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Gentoo's Bugzilla – Attachment 659166 Details for
Bug 741202
sci-biology/wise-2.4.0_alpha-r1 does not respect LDFLAGS
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build.log
build.log (text/plain), 91.12 KB, created by
Agostino Sarubbo
on 2020-09-08 15:00:29 UTC
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Description:
build.log
Filename:
MIME Type:
Creator:
Agostino Sarubbo
Created:
2020-09-08 15:00:29 UTC
Size:
91.12 KB
patch
obsolete
> * Package: sci-biology/wise-2.4.0_alpha > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux 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/d0f82d4a28ee28f2b6e01ce024416f18ed080020 (Tue Sep 8 13:35:28 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, 26820264 free >KiB Swap: 0 total, 0 free >Timestamp of repository gentoo: Tue, 08 Sep 2020 13:35:27 +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-verify-jobs: 1 > sync-rsync-verify-metamanifest: yes > sync-rsync-extra-opts: > sync-rsync-verify-max-age: 24 > >ACCEPT_KEYWORDS="amd64 ~amd64" >ACCEPT_LICENSE="* BSD" >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/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" >CXX="x86_64-pc-linux-gnu-clang++" >CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >DISTDIR="/var/tmp/portage/sci-biology/wise-2.4.0_alpha/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" 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 wise2.4.0alpha.tar.gz to /var/tmp/portage/sci-biology/wise-2.4.0_alpha/work >>>> Unpacking wise-2.4.0_alpha-patchset.tar.bz2 to /var/tmp/portage/sci-biology/wise-2.4.0_alpha/work >>>> Source unpacked in /var/tmp/portage/sci-biology/wise-2.4.0_alpha/work >>>> Preparing source in /var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha ... > * Applying wise-2.4.0_alpha-glibc-2.10.patch ... > [ ok ] > * Applying wise-2.4.0_alpha-cflags.patch ... > [ ok ] > * Applying wise-api.tex.patch ... > [ ok ] >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha ... >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha ... >make -j16 V=1 -C src CC=x86_64-pc-linux-gnu-clang all >make: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src' >(cd base ; make CC="x86_64-pc-linux-gnu-clang" CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread `pkg-config glib-2.0 --cflags`" libwisebase.a ) >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/base' >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wiseconfig.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisestring.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wiseerror.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisememman.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisefile.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wiserandom.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisetime.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wiseoverlay.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisestreaminterface.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include commandline.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include linesubs.c >wisefile.dy:72:33: warning: format specifies type 'int' but the argument has > type 'FILE *' (aka 'struct _IO_FILE *') [-Wformat] > fprintf(stderr,"Closing %d\n",ofp); > ~~ ^~~ >1 warning generated. >ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o >ar: creating libwisebase.a >if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi >if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/base' >(cd HMMer2 ; make CC="x86_64-pc-linux-gnu-clang" CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread `pkg-config glib-2.0 --cflags`" libhmmer.a ) >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/HMMer2' >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c alphabet.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c core_algorithms.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c debug.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c emit.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c emulation.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c histogram.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c hmmio.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c mathsupport.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c masks.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c misc.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c modelmakers.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c plan7.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c plan9.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c prior.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c tophits.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c trace.c >prior.c:102:12: warning: implicitly declaring library function 'strcmp' with > type 'int (const char *, const char *)' [-Wimplicit-function-declaration] > if (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET; > ^ >prior.c:102:12: note: include the header <string.h> or explicitly provide a > declaration for 'strcmp' >alphabet.c:236:9: warning: logical not is only applied to the left hand side of > this bitwise operator [-Wlogical-not-parentheses] > if (! ainfo->sqinfo[idx].flags & SQINFO_LEN) { > ^ ~ >alphabet.c:236:9: note: add parentheses after the '!' to evaluate the bitwise > operator first > if (! ainfo->sqinfo[idx].flags & SQINFO_LEN) { > ^ > ( ) >alphabet.c:236:9: note: add parentheses around left hand side expression to > silence this warning > if (! ainfo->sqinfo[idx].flags & SQINFO_LEN) { > ^ > ( ) >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c aligneval.