* Package: sci-biology/bfast-0.7.0a:0 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * 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'