python-pysam →
0.7.7-1 →
armhf → 2015-03-31 21:23:25
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-02
╔══════════════════════════════════════════════════════════════════════════════╗
║ python-pysam 0.7.7-1 (armhf) 31 Mar 2015 21:06 ║
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Package: python-pysam
Version: 0.7.7-1
Source Version: 0.7.7-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/python-pysam-rxjz2E/python-pysam-0.7.7' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/python-pysam-rxjz2E' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-64a1bd93-e444-4ef9-b87f-ce697a26f496' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
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Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [7730 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8961 kB]
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NOTICE: 'python-pysam' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/python-pysam.git
Need to get 1500 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main python-pysam 0.7.7-1 (dsc) [2168 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main python-pysam 0.7.7-1 (tar) [1479 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main python-pysam 0.7.7-1 (diff) [19.3 kB]
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-lz2ENh/apt_archive/sbuild-build-depends-core-dummy.deb'.
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│ Install core build dependencies (apt-based resolver) │
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The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
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Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), dh-python, python-all-dev, python-setuptools, cython, zlib1g-dev, samtools (>= 0.1.19)
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), dh-python, python-all-dev, python-setuptools, cython, zlib1g-dev, samtools (>= 0.1.19)
dpkg-deb: building package `sbuild-build-depends-python-pysam-dummy' in `/«BUILDDIR»/resolver-540rUR/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'.
OK
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install python-pysam build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
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Building dependency tree...
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The following extra packages will be installed:
bsdmainutils cython debhelper dh-python file gettext gettext-base groff-base
intltool-debian libasprintf0c2 libcroco3 libexpat1 libexpat1-dev libffi6
libglib2.0-0 libmagic1 libmpdec2 libpipeline1 libpython-all-dev
libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev
libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib
libpython3.4-minimal libpython3.4-stdlib libsqlite3-0 libssl1.0.0
libunistring0 libxml2 man-db mime-support po-debconf python python-all
python-all-dev python-dev python-minimal python-pkg-resources
python-setuptools python2.7 python2.7-dev python2.7-minimal python3
python3-minimal python3.4 python3.4-minimal samtools zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser
libmail-box-perl python-doc python-tk python-distribute
python-distribute-doc python2.7-doc binfmt-support python3-doc python3-tk
python3-venv python3.4-venv python3.4-doc
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libglib2.0-data shared-mime-info xdg-user-dirs xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cython debhelper dh-python file gettext gettext-base groff-base
intltool-debian libasprintf0c2 libcroco3 libexpat1 libexpat1-dev libffi6
libglib2.0-0 libmagic1 libmpdec2 libpipeline1 libpython-all-dev
libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev
libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib
libpython3.4-minimal libpython3.4-stdlib libsqlite3-0 libssl1.0.0
libunistring0 libxml2 man-db mime-support po-debconf python python-all
python-all-dev python-dev python-minimal python-pkg-resources
python-setuptools python2.7 python2.7-dev python2.7-minimal python3
python3-minimal python3.4 python3.4-minimal samtools
sbuild-build-depends-python-pysam-dummy zlib1g-dev
0 upgraded, 52 newly installed, 0 to remove and 2 not upgraded.
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Get:47 http://172.17.0.1/private/ jessie-staging/main python-all-dev armhf 2.7.9-1 [1024 B]
Get:48 http://172.17.0.1/private/ jessie-staging/main python-pkg-resources all 5.5.1-1 [64.4 kB]
Get:49 http://172.17.0.1/private/ jessie-staging/main python-setuptools all 5.5.1-1 [242 kB]
Get:50 http://172.17.0.1/private/ jessie-staging/main samtools armhf 0.1.19-1 [523 kB]
Get:51 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-2 [199 kB]
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Selecting previously unselected package python-setuptools.
Preparing to unpack .../python-setuptools_5.5.1-1_all.deb ...
Unpacking python-setuptools (5.5.1-1) ...
Selecting previously unselected package samtools.
Preparing to unpack .../samtools_0.1.19-1_armhf.deb ...
Unpacking samtools (0.1.19-1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-2) ...
Selecting previously unselected package sbuild-build-depends-python-pysam-dummy.
Preparing to unpack .../sbuild-build-depends-python-pysam-dummy.deb ...
Unpacking sbuild-build-depends-python-pysam-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.4.0-1) ...
Setting up libssl1.0.0:armhf (1.0.1k-3) ...
Setting up groff-base (1.22.2-8) ...
Setting up bsdmainutils (9.0.6) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.7.0.2-5) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.19.3-2) ...
Setting up libmagic1:armhf (1:5.22+15-2) ...
Setting up mime-support (3.58) ...
Setting up libexpat1:armhf (2.1.0-6) ...
Setting up libffi6:armhf (3.1-2) ...
Setting up libsqlite3-0:armhf (3.8.7.1-1) ...
Setting up libpython2.7-stdlib:armhf (2.7.9-2) ...
Setting up libpython2.7:armhf (2.7.9-2) ...
Setting up libxml2:armhf (2.9.1+dfsg1-5) ...
Setting up python2.7 (2.7.9-2) ...
Setting up libpython-stdlib:armhf (2.7.9-1) ...
Setting up python (2.7.9-1) ...
Setting up libglib2.0-0:armhf (2.42.1-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-3) ...
Setting up libmpdec2:armhf (2.4.1-1) ...
Setting up libexpat1-dev:armhf (2.1.0-6) ...
Setting up libpython2.7-dev:armhf (2.7.9-2) ...
Setting up libpython3.4-minimal:armhf (3.4.2-1) ...
Setting up libpython3.4-stdlib:armhf (3.4.2-1) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up python3.4-minimal (3.4.2-1) ...
Setting up file (1:5.22+15-2) ...
Setting up gettext-base (0.19.3-2) ...
Setting up cython (0.21.1-1) ...
Setting up gettext (0.19.3-2) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu3) ...
Setting up debhelper (9.20150101) ...
Setting up python3.4 (3.4.2-1) ...
Setting up python3-minimal (3.4.2-2) ...
Setting up libpython3-stdlib:armhf (3.4.2-2) ...
Setting up libpython-dev:armhf (2.7.9-1) ...
Setting up libpython-all-dev:armhf (2.7.9-1) ...
Setting up python-all (2.7.9-1) ...
Setting up python2.7-dev (2.7.9-2) ...
Setting up python-dev (2.7.9-1) ...
Setting up python-all-dev (2.7.9-1) ...
Setting up python-pkg-resources (5.5.1-1) ...
Setting up python-setuptools (5.5.1-1) ...
Setting up samtools (0.1.19-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2) ...
Setting up python3 (3.4.2-2) ...
Setting up dh-python (1.20141111-2) ...
