sci-biology:maq-0.7.1-r3:20231231-200714.log

sci-biology:maq-0.7.1-r3:20231231-200714.log (text/plain), 11.48 KB, created by Toralf Förster on 2023-12-31 21:05:23 UTC

 * Package:    sci-biology/maq-0.7.1-r3:0
 * 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 maq-0.7.1.tar.bz2 to /var/tmp/portage/sci-biology/maq-0.7.1-r3/work
>>> Unpacking calib-36.dat.gz to /var/tmp/portage/sci-biology/maq-0.7.1-r3/work
>>> Source unpacked in /var/tmp/portage/sci-biology/maq-0.7.1-r3/work
>>> Preparing source in /var/tmp/portage/sci-biology/maq-0.7.1-r3/work/maq-0.7.1 ...
 * Applying maq-0.7.1-flags.patch ...
 [ ok ]
 * Applying maq-0.7.1-bfr-overfl.patch ...
 [ ok ]
 * Applying maq-0.7.1-gcc-4.7.patch ...
 [ ok ]
 * Applying maq-0.7.1-remove-64bit-flag.patch ...
 [ ok ]
 * Running eautoreconf in '/var/tmp/portage/sci-biology/maq-0.7.1-r3/work/maq-0.7.1' ...
 * Running 'aclocal --system-acdir=/var/tmp/portage/sci-biology/maq-0.7.1-r3/temp/aclocal' ...
 [ ok ]
 * Running 'autoconf --force' ...
 [ ok ]
 * Running 'autoheader' ...
 [ ok ]
 * Running 'automake --add-missing --copy --force-missing' ...
 [ ok ]
 * Running elibtoolize in: maq-0.7.1/
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/maq-0.7.1-r3/work/maq-0.7.1 ...
 * econf: updating maq-0.7.1/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating maq-0.7.1/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 --datarootdir=/usr/share --disable-silent-rules --docdir=/usr/share/doc/maq-0.7.1-r3 --htmldir=/usr/share/doc/maq-0.7.1-r3/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 host 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 for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
checking whether the compiler supports GNU C++... yes
checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
checking for x86_64-pc-linux-gnu-g++ option to enable C++11 features... none needed
checking if gcc accepts -m64... yes
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 grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for zlib.h... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/maq-0.7.1-r3/work/maq-0.7.1 ...
make -j4 
make  all-am
make[1]: Entering directory '/var/tmp/portage/sci-biology/maq-0.7.1-r3/work/maq-0.7.1'
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -Wall  -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -march=native -fno-diagnostics-color -c -o main.o main.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -Wall  -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -march=native -fno-diagnostics-color -c -o const.o const.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -Wall  -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -march=native -fno-diagnostics-color -c -o seq.o seq.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -Wall  -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -march=native -fno-diagnostics-color -c -o bfa.o bfa.c
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.     -Wall  -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -march=native -fno-diagnostics-color -c -o read.o read.cc
bfa.c: In function ‘nst_load_bfa1’:
bfa.c:31:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   31 |         fread(bfa1->name, sizeof(char), len, fp);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bfa.c:32:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   32 |         fread(&bfa1->ori_len, sizeof(int), 1, fp);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bfa.c:33:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   33 |         fread(&bfa1->len, sizeof(int), 1, fp);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bfa.c:35:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   35 |         fread(bfa1->seq, sizeof(bit64_t), bfa1->len, fp);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bfa.c:37:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   37 |         fread(bfa1->mask, sizeof(bit64_t), bfa1->len, fp);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bfa.c: In function ‘nst_bfa_len’:
bfa.c:46:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   46 |                 fread(&len, sizeof(int), 1, fp);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bfa.c:48:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   48 |                 fread(&len, sizeof(int), 1, fp);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -Wall  -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -march=native -fno-diagnostics-color -c -o fasta2bfa.o fasta2bfa.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -Wall  -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -march=native -fno-diagnostics-color -c -o fastq2bfq.o fastq2bfq.c
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.     -Wall  -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -march=native -fno-diagnostics-color -c -o merge.o merge.cc
fastq2bfq.c: In function ‘fastq2bfq’:
fastq2bfq.c:30:12: error: assignment to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types]
   30 |         fp = gzopen(str, "w");
      |            ^
fastq2bfq.c:36:28: error: assignment to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types]
   36 |                         fp = gzopen(str, "w");
      |                            ^
fastq2bfq.c:47:25: error: passing argument 1 of ‘gzwrite’ from incompatible pointer type [-Wincompatible-pointer-types]
   47 |                 gzwrite(fp, &i, sizeof(int));
      |                         ^~
      |                         |
      |                         struct gzFile_s **
In file included from fastq2bfq.c:1:
/usr/include/zlib.h:1451:36: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
 1451 | ZEXTERN int ZEXPORT gzwrite(gzFile file, voidpc buf, unsigned len);
      |                             ~~~~~~~^~~~
fastq2bfq.c:48:25: error: passing argument 1 of ‘gzwrite’ from incompatible pointer type [-Wincompatible-pointer-types]
   48 |                 gzwrite(fp, name, sizeof(char) * i);
      |                         ^~
      |                         |
      |                         struct gzFile_s **
/usr/include/zlib.h:1451:36: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
 1451 | ZEXTERN int ZEXPORT gzwrite(gzFile file, voidpc buf, unsigned len);
      |                             ~~~~~~~^~~~
fastq2bfq.c:49:25: error: passing argument 1 of ‘gzwrite’ from incompatible pointer type [-Wincompatible-pointer-types]
   49 |                 gzwrite(fp, &l, sizeof(int));
      |                         ^~
      |                         |
      |                         struct gzFile_s **
/usr/include/zlib.h:1451:36: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
 1451 | ZEXTERN int ZEXPORT gzwrite(gzFile file, voidpc buf, unsigned len);
      |                             ~~~~~~~^~~~
fastq2bfq.c:50:25: error: passing argument 1 of ‘gzwrite’ from incompatible pointer type [-Wincompatible-pointer-types]
   50 |                 gzwrite(fp, seq.s, sizeof(char) * l);
      |                         ^~
      |                         |
      |                         struct gzFile_s **
/usr/include/zlib.h:1451:36: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
 1451 | ZEXTERN int ZEXPORT gzwrite(gzFile file, voidpc buf, unsigned len);
      |                             ~~~~~~~^~~~
fastq2bfq.c:53:33: error: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   53 |                         gzclose(fp);
      |                                 ^~
      |                                 |
      |                                 struct gzFile_s **
/usr/include/zlib.h:1634:39: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
 1634 | ZEXTERN int ZEXPORT    gzclose(gzFile file);
      |                                ~~~~~~~^~~~
fastq2bfq.c:62:25: error: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   62 |                 gzclose(fp);
      |                         ^~
      |                         |
      |                         struct gzFile_s **
/usr/include/zlib.h:1634:39: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
 1634 | ZEXTERN int ZEXPORT    gzclose(gzFile file);
      |                                ~~~~~~~^~~~
make[1]: *** [Makefile:485: fastq2bfq.o] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: Leaving directory '/var/tmp/portage/sci-biology/maq-0.7.1-r3/work/maq-0.7.1'
make: *** [Makefile:344: all] Error 2
 * ERROR: sci-biology/maq-0.7.1-r3::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/maq-0.7.1-r3::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/maq-0.7.1-r3::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:maq-0.7.1-r3:20231231-200714.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/maq-0.7.1-r3/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/maq-0.7.1-r3/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/maq-0.7.1-r3/work/maq-0.7.1'
 * S: '/var/tmp/portage/sci-biology/maq-0.7.1-r3/work/maq-0.7.1'