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c alignio.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c cluster.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c dayhoff.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c file.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c getopt.c >1 warning generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c gnuregex.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c interleaved.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c iupac.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c msf.c >gnuregex.c:1616:17: warning: add explicit braces to avoid dangling else > [-Wdangling-else] > else > ^ >gnuregex.c:1636:17: warning: add explicit braces to avoid dangling else > [-Wdangling-else] > else > ^ >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c revcomp.c >1 warning generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c selex.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sqerror.c >gnuregex.c:2821:33: warning: expression which evaluates to zero treated as a > null pointer constant of type 'regoff_t *' (aka 'int *') > [-Wnon-literal-null-conversion] > regs->start = regs->end = (regoff_t) 0; > ^~~~~~~~~~~~ >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sqio.c >gnuregex.c:3758:19: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') > from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] > PUSH_FAILURE_POINT (p1 + mcnt, d, -2); > ^ >gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' > PUSH_FAILURE_ITEM (lowest_active_reg); \ > ^ >gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item > ^ >gnuregex.c:3758:19: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') > from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] >gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' > PUSH_FAILURE_ITEM (highest_active_reg); \ > ^ >gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item > ^ >gnuregex.c:3905:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') > from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] > PUSH_FAILURE_POINT (p + mcnt, NULL, -2); > ^ >gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' > PUSH_FAILURE_ITEM (lowest_active_reg); \ > ^ >gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item > ^ >gnuregex.c:3905:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') > from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] >gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' > PUSH_FAILURE_ITEM (highest_active_reg); \ > ^ >gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item > ^ >gnuregex.c:3958:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') > from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] > PUSH_FAILURE_POINT (p + mcnt, d, -2); > ^ >gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' > PUSH_FAILURE_ITEM (lowest_active_reg); \ > ^ >gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item > ^ >gnuregex.c:3958:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') > from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] >gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' > PUSH_FAILURE_ITEM (highest_active_reg); \ > ^ >gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item > ^ >gnuregex.c:4097:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') > from smaller integer type 'unsigned int' interleaved.c:[-Wint-to-pointer-cast]165:82: >warning: size PUSH_FAILURE_POINT (0, 0, -2); >argument ^ >in 'strncmp'gnuregex.c: call2394: is5: a note comparison: expanded > from[-Wmemsize-comparison] > macro 'PUSH_FAILURE_POINT' > PUSH_FAILURE_ITEM (lowest_active_reg); \ > ^ > ...!= NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) >gnuregex.c: ~~~~~~~~~~~~~~~~~~~~~~^~~~ >2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item > ^ >gnuregex.c:4097:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') > from smaller integerinterleaved.c type :165'unsigned int' :32[-Wint-to-pointer-cast] >: notegnuregex.c:: did2397: you5: mean note to: expanded compare from the result macro of 'PUSH_FAILURE_POINT' >'strncmp' > instead? > PUSH_FAILURE_ITEM (highest_active_reg); \ > ^ >gnuregex.c:2315:42: note ...!= NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) >: ^ ~ >expanded ) >from macro 'PUSH_FAILURE_ITEM' > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item > ^ >interleaved.c:165:60: note: explicitly cast the argument to size_t to silence > this warning > ...!= NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) > ^ > (size_t)( ) >gnuregex.c:4110:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') > from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] > PUSH_FAILURE_POINT (0, 0, -2); > ^ >gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' > PUSH_FAILURE_ITEM (lowest_active_reg); \ > ^ >gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item > ^ >gnuregex.c:4110:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') > from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] >gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' > PUSH_FAILURE_ITEM (highest_active_reg); \ > ^ >gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' > fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item > ^ >interleaved.c:240:82: warning: size argument in 'strncmp' call is a comparison > [-Wmemsize-comparison] > ...!= NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) > ~~~~~~~~~~~~~~~~~~~~~~^~~~ >interleaved.c:240:32: note: did you mean to compare the result of 'strncmp' > instead? > ...!= NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) > ^ ~ > ) >interleaved.c:240:60: note: explicitly cast the argument to size_t to silence > this warning > ...!= NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) > ^ > (size_t)( ) >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sre_ctype.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sre_math.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sre_string.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c stack.c >sqio.c:1033:9: warning: comparison of array 'sp' equal to a null pointer is > always false [-Wtautological-pointer-compare] > if (sp==NULL || *sp=='\0') > ^~ ~~~~ >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c translate.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c types.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c weight.c >2 warnings generated. >1 warning generated. >13 warnings generated. >ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o emit.o emulation.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o prior.o tophits.o trace.o aligneval.o alignio.o cluster.o dayhoff.o file.o getopt.o gnuregex.o interleaved.o iupac.o msf.o revcomp.o selex.o sqerror.o sqio.o sre_ctype.o sre_math.o sre_string.o stack.o translate.o types.o weight.o >a - alphabet.o >a - core_algorithms.o >a - debug.o >a - emit.o >a - emulation.o >a - histogram.o >a - hmmio.o >a - mathsupport.o >a - masks.o >a - misc.o >a - modelmakers.o >a - plan7.o >a - plan9.o >a - prior.o >a - tophits.o >a - trace.o >a - aligneval.o >a - alignio.o >a - cluster.o >a - dayhoff.o >a - file.o >a - getopt.o >a - gnuregex.o >a - interleaved.o >a - iupac.o >a - msf.o >a - revcomp.o >a - selex.o >a - sqerror.o >a - sqio.o >a - sre_ctype.o >a - sre_math.o >a - sre_string.o >a - stack.o >a - translate.o >a - types.o >a - weight.o >if test -x /bin/ranlib; then /bin/ranlib libhmmer.a; else exit 0; fi >if test -x /usr/bin/ranlib; then /usr/bin/ranlib libhmmer.a; else exit 0; fi >if test -x ranlib; then ranlib libhmmer.a; else exit 0; fi >chmod 644 libhmmer.a >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/HMMer2' >(cd dynlibsrc ; make CC="x86_64-pc-linux-gnu-clang" CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread `pkg-config glib-2.0 --cflags`" libdyna.a ) >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/dynlibsrc' >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ packaln.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ aln.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dnamatrix.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ probability.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ alnrange.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ alnconvert.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ basematrix.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ shattermatrix.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ matrixdebug.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dpenvelope.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dbsearchimpl.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dprunimpl.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ complexsequence.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ complexevalset.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ complexconsensi.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ sequence.c >dpenvelope.dy:68:1: warning: non-void function does not return a value in all > control paths [-Wreturn-type] >} >^ >aln.dy:867:65: warning: data argument not used by format string > [-Wformat-extra-args] > fprintf(ofp," {%3.2f} ",(double)(*score_to_double)(cuml),cuml); > ~~~~~~~~~~~~ ^ >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ sequencestream.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ seqalign.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hitlist.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hsp.c >1 warning generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hspstream.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ codon.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ compmat.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ codonmatrix.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ codonmapper.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ sequencedb.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hscore.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ seqlookup.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ arrayseqlookup.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ genericindexresult.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ linkedlist_lookpos.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ singlenumberspace.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ histogram.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ searchstatinterface.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ searchstatlookup.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ proteindb.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ protein.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ pairbase.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ pairbaseseq.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ genomicdb.