+ exec + rm -rf /rpmbuild + mkdir -p /rpmbuild + su -c 'rpmbuild -ba /builddir/build/SPECS/bfast.spec --define "debug_package %{nil}" --undefine _annotated_build --define "_missing_doc_files_terminate_build %{nil}" --define "_emacs_sitestartdir /usr/share/emacs/site-lisp/site-start.d" --define "_emacs_sitelispdir /usr/share/emacs/site-lisp" --nocheck ' mockbuild Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.O0q5Nr + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf bfast-0.7.0a + /usr/bin/gzip -dc /builddir/build/SOURCES/bfast-0.7.0a.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd bfast-0.7.0a + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (bfast-pthread-new.patch):' Patch #0 (bfast-pthread-new.patch): + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 patching file bfast/Makefile.am patching file bfast/Makefile.in patching file butil/Makefile.am patching file butil/Makefile.in patching file scripts/Makefile.am patching file scripts/Makefile.in patching file tests/Makefile.in + sed -i -e 's,^\(CFLAGS="${default_CFLAGS} ${extended_CFLAGS}"\),# \1,' configure configure.ac + touch -r aclocal.m4 configure configure.ac + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.MtPGjz + umask 022 + cd /builddir/build/BUILD + cd bfast-0.7.0a + CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 ' + export CFLAGS + CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 ' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + export LDFLAGS + '[' 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-specs=/usr/lib/rpm/redhat/redhat-hardened-ld ']' ++ find . -name ltmain.sh + ./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 --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline' checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking build system type... riscv64-redhat-linux-gnu checking for riscv64-redhat-linux-gnu-gcc... no checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking whether gcc and cc understand -c and -o together... yes checking for a BSD-compatible install... /usr/bin/install -c ./configure: line 3589: git: command not found checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for an ANSI C-conforming const... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for pow in -lm... yes checking for gzread in -lz... yes checking for floor... yes checking for pow... yes checking for sqrt... yes checking for strchr... yes checking for strdup... yes checking for strpbrk... yes checking for strstr... yes checking for strtok_r... yes checking for _LARGEFILE_SOURCE value needed for large files... no checking for int8_t... yes checking for int32_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for short int... yes checking size of short int... 2 checking for int... yes checking size of int... 4 checking for long int... yes checking size of long int... 8 checking for ANSI C header files... (cached) yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking for inline... inline configure: creating ./config.status config.status: creating Makefile config.status: creating bfast/Makefile config.status: creating butil/Makefile config.status: creating scripts/Makefile config.status: creating tests/Makefile config.status: creating config.h config.status: executing depfiles commands + make -j4 make all-recursive make[1]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a' Making all in bfast make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o AlignedEnd.o AlignedEnd.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o AlignedEntry.o AlignedEntry.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o AlignedRead.o AlignedRead.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o AlignedReadConvert.o AlignedReadConvert.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o BError.o BError.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o BLib.o BLib.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o RGBinary.o RGBinary.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o RGIndex.o RGIndex.c RGBinary.c: In function 'RGBinaryReadBinaryHeader': RGBinary.c:260:10: warning: variable 'numCharsPerByte' set but not used [-Wunused-but-set-variable] int32_t numCharsPerByte; ^~~~~~~~~~~~~~~ RGBinary.c: In function 'RGBinaryWriteBinaryHeader': RGBinary.c:387:10: warning: variable 'numCharsPerByte' set but not used [-Wunused-but-set-variable] int32_t numCharsPerByte; ^~~~~~~~~~~~~~~ RGBinary.c: In function 'RGBinaryWriteBinary': RGBinary.c:421:10: warning: variable 'numCharsPerByte' set but not used [-Wunused-but-set-variable] int32_t numCharsPerByte; ^~~~~~~~~~~~~~~ RGBinary.c: In function 'RGBinaryGetFourBit': RGBinary.c:820:7: warning: variable 'curChar' set but not used [-Wunused-but-set-variable] char curChar; ^~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o RGIndexAccuracy.o RGIndexAccuracy.c RGIndex.c: In function 'RGIndexCreateHelper': RGIndex.c:463:24: warning: variable 'keyEndPos' set but not used [-Wunused-but-set-variable] uint32_t keyStartPos, keyEndPos; ^~~~~~~~~ RGIndex.c: In function 'RGIndexCompareContigPos': RGIndex.c:2428:11: warning: variable 'length' set but not used [-Wunused-but-set-variable] int32_t length; ^~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o RGIndexExons.o RGIndexExons.