Mock Version: 3.5 Mock Version: 3.5 Mock Version: 3.5 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target riscv64 --nodeps /builddir/build/SPECS/bfast.spec'], chrootPath='/var/lib/mock/f39-build-1446366-32670/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=864000uid=996gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --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=1689724800 Wrote: /builddir/build/SRPMS/bfast-0.7.0a-32.fc39.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 --noclean --target riscv64 --nodeps /builddir/build/SPECS/bfast.spec'], chrootPath='/var/lib/mock/f39-build-1446366-32670/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=864000uid=996gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --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=1689724800 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.FSr966 + 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 + rm -rf /builddir/build/BUILD/bfast-0.7.0a-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/bfast-0.7.0a-SPECPARTS + /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.voH8mw + 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 -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 -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 + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + 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 -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 -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 + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + 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 2023-10-27 16:09:27.003566263 -0400 +++ ./configure 2023-10-27 16:09:59.643566632 -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-koji-linux-gnu --host=riscv64-koji-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --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-koji-linux-gnu checking for riscv64-koji-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-koji-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 -j8 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 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 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 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 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 RGBinary.o RGBinary.c 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]: 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 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 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 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 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 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 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 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 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:846:24: note: expected ‘FILE *’ but argument is of type ‘gzFile’ {aka ‘struct gzFile_s *’} 846 | 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 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 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 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 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 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 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 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 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 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 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) * 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]: 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 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,-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 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 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 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 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 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 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 ../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 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,-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 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 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 bindexdist.o bindexdist.c 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]: 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 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 ../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/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/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/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/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/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/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:846:24: note: expected ‘FILE *’ but argument is of type ‘gzFile’ {aka ‘struct gzFile_s *’} 846 | 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,-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/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/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/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/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/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 ../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/AlignNTSpace.o ../bfast/AlignNTSpace.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' ../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]: 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/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 ../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 -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 -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 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 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 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 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 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 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 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.F28Qzv + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.riscv64 ++ dirname /builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.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 -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 -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 + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + 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-32.fc39.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-32.fc39.riscv64/usr/bin' /usr/bin/install -p bfast '/builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.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-32.fc39.riscv64/usr/bin' /usr/bin/install -p balignmentscoredistribution balignsim bevalsim bgeneratereads bindexdist bindexhist bmfmerge brepeat btestindexes '/builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.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-32.fc39.riscv64/usr/bin' /usr/bin/install -p solid2fastq '/builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.riscv64/usr/bin' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.riscv64/usr/bin' /usr/bin/install -p bfast.resubmit.pl bfast.submit.pl ill2fastq.pl '/builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.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-32.fc39.riscv64/usr/share/doc/bfast' /usr/bin/install -p -m 644 LICENSE manual/bfast-book.pdf '/builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.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-32.fc39.riscv64//usr/share/doc/bfast/LICENSE + rm /builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.riscv64//usr/share/doc/bfast/bfast-book.pdf + /usr/bin/find-debuginfo -j8 --strict-build-id -m -i --build-id-seed 0.7.0a-32.fc39 --unique-debug-suffix -0.7.0a-32.fc39.riscv64 --unique-debug-src-base bfast-0.7.0a-32.fc39.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/bfast-0.7.0a find-debuginfo: starting Extracting debug info from 11 files DWARF-compressing 11 files sepdebugcrcfix: Updated 11 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/bfast-0.7.0a-32.fc39.riscv64 1563 blocks find-debuginfo: done + /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 -j8 + /usr/lib/rpm/redhat/brp-python-hardlink Processing files: bfast-0.7.0a-32.fc39.riscv64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.gJndqV + umask 022 + cd /builddir/build/BUILD + cd bfast-0.7.0a + DOCDIR=/builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.riscv64/usr/share/doc/bfast + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.riscv64/usr/share/doc/bfast + cp -pr /builddir/build/BUILD/bfast-0.7.0a/AUTHORS /builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.riscv64/usr/share/doc/bfast + cp -pr /builddir/build/BUILD/bfast-0.7.0a/ChangeLog /builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.riscv64/usr/share/doc/bfast + cp -pr /builddir/build/BUILD/bfast-0.7.0a/NEWS /builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.riscv64/usr/share/doc/bfast + cp -pr /builddir/build/BUILD/bfast-0.7.0a/README /builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.riscv64/usr/share/doc/bfast + cp -pr /builddir/build/BUILD/bfast-0.7.0a/manual/bfast-book.pdf /builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.riscv64/usr/share/doc/bfast + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.6KbAVg + umask 022 + cd /builddir/build/BUILD + cd bfast-0.7.0a + LICENSEDIR=/builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.riscv64/usr/share/licenses/bfast + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.riscv64/usr/share/licenses/bfast + cp -pr /builddir/build/BUILD/bfast-0.7.0a/LICENSE /builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.riscv64/usr/share/licenses/bfast + RPM_EC=0 ++ jobs -p + exit 0 Provides: bfast = 0.7.0a-32.fc39 bfast(riscv-64) = 0.7.0a-32.fc39 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-32.fc39.riscv64 Provides: bfast-debugsource = 0.7.0a-32.fc39 bfast-debugsource(riscv-64) = 0.7.0a-32.fc39 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-32.fc39.riscv64 Provides: bfast-debuginfo = 0.7.0a-32.fc39 bfast-debuginfo(riscv-64) = 0.7.0a-32.fc39 debuginfo(build-id) = 0fb8c091c18eac26a74d14c43c56ef1a3d17987a debuginfo(build-id) = 171ceae37d2ddea0a711a2cf0a0f24a9e1df8d63 debuginfo(build-id) = 28b13abbbfd4e0b3e54c742862718f8034472d87 debuginfo(build-id) = 3201c478e75ef358ce516eab15464e7ae8aa5254 debuginfo(build-id) = 33c8c1a093aabf33d536cc1010f47973b0dc75db debuginfo(build-id) = 469fae6dd9cebc63d5ab1c048bcb4bc141fd5d3a debuginfo(build-id) = 473f4b264adbd05738813380ff480966f9b4bc8c debuginfo(build-id) = 68f0e9c2ff1947b3e00b5e968283f9a725694470 debuginfo(build-id) = 7808bdb455bfd7196d7cba3d7a62690f71bfb129 debuginfo(build-id) = 9c049f689c54a90269e6b846c53df72fab453bf2 debuginfo(build-id) = fd573dcf6990f25aa442a7c86660da4acded0374 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-32.fc39 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bfast-0.7.0a-32.fc39.riscv64 Wrote: /builddir/build/RPMS/bfast-0.7.0a-32.fc39.riscv64.rpm Wrote: /builddir/build/RPMS/bfast-debugsource-0.7.0a-32.fc39.riscv64.rpm Wrote: /builddir/build/RPMS/bfast-debuginfo-0.7.0a-32.fc39.riscv64.rpm RPM build warnings: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Child return code was: 0