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ randommodel.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ randomdb.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ genomic.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ cdna.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ cdnadb.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dna.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ embl.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ genomicregion.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ gene.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ transcript.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ translation.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ btcanvas.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ asciibtcanvas.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dynlibcross.c >1 warning generated. >ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o >ar: creating libdyna.a >if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi >if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/dynlibsrc' >(cd dynlibsrc ; make CC="x86_64-pc-linux-gnu-clang" CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread `pkg-config glib-2.0 --cflags`" libdyna_glib.a ) >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/dynlibsrc' >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ subseqhash.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ intallocator.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ proteinstreamedindex.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ shadowseq.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ shadowseqindex.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hsphandler.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hspscaninterface.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hsp2hitscan.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hsplookupscan.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hsplookupthreaded.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ proteinindexcons.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dnaindexcons.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ staticseq.c >subseqhash.dy:111:29: warning: cast to 'gconstpointer' (aka 'const void *') from > smaller integer type 'int' [-Wint-to-void-pointer-cast] > if( g_hash_table_lookup(h,(gconstpointer)seq_number) == NULL ) { > ^ >subseqhash.dy:128:85: warning: cast to 'gconstpointer' (aka 'const void *') from > smaller integer type 'int' [-Wint-to-void-pointer-cast] > ...*)g_hash_table_lookup(h,(gconstpointer)seq_number)); > ^ >subseqhash.dy:160:54: warning: cast to 'gconstpointer' (aka 'const void *') from > smaller integer type 'int' [-Wint-to-void-pointer-cast] > if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_... > ^ >subseqhash.dy:161:29: warning: cast to 'gpointer' (aka 'void *') from smaller > integer type 'int' [-Wint-to-void-pointer-cast] > g_hash_table_insert(h,(gpointer)seq_number,p); > ^ >subseqhash.dy:188:52: warning: cast to 'gconstpointer' (aka 'const void *') from > smaller integer type 'int' [-Wint-to-void-pointer-cast] > if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_nu... > ^ >subseqhash.dy:189:27: warning: cast to 'gpointer' (aka 'void *') from smaller > integer type 'int' [-Wint-to-void-pointer-cast] > g_hash_table_insert(h,(gpointer)seq_number,p); > ^ >hsplookupthreaded.dy:160:3: warning: implicit declaration of function > 'gettimeofday' is invalid in C99 [-Wimplicit-function-declaration] > gettimeofday(&t1,NULL); > ^ >shadowseqindex.dy:285:59: warning: format specifies type 'double' but the > argument has type 'unsigned long' [-Wformat] > ...%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); > ~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > %.2lu >hsplookupthreaded.dy:211:41: warning: format specifies type 'int' but the > argument has type 'long' [-Wformat] > fprintf(stderr,"Got seq %d numbers\n",current); > ~~ ^~~~~~~ > %ld >hsplookupthreaded.dy:259:55: warning: format specifies type 'int' but the > argument has type 'long' [-Wformat] > fprintf(stderr,"retrieved array with %d elements\n",current_oph); > ~~ ^~~~~~~~~~~ > %ld >hsp2hitscan.dy:210:4: warning: format specifies type 'int' but the argument has > type '__time_t' (aka 'long') [-Wformat] > use.ru_utime.tv_sec, > ^~~~~~~~~~~~~~~~~~~ >hsp2hitscan.dy:211:4: warning: format specifies type 'int' but the argument has > type 'long' [-Wformat] > use.ru_utime.tv_sec/1000, > ^~~~~~~~~~~~~~~~~~~~~~~~ >hsp2hitscan.dy:212:4: warning: format specifies type 'int' but the argument has > type '__time_t' (aka 'long') [-Wformat] > use.ru_stime.tv_sec, > ^~~~~~~~~~~~~~~~~~~ >hsp2hitscan.dy:213:4: warning: format specifies type 'int' but the argument has > type 'long' [-Wformat] > use.ru_stime.tv_sec/1000 > ^~~~~~~~~~~~~~~~~~~~~~~~ >hsp2hitscan.dy:274:4: warning: format specifies type 'int' but the argument has > type '__time_t' (aka 'long') [-Wformat] > use.ru_utime.tv_sec, > ^~~~~~~~~~~~~~~~~~~ >hsp2hitscan.dy:275:4: warning: format specifies type 'int' but the argument has > type 'long' [-Wformat] > use.ru_utime.tv_sec/1000, > ^~~~~~~~~~~~~~~~~~~~~~~~ >hsp2hitscan.dy:276:4: warning: format specifies type 'int' but the argument has > type '__time_t' (aka 'long') [-Wformat] > use.ru_stime.tv_sec, > ^~~~~~~~~~~~~~~~~~~ >hsp2hitscan.dy:277:4: warning: format specifies type 'int' but the argument has > type 'long' [-Wformat] > use.ru_stime.tv_sec/1000 > ^~~~~~~~~~~~~~~~~~~~~~~~ >hsp2hitscan.dy:287:4: warning: format specifies type 'int' but the argument has > type '__time_t' (aka 'long') [-Wformat] > use.ru_utime.tv_sec, > ^~~~~~~~~~~~~~~~~~~ >hsp2hitscan.dy:288:4: warning: format specifies type 'int' but the argument has > type 'long' [-Wformat] > use.ru_utime.tv_sec/1000, > ^~~~~~~~~~~~~~~~~~~~~~~~ >hsp2hitscan.dy:289:4: warning: format specifies type 'int' but the argument has > type '__time_t' (aka 'long') [-Wformat] > use.ru_stime.tv_sec, > ^~~~~~~~~~~~~~~~~~~ >hsp2hitscan.dy:290:4: warning: format specifies type 'int' but the argument has > type 'long' [-Wformat] > use.ru_stime.tv_sec/1000 > ^~~~~~~~~~~~~~~~~~~~~~~~ >hsp2hitscan.dy:303:4: warning: format specifies type 'int' but the argument has > type '__time_t' (aka 'long') [-Wformat] > use.ru_utime.tv_sec, > ^~~~~~~~~~~~~~~~~~~ >hsp2hitscan.dy:304:4: warning: format specifies type 'int' but the argument has > type 'long' [-Wformat] > use.ru_utime.tv_sec/1000, > ^~~~~~~~~~~~~~~~~~~~~~~~ >hsp2hitscan.dy:305:4: warning: format specifies type 'int' but the argument has > type '__time_t' (aka 'long') [-Wformat] > use.ru_stime.tv_sec, > ^~~~~~~~~~~~~~~~~~~ >hsp2hitscan.dy:306:4: warning: format specifies type 'int' but the argument has > type 'long' [-Wformat] > use.ru_stime.tv_sec/1000 > ^~~~~~~~~~~~~~~~~~~~~~~~ >hsplookupthreaded.dy:561:1: warning: non-void function does not return a value > [-Wreturn-type] >} >^ >6 warnings generated. >1 warning generated. >16 warnings generated. >4 warnings generated. >ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o proteinindexcons.o dnaindexcons.o staticseq.o >ar: creating libdyna_glib.a >if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi >if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/dynlibsrc' >(cd external ; make CC="x86_64-pc-linux-gnu-clang" CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread `pkg-config glib-2.0 --cflags`" all ) >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/external' >(cd mott; make CC="x86_64-pc-linux-gnu-clang" CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include " all) >make[2]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/external/mott' >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c -o mott_api.o mott_api.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c -o gaplib.o gaplib.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../../dynlibsrc -I../../base wise2_mott_bridge.c >mott_api.c:64:3: warning: implicit declaration of function 'free' is invalid in > C99 [-Wimplicit-function-declaration] > free(freq0); > ^ >mott_api.c:104:7: warning: implicit declaration of function 'free' is invalid in > C99 [-Wimplicit-function-declaration] > free(freqA); > ^ >mott_api.c:144:5: warning: implicit declaration of function 'free' is invalid in > C99 [-Wimplicit-function-declaration] > free(h+hmin); > ^ >mott_api.c:155:5: warning: implicit declaration of function 'free' is invalid in > C99 [-Wimplicit-function-declaration] > free(h+hmin); > ^ >mott_api.c:179:16: warning: implicitly declaring library function 'calloc' with > type 'void *(unsigned long, unsigned long)' > [-Wimplicit-function-declaration] > h = (double*)calloc(*hmax-*hmin+1,sizeof(double))-*hmin; > ^ >mott_api.c:179:16: note: include the header <stdlib.h> or explicitly provide a > declaration for 'calloc' >mott_api.c:207:12: warning: implicitly declaring library function 'toupper' with > type 'int (int)' [-Wimplicit-function-declaration] > freq[toupper(seq[n])]++; > ^ >mott_api.c:207:12: note: include the header <ctype.h> or explicitly provide a > declaration for 'toupper' >6 warnings generated. >ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o >ar: creating libmott.a >if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi >if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi >make[2]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/external/mott' >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/external' >(cd socket ; make CC="x86_64-pc-linux-gnu-clang" CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread `pkg-config glib-2.0 --cflags`" libwisesocket.a ) >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/socket' >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ functionserver.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ functionclient.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ anonobj.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ transferinterface.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ directsocketwrite.c >functionclient.dy:193:24: warning: incompatible pointer types passing > 'struct sockaddr_in *' to parameter of type 'const struct sockaddr *' > [-Wincompatible-pointer-types] > connect(out->socket, &server, sizeof(server)); > ^~~~~~~ >/usr/include/sys/socket.h:126:52: note: passing argument to parameter '__addr' > here >extern int connect (int __fd, __CONST_SOCKADDR_ARG __addr, socklen_t __len); > ^ >1 warning generated. >ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o >ar: creating libwisesocket.a >if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi >if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisesocket.a; else exit 0; fi >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/socket' >(cd dnaindex ; make CC="x86_64-pc-linux-gnu-clang" CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread `pkg-config glib-2.0 --cflags`" all ) >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/dnaindex' >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_count.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models dnamapping.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c >kmer_assembly_error.dy:351:127: warning: format specifies type 'int' but the > argument has type 'int *' [-Wformat] > ...%d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path... > ~~ ^~~~~~~~~~~~ >kmer_assembly.dy:365:88: warning: format specifies type 'long' but the argument > has type 'KmerAssemblyLink *' (aka 'struct KmerAssemblyLink *') [-Wformat] > ...to remove label %ld from link %ld (%d labels)\n",label,kal,kal->sequence... > ~~~ ^~~ >kmer_assembly.dy:367:36: warning: more '%' conversions than data arguments > [-Wformat] > fprintf(stderr," [%ld] is %d label\n",kal->sequence_label[i]); > ~^ >kmer_assembly_untangler.dy:568:75: warning: incompatible pointer types passing > 'long [10000]' to parameter of type 'int *' [-Wincompatible-pointer-types] > ...transferred_label,transferred_pos,transferred_len); > ^~~~~~~~~~~~~~~~~ >./kmer_assembly_untangler.h:174:116: note: passing argument to parameter > 'start_label' here > ...* kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,S... > ^ >compressed_protein_index.dy:223:10: warning: incompatible pointer to integer > conversion returning 'void *' from a function with result type 'boolean' > (aka 'int') [-Wint-conversion] > return NULL; > ^~~~ >/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stddef.h:89:16: note: > expanded from macro 'NULL' ># define NULL ((void*)0) > ^~~~~~~~~~ >1 warning generated. >2 warnings generated. >1 warning generated. >1 warning generated. >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/dnaindex' >(cd network ; make CC="x86_64-pc-linux-gnu-clang" CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread `pkg-config glib-2.0 --cflags`" all ) >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/network' >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c >x86_64-pc-linux-gnu-clang -g -o wise_proteinindex_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config glib-2.0 --libs` -lpthread >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/network' >(cd models ; make CC="x86_64-pc-linux-gnu-clang" CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread `pkg-config glib-2.0 --cflags`" EXTRALIBS="" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/models' >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ dnal.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ dnaalign.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ seqaligndisplay.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ psw.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ proteinsw.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ sw_wrap.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ abc.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ pba.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ pswdb.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ dbac.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ dba.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ slimdba.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ bigdba.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ dbadisplay.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser21.c >dbac.c:413:45: warning: format specifies type 'int' but the argument has type > 'unsigned long' [-Wformat] > fprintf(stderr,"Got %d with %d vs %d\n",i,strlen(seq),one->len); > ~~ ^~~~~~~~~~~ > %lu >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparameter.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genestats.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisehsp.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ geneutil.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ geneoutput.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatemodel.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genefrequency.c >1 warning generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ splicesitemodeler.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise4.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise6.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genestretch6.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise21.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop21.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop6.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genephase6.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlite.c >genephase6.c:683:1: warning: non-void function does not return a value > [-Wreturn-type] >} >^ >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlitemodel.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ gwrap.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ matchsum.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ estwrap.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodel.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ phasemodel.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ cdparser.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genedisplay.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ estwise3.c >genedisplay.dy:491:37: warning: data argument not used by format string > [-Wformat-extra-args] > sprintf(buffer," Intron ??? ",in_number); > ~~~~~~~~~~~~~~~~ ^ >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ estslim3.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ estloop3.