Setting up sbuild-build-depends-python-pysam-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-15) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25-5 dpkg-dev_1.17.24 g++-4.9_4.9.2-10 gcc-4.8_4.8.4-1 gcc-4.9_4.9.2-10 libc6-dev_2.19-15 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 linux-libc-dev_3.16.7-ckt4-1+rpi1
Package versions: apt_1.0.9.7 base-files_8+rpi1 base-passwd_3.5.37 bash_4.3-11 binutils_2.25-5 bsdmainutils_9.0.6 bsdutils_1:2.25.2-5 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:4.9.2-2 cpp-4.8_4.8.4-1 cpp-4.9_4.9.2-10 cython_0.21.1-1 dash_0.5.7-4 debconf_1.5.56 debfoster_2.7-2 debhelper_9.20150101 debianutils_4.4 dh-python_1.20141111-2 dialog_1.2-20140911-1 diffutils_1:3.3-1 dpkg_1.17.24 dpkg-dev_1.17.24 e2fslibs_1.42.12-1.1 e2fsprogs_1.42.12-1.1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9 g++_4:4.9.2-2 g++-4.9_4.9.2-10 gcc_4:4.9.2-2 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8_4.8.4-1 gcc-4.8-base_4.8.4-1 gcc-4.9_4.9.2-10 gcc-4.9-base_4.9.2-10 gettext_0.19.3-2 gettext-base_0.19.3-2 gnupg_1.4.18-7 gpgv_1.4.18-7 grep_2.20-4.1 groff-base_1.22.2-8 gzip_1.6-4 hostname_3.15 init_1.22 initscripts_2.88dsf-58 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.4-2+rpi1 kmod_18-3 libacl1_2.2.52-2 libapt-pkg4.12_1.0.9.7 libasan0_4.8.4-1 libasan1_4.9.2-10 libasprintf0c2_0.19.3-2 libatomic1_4.9.2-10 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1 libblkid1_2.25.2-5 libbz2-1.0_1.0.6-7 libc-bin_2.19-15 libc-dev-bin_2.19-15 libc6_2.19-15 libc6-dev_2.19-15 libcap2_1:2.24-7 libcgi-pm-perl_4.09-1 libcloog-isl4_0.18.2-1 libcomerr2_1.42.12-1.1 libcroco3_0.6.8-3 libdb5.1_5.1.29-6 libdb5.3_5.3.28-9 libdbus-1-3_1.8.16-1 libdebconfclient0_0.192 libdpkg-perl_1.17.24 libexpat1_2.1.0-6 libexpat1-dev_2.1.0-6 libfakeroot_1.20.2-1 libffi6_3.1-2 libgc1c2_1:7.2d-6.4 libgcc-4.8-dev_4.8.4-1 libgcc-4.9-dev_4.9.2-10 libgcc1_1:4.9.2-10 libgcrypt20_1.6.2-4 libgdbm3_1.8.3-13.1 libglib2.0-0_2.42.1-1 libgmp10_2:6.0.0+dfsg-4+rpi1 libgomp1_4.9.2-10 libgpg-error0_1.17-3 libisl10_0.12.2-2 libklibc_2.0.4-2+rpi1 libkmod2_18-3 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.22+15-2 libmount1_2.25.2-5 libmpc3_1.0.2-1 libmpdec2_2.4.1-1 libmpfr4_3.1.2-2 libncurses5_5.9+20140913-1 libncursesw5_5.9+20140913-1 libpackage-constants-perl_0.04-1 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-3.3 libpipeline1_1.4.0-1 libpng12-0_1.2.50-2 libprocps0_1:3.3.4-2 libprocps3_2:3.3.9-9 libpython-all-dev_2.7.9-1 libpython-dev_2.7.9-1 libpython-stdlib_2.7.9-1 libpython2.7_2.7.9-2 libpython2.7-dev_2.7.9-2 libpython2.7-minimal_2.7.9-2 libpython2.7-stdlib_2.7.9-2 libpython3-stdlib_3.4.2-2 libpython3.4-minimal_3.4.2-1 libpython3.4-stdlib_3.4.2-1 libreadline6_6.3-8 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-2 libsmartcols1_2.25.2-5 libsqlite3-0_3.8.7.1-1 libss2_1.42.12-1.1 libssl1.0.0_1.0.1k-3 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 libsystemd0_215-12 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140913-1 libubsan0_4.9.2-10 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-3 libuuid1_2.25.2-5 libxml2_2.9.1+dfsg1-5 linux-libc-dev_3.16.7-ckt4-1+rpi1 locales_2.19-15 login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.1 makedev_2.3.1-93 man-db_2.7.0.2-5 mawk_1.3.3-17 mime-support_3.58 mount_2.25.2-5 multiarch-support_2.19-15 nano_2.2.6-3 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-2 perl-base_5.20.2-2 perl-modules_5.20.2-2 po-debconf_1.0.16+nmu3 procps_2:3.3.9-9 python_2.7.9-1 python-all_2.7.9-1 python-all-dev_2.7.9-1 python-dev_2.7.9-1 python-minimal_2.7.9-1 python-pkg-resources_5.5.1-1 python-setuptools_5.5.1-1 python2.7_2.7.9-2 python2.7-dev_2.7.9-2 python2.7-minimal_2.7.9-2 python3_3.4.2-2 python3-minimal_3.4.2-2 python3.4_3.4.2-1 python3.4-minimal_3.4.2-1 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 samtools_0.1.19-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 sysv-rc_2.88dsf-58 sysvinit_2.88dsf-58 sysvinit-core_2.88dsf-58 sysvinit-utils_2.88dsf-58 tar_1.27.1-2 tzdata_2015b-1 util-linux_2.25.2-5 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-2 zlib1g-dev_1:1.2.8.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sat Apr 19 05:35:14 2014 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./python-pysam_0.7.7-1.dsc
dpkg-source: info: extracting python-pysam in python-pysam-0.7.7
dpkg-source: info: unpacking python-pysam_0.7.7.orig.tar.gz
dpkg-source: info: unpacking python-pysam_0.7.7-1.debian.tar.xz
dpkg-source: info: applying fix_cleanup_tests.patch
dpkg-source: info: applying do_not_use_distribute_setup.patch
dpkg-source: info: applying offline-tests.patch
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
APT_CONFIG=/var/lib/sbuild/apt.conf
COLUMNS=80
CONSOLE=/dev/console
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INIT_VERSION=sysvinit-2.88
LC_ALL=POSIX
LINES=24
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PREVLEVEL=N
PWD=/
RUNLEVEL=2
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-64a1bd93-e444-4ef9-b87f-ce697a26f496
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
init=/sbin/init
previous=N
rootmnt=/root
runlevel=2
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package python-pysam
dpkg-buildpackage: source version 0.7.7-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build python-pysam-0.7.7
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean --with python2 --buildsystem=pybuild
dh_testdir -O--buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_clean
I: pybuild base:170: python2.7 setup.py clean
running clean
removing '/«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build' (and everything under it)
'build/bdist.linux-armv7l' does not exist -- can't clean it
'build/scripts-2.7' does not exist -- can't clean it
cd tests; make clean
make[2]: Entering directory '/«PKGBUILDDIR»/tests'
mkdir keep_bam_files
mv ex9_fail.bam ex9_nofail.bam example_btag.bam example_empty_header.bam issue100.bam tag_bug.bam test_unaligned.bam keep_bam_files
rm -fr *.bam *.bai *.fai *.pileup* \
*~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam
mv keep_bam_files/* .
