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Gentoo's Bugzilla – Attachment 659146 Details for
Bug 741186
sci-biology/fasta-36.3.5e fails to compile: dropnnw2.c:567:18: error: use of undeclared identifier 'OVERFLOW'
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build.log
build.log (text/plain), 63.35 KB, created by
Agostino Sarubbo
on 2020-09-08 13:09:58 UTC
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Description:
build.log
Filename:
MIME Type:
Creator:
Agostino Sarubbo
Created:
2020-09-08 13:09:58 UTC
Size:
63.35 KB
patch
obsolete
> * Package: sci-biology/fasta-36.3.5e > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: abi_x86_64 amd64 cpu_flags_x86_sse2 elibc_glibc kernel_linux test userland_GNU > * FEATURES: network-sandbox preserve-libs sandbox test userpriv usersandbox > > >@@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@ >This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix; >This ebuild was merged at the following commit: >https://github.com/gentoo-mirror/gentoo/commit/8ee8c827d24103fff75a89608576ea8214b94cb1 (Tue Sep 8 10:05:30 UTC 2020) >@@@@@ END @@@@@ > > > >emerge --info: >Portage 3.0.6 (python 3.8.5-final-0, default/linux/amd64/17.1, gcc-10.2.0, glibc-2.32-r1, 5.4.0-1021-aws x86_64) >================================================================= >System uname: Linux-5.4.0-1021-aws-x86_64-Intel-R-_Xeon-R-_Platinum_8175M_CPU_@_2.50GHz-with-glibc2.2.5 >KiB Mem: 64359960 total, 28204232 free >KiB Swap: 0 total, 0 free >Timestamp of repository gentoo: Tue, 08 Sep 2020 10:05:30 +0000 >sh bash 5.0_p18 >ld GNU ld (Gentoo 2.34 p6) 2.34.0 >app-shells/bash: 5.0_p18::gentoo >dev-lang/perl: 5.30.3-r1::gentoo >dev-lang/python: 2.7.18-r1::gentoo, 3.6.12::gentoo, 3.7.9::gentoo, 3.8.5::gentoo, 3.9.0_rc1::gentoo >dev-util/cmake: 3.18.2::gentoo >sys-apps/baselayout: 2.7::gentoo >sys-apps/openrc: 0.42.1::gentoo >sys-apps/sandbox: 2.20::gentoo >sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r5::gentoo >sys-devel/automake: 1.16.2::gentoo >sys-devel/binutils: 2.34-r2::gentoo >sys-devel/gcc: 10.2.0-r1::gentoo >sys-devel/gcc-config: 2.3.2::gentoo >sys-devel/libtool: 2.4.6-r6::gentoo >sys-devel/make: 4.3::gentoo >sys-kernel/linux-headers: 5.8::gentoo (virtual/os-headers) >sys-libs/glibc: 2.32-r1::gentoo >Repositories: > >gentoo > location: /usr/portage > sync-type: rsync > sync-uri: rsync://rsync.gentoo.org/gentoo-portage > priority: -1000 > sync-rsync-extra-opts: > sync-rsync-verify-jobs: 1 > sync-rsync-verify-metamanifest: yes > sync-rsync-verify-max-age: 24 > >ACCEPT_KEYWORDS="amd64 ~amd64" >ACCEPT_LICENSE="* fasta" >CBUILD="x86_64-pc-linux-gnu" >CC="x86_64-pc-linux-gnu-clang" >CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >CHOST="x86_64-pc-linux-gnu" >CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" >CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" >CXX="x86_64-pc-linux-gnu-clang++" >CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >DISTDIR="/var/tmp/portage/sci-biology/fasta-36.3.5e/distdir" >EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -b -k" >ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" >FCFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" >FFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >GENTOO_MIRRORS="http://distfiles.gentoo.org" >LANG="C.UTF-8" >LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld" >MAKEOPTS="-j16 V=1" >PKGDIR="/root/.packages" >PORTAGE_CONFIGROOT="/" >PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" >PORTAGE_TMPDIR="/var/tmp" >USE="acl amd64 berkdb bzip2 cli crypt dri elogind fortran gdbm iconv ipv6 jumbo-build libglvnd libtirpc multilib native-symlinks ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd test unicode xattr zlib" ABI_X86="64" CPU_FLAGS_X86="sse2" ELIBC="glibc" KERNEL="linux" USERLAND="GNU" >Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS > > > >>>> Unpacking source... >>>> Unpacking