* Package: sci-biology/wise-2.4.0_alpha-r1:0 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking wise2.4.0alpha.tar.gz to /var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work >>> Unpacking wise-2.4.0_alpha-patchset.tar.bz2 to /var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work >>> Source unpacked in /var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work >>> Preparing source in /var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/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 ... patching file api.tex Hunk #4 succeeded at 5551 with fuzz 1 (offset 496 lines). [ ok ] >>> Source prepared. * Clang 16 testing: this build is using a /etc/portage/bashrc hook (2022-11-24T21:47)! * Clang 16 testing: see https://wiki.gentoo.org/wiki/Modern_C_porting for more info. >>> Configuring source in /var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha ... make -j4 -C src all make: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src' (cd base ; make CC="clang" CFLAGS="-pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread `pkg-config glib-2.0 --cflags`" libwisebase.a ) make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/base' clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wiseconfig.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisestring.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wiseerror.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisememman.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisefile.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wiserandom.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisetime.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); ~~ ^~~ clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wiseoverlay.c 1 warning generated. clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisestreaminterface.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include commandline.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include linesubs.c 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-r1/work/wise2.4.0alpha/src/base' (cd HMMer2 ; make CC="clang" CFLAGS="-pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread `pkg-config glib-2.0 --cflags`" libhmmer.a ) make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/HMMer2' clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c alphabet.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c core_algorithms.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c debug.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c emit.c 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) { ^ ( ) clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c emulation.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c histogram.c 1 warning generated. clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c hmmio.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c mathsupport.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c masks.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c misc.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c modelmakers.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c plan7.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c plan9.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c prior.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c tophits.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c trace.c prior.c:102:12: error: call to undeclared library function 'strcmp' with type 'int (const char *, const char *)'; ISO C99 and later do not support implicit function declarations [-Werror,-Wimplicit-function-declaration] if (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET; ^ prior.c:102:12: note: include the header or explicitly provide a declaration for 'strcmp' 1 error generated. make[1]: *** [Makefile:69: prior.o] Error 1 make[1]: *** Waiting for unfinished jobs.... make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/HMMer2' make: *** [makefile:81: realall] Error 2 make: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src' * ERROR: sci-biology/wise-2.4.0_alpha-r1::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/wise-2.4.0_alpha-r1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/wise-2.4.0_alpha-r1::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:wise-2.4.0_alpha-r1:20221201-104434.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha' * S: '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha'