sci-biology:wise-2.4.0_alpha-r1:20221201-104434.log

sci-biology:wise-2.4.0_alpha-r1:20221201-104434.log (text/plain), 9.98 KB, created by Toralf Förster on 2022-12-01 20:15:40 UTC

 * Package:    sci-biology/wise-2.4.0_alpha-r1:0
 * Repository: gentoo
 * Maintainer: [e-mail]
 * 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 <string.h> 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'