fastdnaml →
1.2.2-11 →
armhf → 2016-01-21 06:01:53
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-02
╔══════════════════════════════════════════════════════════════════════════════╗
║ fastdnaml 1.2.2-11 (armhf) 21 Jan 2016 05:55 ║
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Package: fastdnaml
Version: 1.2.2-11
Source Version: 1.2.2-11
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/fastdnaml-qIqQpd/fastdnaml-1.2.2' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/fastdnaml-qIqQpd' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-2b99cbb4-f6b4-4292-8d80-50fb9d199a01' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
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Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [8628 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [10.7 MB]
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Check APT
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NOTICE: 'fastdnaml' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/fastdnaml/trunk/
Need to get 79.0 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main fastdnaml 1.2.2-11 (dsc) [2014 B]
Get:2 http://172.17.0.1/private stretch-staging/main fastdnaml 1.2.2-11 (tar) [70.0 kB]
Get:3 http://172.17.0.1/private stretch-staging/main fastdnaml 1.2.2-11 (diff) [6956 B]
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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-R3yeHu/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/«BUILDDIR»/resolver-R3yeHu/apt_archive ./ InRelease
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Get:2 file:/«BUILDDIR»/resolver-R3yeHu/apt_archive ./ Release [2119 B]
Get:3 file:/«BUILDDIR»/resolver-R3yeHu/apt_archive ./ Release.gpg [299 B]
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Get:4 file:/«BUILDDIR»/resolver-R3yeHu/apt_archive ./ Sources [188 B]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
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Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libapt-pkg4.16 libisl13 libprocps4
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 22 not upgraded.
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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)
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9)
dpkg-deb: building package 'sbuild-build-depends-fastdnaml-dummy' in '/«BUILDDIR»/resolver-Kwy_Ck/apt_archive/sbuild-build-depends-fastdnaml-dummy.deb'.
OK
Get:1 file:/«BUILDDIR»/resolver-Kwy_Ck/apt_archive ./ InRelease
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Get:2 file:/«BUILDDIR»/resolver-Kwy_Ck/apt_archive ./ Release [2119 B]
Get:3 file:/«BUILDDIR»/resolver-Kwy_Ck/apt_archive ./ Release.gpg [299 B]
Get:3 file:/«BUILDDIR»/resolver-Kwy_Ck/apt_archive ./ Release.gpg [299 B]
Get:4 file:/«BUILDDIR»/resolver-Kwy_Ck/apt_archive ./ Sources [295 B]
Get:5 file:/«BUILDDIR»/resolver-Kwy_Ck/apt_archive ./ Packages [549 B]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install fastdnaml build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libapt-pkg4.16 libisl13 libprocps4
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
bsdmainutils debhelper dh-strip-nondeterminism file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libcroco3 libffi6
libfile-stripnondeterminism-perl libglib2.0-0 libicu55 libmagic1
libpipeline1 libunistring0 libxml2 man-db po-debconf
Suggested packages:
wamerican | wordlist whois vacation dh-make gettext-doc autopoint
libasprintf-dev libgettextpo-dev groff less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils debhelper dh-strip-nondeterminism file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libcroco3 libffi6
libfile-stripnondeterminism-perl libglib2.0-0 libicu55 libmagic1
libpipeline1 libunistring0 libxml2 man-db po-debconf
sbuild-build-depends-fastdnaml-dummy
0 upgraded, 21 newly installed, 0 to remove and 22 not upgraded.
Need to get 16.4 MB/16.4 MB of archives.
After this operation, 57.4 MB of additional disk space will be used.
Get:1 file:/«BUILDDIR»/resolver-Kwy_Ck/apt_archive ./ sbuild-build-depends-fastdnaml-dummy 0.invalid.0 [806 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-5 [1083 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.6 [177 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libicu55 armhf 55.1-7 [7380 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.3+dfsg1-1 [800 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.46.2-3 [2482 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.56-2 [94.9 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.014-1 [7472 B]
Get:21 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20151225 [830 kB]
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Processing triggers for libc-bin (2.21-6) ...
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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 libpipeline1:armhf (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
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Setting up libicu55:armhf (55.1-7) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1) ...