fasta-36.3.5e.tar.gz to /var/tmp/portage/sci-biology/fasta-36.3.5e/work >>>> Source unpacked in /var/tmp/portage/sci-biology/fasta-36.3.5e/work >>>> Preparing source in /var/tmp/portage/sci-biology/fasta-36.3.5e/work/fasta-36.3.5e ... > * Applying fasta-36.3.5e-ldflags.patch ... > [ ok ] >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/fasta-36.3.5e/work/fasta-36.3.5e ... >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/fasta-36.3.5e/work/fasta-36.3.5e ... >make -j16 V=1 -f ../make/Makefile.linux64_sse2 'CC=x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math' 'HFLAGS=-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -o' all >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_THR -DCOMP_MLIB -c comp_lib8.c -o comp_mthr8.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c work_thr2.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c pthr_subs2.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_THR -DCOMP_MLIB -c compacc2.c -o compacc2_t.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c mshowbest.c -o showbest.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c build_ares.c -o build_ares.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c re_getlib.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_THR -c mshowalign2.c -o mshowalign2_t.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c htime.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c apam.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c doinit.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTA initfa.c -o init_fa.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DLOCAL_SCORE -c scaleswn.c -o scale_se.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c karlin.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropnfa.c -o drop_nfa.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c wm_align.c >mshowalign2.c:272:20: warning: sizeof on pointer operation will return size of > 'char *' instead of 'char [2048]' [-Wsizeof-array-decay] > bline[sizeof(bline-1)]='\0'; > ~~~~~^ >mshowbest.c:355:11: warning: logical not is only applied to the left hand side > of this bitwise operator [-Wlogical-not-parentheses] > if (!bbp->have_ares & 0x1) { > ^ ~ >mshowbest.c:355:11: note: add parentheses after the '!' to evaluate the bitwise > operator first > if (!bbp->have_ares & 0x1) { > ^ > ( ) >mshowalign2.cmshowbest.c:346:355:10:11: : warning: note: logical addnot parentheses is around only left handapplied sideto expressionthe toleft > hand silence sidethis > warning >of this bitwise operator if (!bbp->have_ares & 0x1) { > [-Wlogical-not-parentheses] ^ > > ( ) > if ((!m_msp->markx & MX_M10FORM)) name1[nml]='\0'; > ^ ~ >mshowalign2.c:346:10: note: add parentheses after the '!' to evaluate the > bitwise operator first > if ((!m_msp->markx & MX_M10FORM)) name1[nml]='\0'; > ^ > ( ) >mshowalign2.c:346:10: note: add parentheses around left hand side expression to > silence this warning > if ((!m_msp->markx & MX_M10FORM)) name1[nml]='\0'; > ^ > ( ) >mshowalign2.c:361:27: warning: the value of the size argument in 'strncat' is > too large, might lead to a buffer overflow [-Wstrncat-size] > strncat(l_name,"_r",sizeof(l_name)); > ^~~~~~~~~~~~~~ >mshowalign2.c:361:27: note: change the argument to be the free space in the > destination buffer minus the terminating null byte > strncat(l_name,"_r",sizeof(l_name)); > ^~~~~~~~~~~~~~ > sizeof(l_name) - strlen(l_name) - 1 >mshowalign2.c:364:30: warning: the value of the size argument in 'strncat' is > too large, might lead to a buffer overflow [-Wstrncat-size] > strncat(l_name,tmp_str,sizeof(l_name)-strlen(l_name)); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >mshowalign2.c:364:30: note: change the argument to be the free space in the > destination buffer minus the terminating null byte > strncat(l_name,tmp_str,sizeof(l_name)-strlen(l_name)); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > sizeof(l_name) - strlen(l_name) - 