Mock Version: 2.15 Mock Version: 2.15 Mock Version: 2.15 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/bfast.spec'], chrootPath='/var/lib/mock/f38-build-710843-93550/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=432000uid=991gid=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': 'C.UTF-8'} and shell False warning: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1674000000 Wrote: /builddir/build/SRPMS/bfast-0.7.0a-31.fc38.src.rpm RPM build warnings: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/bfast.spec'], chrootPath='/var/lib/mock/f38-build-710843-93550/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=432000uid=991gid=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': 'C.UTF-8'} and shell False warning: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1674000000 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.AzH1yU + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf bfast-0.7.0a + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/bfast-0.7.0a.tar.gz + 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 -f -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 configure.ac:23: warning: The macro `AC_GNU_SOURCE' is obsolete. configure.ac:23: You should run autoupdate. ./lib/autoconf/specific.m4:312: AC_GNU_SOURCE is expanded from... configure.ac:23: the top level configure.ac:87: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:87: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:87: the top level parallel-tests: installing 'config/test-driver' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.XKpQaz + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bfast-0.7.0a + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + 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 2023-05-11 15:18:43.491997464 -0400 +++ ./configure 2023-05-11 15:18:49.821969258 -0400 @@ -1692,7 +1692,7 @@ #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.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' + 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' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=riscv64-redhat-linux-gnu --host=riscv64-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/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline' checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free 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-redhat-linux-gnu checking for riscv64-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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... 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 for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for wchar.h... yes checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no ./configure: line 4851: git: command not found 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 host system type... riscv64-redhat-linux-gnu checking for GNU libc compatible malloc... 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 grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for limits.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for float.h... yes checking for zlib.h... 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 -j4 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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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:788:24: note: expected 'FILE *' but argument is of type 'gzFile' {aka 'struct gzFile_s *'} 788 | 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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -c -o RGIndex.o RGIndex.c 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]: 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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -c -o Align.o Align.c 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]: 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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -c -o AlignColorSpace.o AlignColorSpace.c AlignColorSpace.c: In function 'AlignColorSpaceGappedConstrained': AlignColorSpace.c:379:68: warning: operation on '(*(matrix->cells + ((sizetype)i + 1) * 8) + ((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]: 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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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 -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -c -o RunPostProcess.o RunPostProcess.c 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]: 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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -c -o balignsim.o balignsim.c 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]: 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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -c -o ../bfast/RGBinary.o ../bfast/RGBinary.c ../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]: 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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -c -o ../bfast/RGMatch.o ../bfast/RGMatch.c ../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:788:24: note: expected 'FILE *' but argument is of type 'gzFile' {aka 'struct gzFile_s *'} 788 | extern int feof (FILE *__stream) __THROW __wur; | ~~~~~~^~~~~~~~ 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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -c -o ../bfast/AlignMatrix.o ../bfast/AlignMatrix.c ../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]: 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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -c -o ../bfast/AlignColorSpace.o ../bfast/AlignColorSpace.