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25.90.20160101-1 dpkg-dev_1.18.4 g++-5_5.3.1-5+rpi1 gcc-5_5.3.1-5+rpi1 libc6-dev_2.21-6 libstdc++-4.9-dev_4.9.3-10 libstdc++-5-dev_5.3.1-5+rpi1 libstdc++6_5.3.1-5+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.1.10 base-files_9.4+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.25.90.20160101-1 bsdmainutils_9.0.6 bsdutils_1:2.27.1-1 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-5+rpi1 dash_0.5.7-4 debconf_1.5.58 debfoster_2.7-2 debhelper_9.20151225 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-3 dmsetup_2:1.02.114-1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.4.2-10 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-5+rpi1 gcc_4:5.3.1-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-3 gcc-4.9-base_4.9.3-10 gcc-5_5.3.1-5+rpi1 gcc-5-base_5.3.1-5+rpi1 gettext_0.19.7-2 gettext-base_0.19.7-2 gnupg_1.4.20-1 gpgv_1.4.20-1 grep_2.22-1 groff-base_1.22.3-5 gzip_1.6-4 hostname_3.16 init_1.24 init-system-helpers_1.24 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-4+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.10-2+b3 libapt-pkg4.12_1.0.9.10 libapt-pkg4.16_1.0.10.2 libapt-pkg5.0_1.1.10 libarchive-zip-perl_1.56-2 libasan1_4.9.3-10 libasan2_5.3.1-5+rpi1 libatomic1_5.3.1-5+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libblkid1_2.27.1-1 libbz2-1.0_1.0.6-8 libc-bin_2.21-6 libc-dev-bin_2.21-6 libc6_2.21-6 libc6-dev_2.21-6 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-5+rpi1 libcomerr2_1.42.13-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1 libdebconfclient0_0.201 libdevmapper1.02.1_2:1.02.114-1 libdpkg-perl_1.18.4 libdrm2_2.4.65-3 libfakeroot_1.20.2-1 libfdisk1_2.27.1-1 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.014-1 libgc1c2_1:7.4.2-7.3 libgcc-4.9-dev_4.9.3-10 libgcc-5-dev_5.3.1-5+rpi1 libgcc1_1:5.3.1-5+rpi1 libgcrypt20_1.6.4-4 libgdbm3_1.8.3-13.1 libglib2.0-0_2.46.2-3 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-5+rpi1 libgpg-error0_1.21-1 libicu55_55.1-7 libisl13_0.14-2 libisl15_0.15-3 libklibc_2.0.4-4+rpi1 libkmod2_21-1 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-1 libmpc3_1.0.3-1 libmpfr4_3.1.3-2 libncurses5_6.0+20151024-2 libncursesw5_6.0+20151024-2 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_2:8.35-8 libperl5.22_5.22.1-3 libpipeline1_1.4.1-2 libpng12-0_1.2.54-1 libprocps3_2:3.3.9-9 libprocps4_2:3.3.10-2 libprocps5_2:3.3.11-3 libreadline6_6.3-8+b3 libseccomp2_2.2.3-2 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libslang2_2.3.0-2+b1 libsmartcols1_2.27.1-1 libss2_1.42.13-1 libstdc++-4.9-dev_4.9.3-10 libstdc++-5-dev_5.3.1-5+rpi1 libstdc++6_5.3.1-5+rpi1 libsystemd0_228-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20151024-2 libubsan0_5.3.1-5+rpi1 libudev1_228-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1 libxml2_2.9.3+dfsg1-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.2 makedev_2.3.1-93 man-db_2.7.5-1 manpages_3.74-1 mawk_1.3.3-17 mount_2.27.1-1 multiarch-support_2.21-6 nano_2.4.2-1 ncurses-base_6.0+20151024-2 ncurses-bin_6.0+20151024-2 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-3 perl-base_5.22.1-3 perl-modules-5.22_5.22.1-3 po-debconf_1.0.19 procps_2:3.3.11-3 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-fastdnaml-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_228-2 systemd-sysv_228-2 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-2.1 tzdata_2015g-1 udev_228-2 util-linux_2.27.1-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sat Jan 9 17:35:56 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./fastdnaml_1.2.2-11.dsc
dpkg-source: info: extracting fastdnaml in fastdnaml-1.2.2
dpkg-source: info: unpacking fastdnaml_1.2.2.orig.tar.gz
dpkg-source: info: unpacking fastdnaml_1.2.2-11.debian.tar.xz
dpkg-source: info: applying Makefile.patch
dpkg-source: info: applying scripts.patch
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-2b99cbb4-f6b4-4292-8d80-50fb9d199a01
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package fastdnaml
dpkg-buildpackage: source version 1.2.2-11
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build fastdnaml-1.2.2
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j1 clean
make[1]: Entering directory '/«PKGBUILDDIR»'
(cd source; rm -f *.o fastDNAml)
rm -rf tests
rm -f checkpoint.*
make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_clean
make[1]: Entering directory '/«PKGBUILDDIR»'
rm -fr source/fastDNAml
make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_auto_configure -a
dh_auto_build -a
make -j1
make[1]: Entering directory '/«PKGBUILDDIR»'
(cd source; cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security fastDNAml.c -o fastDNAml -lm -Wl,-z,relro)
In file included from fastDNAml.c:207:0:
fastDNAml.h:222:10: warning: conflicting types for built-in function 'malloc'
char *malloc();
^
fastDNAml.c: In function 'freeTopol':
fastDNAml.h:228:28: warning: implicit declaration of function 'free' [-Wimplicit-function-declaration]
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:342:5: note: in expansion of macro 'Free'
Free(tpl->links);
^
fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free'
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:342:5: note: in expansion of macro 'Free'