1 >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTA -c cal_cons.c -o calcons_fa.o >doinit.c:318:37: warning: the value of the size argument in 'strncat' is too > large, might lead to a buffer overflow [-Wstrncat-size] > strncat (optstring, f_optstring, sizeof (optstring)); > ^~~~~~~~~~~~~~~~~~ >doinit.c:318:37: note: change the argument to be the free space in the > destination buffer minus the terminating null byte > strncat (optstring, f_optstring, sizeof (optstring)); > ^~~~~~~~~~~~~~~~~~ > sizeof(optstring) - strlen(optstring) - 1 >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c nmgetlib.c -o lgetlib.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c mmgetaa.c -o lgetaa_m.o >compacc2.c:1601:28: warning: format specifies type 'long long' but the argument > has type 'off_t' (aka 'long') [-Wformat] > rbuf_dp->stats_idx, rbuf_dp->mseq->lseek); > ^~~~~~~~~~~~~~~~~~~~ >mmgetaa.c:117:87: warning: format specifies type 'long long' but the argument > has type 'fseek_t' (aka 'long') [-Wformat] > ...*** Warning *** database too large (%lld) for 32-bit mmap()\n",f_size); > ~~~~ ^~~~~~ > %ld >mmgetaa.c:140:12: warning: format specifies type 'long long' but the argument > has type '__off_t' (aka 'long') [-Wformat] > sname,statbuf.st_size,f_size); > ^~~~~~~~~~~~~~~ >mmgetaa.c:140:28: warning: format specifies type 'long long' but the argument > has type 'fseek_t' (aka 'long') [-Wformat] > sname,statbuf.st_size,f_size); > ^~~~~~ >mmgetaa.c:795:10: warning: format specifies type 'long long' but the argument > has type 'MM_OFF' (aka 'long') [-Wformat] > i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], > ^~~~~~~~~~~~~~~~~~ >mmgetaa.c:795:29: warning: format specifies type 'long long' but the argument > has type 'MM_OFF' (aka 'long') [-Wformat] > i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], > ^~~~~~~~~~~~~~~~~~ >mmgetaa.c:796:8: warning: format specifies type 'long long' but the argument has > type 'long' [-Wformat] > m_fd->d_pos_arr[i+1]-m_fd->s_pos_arr[i]); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c c_dispn.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c ncbl2_mlib.c >c_dispn.c:413:49: warning: the value of the size argument in 'strncat' is too > large, might lead to a buffer overflow [-Wstrncat-size] > strncat(afmtf," %4ld-%4ld: %5.1f%%:%s:\n",sizeof(afmtf)); > ^~~~~~~~~~~~~ >c_dispn.c:413:49: note: change the argument to 1 warning generated. >be the free space in the > destination buffer minus x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c lib_sel.c >ncbl2_mlib.cthe :312terminating:31: nullwarning: byte >the value of the size argument in 'strncat' is too > large, might lead to a ...%4ld-%4ld: %5.1f%%:%s:\n",sizeof(afmtf)); > buffer ^~~~~~~~~~~~~overflow > sizeof(afmtf) - strlen(afmtf) - 1[-Wstrncat-size] > > strncat(tname,msk_name, sizeof(tname)); > ^~~~~~~~~~~~~ >ncbl2_mlib.c:312:31: note: change the argument to be the free space in the > destination buffer minus the terminating null byte > strncat(tname,msk_name, sizeof(tname)); > ^~~~~~~~~~~~~ > sizeof(tname) - strlen(tname) - 1 >ncbl2_mlib.cc_dispn.c:316::28:441: warning51:: the warning value: the of the value size argument of in the 'strncat' size is argument too >in large,'strncat' mightis lead tooto > a large, buffer might overflow lead [-Wstrncat-size] >to a buffer overflow strncat(tname,dname, sizeof(tname));[-Wstrncat-size] > > ^~~~~~~~~~~~~ > strncat(afmtf," %4ld-%4ld:%4d %5.1f%%:%s\n",sizeof(afmtf)); > ^~~~~~~~~~~~~ >ncbl2_mlib.c:316:28: note: change the argumentc_dispn.c to be :441the free :51space : in note: the > destinationchange buffer minus the the argument terminating to null be byte >the free space in the strncat(tname,dname, sizeof(tname)); > > ^~~~~~~~~~~~~destination > sizeof(tname) - strlen(tname) - 1buffer >minus the terminating null byte > ...