sci-biology:bfast-0.7.0a:20231205-064340.log

sci-biology:bfast-0.7.0a:20231205-064340.log (text/plain), 10.60 KB, created by Toralf Förster on 2023-12-05 08:11:08 UTC

 * Package:    sci-biology/bfast-0.7.0a:0
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox

>>> Unpacking source...
>>> Unpacking bfast-0.7.0a.tar.gz to /var/tmp/portage/sci-biology/bfast-0.7.0a/work
>>> Source unpacked in /var/tmp/portage/sci-biology/bfast-0.7.0a/work
>>> Preparing source in /var/tmp/portage/sci-biology/bfast-0.7.0a/work/bfast-0.7.0a ...
 * Applying bfast-0.7.0a-autotools.patch ...
 [ ok ]
 * Applying bfast-0.7.0a-test-sourcing.patch ...
 [ ok ]
 * Applying bfast-0.7.0a-C99-inline.patch ...
 [ ok ]
 * Running eautoreconf in '/var/tmp/portage/sci-biology/bfast-0.7.0a/work/bfast-0.7.0a' ...
 * Running 'aclocal --system-acdir=/var/tmp/portage/sci-biology/bfast-0.7.0a/temp/aclocal' ...
 [ ok ]
 * Running 'autoconf --force' ...
 [ ok ]
 * Running 'autoheader' ...
 [ ok ]
 * Running 'automake --add-missing --copy --force-missing' ...
 [ ok ]
 * Running elibtoolize in: bfast-0.7.0a/
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/bfast-0.7.0a/work/bfast-0.7.0a ...
 * econf: updating bfast-0.7.0a/config/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating bfast-0.7.0a/config/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating bfast-0.7.0a/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating bfast-0.7.0a/config.sub with /usr/share/gnuconfig/config.sub
./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/bfast-0.7.0a --htmldir=/usr/share/doc/bfast-0.7.0a/html --libdir=/usr/lib64
configure: loading site script /usr/share/config.site
checking for a BSD-compatible install... /usr/lib/portage/python3.11/ebuild-helpers/xattr/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking build system type... x86_64-pc-linux-gnu
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to enable C11 features... none needed
checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of x86_64-pc-linux-gnu-gcc... none
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for wchar.h... yes
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking whether _XOPEN_SOURCE should be defined... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
fatal: not a git repository (or any parent up to mount point /var/tmp)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
checking for bzlib.h... yes
checking for special C compiler options needed for large files... (cached) no
checking for _FILE_OFFSET_BITS value needed for large files... (cached) no
checking for an ANSI C-conforming const... yes
checking host system type... x86_64-pc-linux-gnu
checking for GNU libc compatible malloc... yes
checking for GNU libc compatible realloc... yes
checking for pow in -lm... yes
checking for gzread in -lz... yes
checking for floor... yes
checking for pow... yes
checking for sqrt... yes
checking for strchr... yes
checking for strdup... yes
checking for strpbrk... yes
checking for strstr... yes
checking for strtok_r... yes
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for int8_t... yes
checking for int32_t... yes
checking for int64_t... yes
checking for uint8_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking size of short int... 2
checking size of int... 4
checking size of long int... 8
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for limits.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for float.h... yes
checking for zlib.h... yes
checking for fcntl.h... yes
checking for inline... inline
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating bfast/Makefile
config.status: creating butil/Makefile
config.status: creating scripts/Makefile
config.status: creating tests/Makefile
config.status: creating config.h
config.status: executing depfiles commands
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/bfast-0.7.0a/work/bfast-0.7.0a ...
make -j4 
make  all-recursive
make[1]: Entering directory '/var/tmp/portage/sci-biology/bfast-0.7.0a/work/bfast-0.7.0a'
Making all in bfast
make[2]: Entering directory '/var/tmp/portage/sci-biology/bfast-0.7.0a/work/bfast-0.7.0a/bfast'