Free(tpl->links);
^
fastDNAml.h:228:28: note: include '<stdlib.h>' or provide a declaration of 'free'
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:342:5: note: in expansion of macro 'Free'
Free(tpl->links);
^
fastDNAml.c: In function 'freeTreeNode':
fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free'
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:1533:23: note: in expansion of macro 'Free'
if (p->x->lv) Free(p->x->lv);
^
fastDNAml.h:228:28: note: include '<stdlib.h>' or provide a declaration of 'free'
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:1533:23: note: in expansion of macro 'Free'
if (p->x->lv) Free(p->x->lv);
^
fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free'
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:1534:9: note: in expansion of macro 'Free'
Free(p->x);
^
fastDNAml.h:228:28: note: include '<stdlib.h>' or provide a declaration of 'free'
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:1534:9: note: in expansion of macro 'Free'
Free(p->x);
^
fastDNAml.c: In function 'freeTree':
fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free'
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:1560:5: note: in expansion of macro 'Free'
Free(tr->nodep[1]); /* Free the actual nodes */
^
fastDNAml.h:228:28: note: include '<stdlib.h>' or provide a declaration of 'free'
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:1560:5: note: in expansion of macro 'Free'
Free(tr->nodep[1]); /* Free the actual nodes */
^
fastDNAml.c: In function 'setupxarray':
fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free'
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:2028:9: note: in expansion of macro 'Free'
Free(x);
^
fastDNAml.h:228:28: note: include '<stdlib.h>' or provide a declaration of 'free'
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:2028:9: note: in expansion of macro 'Free'
Free(x);
^
fastDNAml.c: In function 'makenewz':
fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free'
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:2604:5: note: in expansion of macro 'Free'
Free(abi);
^
fastDNAml.h:228:28: note: include '<stdlib.h>' or provide a declaration of 'free'
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:2604:5: note: in expansion of macro 'Free'
Free(abi);
^
fastDNAml.c: In function 'readKeyValue':
fastDNAml.c:2886:15: warning: implicit declaration of function 'strlen' [-Wimplicit-function-declaration]
string += strlen(key);
^
fastDNAml.c:2886:15: warning: incompatible implicit declaration of built-in function 'strlen'
fastDNAml.c:2886:15: note: include '<string.h>' or provide a declaration of 'strlen'
fastDNAml.c: In function 'fopen_pid':
fastDNAml.c:3231:47: warning: implicit declaration of function 'getpid' [-Wimplicit-function-declaration]
(void) sprintf(name_pid, "%s.%d", filenm, getpid());
^
In file included from fastDNAml.c:207:0:
fastDNAml.c: In function 'treeOut':
fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free'
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:3683:5: note: in expansion of macro 'Free'
Free(treestr);
^
fastDNAml.h:228:28: note: include '<stdlib.h>' or provide a declaration of 'free'
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:3683:5: note: in expansion of macro 'Free'
Free(treestr);
^
fastDNAml.c: In function 'cmpBestTrees':
fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free'
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:4535:5: note: in expansion of macro 'Free'
Free(log_f0);
^
fastDNAml.h:228:28: note: include '<stdlib.h>' or provide a declaration of 'free'
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:4535:5: note: in expansion of macro 'Free'
Free(log_f0);
^
fastDNAml.c: In function 'makeDenovoTree':
fastDNAml.h:228:28: warning: incompatible implicit declaration of built-in function 'free'
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:4765:5: note: in expansion of macro 'Free'
Free(enterorder);
^
fastDNAml.h:228:28: note: include '<stdlib.h>' or provide a declaration of 'free'
#define Free(x) (void) free((char *) (x)) /* BSD */
^
fastDNAml.c:4765:5: note: in expansion of macro 'Free'
Free(enterorder);
^
fastDNAml.c: At top level:
fastDNAml.c:4775:3: warning: return type defaults to 'int' [-Wimplicit-int]
main ()
^
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_auto_test -a
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_installdirs -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/«PKGBUILDDIR»'
# do nothing
make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_install
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_install
cp -a docs/fastDNAml_doc_1.2.txt `pwd`/debian/`dh_listpackages`/usr/share/`dh_listpackages`/fastdnaml_help
# the scripts have to be executable thus mentioning these in debian/install is not enough
cp -a scripts/* `pwd`/debian/`dh_listpackages`/usr/lib/`dh_listpackages`/bin
chmod 755 `pwd`/debian/`dh_listpackages`/usr/lib/`dh_listpackages`/bin/*
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_installmenu -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/fastdnaml/usr/bin/fastDNAml was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'fastdnaml-dbgsym' in '../fastdnaml-dbgsym_1.2.2-11_armhf.deb'.