%4ld-%4ld:%4d %5.1f%%:%s\n",sizeof(afmtf)); > ^~~~~~~~~~~~~ > sizeof(afmtf) - strlen(afmtf) - 1 >c_dispn.c:447:39: warning: the value of the size argument in 'strncat' is too > large, might lead to a buffer overflow [-Wstrncat-size] > strncat(afmtf," %4ld-%4ld:%s\n",sizeof(afmtf)); > ^~~~~~~~~~~~~ >c_dispn.c:447:39: note: change the argument to be the free space in the > destination buffer minus the terminating null byte > strncat(afmtf," %4ld-%4ld:%s\n",sizeof(afmtf)); > ^~~~~~~~~~~~~ > sizeof(afmtf) - strlen(afmtf) - 1 >ncbl2_mlib.c:608:29: warning: the value of the size argument in 'strncat' is too > large, might lead to a buffer overflow [-Wstrncat-size] > strncat(tname,msk_name, sizeof(tname)); > ^~~~~~~~~~~~~ >ncbl2_mlib.c:608:29: note: change the argument to be the free space in the > destination buffer minus the terminating null byte > strncat(tname,msk_name, sizeof(tname)); > ^~~~~~~~~~~~~ > sizeof(tname) - strlen(tname) - 1 >ncbl2_mlib.c:612:26: warning: the value of the size argument in 'strncat' is too > large, might lead to a buffer overflow [-Wstrncat-size] > strncat(tname,dname, sizeof(tname)); > ^~~~~~~~~~~~~ >ncbl2_mlib.c:612:26: note: change the argument to be the free space in the > destination buffer minus the terminating null byte > strncat(tname,dname, sizeof(tname)); > ^~~~~~~~~~~~~ > sizeof(tname) - strlen(tname) - 1 >ncbl2_mlib.c:1044:8: warning: format specifies type 'long long' but the argument > has type 'fseek_t' (aka 'long') [-Wformat] > *libpos,tmp,seq_len); > ^~~~~~~ >ncbl2_mlib.c:1084:60: warning: format specifies type 'long long' but the > argument has type 'fseek_t' (aka 'long') [-Wformat] >error: fprintf(stderr," error reading %s at %lld\n",libstr,*libpos); > ~~~~ ^~~~~~~ > %ld >ncbl2_mlib.c:1218:10: warning: format specifies type 'long long' but the > argument has type 'fseek_t' (aka 'long') [-Wformat] > libstr,*libpos,tmp,seqcnt,*seq); > ^~~~~~~ >ncbl2_mlib.c:1238:3: warning: format specifies type 'long long' but the argument > has type 'fseek_t' (aka 'long') [-Wformat] > *libpos,tmp,seqcnt); > ^~~~~~~ >ncbl2_mlib.c:1349:60: warning: format specifies type 'long long' but the > argument has type 'fseek_t' (aka 'long') [-Wformat] >error: fprintf(stderr," error reading %s at %lld\n",libstr,*libpos); > ~~~~ ^~~~~~~ > %ld >ncbl2_mlib.c:1514:36: warning: operator '<<' has lower precedence than '+'; '+' > will be evaluated first [-Wshift-op-parentheses] > *val = (int)((int)((int)(b[0]<<8)+(int)b[1]<<8)+(int)b[2]<<8) > ~~~~~~~~~~~~~~^~~~~~~~~~~~ >ncbl2_mlib.c:1514:36: note: place parentheses around the '+' expression to > silence this warning > *val = (int)((int)((int)(b[0]<<8)+(int)b[1]<<8)+(int)b[2]<<8) > ^ > ( ) >ncbl2_mlib.c:1514:50: warning: operator '<<' has lower precedence than '+'; '+' > will be evaluated first [-Wshift-op-parentheses] > *val = (int)((int)((int)(b[0]<<8)+(int)b[1]<<8)+(int)b[2]<<8) > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ >ncbl2_mlib.c:1514:50: note: place parentheses around the '+' expression to > silence this warning > *val = (int)((int)((int)(b[0]<<8)+(int)b[1]<<8)+(int)b[2]<<8) > ^ > ( ) >ncbl2_mlib.c:1530:36: warning: operator '<<' has lower precedence than '+'; '+' > will be evaluated first [-Wshift-op-parentheses] > val4 = (int)((int)((int)(b[0]<<8)+(int)b[1]<<8)+(int)b[2]<<8) > ~~~~~~~~~~~~~~^~~~~~~~~~~~ >ncbl2_mlib.c:1530:36: note: place parentheses around the '+' expression to > silence this warning > val4 = (int)((int)((int)(b[0]<<8)+(int)b[1]<<8)+(int)b[2]<<8) > ^ > ( ) >ncbl2_mlib.c:1530:50: warning: operator '<<' has lower precedence than '+'; '+' > will be evaluated first [-Wshift-op-parentheses] > val4 = (int)((int)((int)(b[0]<<8)+(int)b[1]<<8)+(int)b[2]<<8) > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ >ncbl2_mlib.c:1530:50: note: place parentheses around the '+' expression to > silence this warning > val4 = (int)((int)((int)(b[0]<<8)+(int)b[1]<<8)+(int)b[2]<<8) > ^ > ( ) >ncbl2_mlib.c:1545:46: warning: operator '<<' has