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ estfrag3.c >1 warning generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ estslimloop.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ gwquickdb.c >gwquickdb.dy:46:1: warning: non-void function does not return a value in all > control paths [-Wreturn-type] >} >^ >gwquickdb.dy:65:1: warning: non-void function does not return a value in all > control paths [-Wreturn-type] >} >^ >2 warnings generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatedb.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ pfamhmmer1db.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ pwmdna.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodeldb.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ seqhit.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ standardout.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser4.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ estquick3.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise9.c >genomewise9.c:745:1: warning: non-void function does not return a value > [-Wreturn-type] >} >^ >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ genome_evidence.c >genome_evidence.dy:61:1: warning: non-void function does not return a value > [-Wreturn-type] >} >^ >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ est_evidence.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise.c >1 warning generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise20.c >est_evidence.dy:142:16: warning: incompatible pointer types assigning to > 'int (*)(void *)' from 'Wise2_EstEvidence *(Wise2_EstEvidence *)' (aka > 'struct Wise2_EstEvidence *(struct Wise2_EstEvidence *)') > [-Wincompatible-pointer-types] > in->geu_free = free_EstEvidence; > ^ ~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ syexonmodel.c >sywise20.c:764:1: warning: non-void function does not return a value > [-Wreturn-type] >} >^ >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise7.c >1 warning generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` promoterwise.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ localdba.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` localcishit.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ localcispara.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrix.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrixdp.c >motifmatrix.c:408:24: warning: incompatible pointer to integer conversion > assigning to 'char' from 'void *' [-Wint-conversion] > out->mat[i][j] = NULL; > ^ ~~~~ >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ transfactor.c >transfactor.dy:339:1: warning: non-void function does x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ pairwiseshortdna.c >not return a value in all > control paths [-Wreturn-type] >} >^ >1 warning generated. >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../external/mott `pkg-config glib-2.0 --cflags` scanwisep.c >x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` hsp2aln_sw.c >1 warning generated. >x86_64-pc-linux-gnu-clang -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c `pkg-config glib-2.0 --libs` >x86_64-pc-linux-gnu-clang -o dnal dnal.o dnaalign.o seqaligndisplay.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm >clang-10: warning: -Wl,-O1: 'linker' input unused [-Wunused-command-line-argument] >clang-10: warning: -Wl,--as-needed: 'linker' input unused [-Wunused-command-line-argument] >clang-10: warning: -Wl,--defsym=__gentoo_check_ldflags__=0: 'linker' input unused [-Wunused-command-line-argument] >clang-10: warning: -lglib-2.0: 'linker' input unused [-Wunused-command-line-argument] >clang-10: warning: argument unused during compilation: '-fuse-ld=lld' [-Wunused-command-line-argument] >x86_64-pc-linux-gnu-clang -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm >x86_64-pc-linux-gnu-clang -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm >x86_64-pc-linux-gnu-clang -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm >x86_64-pc-linux-gnu-clang -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase -lm `pkg-config glib-2.0 --libs` -lpthread >x86_64-pc-linux-gnu-clang -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm -lpthread `pkg-config glib-2.0 --libs` >1 warning generated. >1 warning generated. >x86_64-pc-linux-gnu-clang -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm >x86_64-pc-linux-gnu-clang -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm `pkg-config glib-2.0 --libs` -lpthread >1 warning generated. >x86_64-pc-linux-gnu-clang -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -ldyna_glib -ldyna -lwisebase -lm >x86_64-pc-linux-gnu-clang -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -o estwise estwise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm `pkg-config glib-2.0 --libs` >x86_64-pc-linux-gnu-clang -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -o genewise genewise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm `pkg-config glib-2.0 --libs` >x86_64-pc-linux-gnu-clang -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -o genewisedb genewisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm `pkg-config glib-2.0 --libs` >x86_64-pc-linux-gnu-clang -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -o estwisedb estwisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm `pkg-config glib-2.0 --libs` >x86_64-pc-linux-gnu-clang -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -o pseudowise pseudowise.o pseudowise7.