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=native -fno-diagnostics-color -Wall -pthread  -c -o AlignedEnd.o AlignedEnd.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=native -fno-diagnostics-color -Wall -pthread  -c -o AlignedEntry.o AlignedEntry.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=native -fno-diagnostics-color -Wall -pthread  -c -o AlignedRead.o AlignedRead.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=native -fno-diagnostics-color -Wall -pthread  -c -o AlignedReadConvert.o AlignedReadConvert.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=native -fno-diagnostics-color -Wall -pthread  -c -o BError.o BError.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=native -fno-diagnostics-color -Wall -pthread  -c -o BLib.o BLib.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=native -fno-diagnostics-color -Wall -pthread  -c -o RGBinary.o RGBinary.c
RGBinary.c: In function ‘RGBinaryReadBinaryHeader’:
RGBinary.c:260:17: warning: variable ‘numCharsPerByte’ set but not used [-Wunused-but-set-variable]
  260 |         int32_t numCharsPerByte;
      |                 ^~~~~~~~~~~~~~~
RGBinary.c: In function ‘RGBinaryWriteBinaryHeader’:
RGBinary.c:387:17: warning: variable ‘numCharsPerByte’ set but not used [-Wunused-but-set-variable]
  387 |         int32_t numCharsPerByte;
      |                 ^~~~~~~~~~~~~~~
RGBinary.c: In function ‘RGBinaryWriteBinary’:
RGBinary.c:421:17: warning: variable ‘numCharsPerByte’ set but not used [-Wunused-but-set-variable]
  421 |         int32_t numCharsPerByte;
      |                 ^~~~~~~~~~~~~~~
RGBinary.c: In function ‘RGBinaryGetFourBit’:
RGBinary.c:820:14: warning: variable ‘curChar’ set but not used [-Wunused-but-set-variable]
  820 |         char curChar;
      |              ^~~~~~~
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=native -fno-diagnostics-color -Wall -pthread  -c -o RGIndex.o RGIndex.c
RGIndex.c: In function ‘RGIndexCreateHelper’:
RGIndex.c:463:31: warning: variable ‘keyEndPos’ set but not used [-Wunused-but-set-variable]
  463 |         uint32_t keyStartPos, keyEndPos;
      |                               ^~~~~~~~~
RGIndex.c: In function ‘RGIndexCompareContigPos’:
RGIndex.c:2428:25: warning: variable ‘length’ set but not used [-Wunused-but-set-variable]
 2428 |                 int32_t length;
      |                         ^~~~~~
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=native -fno-diagnostics-color -Wall -pthread  -c -o RGIndexAccuracy.o RGIndexAccuracy.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=native -fno-diagnostics-color -Wall -pthread  -c -o RGIndexExons.o RGIndexExons.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=native -fno-diagnostics-color -Wall -pthread  -c -o RGIndexLayout.o RGIndexLayout.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=native -fno-diagnostics-color -Wall -pthread  -c -o RGMatch.o RGMatch.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -O2 -pipe -march=native -fno-diagnostics-color -Wall -pthread  -c -o RGMatches.o RGMatches.c
RGMatch.c: In function ‘RGMatchRead’:
RGMatch.c:23:25: error: passing argument 1 of ‘feof’ from incompatible pointer type [-Wincompatible-pointer-types]
   23 |                 if(feof(fp) != 0) {
      |                         ^~
      |                         |
      |                         gzFile {aka struct gzFile_s *}
In file included from RGMatch.c:2:
/usr/include/stdio.h:846:24: note: expected ‘FILE *’ but argument is of type ‘gzFile’ {aka ‘struct gzFile_s *’}
  846 | extern int feof (FILE *__stream) __THROW __wur;
      |                  ~~~~~~^~~~~~~~
make[2]: *** [Makefile:472: RGMatch.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/var/tmp/portage/sci-biology/bfast-0.7.0a/work/bfast-0.7.0a/bfast'
make[1]: *** [Makefile:436: all-recursive] Error 1
make[1]: Leaving directory '/var/tmp/portage/sci-biology/bfast-0.7.0a/work/bfast-0.7.0a'
make: *** [Makefile:356: all] Error 2
 * ERROR: sci-biology/bfast-0.7.0a::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/bfast-0.7.0a::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/bfast-0.7.0a::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:bfast-0.7.0a:20231205-064340.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/bfast-0.7.0a/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/bfast-0.7.0a/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/bfast-0.7.0a/work/bfast-0.7.0a'
 * S: '/var/tmp/portage/sci-biology/bfast-0.7.0a/work/bfast-0.7.0a'