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o RGIndexLayout.o RGIndexLayout.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o RGMatch.o RGMatch.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o RGMatches.o RGMatches.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o RGRanges.o RGRanges.c RGMatch.c: In function 'RGMatchRead': RGMatch.c:23:11: warning: passing argument 1 of 'feof' from incompatible pointer type [-Wincompatible-pointer-types] if(feof(fp) != 0) { ^~ In file included from RGMatch.c:2:0: /usr/include/stdio.h:759:12: note: expected 'FILE * {aka struct _IO_FILE *}' but argument is of type 'gzFile {aka struct gzFile_s *}' extern int feof (FILE *__stream) __THROW __wur; ^~~~ gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o RGReads.o RGReads.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ScoringMatrix.o ScoringMatrix.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o Align.o Align.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o AlignNTSpace.o AlignNTSpace.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o AlignColorSpace.o AlignColorSpace.c Align.c: In function 'AlignExact': Align.c:499:8: warning: variable 'colorErrorAligned' set but not used [-Wunused-but-set-variable] char colorErrorAligned[SEQUENCE_LENGTH]="\0"; ^~~~~~~~~~~~~~~~~ AlignNTSpace.c: In function 'AlignNTSpaceRecoverAlignmentFromMatrix': AlignNTSpace.c:225:7: warning: variable 'curReadBase' set but not used [-Wunused-but-set-variable] char curReadBase; ^~~~~~~~~~~ AlignColorSpace.c: In function 'AlignColorSpaceGappedConstrained': AlignColorSpace.c:379:40: warning: operation on '(*(matrix->cells + ((sizetype)i + 1) * 8) + ((sizetype)j + 1) * 180)->s.score[k]' may be undefined [-Wsequence-point] matrix->cells[i+1][j+1].s.score[k] = LOWERBOUNDSCORE(matrix->cells[i+1][j+1].s.score[k]); AlignColorSpace.c:384:10: warning: variable 'max' set but not used [-Wunused-but-set-variable] char max = GAP; ^~~ AlignColorSpace.c: In function 'AlignColorSpaceFillInCell': AlignColorSpace.c:848:9: warning: variable 'max' set but not used [-Wunused-but-set-variable] char max = GAP; ^~~ AlignColorSpace.c:899:8: warning: variable 'max' set but not used [-Wunused-but-set-variable] char max = GAP; ^~~ AlignColorSpace.c:986:9: warning: variable 'max' set but not used [-Wunused-but-set-variable] char max = GAP; ^~~ gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o AlignMatrix.o AlignMatrix.c AlignMatrix.c: In function 'AlignMatrixReallocate': AlignMatrix.c:12:23: warning: variable 'prevNCol' set but not used [-Wunused-but-set-variable] int32_t i, prevNRow, prevNCol; ^~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o MatchesReadInputFiles.o MatchesReadInputFiles.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o RunMatch.o RunMatch.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o RunLocalAlign.o RunLocalAlign.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o RunPostProcess.o RunPostProcess.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o RunAlign.o RunAlign.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o BfastFasta2BRG.o BfastFasta2BRG.c RunPostProcess.c: In function 'FilterAlignedRead': RunPostProcess.c:685:16: warning: variable 'bestIndex' set but not used [-Wunused-but-set-variable] int32_t best, bestIndex, numBest; ^~~~~~~~~ RunPostProcess.c: In function 'GetPEDBins': RunPostProcess.c:850:10: warning: variable 'alignQueueLength' set but not used [-Wunused-but-set-variable] int32_t alignQueueLength; ^~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o BfastIndex.o BfastIndex.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o BfastMatch.o BfastMatch.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o BfastLocalAlign.o BfastLocalAlign.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o BfastPostProcess.o BfastPostProcess.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o BfastBAFConvert.o BfastBAFConvert.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o BfastHeader.o BfastHeader.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o BfastBMFConvert.o BfastBMFConvert.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o BfastBRG2Fasta.o BfastBRG2Fasta.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o BfastAlign.o BfastAlign.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o aflib.o aflib.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o Main.o Main.