lower precedence than '+'; '+' > will be evaluated first [-Wshift-op-parentheses] > *valp = (unsigned int)((int)((int)(b[0]<<8)+(int)b[1]<<8)+(int)b[2]<<8) > ~~~~~~~~~~~~~~^~~~~~~~~~~~ >ncbl2_mlib.c:1545:46: note: place parentheses around the '+' expression to > silence this warning > *valp = (unsigned int)((int)((int)(b[0]<<8)+(int)b[1]<<8)+(int)b[2]<<8) > ^ > ( ) >ncbl2_mlib.c:1545:60: warning: operator '<<' has lower precedence than '+'; '+' > will be evaluated first [-Wshift-op-parentheses] > *valp = (unsigned int)((int)((int)(b[0]<<8)+(int)b[1]<<8)+(int)b[2]<<8) > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ >ncbl2_mlib.c:1545:60: note: place parentheses around the '+' expression to > silence this warning > *valp = (unsigned int)((int)((int)(b[0]<<8)+(int)b[1]<<8)+(int)b[2]<<8) > ^ > ( ) >ncbl2_mlib.c:1562:40: warning: operator '<<' has lower precedence than '+'; '+' > will be evaluated first [-Wshift-op-parentheses] > val_h = (long)((long)((long)(b[0]<<8)+(long)b[1]<<8)+(long)b[2]<<8)+(l... > ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ >ncbl2_mlib.c:1562:40: note: place parentheses around the '+' expression to > silence this warning > val_h = (long)((long)((long)(b[0]<<8)+(long)b[1]<<8)+(long)b[2]<<8)+(l... > ^ > ( ) >ncbl2_mlib.c:1562:55: warning: operator '<<' has lower precedence than '+'; '+' > will be evaluated first [-Wshift-op-parentheses] > val_h = (long)((long)((long)(b[0]<<8)+(long)b[1]<<8)+(long)b[2]<<8)+(l... > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ >ncbl2_mlib.c:1562:55: note: place parentheses around the '+' expression to > silence this warning > val_h = (long)((long)((long)(b[0]<<8)+(long)b[1]<<8)+(long)b[2]<<8)+(l... > ^ > ( ) >ncbl2_mlib.c:1563:40: warning: operator '<<' has lower precedence than '+'; '+' > will be evaluated first [-Wshift-op-parentheses] > val_l = (long)((long)((long)(b[4]<<8)+(long)b[5]<<8)+(long)b[6]<<8)+(l... > ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ >ncbl2_mlib.c:1563:40: note: place parentheses around the '+' expression to > silence this warning > val_l = (long)((long)((long)(b[4]<<8)+(long)b[5]<<8)+(long)b[6]<<8)+(l... > ^ > ( ) >ncbl2_mlib.c:1563:55: warning: operator '<<' has lower precedence than '+'; '+' > will be evaluated first [-Wshift-op-parentheses] > val_l = (long)((long)((long)(b[4]<<8)+(long)b[5]<<8)+(long)b[6]<<8)+(l... > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ >ncbl2_mlib.c:1563:55: note: place parentheses around the '+' expression to > silence this warning > val_l = (long)((long)((long)(b[4]<<8)+(long)b[5]<<8)+(long)b[6]<<8)+(l... > ^ > ( ) >ncbl2_mlib.c:1581:43: warning: operator '<<' has lower precedence than '+'; '+' > will be evaluated first [-Wshift-op-parentheses] > *val = (long)((((((long)((long)(b[7]<<8)+(long)b[6]<<8)+(long)b[5]<<8) > ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ >ncbl2_mlib.c:1581:43: note: place parentheses around the '+' expression to > silence this warning > *val = (long)((((((long)((long)(b[7]<<8)+(long)b[6]<<8)+(long)b[5]<<8) > ^ > ( ) >ncbl2_mlib.c:1581:58: warning: operator '<<' has lower precedence than '+'; '+' > will be evaluated first [-Wshift-op-parentheses] > *val = (long)((((((long)((long)(b[7]<<8)+(long)b[6]<<8)+(long)b[5]<<8) > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ >ncbl2_mlib.c:1581:58: note: place parentheses around the '+' expression to > silence this warning > *val = (long)((((((long)((long)(b[7]<<8)+(long)b[6]<<8)+(long)b[5]<<8) > ^ > ( ) >ncbl2_mlib.c:1582:5: warning: operator '<<' has lower precedence than '+'; '+' > will be evaluated first [-Wshift-op-parentheses] > +(long)b[4]<<8)+(long)b[3]<<8)+(long)b[2]<<8) > ^~~~~~~~~~~~~ >ncbl2_mlib.c:1582:5: note: place parentheses around the '+' expression to > silence this warning > +(long)b[4]<<8)+(long)b[3]<<8)+(long)b[2]<<8) > ^ > ) >ncbl2_mlib.c:1582:20: warning: operator '<<' has lower precedence than '+'; '+' > will