* Package: sci-biology/maq-0.7.1-r3:0 * 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 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'