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -lpthread -o bfast AlignedEnd.o AlignedEntry.o AlignedRead.o AlignedReadConvert.o BError.o BLib.o RGBinary.o RGIndex.o RGIndexAccuracy.o RGIndexExons.o RGIndexLayout.o RGMatch.o RGMatches.o RGRanges.o RGReads.o ScoringMatrix.o Align.o AlignNTSpace.o AlignColorSpace.o AlignMatrix.o MatchesReadInputFiles.o RunMatch.o RunLocalAlign.o RunPostProcess.o RunAlign.o BfastFasta2BRG.o BfastIndex.o BfastMatch.o BfastLocalAlign.o BfastPostProcess.o BfastBAFConvert.o BfastHeader.o BfastBMFConvert.o BfastBRG2Fasta.o BfastAlign.o aflib.o Main.o -lpthread -lm -lbz2 -lz make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' Making all in butil make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/butil' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o balignmentscoredistribution.o balignmentscoredistribution.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o SimRead.o SimRead.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o balignsim.o balignsim.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o bevalsim.o bevalsim.c balignsim.c: In function 'Run': balignsim.c:174:9: warning: variable 'mismatchScore' set but not used [-Wunused-but-set-variable] double mismatchScore; ^~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o bgeneratereads.o bgeneratereads.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/RGReads.o ../bfast/RGReads.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o bindexdist.o bindexdist.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o bindexhist.o bindexhist.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/MatchesReadInputFiles.o ../bfast/MatchesReadInputFiles.c bindexdist.c: In function 'PrintDistribution': bindexdist.c:128:10: warning: variable 'numDifferent' set but not used [-Wunused-but-set-variable] int64_t numDifferent = 0; ^~~~~~~~~~~~ bindexhist.c: In function 'PrintHistogramThread': bindexhist.c:372:6: warning: variable 'skip' set but not used [-Wunused-but-set-variable] int skip; ^~~~ gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/aflib.o ../bfast/aflib.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o bmfmerge.o bmfmerge.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o brepeat.o brepeat.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o btestindexes.o btestindexes.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/BError.o ../bfast/BError.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/RGIndex.o ../bfast/RGIndex.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/BLib.o ../bfast/BLib.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/RGBinary.o ../bfast/RGBinary.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/RGRanges.o ../bfast/RGRanges.c ../bfast/RGIndex.c: In function 'RGIndexCreateHelper': ../bfast/RGIndex.c:463:24: warning: variable 'keyEndPos' set but not used [-Wunused-but-set-variable] uint32_t keyStartPos, keyEndPos; ^~~~~~~~~ ../bfast/RGBinary.c: In function 'RGBinaryReadBinaryHeader': ../bfast/RGBinary.c:260:10: warning: variable 'numCharsPerByte' set but not used [-Wunused-but-set-variable] int32_t numCharsPerByte; ^~~~~~~~~~~~~~~ ../bfast/RGBinary.c: In function 'RGBinaryWriteBinaryHeader': ../bfast/RGBinary.c:387:10: warning: variable 'numCharsPerByte' set but not used [-Wunused-but-set-variable] int32_t numCharsPerByte; ^~~~~~~~~~~~~~~ ../bfast/RGBinary.c: In function 'RGBinaryWriteBinary': ../bfast/RGBinary.c:421:10: warning: variable 'numCharsPerByte' set but not used [-Wunused-but-set-variable] int32_t numCharsPerByte; ^~~~~~~~~~~~~~~ ../bfast/RGBinary.c: In function 'RGBinaryGetFourBit': ../bfast/RGBinary.c:820:7: warning: variable 'curChar' set but not used [-Wunused-but-set-variable] char curChar; ^~~~~~~ ../bfast/RGIndex.c: In function 'RGIndexCompareContigPos': ../bfast/RGIndex.c:2428:11: warning: variable 'length' set but not used [-Wunused-but-set-variable] int32_t length; ^~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/RGMatch.o ../bfast/RGMatch.c ../bfast/RGMatch.c: In function 'RGMatchRead': ../bfast/RGMatch.c:23:11: warning: passing argument 1 of 'feof' from incompatible pointer type [-Wincompatible-pointer-types] if(feof(fp) != 0) { ^~ In file included from ../bfast/RGMatch.c:2:0: /usr/include/stdio.h:759:12: note: expected 'FILE * {aka struct _IO_FILE *}' but argument is of type 'gzFile {aka struct gzFile_s *}' extern int feof (FILE *__stream) __THROW __wur; ^~~~ gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/AlignedRead.o ../bfast/AlignedRead.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/AlignedReadConvert.o ../bfast/AlignedReadConvert.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/AlignedEnd.o ../bfast/AlignedEnd.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/AlignedEntry.o ../bfast/AlignedEntry.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/RGIndexExons.o ../bfast/RGIndexExons.