rmdir keep_bam_files
rm -rf pysam_test_work/
make[2]: Leaving directory '/«PKGBUILDDIR»/tests'
rm -f tests/log.txt
make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_clean
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_clean
# restore cython generated files
if [ -d debian/savefiles ] ; then \
mv debian/savefiles/* pysam ; \
rm -rf debian/savefiles ; \
fi
make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules build-arch
dh build-arch --with python2 --buildsystem=pybuild
dh_testdir -a -O--buildsystem=pybuild
dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:170: python2.7 setup.py config
running config
debian/rules override_dh_auto_build
make[1]: Entering directory '/«PKGBUILDDIR»'
mkdir -p debian/savefiles
cp -a `grep -l "Generated by Cython" pysam/*.c` debian/savefiles
dh_auto_build
I: pybuild base:170: /usr/bin/python setup.py build
running build
running build_py
creating /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/version.py -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/Pileup.py -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/namedtuple.py -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/__init__.py -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam
creating /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include
copying pysam/include/__init__.py -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include
creating /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/__init__.py -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
creating /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bcftools
copying samtools/bcftools/__init__.py -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bcftools
creating /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying samtools/win32/__init__.py -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
creating /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/tabix
copying tabix/__init__.py -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/tabix
copying pysam/TabProxies.pxd -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/cvcf.pxd -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/csamtools.pxd -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/ctabix.pxd -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/pysam_util.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/tabix_util.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam
copying samtools/bam.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/klist.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/razf.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sam_header.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/kprobaln.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/errmod.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/khash.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/kseq.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sample.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/pysam.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bgzf.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_tview.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sam.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/knetfile.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/faidx.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_endian.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/kaln.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/ksort.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/kstring.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bcftools/prob1.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bcftools
copying samtools/bcftools/kmin.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bcftools
copying samtools/bcftools/bcf.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bcftools
copying samtools/win32/zconf.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying tabix/khash.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/tabix
copying tabix/tabix.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/tabix
copying tabix/kseq.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/tabix
copying tabix/pysam.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/tabix
copying tabix/bgzf.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/tabix
copying tabix/knetfile.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/tabix
copying tabix/bam_endian.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/tabix
copying tabix/ksort.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/tabix
copying tabix/kstring.h -> /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/include/tabix
running build_ext
skipping 'pysam/csamtools.c' Cython extension (up-to-date)
building 'pysam.csamtools' extension
creating build
creating build/temp.linux-armv7l-2.7
creating build/temp.linux-armv7l-2.7/pysam
creating build/temp.linux-armv7l-2.7/samtools
creating build/temp.linux-armv7l-2.7/samtools/misc
creating build/temp.linux-armv7l-2.7/samtools/bcftools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c pysam/csamtools.c -o build/temp.linux-armv7l-2.7/pysam/csamtools.o
In file included from pysam/csamtools.c:262:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
In file included from pysam/csamtools.c:265:0:
pysam/pysam_util.h:22:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void pysam_unset_stderr();
^
pysam/csamtools.c: In function '__pyx_pf_5pysam_9csamtools_7Samfile_20fetch':
pysam/csamtools.c:12717:167: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type
__pyx_t_5 = PyInt_FromLong(bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)__pyx_v_callback), __pyx_f_5pysam_9csamtools_fetch_callback)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1071; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
^
In file included from pysam/csamtools.c:262:0:
samtools/bam.h:644:6: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)'
int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func);
^
pysam/csamtools.c: In function '__pyx_pf_5pysam_9csamtools_7Samfile_22mate':
pysam/csamtools.c:13182:210: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type
bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_read->_delegate->core.mtid, __pyx_v_read->_delegate->core.mpos, (__pyx_v_read->_delegate->core.mpos + 1), ((void *)(&__pyx_v_mate_data)), __pyx_f_5pysam_9csamtools_mate_callback);
^
In file included from pysam/csamtools.c:262:0:
samtools/bam.h:644:6: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)'
int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func);
^
pysam/csamtools.c: In function '__pyx_pf_5pysam_9csamtools_7Samfile_24count':
pysam/csamtools.c:13680:140: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type
bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)(&__pyx_v_counter)), __pyx_f_5pysam_9csamtools_count_callback);
^
In file included from pysam/csamtools.c:262:0:
samtools/bam.h:644:6: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)'
int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func);
^
pysam/csamtools.c: In function '__pyx_pf_5pysam_9csamtools_7Samfile_26pileup':
pysam/csamtools.c:14120:125: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type
bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, __pyx_v_buf, __pyx_f_5pysam_9csamtools_pileup_fetch_callback);
^
In file included from pysam/csamtools.c:262:0:
samtools/bam.h:644:6: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)'
int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func);
^
pysam/csamtools.c: In function '__pyx_f_5pysam_9csamtools___advance_snpcalls':
pysam/csamtools.c:20819:7: warning: implicit declaration of function 'bam_prob_realn' [-Wimplicit-function-declaration]
bam_prob_realn(__pyx_v_b, __pyx_v_d->seq);
^
pysam/csamtools.c:20847:7: warning: implicit declaration of function 'bam_cap_mapQ' [-Wimplicit-function-declaration]
__pyx_v_q = bam_cap_mapQ(__pyx_v_b, __pyx_v_d->seq, __pyx_v_capQ_thres);
^
pysam/csamtools.c: In function '__pyx_pf_5pysam_9csamtools_20IteratorColumnRegion_2__next__':
pysam/csamtools.c:22394:59: warning: passing argument 1 of '__pyx_f_5pysam_9csamtools_makePileupProxy' from incompatible pointer type
__pyx_t_2 = __pyx_f_5pysam_9csamtools_makePileupProxy((&__pyx_v_self->__pyx_base.plp), __pyx_v_self->__pyx_base.tid, __pyx_v_self->__pyx_base.pos, __pyx_v_self->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
^
pysam/csamtools.c:3832:18: note: expected 'struct bam_pileup1_t **' but argument is of type 'const struct bam_pileup1_t **'
static PyObject *__pyx_f_5pysam_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp, int __pyx_v_tid, int __pyx_v_pos, int __pyx_v_n) {
^
pysam/csamtools.c: In function '__pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__':
pysam/csamtools.c:22647:61: warning: passing argument 1 of '__pyx_f_5pysam_9csamtools_makePileupProxy' from incompatible pointer type