be evaluated first [-Wshift-op-parentheses] > +(long)b[4]<<8)+(long)b[3]<<8)+(long)b[2]<<8) > ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ >ncbl2_mlib.c:1582:20: note: place parentheses around the '+' expression to > silence this warning > +(long)b[4]<<8)+(long)b[3]<<8)+(long)b[2]<<8) > ^ > ) >ncbl2_mlib.c:1582:35: warning: operator '<<' has lower precedence than '+'; '+' > will be evaluated first [-Wshift-op-parentheses] > +(long)b[4]<<8)+(long)b[3]<<8)+(long)b[2]<<8) > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ >ncbl2_mlib.c:1582:35: note: place parentheses around the '+' expression to > silence this warning > +(long)b[4]<<8)+(long)b[3]<<8)+(long)b[2]<<8) > ^ > ) >ncbl2_mlib.c:1583:3: warning: operator '<<' has lower precedence than '+'; '+' > will be evaluated first [-Wshift-op-parentheses] > +(long)b[1]<<8)+(long)b[0]; > ^~~~~~~~~~~~~ >ncbl2_mlib.c:1583:3: note: place parentheses around the '+' expression to > silence this warning > +(long)b[1]<<8)+(long)b[0]; > ^ > ) >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c url_subs.c >1 warning generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -o mrandom.o mrandom.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DSW_SSE2 -DSSEARCH initfa.c -o init_sw_sse.o >4 warnings generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c dropgsw2.c -o dropgsw2_sse.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c smith_waterman_sse2.c >url_subs.c:51:34: warning: the value of the size argument in 'strncat' is too > large, might lead to a buffer overflow [-Wstrncat-size] > strncat(lib,&m_msg->lname[1],sizeof(lib)); > ^~~~~~~~~~~ >url_subs.c:51:34: note: change the argument to be the free space in the > destination buffer minus the terminating null byte > strncat(lib,&m_msg->lname[1],sizeof(lib)); > ^~~~~~~~~~~ > sizeof(lib) - strlen(lib) - 1 >1 warning generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSSEARCH -c cal_cons.c -o calcons_sw.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c pssm_asn_subs.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_MLIB -c comp_lib8.c -o comp_mlib8.o >6 warnings generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_MLIB -c compacc2.c -o compacc2_s.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DLALIGN -c mshowalign2.c -o lshowalign.o >3 warnings generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DLALIGN initfa.c -o init_lal.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c last_thresh.c >mshowalign2.c:272:20: warning: sizeof on pointer operation will return size of > 'char *' instead of 'char [2048]' [-Wsizeof-array-decay] > bline[sizeof(bline-1)]='\0'; > ~~~~~^ >mshowalign2.c:346:10: warning: logical not is only applied to the left hand side > of this bitwise operator [-Wlogical-not-parentheses] > if ((!m_msp->markx & MX_M10FORM)) name1[nml]='\0'; > ^ ~ >mshowalign2.c:346:10: note: add parentheses after the '!' to evaluate the > bitwise operator first > if ((!m_msp->markx & MX_M10FORM)) name1[nml]='\0'; > ^ > ( ) >mshowalign2.c:346:10: note: add parentheses around left hand side expression to > silence this warning > if ((!m_msp->markx & MX_M10FORM)) name1[nml]='\0'; > ^ > ( ) >mshowalign2.c:361:27: warning: the value of the size argument in 'strncat' is > too large, might lead to a buffer overflow [-Wstrncat-size] > strncat(l_name,"_r",sizeof(l_name)); > ^~~~~~~~~~~~~~ >mshowalign2.c:361:27: note: change the argument to be the free space in the > destination buffer minus the terminating null byte > strncat(l_name,"_r",sizeof(l_name)); > ^~~~~~~~~~~~~~ > sizeof(l_name) - strlen(l_name) - 1 >mshowalign2.c:364:30: warning: the value of the size argument in 'strncat' is > too large, might lead to a buffer overflow [-Wstrncat-size] > strncat(l_name,tmp_str,sizeof(l_name)-strlen(l_name)); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >mshowalign2.c:364:30: note: change the argument to be the free space in the > destination buffer minus the terminating null byte > strncat(l_name,tmp_str,sizeof(l_name)-strlen(l_name)); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > sizeof(l_name) - strlen(l_name) - 1 >compacc2.c:1601:28: warning: format specifies type 'long long' but the argument > has type 'off_t' (aka 'long') [-Wformat] > rbuf_dp->stats_idx, rbuf_dp->mseq->lseek); > ^~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DLALIGN -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c dropgsw2.c -o droplal2_sse.