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/RGMatches.o ../bfast/RGMatches.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/RGIndexAccuracy.o ../bfast/RGIndexAccuracy.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/RunLocalAlign.o ../bfast/RunLocalAlign.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/ScoringMatrix.o ../bfast/ScoringMatrix.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/Align.o ../bfast/Align.c ../bfast/Align.c: In function 'AlignExact': ../bfast/Align.c:499:8: warning: variable 'colorErrorAligned' set but not used [-Wunused-but-set-variable] char colorErrorAligned[SEQUENCE_LENGTH]="\0"; ^~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/AlignColorSpace.o ../bfast/AlignColorSpace.c gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/AlignNTSpace.o ../bfast/AlignNTSpace.c ../bfast/AlignColorSpace.c: In function 'AlignColorSpaceGappedConstrained': ../bfast/AlignColorSpace.c:379:40: warning: operation on '(*(matrix->cells + ((sizetype)i + 1) * 8) + ((sizetype)j + 1) * 180)->s.score[k]' may be undefined [-Wsequence-point] matrix->cells[i+1][j+1].s.score[k] = LOWERBOUNDSCORE(matrix->cells[i+1][j+1].s.score[k]); ../bfast/AlignColorSpace.c:384:10: warning: variable 'max' set but not used [-Wunused-but-set-variable] char max = GAP; ^~~ ../bfast/AlignColorSpace.c: In function 'AlignColorSpaceFillInCell': ../bfast/AlignColorSpace.c:848:9: warning: variable 'max' set but not used [-Wunused-but-set-variable] char max = GAP; ^~~ ../bfast/AlignColorSpace.c:899:8: warning: variable 'max' set but not used [-Wunused-but-set-variable] char max = GAP; ^~~ ../bfast/AlignColorSpace.c:986:9: warning: variable 'max' set but not used [-Wunused-but-set-variable] char max = GAP; ^~~ ../bfast/AlignNTSpace.c: In function 'AlignNTSpaceRecoverAlignmentFromMatrix': ../bfast/AlignNTSpace.c:225:7: warning: variable 'curReadBase' set but not used [-Wunused-but-set-variable] char curReadBase; ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o ../bfast/AlignMatrix.o ../bfast/AlignMatrix.c ../bfast/AlignMatrix.c: In function 'AlignMatrixReallocate': ../bfast/AlignMatrix.c:12:23: warning: variable 'prevNCol' set but not used [-Wunused-but-set-variable] int32_t i, prevNRow, prevNCol; ^~~~~~~~ gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -lpthread -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 -lm -lbz2 -lz gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -lpthread -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 -lm -lbz2 -lz gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -lpthread -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 -lm -lbz2 -lz gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -lpthread -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 -lm -lbz2 -lz gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -lpthread -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 -lm -lbz2 -lz gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -lpthread -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 -lm -lbz2 -lz gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -lpthread -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 -lm -lbz2 -lz gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -lpthread -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 -lm -lbz2 -lz gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -lpthread -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 -lm -lbz2 -lz make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/butil' Making all in scripts make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/scripts' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -c -o solid2fastq.o solid2fastq.c gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -lpthread -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 -lm -lbz2 -lz make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/scripts' Making all in tests make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/tests' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/tests' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a' make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a' make[1]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a' + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.glzinP + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64 ++ dirname /builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64 + cd bfast-0.7.0a + make install DESTDIR=/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64 Making install in bfast make[1]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fgnu89-inline -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -lpthread -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' test -z "/usr/bin" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin" /usr/bin/install -c 'bfast' '/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin/bfast' 