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -g -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config glib-2.0 --libs` -lhmmer -ldyna_glib -ldyna -lwisebase -lm `pkg-config glib-2.0 --libs` >ar ru libmodel.a geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o >ar: creating libmodel.a >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/models' >make bin >make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src' >mkdir bin >cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise ./bin >csh welcome.csh > >Welcome to Wise2.4 > >The executable programs are in the ./bin directory > >You must set your WISECONFIGDIR to the config directory >before using the programs > >ie, type setenv WISECONFIGDIR /var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src/../wisecfg/ > >to try an example, try cd example and then >../bin/genewise road.pep human.genomic > >to build perl, type make perl and follow the instructions > >to test the package, type make test >make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src' >make: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha/work/wise2.4.0alpha/src' >>>> Source compiled. >>>> Test phase: sci-biology/wise-2.4.0_alpha >make -j16 V=1 test >cd test ; perl testman.pl -cf ../wisecfg < short.test >>>> Doing promoterwise promoterwise standard test >>>> Calling [../bin/promoterwise -silent pw.human pw.mouse > TEMP-PW] >working with 59 forward matches >Breaking out of loop.... >>>> promoterwise ... Passed >>>> Doing basic-cdna cdna test case (protein v cdna), all outputs >>>> Calling [../bin/estwise short.pep short.dna -indel 1e-5 -subs 1e-5 -pretty -para -sum -alb -pal -silent -alg 333 > TEMP] >>>> basic-cdna ... Passed >>>> Doing basic-genomic genomic test case (protein v genomic), all outputs >>>> Calling [../bin/genewise short.pep short.dna -pretty -para -genes -sum -cdna -trans -ace -gener -alb -pal -quiet > TEMP] >>>> basic-genomic ... Passed >>>> Doing hmm-binary-cdna cdna test case (protein v cdna), all outputs >>>> Calling [../bin/estwise HMM.binary -indel 1e-5 -subs 1e-5 -hmmer short.dna -pretty -para -sum -alb -pal -quiet -alg 333L > TEMP] >>>> hmm-binary-cdna ... Passed >>>> Doing hmm-wrong-dna HMMs vs DNA sequence when there is no match >>>> Calling [../bin/genewise wrong.hmm -hmmer short.dna -alg 623 -pal > TEMP] >Information > In making HSHNCPA1 a genomic sequence, converted 2 bases (0.5%) to >N's from non ATGCN >GeneWise6 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 61%[ 21000] Cells 64%[ 22000] Cells 67%[ 23000] Cells 70%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% >>>> hmm-wrong-dna ... Passed >>>> Doing hmm-wrong-dna-est HMMs vs DNA sequence when there is no match >>>> Calling [../bin/estwise wrong.hmm -hmmer short.dna -alg 333 -pal > TEMP] >Information > In making HSHNCPA1 a cdna sequence, converted 2 bases (0.5%) to N's >from non ATGCN >EstWise3 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 61%[ 21000] Cells 64%[ 22000] Cells 67%[ 23000] Cells 70%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% >EstWise3 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 61%[ 21000] Cells 64%[ 22000] Cells 67%[ 23000] Cells 70%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% >>>> hmm-wrong-dna-est ... Passed >>>> Doing hmm-ascii-genomic cdna test case (protein v cdna), all outputs >>>> Calling [../bin/genewise -init local HMM.ascii -hmmer short.dna -pretty -para -genes -sum -cdna -trans -ace -gener -alb -pal -quiet > TEMP] >>>> hmm-ascii-genomic ... Passed >>>> Doing genewise-db genewisedb hmm vs DNA sequences. Could take a while >>>> Calling [../bin/genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init global > TEMP] >>>> genewise-db ... Passed >>>> Doing genewise-db-lite genewisedb hmm vs DNA sequences, using GWLITE. Could take a while >>>> Calling [../bin/genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init global -alg 6LITE > TEMP] >>>> genewise-db-lite ... Passed >>>> Doing estwise-db estwisedb hmm vs DNA sequences. Could take a while >>>> Calling [../bin/estwisedb -init local rrm.HMM -hmmer dna.db -pretty -para -alb -quiet -alg 333 -aalg 333 > TEMP] >>>> estwise-db ... Passed >>>> Doing pswdb Protein smith waterman db search >>>> Calling [../bin/pswdb road.pep pep.fa -quiet > TEMP ] >>>> pswdb ... Passed >>>> Doing genewisedb-pfam-mode genewisedb designed for Pfam searching >>>> Calling [../bin/genewisedb -pfam rrm.HMM -dnas short.dna -pretty -para -alb -quiet -alg 623 -aalg 623L > TEMP] >>>> genewisedb-pfam-mode ... Passed >Tests passed >>>> Completed testing sci-biology/wise-2.4.0_alpha > >>>> Install sci-biology/wise-2.4.0_alpha into /var/tmp/portage/sci-biology/wise-2.4.0_alpha/image/ >>>> Completed installing sci-biology/wise-2.4.0_alpha into /var/tmp/portage/sci-biology/wise-2.4.0_alpha/image/ > > * Final size of build directory: 62052 KiB (60.5 MiB) > * Final size of installed tree: 11572 KiB (11.3 MiB) > > > * QA Notice: Files built without respecting LDFLAGS have been detected > * Please include the following list of files in your report: > * /usr/bin/dba > * /usr/bin/dnal > * /usr/bin/psw > * /usr/bin/pswdb > >strip: llvm-strip --strip-unneeded -N __gentoo_check_ldflags__ -R .comment -R .GCC.command.line -R .note.gnu.gold-version > /usr/bin/dba > /usr/bin/dnal > /usr/bin/psw > /usr/bin/promoterwise > /usr/bin/genewise > /usr/bin/genewisedb > /usr/bin/estwise > /usr/bin/pswdb > /usr/bin/estwisedb >>>> Done.
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