostProcess.c:850:17: warning: variable 'alignQueueLength' set but not used [-Wunused-but-set-variable] 850 | int32_t alignQueueLength; | ^~~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o BfastMatch.o BfastMatch.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o BfastBMFConvert.o BfastBMFConvert.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o BfastBRG2Fasta.o BfastBRG2Fasta.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o Main.o Main.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o BfastAlign.o BfastAlign.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o aflib.o aflib.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o BfastPostProcess.o BfastPostProcess.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o balignmentscoredistribution.o balignmentscoredistribution.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o bgeneratereads.o bgeneratereads.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o balignsim.o balignsim.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' balignsim.c: In function 'Run': balignsim.c:174:16: warning: variable 'mismatchScore' set but not used [-Wunused-but-set-variable] 174 | double mismatchScore; | ^~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o bevalsim.o bevalsim.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o bindexhist.o bindexhist.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' bindexhist.c: In function 'PrintHistogramThread': bindexhist.c:372:13: warning: variable 'skip' set but not used [-Wunused-but-set-variable] 372 | int skip; | ^~~~ make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o SimRead.o SimRead.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/RGReads.o ../bfast/RGReads.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o bindexdist.o bindexdist.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' bindexdist.c: In function 'PrintDistribution': bindexdist.c:128:17: warning: variable 'numDifferent' set but not used [-Wunused-but-set-variable] 128 | int64_t numDifferent = 0; | ^~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/aflib.o ../bfast/aflib.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o bmfmerge.o bmfmerge.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o btestindexes.o btestindexes.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/MatchesReadInputFiles.o ../bfast/MatchesReadInputFiles.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/BError.o ../bfast/BError.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o brepeat.o brepeat.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/RGRanges.o ../bfast/RGRanges.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/AlignedRead.o ../bfast/AlignedRead.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/RGBinary.o ../bfast/RGBinary.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' ../bfast/RGBinary.c: In function 'RGBinaryReadBinaryHeader': ../bfast/RGBinary.c:260:17: warning: variable 'numCharsPerByte' set but not used [-Wunused-but-set-variable] 260 | int32_t numCharsPerByte; | ^~~~~~~~~~~~~~~ ../bfast/RGBinary.c: In function 'RGBinaryWriteBinaryHeader': ../bfast/RGBinary.c:387:17: warning: variable 'numCharsPerByte' set but not used [-Wunused-but-set-variable] 387 | int32_t numCharsPerByte; | ^~~~~~~~~~~~~~~ ../bfast/RGBinary.c: In function 'RGBinaryWriteBinary': ../bfast/RGBinary.c:421:17: warning: variable 'numCharsPerByte' set but not used [-Wunused-but-set-variable] 421 | int32_t numCharsPerByte; | ^~~~~~~~~~~~~~~ ../bfast/RGBinary.c: In function 'RGBinaryGetFourBit': ../bfast/RGBinary.c:820:14: warning: variable 'curChar' set but not used [-Wunused-but-set-variable] 820 | char curChar; | ^~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/AlignedEnd.o ../bfast/AlignedEnd.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/RGIndexExons.o ../bfast/RGIndexExons.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/RGMatch.o ../bfast/RGMatch.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' ../bfast/RGMatch.c: In function 'RGMatchRead': ../bfast/RGMatch.c:23:25: warning: passing argument 1 of 'feof' from incompatible pointer type [-Wincompatible-pointer-types] 23 | if(feof(fp) != 0) { | ^~ | | | gzFile {aka struct gzFile_s *} In file included from ../bfast/RGMatch.c:2: /usr/include/stdio.h:764:24: note: expected 'FILE *' but argument is of type 'gzFile' {aka 'struct gzFile_s *'} 764 | extern int feof (FILE *__stream) __THROW __wur; | ~~~~~~^~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/BLib.o ../bfast/BLib.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/AlignedEntry.o ../bfast/AlignedEntry.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/AlignedReadConvert.o ../bfast/AlignedReadConvert.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/ScoringMatrix.o ../bfast/ScoringMatrix.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/RunLocalAlign.o ../bfast/RunLocalAlign.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/Align.o ../bfast/Align.