__pyx_t_2 = __pyx_f_5pysam_9csamtools_makePileupProxy((&__pyx_v_self->__pyx_base.plp), __pyx_v_self->__pyx_base.tid, __pyx_v_self->__pyx_base.pos, __pyx_v_self->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
^
pysam/csamtools.c:3832:18: note: expected 'struct bam_pileup1_t **' but argument is of type 'const struct bam_pileup1_t **'
static PyObject *__pyx_f_5pysam_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp, int __pyx_v_tid, int __pyx_v_pos, int __pyx_v_n) {
^
pysam/csamtools.c: In function '__Pyx_InitGlobals':
pysam/csamtools.c:44422:3: warning: this decimal constant is unsigned only in ISO C90
__pyx_int_neg_2147483648 = PyInt_FromLong(-2147483648); if (unlikely(!__pyx_int_neg_2147483648)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-armv7l-2.7/pysam/pysam_util.o
In file included from pysam/pysam_util.c:3:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
In file included from pysam/pysam_util.c:6:0:
samtools/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes]
static inline int bam_is_big_endian()
^
In file included from pysam/pysam_util.c:8:0:
pysam/pysam_util.h:22:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void pysam_unset_stderr();
^
pysam/pysam_util.c:30:6: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void pysam_unset_stderr()
^
In file included from pysam/pysam_util.c:4:0:
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:495:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
^
pysam/pysam_util.c:66:1: note: in expansion of macro 'KHASH_MAP_INIT_INT'
KHASH_MAP_INIT_INT(i, bam_binlist_t);
^
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:526:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
pysam/pysam_util.c:67:1: note: in expansion of macro 'KHASH_MAP_INIT_STR'
KHASH_MAP_INIT_STR(s, int)
^
pysam/pysam_util.c:99:19: warning: function declaration isn't a prototype [-Wstrict-prototypes]
static mempool_t *mp_init()
^
pysam/pysam_util.c: In function 'pysam_pileup_next':
pysam/pysam_util.c:196:8: warning: assignment discards 'const' qualifier from pointer target type
*plp = bam_plp_next(buf->iter, tid, pos, n_plp);
^
In file included from pysam/pysam_util.h:4:0,
from pysam/pysam_util.c:8:
pysam/pysam_util.c: At top level:
samtools/kseq.h:152:16: warning: 'kseq_init' defined but not used [-Wunused-function]
SCOPE kseq_t *kseq_init(type_t fd) \
^
samtools/kseq.h:223:2: note: in expansion of macro '__KSEQ_BASIC'
__KSEQ_BASIC(SCOPE, type_t) \
^
samtools/kseq.h:226:35: note: in expansion of macro 'KSEQ_INIT2'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
pysam/pysam_util.h:8:1: note: in expansion of macro 'KSEQ_INIT'
KSEQ_INIT(gzFile, gzread)
^
samtools/kseq.h:158:13: warning: 'kseq_destroy' defined but not used [-Wunused-function]
SCOPE void kseq_destroy(kseq_t *ks) \
^
samtools/kseq.h:223:2: note: in expansion of macro '__KSEQ_BASIC'
__KSEQ_BASIC(SCOPE, type_t) \
^
samtools/kseq.h:226:35: note: in expansion of macro 'KSEQ_INIT2'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
pysam/pysam_util.h:8:1: note: in expansion of macro 'KSEQ_INIT'
KSEQ_INIT(gzFile, gzread)
^
samtools/kseq.h:172:12: warning: 'kseq_read' defined but not used [-Wunused-function]
SCOPE int kseq_read(kseq_t *seq) \
^
samtools/kseq.h:224:2: note: in expansion of macro '__KSEQ_READ'
__KSEQ_READ(SCOPE)
^
samtools/kseq.h:226:35: note: in expansion of macro 'KSEQ_INIT2'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^
pysam/pysam_util.h:8:1: note: in expansion of macro 'KSEQ_INIT'
KSEQ_INIT(gzFile, gzread)
^
pysam/pysam_util.c:99:19: warning: 'mp_init' defined but not used [-Wunused-function]
static mempool_t *mp_init()
^
pysam/pysam_util.c:105:13: warning: 'mp_destroy' defined but not used [-Wunused-function]
static void mp_destroy(mempool_t *mp)
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_sort.c.pysam.o
In file included from samtools/bam_sort.c.pysam.c:10:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_color.c.pysam.o
In file included from samtools/bam_color.c.pysam.c:4:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_pileup.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_pileup.c.pysam.o
In file included from samtools/sam.h:4:0,
from samtools/bam_pileup.c.pysam.c:7:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
samtools/bam_pileup.c.pysam.c:29:19: warning: function declaration isn't a prototype [-Wstrict-prototypes]
static mempool_t *mp_init()
^
samtools/bam_pileup.c.pysam.c: In function 'resolve_cigar2':
samtools/bam_pileup.c.pysam.c:77:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
int k, is_head = 0;
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/kaln.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/kaln.c.pysam.o
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bamshuf.c.pysam.o
In file included from samtools/sam.h:4:0,
from samtools/bamshuf.c.pysam.c:8:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
samtools/bamshuf.c.pysam.c: In function 'bamshuf':
samtools/bamshuf.c.pysam.c:107:8: warning: unused variable '_l' [-Wunused-variable]
int _l = bam_read1(fp, a[j].b);
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/kprobaln.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/kprobaln.c.pysam.o
samtools/kprobaln.c.pysam.c: In function 'kpa_glocal':
samtools/kprobaln.c.pysam.c:80:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/faidx.c.pysam.o
In file included from samtools/faidx.c.pysam.c:9:0:
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:526:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
samtools/faidx.c.pysam.c:16:1: note: in expansion of macro 'KHASH_MAP_INIT_STR'
KHASH_MAP_INIT_STR(s, faidx1_t)
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_reheader.c.pysam.o
In file included from samtools/bam_reheader.c.pysam.c:7:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
samtools/bam_reheader.c.pysam.c: In function 'bam_reheader':
samtools/bam_reheader.c.pysam.c:14:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
bam_header_t *old;
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_rmdup.c.pysam.o
In file included from samtools/sam.h:4:0,
from samtools/bam_rmdup.c.pysam.c:8:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
In file included from samtools/bam_rmdup.c.pysam.c:12:0:
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:518:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
^
samtools/bam_rmdup.c.pysam.c:13:1: note: in expansion of macro 'KHASH_SET_INIT_STR'
KHASH_SET_INIT_STR(name)
^
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:510:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
^
samtools/bam_rmdup.c.pysam.c:14:1: note: in expansion of macro 'KHASH_MAP_INIT_INT64'
KHASH_MAP_INIT_INT64(pos, bam1_p)
^
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:526:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
samtools/bam_rmdup.c.pysam.c:22:1: note: in expansion of macro 'KHASH_MAP_INIT_STR'
KHASH_MAP_INIT_STR(lib, lib_aux_t)
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/cut_target.c.pysam.o
In file included from samtools/cut_target.c.pysam.c:6:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
samtools/cut_target.c.pysam.c: In function 'main_cut_target':
samtools/cut_target.c.pysam.c:139:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l;
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_import.c.pysam.o
In file included from samtools/bam_import.c.pysam.c:14:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
In file included from samtools/bam_import.c.pysam.c:17:0:
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:526:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
samtools/bam_import.c.pysam.c:20:1: note: in expansion of macro 'KHASH_MAP_INIT_STR'
KHASH_MAP_INIT_STR(ref, uint64_t)
^
samtools/bam_import.c.pysam.c: In function 'append_text':
samtools/bam_import.c.pysam.c:181:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat=]
fprintf(pysamerr,"realloc failed to alloc %ld bytes\n", y);
^
samtools/bam_import.c.pysam.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint32_t' [-Wformat=]
fprintf(pysamerr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,(long)header->n_text,x,y);
^
samtools/bam_import.c.pysam.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat=]
samtools/bam_import.c.pysam.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat=]
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_index.c.pysam.o
In file included from samtools/bam_index.c.pysam.c:5:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
In file included from samtools/bam_index.c.pysam.c:8:0:
samtools/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes]
static inline int bam_is_big_endian()
^
In file included from samtools/bam_index.c.pysam.c:6:0:
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:495:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
^
samtools/bam_index.c.pysam.c:66:1: note: in expansion of macro 'KHASH_MAP_INIT_INT'
KHASH_MAP_INIT_INT(i, bam_binlist_t)
^
samtools/bam_index.c.pysam.c: In function 'bam_index_load_core':
samtools/bam_index.c.pysam.c:337:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic, 1, 4, fp);
^
samtools/bam_index.c.pysam.c:344:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&idx->n, 4, 1, fp);
^
samtools/bam_index.c.pysam.c:357:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&size, 4, 1, fp);
^
samtools/bam_index.c.pysam.c:360:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&key, 4, 1, fp);
^
samtools/bam_index.c.pysam.c:364:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&p->n, 4, 1, fp);
^
samtools/bam_index.c.pysam.c:368:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(p->list, 16, p->n, fp);
^
samtools/bam_index.c.pysam.c:378:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&index2->n, 4, 1, fp);
^
samtools/bam_index.c.pysam.c:382:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(index2->offset, index2->n, 8, fp);
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/errmod.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/errmod.c.pysam.o
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bedcov.c.pysam.o
In file included from samtools/bedcov.c.pysam.c:11:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sample.c.pysam.o
In file included from samtools/sample.c.pysam.c:6:0:
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:526:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
samtools/sample.c.pysam.c:7:1: note: in expansion of macro 'KHASH_MAP_INIT_STR'
KHASH_MAP_INIT_STR(sm, int)
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_tview.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_tview.c.pysam.o
In file included from samtools/bam_tview.h:10:0,
from samtools/bam_tview.c.pysam.c:4:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
In file included from samtools/bam2bcf.h:6:0,
from samtools/bam_tview.h:12,
from samtools/bam_tview.c.pysam.c:4:
samtools/bcftools/bcf.h:173:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bcf_str2id_init();
^
In file included from samtools/bam_tview.h:14:0,
from samtools/bam_tview.c.pysam.c:4:
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:526:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
samtools/bam_tview.h:16:1: note: in expansion of macro 'KHASH_MAP_INIT_STR'
KHASH_MAP_INIT_STR(kh_rg, const char *)
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_mate.c.pysam.o
In file included from samtools/bam_mate.c.pysam.c:7:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
samtools/bam_mate.c.pysam.c:105:6: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void usage()
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sam.c.pysam.o
In file included from samtools/sam.h:4:0,
from samtools/sam.c.pysam.c:6:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/knetfile.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/knetfile.c.pysam.o
In file included from samtools/knetfile.c.pysam.c:48:0:
samtools/knetfile.c.pysam.c: In function 'kftp_send_cmd':
samtools/knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
#define netwrite(fd, ptr, len) write(fd, ptr, len)
^
samtools/knetfile.c.pysam.c:238:2: note: in expansion of macro 'netwrite'
netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
^
samtools/knetfile.c.pysam.c: In function 'khttp_connect_file':
samtools/knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
#define netwrite(fd, ptr, len) write(fd, ptr, len)
^
samtools/knetfile.c.pysam.c:417:2: note: in expansion of macro 'netwrite'
netwrite(fp->fd, buf, l);
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sam_view.c.pysam.o
In file included from samtools/sam.h:4:0,
from samtools/sam_view.c.pysam.c:10:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
In file included from samtools/sam_view.c.pysam.c:13:0:
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:518:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
^
samtools/sam_view.c.pysam.c:14:1: note: in expansion of macro 'KHASH_SET_INIT_STR'
KHASH_SET_INIT_STR(rg)
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam2bcf_indel.c.pysam.o
In file included from samtools/bam2bcf_indel.c.pysam.c:6:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
In file included from samtools/bam2bcf.h:6:0,
from samtools/bam2bcf_indel.c.pysam.c:7:
samtools/bcftools/bcf.h:173:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bcf_str2id_init();
^
In file included from samtools/bam2bcf_indel.c.pysam.c:10:0:
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:518:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
^
samtools/bam2bcf_indel.c.pysam.c:11:1: note: in expansion of macro 'KHASH_SET_INIT_STR'
KHASH_SET_INIT_STR(rg)
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/razf.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/razf.c.pysam.o
samtools/razf.c.pysam.c:76:19: warning: function declaration isn't a prototype [-Wstrict-prototypes]
static inline int is_big_endian(){
^
samtools/razf.c.pysam.c: In function 'razf_flush':
samtools/razf.c.pysam.c:223:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
^
samtools/razf.c.pysam.c:236:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
^
samtools/razf.c.pysam.c: In function '_razf_write':
samtools/razf.c.pysam.c:203:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
^
samtools/razf.c.pysam.c: In function 'razf_close':
samtools/razf.c.pysam.c:806:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, &rz->in, sizeof(int64_t));
^
samtools/razf.c.pysam.c:807:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, &rz->out, sizeof(int64_t));
^
samtools/razf.c.pysam.c:810:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, &v64, sizeof(int64_t));
^
samtools/razf.c.pysam.c:812:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, &v64, sizeof(int64_t));
^
samtools/razf.c.pysam.c: In function 'razf_end_flush':
samtools/razf.c.pysam.c:260:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
^
samtools/razf.c.pysam.c: In function 'save_zindex':
samtools/razf.c.pysam.c:98:12: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
if(is_be) write(fd, &rz->index->size, sizeof(int));
^
samtools/razf.c.pysam.c:101:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(fd, &v32, sizeof(uint32_t));
^
samtools/razf.c.pysam.c:108:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
^
samtools/razf.c.pysam.c:109:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size);
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_plcmd.c.pysam.o
In file included from samtools/sam.h:4:0,
from samtools/bam_plcmd.c.pysam.c:11:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
In file included from samtools/bam2bcf.h:6:0,
from samtools/bam_plcmd.c.pysam.c:67:
samtools/bcftools/bcf.h:173:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bcf_str2id_init();
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_lpileup.c.pysam.o
In file included from samtools/bam_lpileup.c.pysam.c:6:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
samtools/bam_lpileup.c.pysam.c:25:19: warning: function declaration isn't a prototype [-Wstrict-prototypes]
static mempool_t *mp_init()
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/padding.c.pysam.o
In file included from samtools/sam.h:4:0,
from samtools/padding.c.pysam.c:8:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
samtools/padding.c.pysam.c: In function 'bam_pad2unpad':
samtools/padding.c.pysam.c:175:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat=]
fprintf(pysamerr, "[depad] ERROR: (Padded) length of '%s' is %d in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_cat.c.pysam.o
In file included from samtools/bam_cat.c.pysam.c:66:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam2bcf.c.pysam.o
In file included from samtools/bam2bcf.c.pysam.c:6:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
In file included from samtools/bam2bcf.h:6:0,
from samtools/bam2bcf.c.pysam.c:8:
samtools/bcftools/bcf.h:173:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bcf_str2id_init();
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_tview_curses.c.pysam.o
In file included from samtools/bam_tview.h:10:0,
from samtools/bam_tview_curses.c.pysam.c:21:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
In file included from samtools/bam2bcf.h:6:0,
from samtools/bam_tview.h:12,
from samtools/bam_tview_curses.c.pysam.c:21:
samtools/bcftools/bcf.h:173:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bcf_str2id_init();
^
In file included from samtools/bam_tview.h:14:0,
from samtools/bam_tview_curses.c.pysam.c:21:
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:526:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
samtools/bam_tview.h:16:1: note: in expansion of macro 'KHASH_MAP_INIT_STR'
KHASH_MAP_INIT_STR(kh_rg, const char *)
^
samtools/bam_tview_curses.c.pysam.c:289:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp]
#warning "No curses library is available; tview with curses is disabled."