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' test -z "/usr/bin" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin" /usr/bin/install -c 'balignmentscoredistribution' '/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin/balignmentscoredistribution' /usr/bin/install -c 'balignsim' '/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin/balignsim' /usr/bin/install -c 'bevalsim' '/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin/bevalsim' /usr/bin/install -c 'bgeneratereads' '/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin/bgeneratereads' /usr/bin/install -c 'bindexdist' '/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin/bindexdist' /usr/bin/install -c 'bindexhist' '/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin/bindexhist' /usr/bin/install -c 'bmfmerge' '/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin/bmfmerge' /usr/bin/install -c 'brepeat' '/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin/brepeat' /usr/bin/install -c 'btestindexes' '/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin/btestindexes' 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' test -z "/usr/bin" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin" /usr/bin/install -c 'solid2fastq' '/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin/solid2fastq' test -z "/usr/bin" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin" /usr/bin/install -c 'bfast.resubmit.pl' '/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin/bfast.resubmit.pl' /usr/bin/install -c 'bfast.submit.pl' '/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin/bfast.submit.pl' /usr/bin/install -c 'ill2fastq.pl' '/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin/ill2fastq.pl' 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' test -z "/usr/bin" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/bin" 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'. test -z "/usr/share/doc/bfast" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/share/doc/bfast" /usr/bin/install -c -m 644 'LICENSE' '/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/share/doc/bfast/LICENSE' /usr/bin/install -c -m 644 'manual/bfast-book.pdf' '/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/share/doc/bfast/bfast-book.pdf' 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-17.fc28.riscv64//usr/share/doc/bfast/LICENSE + rm /builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64//usr/share/doc/bfast/bfast-book.pdf + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig /sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip /usr/bin/strip + /usr/lib/rpm/brp-strip-comment-note /usr/bin/strip /usr/bin/objdump + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs Processing files: bfast-0.7.0a-17.fc28.riscv64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.TTfvHU + umask 022 + cd /builddir/build/BUILD + cd bfast-0.7.0a + DOCDIR=/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.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-17.fc28.riscv64/usr/share/doc/bfast + cp -pr AUTHORS /builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/share/doc/bfast + cp -pr ChangeLog /builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/share/doc/bfast + cp -pr NEWS /builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/share/doc/bfast + cp -pr README /builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/share/doc/bfast + cp -pr manual/bfast-book.pdf /builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/share/doc/bfast + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.MI6IgM + umask 022 + cd /builddir/build/BUILD + cd bfast-0.7.0a + LICENSEDIR=/builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.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-17.fc28.riscv64/usr/share/licenses/bfast + cp -pr LICENSE /builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64/usr/share/licenses/bfast + exit 0 Provides: bfast = 0.7.0a-17.fc28 bfast(riscv-64) = 0.7.0a-17.fc28 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/perl ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.27)(64bit) libz.so.1()(64bit) perl(Cwd) perl(Data::Dumper) perl(File::Path) perl(Getopt::Long) perl(Getopt::Std) perl(Pod::Usage) perl(XML::Simple) perl(constant) perl(strict) perl(warnings) rtld(GNU_HASH) Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64 Wrote: /builddir/build/SRPMS/bfast-0.7.0a-17.fc28.src.rpm Wrote: /builddir/build/RPMS/riscv64/bfast-0.7.0a-17.fc28.riscv64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.R1yQNQ + umask 022 + cd /builddir/build/BUILD + cd bfast-0.7.0a + /usr/bin/rm -rf /builddir/build/BUILDROOT/bfast-0.7.0a-17.fc28.riscv64 + exit 0 + touch /buildok + cleanup + set +e + sync + sleep 5 + sync + poweroff Terminated ++ cleanup ++ set +e ++ sync Terminated +++ cleanup +++ set +e +++ sync +++ sleep 5 +++ sync +++ poweroff