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' ../bfast/Align.c: In function 'AlignExact': ../bfast/Align.c:499:22: warning: variable 'colorErrorAligned' set but not used [-Wunused-but-set-variable] 499 | char colorErrorAligned[SEQUENCE_LENGTH]="\0"; | ^~~~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/RGMatches.o ../bfast/RGMatches.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/AlignMatrix.o ../bfast/AlignMatrix.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' ../bfast/AlignMatrix.c: In function 'AlignMatrixReallocate': ../bfast/AlignMatrix.c:12:30: warning: variable 'prevNCol' set but not used [-Wunused-but-set-variable] 12 | int32_t i, prevNRow, prevNCol; | ^~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/RGIndex.o ../bfast/RGIndex.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' ../bfast/RGIndex.c: In function 'RGIndexCreateHelper': ../bfast/RGIndex.c:463:31: warning: variable 'keyEndPos' set but not used [-Wunused-but-set-variable] 463 | uint32_t keyStartPos, keyEndPos; | ^~~~~~~~~ ../bfast/RGIndex.c: In function 'RGIndexCompareContigPos': ../bfast/RGIndex.c:2428:25: warning: variable 'length' set but not used [-Wunused-but-set-variable] 2428 | int32_t length; | ^~~~~~ make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/RGIndexAccuracy.o ../bfast/RGIndexAccuracy.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/AlignNTSpace.o ../bfast/AlignNTSpace.c ../bfast/AlignNTSpace.c: In function 'AlignNTSpaceRecoverAlignmentFromMatrix': ../bfast/AlignNTSpace.c:225:14: warning: variable 'curReadBase' set but not used [-Wunused-but-set-variable] 225 | char curReadBase; | ^~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o ../bfast/AlignColorSpace.o ../bfast/AlignColorSpace.c ../bfast/AlignColorSpace.c: In function 'AlignColorSpaceGappedConstrained': ../bfast/AlignColorSpace.c:379:68: warning: operation on '(*(matrix->cells + ((sizetype)i + 1) * 4) + ((sizetype)j + 1) * 180)->s.score[k]' may be undefined [-Wsequence-point] 379 | matrix->cells[i+1][j+1].s.score[k] = LOWERBOUNDSCORE(matrix->cells[i+1][j+1].s.score[k]); ../bfast/AlignColorSpace.c:384:38: warning: variable 'max' set but not used [-Wunused-but-set-variable] 384 | char max = GAP; | ^~~ ../bfast/AlignColorSpace.c: In function 'AlignColorSpaceFillInCell': ../bfast/AlignColorSpace.c:848:30: warning: variable 'max' set but not used [-Wunused-but-set-variable] 848 | char max = GAP; | ^~~ ../bfast/AlignColorSpace.c:899:22: warning: variable 'max' set but not used [-Wunused-but-set-variable] 899 | char max = GAP; | ^~~ ../bfast/AlignColorSpace.c:986:30: warning: variable 'max' set but not used [-Wunused-but-set-variable] 986 | char max = GAP; | ^~~ make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 ../bfast/AlignedReadConvert.o ../bfast/AlignedEnd.o ../bfast/AlignedEntry.o balignmentscoredistribution.o -lpthread -lm -lbz2 -lz make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fgnu89-inline -c -o solid2fastq.o solid2fastq.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/scripts' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/scripts' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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]: Nothing to be done for 'all'. + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.5FoysL + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386 ++ dirname /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386 + cd bfast-0.7.0a + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386 'INSTALL=/usr/bin/install -p' Making install in bfast make[1]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-26.fc34.i386/usr/bin' /usr/bin/install -p bfast '/builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/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-26.fc34.i386/usr/bin' /usr/bin/install -p balignmentscoredistribution balignsim bevalsim bgeneratereads bindexdist bindexhist bmfmerge brepeat btestindexes '/builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/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-26.fc34.i386/usr/bin' /usr/bin/install -p solid2fastq '/builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin' /usr/bin/install -p bfast.resubmit.pl bfast.submit.pl ill2fastq.pl '/builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/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-26.fc34.i386/usr/share/doc/bfast' /usr/bin/install -p -m 644 LICENSE manual/bfast-book.pdf '/builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/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' + rm /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386//usr/share/doc/bfast/LICENSE + rm /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386//usr/share/doc/bfast/bfast-book.pdf + /usr/lib/rpm/find-debuginfo.sh -j6 --strict-build-id -m -i --build-id-seed 0.7.0a-26.fc34 --unique-debug-suffix -0.7.0a-26.fc34.i386 --unique-debug-src-base bfast-0.7.0a-26.fc34.i386 