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' ../bfast/AlignColorSpace.c: In function 'AlignColorSpaceGappedConstrained': ../bfast/AlignColorSpace.c:379:68: warning: operation on '(*(matrix->cells + ((sizetype)i + 1) * 8) + ((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]: 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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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.Y4Qi4q + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64 ++ dirname /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bfast-0.7.0a + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64 '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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -fgnu89-inline -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -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-31.fc38.riscv64/usr/bin' /usr/bin/install -p bfast '/builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.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-31.fc38.riscv64/usr/bin' /usr/bin/install -p balignmentscoredistribution balignsim bevalsim bgeneratereads bindexdist bindexhist bmfmerge brepeat btestindexes '/builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.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-31.fc38.riscv64/usr/bin' /usr/bin/install -p solid2fastq '/builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/bin' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/bin' /usr/bin/install -p bfast.resubmit.pl bfast.submit.pl ill2fastq.pl '/builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.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-31.fc38.riscv64/usr/share/doc/bfast' /usr/bin/install -p -m 644 LICENSE manual/bfast-book.pdf '/builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.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' + rm /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64//usr/share/doc/bfast/LICENSE + rm /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64//usr/share/doc/bfast/bfast-book.pdf + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 0.7.0a-31.fc38 --unique-debug-suffix -0.7.0a-31.fc38.riscv64 --unique-debug-src-base bfast-0.7.0a-31.fc38.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/bfast-0.7.0a extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/bin/balignmentscoredistribution extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/bin/balignsim extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/bin/bevalsim extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/bin/bfast extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/bin/bgeneratereads extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/bin/bindexdist extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/bin/bindexhist extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/bin/bmfmerge extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/bin/brepeat extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/bin/btestindexes extracting debug info from /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/bin/solid2fastq original debug info size: 13056kB, size after compression: 12716kB /usr/bin/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/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 + /usr/lib/rpm/redhat/brp-python-hardlink Processing files: bfast-0.7.0a-31.fc38.riscv64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.vB4i30 + umask 022 + cd /builddir/build/BUILD + cd bfast-0.7.0a + DOCDIR=/builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.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-31.fc38.riscv64/usr/share/doc/bfast + cp -pr AUTHORS /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/share/doc/bfast + cp -pr ChangeLog /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/share/doc/bfast + cp -pr NEWS /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/share/doc/bfast + cp -pr README /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/share/doc/bfast + cp -pr manual/bfast-book.pdf /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/share/doc/bfast + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.kS1vQs + umask 022 + cd /builddir/build/BUILD + cd bfast-0.7.0a + LICENSEDIR=/builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.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-31.fc38.riscv64/usr/share/licenses/bfast + cp -pr LICENSE /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64/usr/share/licenses/bfast + RPM_EC=0 ++ jobs -p + exit 0 Provides: bfast = 0.7.0a-31.fc38 bfast(riscv-64) = 0.7.0a-31.fc38 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) libc.so.6(GLIBC_2.34)(64bit) libm.so.6()(64bit) libm.so.6(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-31.fc38.riscv64 Provides: bfast-debugsource = 0.7.0a-31.fc38 bfast-debugsource(riscv-64) = 0.7.0a-31.fc38 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-31.fc38.riscv64 Provides: bfast-debuginfo = 0.7.0a-31.fc38 bfast-debuginfo(riscv-64) = 0.7.0a-31.fc38 debuginfo(build-id) = 05bbcdbd6609fdb5c190be36659fca2ce6c9c7ee debuginfo(build-id) = 07d44b44cb36710577a4968bf3791d447813fc5c debuginfo(build-id) = 152ee1a3110b4623224be042553dc18894408ede debuginfo(build-id) = 19b4ba9b7952ac8c308c9e6ebbc9bd9cad2fafd6 debuginfo(build-id) = 38d12bd8177b193ebe3dc78c10190af84351d747 debuginfo(build-id) = 40683baaa1ce2ec093d3d5d92a75aea15cd5a457 debuginfo(build-id) = 6724f7435010310f3c4a5eff8180b5ebd23b5b7b debuginfo(build-id) = 827a95e01c8666c8d744bfef6cec9bd8d8fddd9f debuginfo(build-id) = 8787800086469932e96daf10fc8d5ed6fc855e25 debuginfo(build-id) = a5efa80df48618bb90d6de21f234a00f5e55d427 debuginfo(build-id) = d78e5c78802f19aee4639a10c19f82a0ce857ca6 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-31.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64 Wrote: /builddir/build/RPMS/bfast-0.7.0a-31.fc38.riscv64.rpm Wrote: /builddir/build/RPMS/bfast-debugsource-0.7.0a-31.fc38.riscv64.rpm Wrote: /builddir/build/RPMS/bfast-debuginfo-0.7.0a-31.fc38.riscv64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.UbZI6s + umask 022 + cd /builddir/build/BUILD + cd bfast-0.7.0a + /usr/bin/rm -rf /builddir/build/BUILDROOT/bfast-0.7.0a-31.fc38.riscv64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.nU02QW + umask 022 + cd /builddir/build/BUILD + rm -rf bfast-0.7.0a bfast-0.7.0a.gemspec + RPM_EC=0 ++ jobs -p + exit 0 RPM build warnings: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Child return code was: 0