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bgzf.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bgzf.c.pysam.o
samtools/bgzf.c.pysam.c:106:14: warning: function declaration isn't a prototype [-Wstrict-prototypes]
static BGZF *bgzf_read_init()
^
samtools/bgzf.c.pysam.c: In function 'worker_aux':
samtools/bgzf.c.pysam.c:394:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
int i, tmp, stop = 0;
^
samtools/bgzf.c.pysam.c: In function 'bgzf_close':
samtools/bgzf.c.pysam.c:574:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int ret, count, block_length;
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_md.c.pysam.o
In file included from samtools/sam.h:4:0,
from samtools/bam_md.c.pysam.c:9:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bedidx.c.pysam.o
In file included from samtools/bedidx.c.pysam.c:25:0:
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:526:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
samtools/bedidx.c.pysam.c:26:1: note: in expansion of macro 'KHASH_MAP_INIT_STR'
KHASH_MAP_INIT_STR(reg, bed_reglist_t)
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam2depth.c.pysam.o
In file included from samtools/bam2depth.c.pysam.c:13:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_rmdupse.c.pysam.o
In file included from samtools/sam.h:4:0,
from samtools/bam_rmdupse.c.pysam.c:4:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
In file included from samtools/bam_rmdupse.c.pysam.c:6:0:
samtools/klist.h:11:32: warning: function declaration isn't a prototype [-Wstrict-prototypes]
static inline kmp_##name##_t *kmp_init_##name() { \
^
samtools/klist.h:47:2: note: in expansion of macro 'KMEMPOOL_INIT'
KMEMPOOL_INIT(name, kl1_##name, kmpfree_t) \
^
samtools/bam_rmdupse.c.pysam.c:17:1: note: in expansion of macro 'KLIST_INIT'
KLIST_INIT(q, elem_t, __free_elem)
^
samtools/klist.h:53:31: warning: function declaration isn't a prototype [-Wstrict-prototypes]
static inline kl_##name##_t *kl_init_##name() { \
^
samtools/bam_rmdupse.c.pysam.c:17:1: note: in expansion of macro 'KLIST_INIT'
KLIST_INIT(q, elem_t, __free_elem)
^
In file included from samtools/bam_rmdupse.c.pysam.c:5:0:
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:495:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
^
samtools/bam_rmdupse.c.pysam.c:20:1: note: in expansion of macro 'KHASH_MAP_INIT_INT'
KHASH_MAP_INIT_INT(best, elem_p)
^
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:526:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
samtools/bam_rmdupse.c.pysam.c:27:1: note: in expansion of macro 'KHASH_MAP_INIT_STR'
KHASH_MAP_INIT_STR(lib, lib_aux_t)
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_aux.c.pysam.o
In file included from samtools/bam_aux.c.pysam.c:4:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
In file included from samtools/bam_aux.c.pysam.c:5:0:
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:526:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
samtools/bam_aux.c.pysam.c:7:1: note: in expansion of macro 'KHASH_MAP_INIT_STR'
KHASH_MAP_INIT_STR(s, int)
^
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:526:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
samtools/bam_aux.c.pysam.c:8:1: note: in expansion of macro 'KHASH_MAP_INIT_STR'
KHASH_MAP_INIT_STR(r2l, str_p)
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam.c.pysam.o
In file included from samtools/bam.c.pysam.c:7:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
In file included from samtools/bam.c.pysam.c:8:0:
samtools/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes]
static inline int bam_is_big_endian()
^
samtools/bam.c.pysam.c:59:15: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init()
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_stat.c.pysam.o
In file included from samtools/bam_stat.c.pysam.c:5:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/phase.c.pysam.o
In file included from samtools/phase.c.pysam.c:9:0:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
In file included from samtools/phase.c.pysam.c:46:0:
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:502:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)
^
samtools/phase.c.pysam.c:47:1: note: in expansion of macro 'KHASH_SET_INIT_INT64'
KHASH_SET_INIT_INT64(set64)
^
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:510:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
^
samtools/phase.c.pysam.c:48:1: note: in expansion of macro 'KHASH_MAP_INIT_INT64'
KHASH_MAP_INIT_INT64(64, frag_t)
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sam_header.c.pysam.o
In file included from samtools/sam_header.c.pysam.c:10:0:
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:526:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
samtools/sam_header.c.pysam.c:11:1: note: in expansion of macro 'KHASH_MAP_INIT_STR'
KHASH_MAP_INIT_STR(str, const char *)
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/kstring.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/kstring.c.pysam.o
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_tview_html.c.pysam.o
In file included from samtools/bam_tview.h:10:0,
from samtools/bam_tview_html.c.pysam.c:4:
samtools/bam.h:383:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bam_strmap_init();
^
samtools/bam.h:398:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
bam_header_t *bam_header_init();
^
In file included from samtools/bam2bcf.h:6:0,
from samtools/bam_tview.h:12,
from samtools/bam_tview_html.c.pysam.c:4:
samtools/bcftools/bcf.h:173:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bcf_str2id_init();
^
In file included from samtools/bam_tview.h:14:0,
from samtools/bam_tview_html.c.pysam.c:4:
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:526:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
samtools/bam_tview.h:16:1: note: in expansion of macro 'KHASH_MAP_INIT_STR'
KHASH_MAP_INIT_STR(kh_rg, const char *)
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/misc/ace2sam.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/misc/ace2sam.c.pysam.o
samtools/misc/ace2sam.c.pysam.c: In function 'main':
samtools/misc/ace2sam.c.pysam.c:114:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat=]
fprintf(pysamerr, "H @SQ\tSN:%s\tLN:%ld\n", t[0].s, t[is_padded?1:2].l); // The SAM header line
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/misc/md5.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/misc/md5.c.pysam.o
samtools/misc/md5.c.pysam.c:33:6: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void byteReverse(buf, longs)
^
samtools/misc/md5.c.pysam.c: In function 'MD5Final':
samtools/misc/md5.c.pysam.c:157:26: warning: argument to 'sizeof' in 'memset' call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess]
memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/kmin.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bcftools/kmin.c.pysam.o
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/bcfutils.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bcftools/bcfutils.c.pysam.o
In file included from samtools/bcftools/bcfutils.c.pysam.c:6:0:
samtools/bcftools/bcf.h:173:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bcf_str2id_init();
^
In file included from samtools/bcftools/bcfutils.c.pysam.c:8:0:
samtools/khash.h:168:23: warning: function declaration isn't a prototype [-Wstrict-prototypes]
SCOPE kh_##name##_t *kh_init_##name() { \
^
samtools/khash.h:307:2: note: in expansion of macro 'KHASH_INIT2'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
samtools/khash.h:526:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
samtools/bcftools/bcfutils.c.pysam.c:9:1: note: in expansion of macro 'KHASH_MAP_INIT_STR'
KHASH_MAP_INIT_STR(str2id, int)
^
samtools/bcftools/bcfutils.c.pysam.c:30:7: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bcf_str2id_init()
^
samtools/bcftools/bcfutils.c.pysam.c: In function 'bcf_fit_alt':
samtools/bcftools/bcfutils.c.pysam.c:121:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
int ipl=-1, igt=-1;
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/kfunc.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bcftools/kfunc.c.pysam.o
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/index.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bcftools/index.c.pysam.o
In file included from samtools/bcftools/index.c.pysam.c:6:0:
samtools/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes]
static inline int bam_is_big_endian()
^
In file included from samtools/bcftools/index.c.pysam.c:8:0:
samtools/bcftools/bcf.h:173:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bcf_str2id_init();