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/bfast-0.7.0a explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/balignsim explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/balignmentscoredistribution explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/bevalsim explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/bfast extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/balignsim extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/balignmentscoredistribution explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/bindexdist extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/bevalsim explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/bgeneratereads extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/bfast extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/bindexdist extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/bgeneratereads explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/bindexhist extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/bindexhist explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/bmfmerge explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/brepeat extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/bmfmerge extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/brepeat explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/btestindexes extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/btestindexes explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/solid2fastq extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/bin/solid2fastq original debug info size: 2788kB, size after compression: 2140kB /usr/lib/rpm/sepdebugcrcfix: Updated 11 CRC32s, 0 CRC32s did match. 1563 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs Processing files: bfast-0.7.0a-26.fc34.i686 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.V54EnK + umask 022 + cd /builddir/build/BUILD + cd bfast-0.7.0a + DOCDIR=/builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/share/doc/bfast + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/share/doc/bfast + cp -pr AUTHORS /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/share/doc/bfast + cp -pr ChangeLog /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/share/doc/bfast + cp -pr NEWS /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/share/doc/bfast + cp -pr README /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/share/doc/bfast + cp -pr manual/bfast-book.pdf /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/share/doc/bfast + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.gEuD2L + umask 022 + cd /builddir/build/BUILD + cd bfast-0.7.0a + LICENSEDIR=/builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/share/licenses/bfast + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/share/licenses/bfast + cp -pr LICENSE /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386/usr/share/licenses/bfast + RPM_EC=0 ++ jobs -p + exit 0 Provides: bfast = 0.7.0a-26.fc34 bfast(x86-32) = 0.7.0a-26.fc34 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/perl libbz2.so.1 libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.4) libc.so.6(GLIBC_2.7) libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.29) libpthread.so.0 libpthread.so.0(GLIBC_2.0) libpthread.so.0(GLIBC_2.1) libz.so.1 libz.so.1(ZLIB_1.2.3.3) 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-26.fc34.i686 Provides: bfast-debugsource = 0.7.0a-26.fc34 bfast-debugsource(x86-32) = 0.7.0a-26.fc34 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-26.fc34.i686 Provides: bfast-debuginfo = 0.7.0a-26.fc34 bfast-debuginfo(x86-32) = 0.7.0a-26.fc34 debuginfo(build-id) = 02bdaa25ca8f07b8f5d56de53148d905a7a31983 debuginfo(build-id) = 465405320265bb7a2b089941a09acadaada8c472 debuginfo(build-id) = 4e4072e7819e130d963b4bbb4ce6993644875d2a debuginfo(build-id) = 6f6f9df0679606213e0917b35e8af7e8d5ce7c02 debuginfo(build-id) = 80047ef0707cffaaa01a8353117830862af803ee debuginfo(build-id) = 84994785cffdf06b84fcf8e759a6fb8b2dd28591 debuginfo(build-id) = 97cdde714a85e4f8b0ad8dd780c2492772e4f138 debuginfo(build-id) = 9d67f00a45092e8c0e03ff1fdfd7ed65a3d09bb2 debuginfo(build-id) = e0479dd67ac62b5580f5d55fa0ffbe50bdd01af1 debuginfo(build-id) = ea0e8e40ace924728862d8f31947e560afe0169c debuginfo(build-id) = fa73c00f1ba468849f82856d8b5250876d7a0725 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bfast-debugsource(x86-32) = 0.7.0a-26.fc34 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386 Wrote: /builddir/build/RPMS/bfast-0.7.0a-26.fc34.i686.rpm Wrote: /builddir/build/RPMS/bfast-debugsource-0.7.0a-26.fc34.i686.rpm Wrote: /builddir/build/RPMS/bfast-debuginfo-0.7.0a-26.fc34.i686.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.zPSr0I + umask 022 + cd /builddir/build/BUILD + cd bfast-0.7.0a + /usr/bin/rm -rf /builddir/build/BUILDROOT/bfast-0.7.0a-26.fc34.i386 + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0