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c lsim4.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DLALIGN -DLCAL_CONS -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c cal_cons.c -o calcons_la.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTS initfa.c -o init_fs.o >4 warnings generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c scaleswt.c -o scaleswts.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c last_tat.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTS tatstats.c -o tatstats_fs.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTS -c dropfs2.c -o drop_fs2.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTS -c cal_consf.c -o calcons_fs.o >25 warnings generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTX initfa.c -o init_fx.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c faatran.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropfx.c -o drop_fx.o >1 warning generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTX -DTFAST initfa.c -o init_tfx.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST dropfx.c -o drop_tfx.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTY initfa.c -o init_fy.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropfz2.c -o drop_fz.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTY -DTFAST initfa.c -o init_tfy.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST dropfz2.c -o drop_tfz.o >dropfz2.c:320:14: warning: operator '<<' has lower precedence than '-'; '-' will > be evaluated first [-Wshift-op-parentheses] > dnav = (3-hnt[aa0[n0-1]]<<2) + 3-hnt[aa0[n0-2]]; > ~^~~~~~~~~~~~~~~~~ >dropfz2.c:320:14: note: place parentheses around the '-' expression to silence > this warning > dnav = (3-hnt[aa0[n0-1]]<<2) + 3-hnt[aa0[n0-2]]; > ^ > ( ) >dropfz2.c:320:14: warning: operator '<<' has lower precedence than '-'; '-' will > be evaluated first [-Wshift-op-parentheses] > dnav = (3-hnt[aa0[n0-1]]<<2) + 3-hnt[aa0[n0-2]]; > ~^~~~~~~~~~~~~~~~~ >dropfz2.c:320:14: note: place parentheses around the '-' expression to silence > this warning > dnav = (3-hnt[aa0[n0-1]]<<2) + 3-hnt[aa0[n0-2]]; > ^ > ( ) >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTS -DTFAST initfa.c -o init_tfs.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST -DFASTS dropfs2.c -o drop_tfs.o >1 warning generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DTFAST -DFASTS -c cal_consf.c -o calcons_tfs.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM initfa.c -o init_fm.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM tatstats.c -o tatstats_fm.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM dropfs2.c -o drop_fm.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTM -c cal_consf.c -o calcons_fm.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c mshowalign2.c -o mshowalign2_s.