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/bcf.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bcftools/bcf.c.pysam.o
In file included from samtools/bcftools/bcf.c.pysam.c:7:0:
samtools/bcftools/bcf.h:173:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bcf_str2id_init();
^
samtools/bcftools/bcf.c.pysam.c: In function 'bcf_fmt_core':
samtools/bcftools/bcf.c.pysam.c:235:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
int iPL = -1;
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/bcf2qcall.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bcftools/bcf2qcall.c.pysam.o
In file included from samtools/bcftools/bcf2qcall.c.pysam.c:7:0:
samtools/bcftools/bcf.h:173:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bcf_str2id_init();
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/prob1.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bcftools/prob1.c.pysam.o
In file included from samtools/bcftools/prob1.h:4:0,
from samtools/bcftools/prob1.c.pysam.c:11:
samtools/bcftools/bcf.h:173:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bcf_str2id_init();
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/fet.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bcftools/fet.c.pysam.o
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/em.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bcftools/em.c.pysam.o
In file included from samtools/bcftools/em.c.pysam.c:6:0:
samtools/bcftools/bcf.h:173:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bcf_str2id_init();
^
samtools/bcftools/em.c.pysam.c: In function 'bcf_em1':
samtools/bcftools/em.c.pysam.c:176:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
int i, n, n2;
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/vcf.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bcftools/vcf.c.pysam.o
In file included from samtools/bcftools/vcf.c.pysam.c:7:0:
samtools/bcftools/bcf.h:173:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bcf_str2id_init();
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/call1.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bcftools/call1.c.pysam.o
In file included from samtools/bcftools/call1.c.pysam.c:8:0:
samtools/bcftools/bcf.h:173:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bcf_str2id_init();
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.7 -c samtools/bcftools/mut.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bcftools/mut.c.pysam.o
In file included from samtools/bcftools/mut.c.pysam.c:5:0:
samtools/bcftools/bcf.h:173:2: warning: function declaration isn't a prototype [-Wstrict-prototypes]
void *bcf_str2id_init();
^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/csamtools.o build/temp.linux-armv7l-2.7/pysam/pysam_util.o build/temp.linux-armv7l-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_color.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_pileup.c.pysam.o build/temp.linux-armv7l-2.7/samtools/kaln.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-armv7l-2.7/samtools/kprobaln.c.pysam.o build/temp.linux-armv7l-2.7/samtools/faidx.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-armv7l-2.7/samtools/cut_target.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_import.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_index.c.pysam.o build/temp.linux-armv7l-2.7/samtools/errmod.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bedcov.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sample.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_tview.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sam.c.pysam.o build/temp.linux-armv7l-2.7/samtools/knetfile.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sam_view.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-2.7/samtools/razf.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-armv7l-2.7/samtools/padding.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_tview_curses.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bgzf.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_md.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bedidx.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-armv7l-2.7/samtools/phase.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sam_header.c.pysam.o build/temp.linux-armv7l-2.7/samtools/kstring.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_tview_html.c.pysam.o build/temp.linux-armv7l-2.7/samtools/misc/ace2sam.c.pysam.o build/temp.linux-armv7l-2.7/samtools/misc/md5.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bcftools/kmin.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bcftools/bcfutils.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bcftools/kfunc.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bcftools/index.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bcftools/bcf.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bcftools/bcf2qcall.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bcftools/prob1.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bcftools/fet.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bcftools/em.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bcftools/vcf.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bcftools/call1.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bcftools/mut.c.pysam.o -lz -o /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/csamtools.so
skipping 'pysam/ctabix.c' Cython extension (up-to-date)
building 'pysam.ctabix' extension
creating build/temp.linux-armv7l-2.7/tabix
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/usr/include/python2.7 -c pysam/ctabix.c -o build/temp.linux-armv7l-2.7/pysam/ctabix.o
pysam/ctabix.c: In function '__pyx_pf_5pysam_6ctabix_9Tabixfile_7contigs___get__':
pysam/ctabix.c:4151:21: warning: assignment from incompatible pointer type
__pyx_v_sequences = ti_seqname(__pyx_v_self->tabixfile->idx, (&__pyx_v_nsequences));
^
pysam/ctabix.c: In function '__pyx_pf_5pysam_6ctabix_13TabixIterator_4__next__':
pysam/ctabix.c:4652:15: warning: assignment discards 'const' qualifier from pointer target type
__pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len));
^
pysam/ctabix.c: In function '__pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_4__next__':
pysam/ctabix.c:5004:13: warning: assignment discards 'const' qualifier from pointer target type
__pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len));
^
pysam/ctabix.c: In function '__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_4__next__':
pysam/ctabix.c:5837:15: warning: assignment discards 'const' qualifier from pointer target type
__pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len));
^
pysam/ctabix.c: At top level:
pysam/ctabix.c:1560:18: warning: '__pyx_f_5pysam_6ctabix_from_string_and_size' defined but not used [-Wunused-function]
static PyObject *__pyx_f_5pysam_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) {
^
pysam/ctabix.c:2030:18: warning: '__pyx_f_5pysam_6ctabix__force_str' defined but not used [-Wunused-function]
static PyObject *__pyx_f_5pysam_6ctabix__force_str(PyObject *__pyx_v_s) {
^
pysam/ctabix.c:7363:18: warning: '__pyx_f_5pysam_6ctabix_buildGzipError' defined but not used [-Wunused-function]
static PyObject *__pyx_f_5pysam_6ctabix_buildGzipError(void *__pyx_v_gzfp) {
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/usr/include/python2.7 -c pysam/tabix_util.c -o build/temp.linux-armv7l-2.7/pysam/tabix_util.o
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/usr/include/python2.7 -c tabix/index.c.pysam.c -o build/temp.linux-armv7l-2.7/tabix/index.c.pysam.o
In file included from tabix/index.c.pysam.c:9:0:
tabix/bam_endian.h:6:19: warning: function declaration isn't a prototype [-Wstrict-prototypes]
static inline int bam_is_big_endian()
^
In file included from tabix/index.c.pysam.c:6:0:
tabix/khash.h:129:31: warning: function declaration isn't a prototype [-Wstrict-prototypes]
static inline kh_##name##_t *kh_init_##name() { \
^
tabix/khash.h:453:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
^
tabix/index.c.pysam.c:36:1: note: in expansion of macro 'KHASH_MAP_INIT_INT'
KHASH_MAP_INIT_INT(i, ti_binlist_t)
^
tabix/khash.h:129:31: warning: function declaration isn't a prototype [-Wstrict-prototypes]
static inline kh_##name##_t *kh_init_##name() { \
^
tabix/khash.h:484:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
tabix/index.c.pysam.c:37:1: note: in expansion of macro 'KHASH_MAP_INIT_STR'
KHASH_MAP_INIT_STR(s, int)
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/usr/include/python2.7 -c tabix/bgzip.c.pysam.c -o build/temp.linux-armv7l-2.7/tabix/bgzip.c.pysam.o
tabix/bgzip.c.pysam.c:38:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
static int bgzip_main_usage()
^
tabix/bgzip.c.pysam.c: In function 'main':
tabix/bgzip.c.pysam.c:200:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(f_dst, buffer, c);
^
tabix/bgzip.c.pysam.c: In function 'write_open':
tabix/bgzip.c.pysam.c:59:4: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
scanf("%c", &c);
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/usr/include/python2.7 -c tabix/knetfile.c.pysam.c -o build/temp.linux-armv7l-2.7/tabix/knetfile.c.pysam.o
In file included from tabix/knetfile.c.pysam.c:51:0:
tabix/knetfile.c.pysam.c: In function 'kftp_send_cmd':
tabix/knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
#define netwrite(fd, ptr, len) write(fd, ptr, len)
^
tabix/knetfile.c.pysam.c:241:2: note: in expansion of macro 'netwrite'
netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
^
tabix/knetfile.c.pysam.c: In function 'khttp_connect_file':
tabix/knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
#define netwrite(fd, ptr, len) write(fd, ptr, len)
^
tabix/knetfile.c.pysam.c:420:2: note: in expansion of macro 'netwrite'
netwrite(fp->fd, buf, l);
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/usr/include/python2.7 -c tabix/bgzf.c.pysam.c -o build/temp.linux-armv7l-2.7/tabix/bgzf.c.pysam.o
tabix/bgzf.c.pysam.c:104:14: warning: function declaration isn't a prototype [-Wstrict-prototypes]
static BGZF *bgzf_read_init()
^
tabix/bgzf.c.pysam.c: In function 'bgzf_close':
tabix/bgzf.c.pysam.c:437:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
int ret, count, block_length;
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/usr/include/python2.7 -c tabix/bedidx.c.pysam.c -o build/temp.linux-armv7l-2.7/tabix/bedidx.c.pysam.o
In file included from tabix/bedidx.c.pysam.c:21:0:
tabix/khash.h:129:31: warning: function declaration isn't a prototype [-Wstrict-prototypes]
static inline kh_##name##_t *kh_init_##name() { \
^
tabix/khash.h:484:2: note: in expansion of macro 'KHASH_INIT'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
tabix/bedidx.c.pysam.c:22:1: note: in expansion of macro 'KHASH_MAP_INIT_STR'
KHASH_MAP_INIT_STR(reg, bed_reglist_t)
^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/usr/include/python2.7 -c tabix/kstring.c.pysam.c -o build/temp.linux-armv7l-2.7/tabix/kstring.c.pysam.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/ctabix.o build/temp.linux-armv7l-2.7/pysam/tabix_util.o build/temp.linux-armv7l-2.7/tabix/index.c.pysam.o build/temp.linux-armv7l-2.7/tabix/bgzip.c.pysam.o build/temp.linux-armv7l-2.7/tabix/knetfile.c.pysam.o build/temp.linux-armv7l-2.7/tabix/bgzf.c.pysam.o build/temp.linux-armv7l-2.7/tabix/bedidx.c.pysam.o build/temp.linux-armv7l-2.7/tabix/kstring.c.pysam.o -lz -o /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/ctabix.so
skipping 'pysam/TabProxies.c' Cython extension (up-to-date)
building 'pysam.TabProxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c pysam/TabProxies.c -o build/temp.linux-armv7l-2.7/pysam/TabProxies.o
pysam/TabProxies.c:1180:18: warning: '__pyx_f_5pysam_10TabProxies_from_string_and_size' defined but not used [-Wunused-function]
static PyObject *__pyx_f_5pysam_10TabProxies_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) {
^
pysam/TabProxies.c:1253:18: warning: '__pyx_f_5pysam_10TabProxies__my_encodeFilename' defined but not used [-Wunused-function]
static PyObject *__pyx_f_5pysam_10TabProxies__my_encodeFilename(PyObject *__pyx_v_filename) {
^
pysam/TabProxies.c:1577:18: warning: '__pyx_f_5pysam_10TabProxies__charptr_to_str' defined but not used [-Wunused-function]
static PyObject *__pyx_f_5pysam_10TabProxies__charptr_to_str(char *__pyx_v_s) {
^
pysam/TabProxies.c:1775:14: warning: '__pyx_f_5pysam_10TabProxies_nextItem' defined but not used [-Wunused-function]
static char *__pyx_f_5pysam_10TabProxies_nextItem(char *__pyx_v_buffer) {
^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/TabProxies.o -lz -o /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/TabProxies.so
skipping 'pysam/cvcf.c' Cython extension (up-to-date)
building 'pysam.cvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -Itabix -I/usr/include/python2.7 -c pysam/cvcf.c -o build/temp.linux-armv7l-2.7/pysam/cvcf.o
In file included from pysam/tabix_util.h:5:0,
from pysam/cvcf.c:266:
tabix/kseq.h:97:13: warning: 'ks_getuntil' defined but not used [-Wunused-function]
static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
^
tabix/kseq.h:147:2: note: in expansion of macro '__KS_GETUNTIL'
__KS_GETUNTIL(__read, __bufsize)
^
pysam/tabix_util.h:12:1: note: in expansion of macro 'KSTREAM_INIT'
KSTREAM_INIT( gzFile, gzread, 16384)
^
pysam/cvcf.c: In function '__pyx_pw_5pysam_4cvcf_3VCF_33parse_data':
pysam/cvcf.c:19055:14: warning: '__pyx_v_qual' may be used uninitialized in this function [-Wmaybe-uninitialized]
__pyx_t_24 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
^
pysam/cvcf.c:14923:10: note: '__pyx_v_qual' was declared here
double __pyx_v_qual;
^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/cvcf.o -lz -o /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build/pysam/cvcf.so
make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_test
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_test # default tests
I: pybuild base:170: cd /«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build; python2.7 -m unittest discover -v
----------------------------------------------------------------------
Ran 0 tests in 0.000s
OK
PYBUILD_SYSTEM=custom \
PYBUILD_TEST_ARGS="cd tests && PYTHONPATH={build_dir} {interpreter} ./pysam_test_offline.py" \
dh_auto_test --buildsystem=pybuild
I: pybuild base:170: cd tests && PYTHONPATH=/«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build python2.7 ./pysam_test_offline.py
make[2]: Entering directory '/«PKGBUILDDIR»/tests'
samtools faidx ex1.fa
samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
[main] The `pileup' command has been removed. Please use `mpileup' instead.
samtools index ex1.bam
samtools view -h ex1.bam | gzip > ex2.sam.gz
gunzip < ex2.sam.gz > ex2.sam
gunzip < ex1.sam.gz > ex1.sam
samtools import ex1.fa.fai ex2.sam ex2.bam
[samopen] SAM header is present: 2 sequences.
samtools import ex1.fa.fai ex3.sam ex3.bam
[samopen] SAM header is present: 2 sequences.
samtools index ex3.bam
samtools import ex1.fa.fai ex4.sam ex4.bam
[samopen] SAM header is present: 2 sequences.
samtools index ex4.bam
samtools import ex1.fa.fai ex5.sam ex5.bam
[samopen] SAM header is present: 2 sequences.
Parse warning at line 4: mapped sequence without CIGAR
Parse warning at line 5: mapped sequence without CIGAR
samtools index ex5.bam
samtools import ex1.fa.fai ex6.sam ex6.bam
[samopen] SAM header is present: 2 sequences.
samtools import ex1.fa.fai ex8.sam ex8.bam
[samopen] SAM header is present: 1 sequences.
samtools index ex8.bam
samtools index ex9_nofail.bam
samtools index ex9_fail.bam
samtools import ex1.fa.fai ex10.sam ex10.bam
[samopen] SAM header is present: 1 sequences.
Makefile:22: recipe for target 'ex10.bam' failed
make[2]: *** [ex10.bam] Bus error
make[2]: *** Deleting file 'ex10.bam'
make[2]: Leaving directory '/«PKGBUILDDIR»/tests'
building data files
starting tests
.....................E...E../pysam_test_offline.py:473: UserWarning: fetch called for samfile without header
result = list(infile.fetch())
................................................................EE.....................Bus error
E: pybuild pybuild:256: test: plugin custom failed with: exit code=135: cd tests && PYTHONPATH=/«PKGBUILDDIR»/.pybuild/pythonX.Y_2.7/build python2.7 ./pysam_test_offline.py
dh_auto_test: pybuild --test -i python{version} -p 2.7 --dir . returned exit code 13
make[1]: *** [override_dh_auto_test] Error 13
debian/rules:29: recipe for target 'override_dh_auto_test' failed
make[1]: Leaving directory '/«PKGBUILDDIR»'
make: *** [build-arch] Error 2
debian/rules:9: recipe for target 'build-arch' failed
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
Build finished at 20150331-2123
Finished
────────
E: Build failure (dpkg-buildpackage died)
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 38868
Build-Time: 643
Distribution: jessie-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 324
Job: python-pysam_0.7.7-1
Machine Architecture: armhf
Package: python-pysam
Package-Time: 1023
Source-Version: 0.7.7-1
Space: 38868
Status: attempted
Version: 0.7.7-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20150331-2123
Build needed 00:17:03, 38868k disc space