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTM -DTFAST initfa.c -o init_tfm.o >mshowalign2.c:272:20: warning: sizeof on pointer operation will return size of > 'char *' instead of 'char [2048]' [-Wsizeof-array-decay] > bline[sizeof(bline-1)]='\0'; > ~~~~~^ >mshowalign2.c:346:10: warning: logical not is only applied to the left hand side > of this bitwise operator [-Wlogical-not-parentheses] > if ((!m_msp->markx & MX_M10FORM)) name1[nml]='\0'; > ^ ~ >mshowalign2.c:346:10: note: add parentheses after the '!' to evaluate the > bitwise operator first > if ((!m_msp->markx & MX_M10FORM)) name1[nml]='\0'; > ^ > ( ) >mshowalign2.c:346:10: note: add parentheses around left hand side expression to > silence this warning > if ((!m_msp->markx & MX_M10FORM)) name1[nml]='\0'; > ^ > ( ) >mshowalign2.c:361:27: warning: the value of the size argument in 'strncat' is > too large, might lead to a buffer overflow [-Wstrncat-size] > strncat(l_name,"_r",sizeof(l_name)); > ^~~~~~~~~~~~~~ >mshowalign2.c:361:27: note: change the argument to be the free space in the > destination buffer minus the terminating null byte > strncat(l_name,"_r",sizeof(l_name)); > ^~~~~~~~~~~~~~ > sizeof(l_name) - strlen(l_name) - 1 >mshowalign2.c:364:30: warning: the value of the size argument in 'strncat' is > too large, might lead to a buffer overflow [-Wstrncat-size] > strncat(l_name,tmp_str,sizeof(l_name)-strlen(l_name)); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >mshowalign2.c:364:30: note: change the argument to be the free space in the > destination buffer minus the terminating null byte > strncat(l_name,tmp_str,sizeof(l_name)-strlen(l_name)); > ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > sizeof(l_name) - strlen(l_name) - 1 >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DTFAST -DFASTM dropfs2.c -o drop_tfm.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DTFAST -DFASTM -c cal_consf.c -o calcons_tfm.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF initfa.c -o init_ff.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTF -c scaleswt.c -o scaleswtf.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF tatstats.c -o tatstats_ff.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF dropff2.c -o drop_ff2.o >4 warnings generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DFASTF -c cal_consf.c -o calcons_ff.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF -DTFAST initfa.c -o init_tf.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTF -DTFAST dropff2.c -o drop_tff.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DTFAST -DFASTF -c cal_consf.c -o calcons_tff.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DNORMAL_DIST -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c scaleswn.c -o scale_sn.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DSW_SSE2 -DGLSEARCH initfa.c -o init_lnw_sse.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSW_SSE2 -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropnnw2.c -o droplnw_sse.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c glocal_sse2.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DSW_SSE2 -DGGSEARCH initfa.c -o init_gnw_sse.o >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -msse2 -ffast-math -DGLOBAL_GLOBAL -DSW_SSE2 -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c dropnnw2.c -o dropgnw_sse.o >dropnnw2.c:567:18: error: use of undeclared identifier 'OVERFLOW' > if (score == OVERFLOW) { > ^ >1 error generated. >make: *** [../make/Makefile.fcom:244: droplnw_sse.o] Error 1 >make: *** Waiting for unfinished jobs.... >dropnnw2.c:567:18: error: use of undeclared identifier 'OVERFLOW' > if (score == OVERFLOW) { > ^ >1 error generated. >make: *** [../make/Makefile.fcom:250: dropgnw_sse.o] Error 1 >1 warning generated. >1 warning generated. > * ERROR: sci-biology/fasta-36.3.5e::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-biology/fasta-36.3.5e::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-biology/fasta-36.3.5e::gentoo'`. > * The complete build log is located at '/var/log/emerge-log/build/sci-biology/fasta-36.3.5e:20200908-113907.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/fasta-36.3.5e/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/fasta-36.3.5e/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/fasta-36.3.5e/work/fasta-36.3.5e/src' > * S: '/var/tmp/portage/sci-biology/fasta-36.3.5e/work/fasta-36.3.5e'
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bug 741186
: 659146