dpkg-deb: building package 'fastdnaml' in '../fastdnaml_1.2.2-11_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../fastdnaml_1.2.2-11_armhf.changes
dpkg-genchanges: warning: package fastdnaml-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build fastdnaml-1.2.2
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20160121-0559
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
fastdnaml_1.2.2-11_armhf.changes:
─────────────────────────────────
Format: 1.8
Date: Sat, 09 Jan 2016 18:35:08 +0100
Source: fastdnaml
Binary: fastdnaml
Architecture: armhf
Version: 1.2.2-11
Distribution: stretch-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
fastdnaml - Tool for construction of phylogenetic trees of DNA sequences
Changes:
fastdnaml (1.2.2-11) unstable; urgency=low
.
* debian/upstream/metadata: Add citation information
* cme fix dpkg-control
* debhelper 9
* DEP5
* add fake debian/watch
* propagate hardening options
Checksums-Sha1:
1642bbccb5168fced3742b28bdd398d20c874348 47986 fastdnaml-dbgsym_1.2.2-11_armhf.deb
b3d8eb507fa11612f087100e7f9c8258e2ec55b3 53840 fastdnaml_1.2.2-11_armhf.deb
Checksums-Sha256:
41191e142236ea37553dbf7347216d34994064d6d86389d3a8b8b5fe144653eb 47986 fastdnaml-dbgsym_1.2.2-11_armhf.deb
62affcf8324cf0a3ddff448eb87c5d78e814ffa1f9fb85e0df1dd380993e55be 53840 fastdnaml_1.2.2-11_armhf.deb
Files:
1f45caa21596629faf7f69f48ef152bf 47986 debug extra fastdnaml-dbgsym_1.2.2-11_armhf.deb
b80dc67e4b8d6411e45a11f8639fce32 53840 science optional fastdnaml_1.2.2-11_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
fastdnaml-dbgsym_1.2.2-11_armhf.deb
───────────────────────────────────
new debian package, version 2.0.
size 47986 bytes: control archive=509 bytes.
451 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: fastdnaml-dbgsym
Source: fastdnaml
Version: 1.2.2-11
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 64
Depends: fastdnaml (= 1.2.2-11)
Section: debug
Priority: extra
Homepage: ftp://ftp.bio.indiana.edu/molbio/evolve/fastdnaml/fastDNAml.html
Description: Debug symbols for fastdnaml
Auto-Built-Package: debug-symbols
Build-Ids: 12d4e0e25b783fd0a039b2865072b7fd58844918
drwxr-xr-x root/root 0 2016-01-21 05:59 ./
drwxr-xr-x root/root 0 2016-01-21 05:59 ./usr/
drwxr-xr-x root/root 0 2016-01-21 05:59 ./usr/lib/
drwxr-xr-x root/root 0 2016-01-21 05:59 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-01-21 05:59 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-01-21 05:59 ./usr/lib/debug/.build-id/12/
-rw-r--r-- root/root 54708 2016-01-21 05:59 ./usr/lib/debug/.build-id/12/d4e0e25b783fd0a039b2865072b7fd58844918.debug
drwxr-xr-x root/root 0 2016-01-21 05:59 ./usr/share/
drwxr-xr-x root/root 0 2016-01-21 05:59 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-01-21 05:59 ./usr/share/doc/fastdnaml-dbgsym -> fastdnaml
fastdnaml_1.2.2-11_armhf.deb
────────────────────────────
new debian package, version 2.0.
size 53840 bytes: control archive=2928 bytes.
978 bytes, 22 lines control
5023 bytes, 70 lines md5sums
185 bytes, 7 lines * postinst #!/bin/sh
160 bytes, 5 lines * postrm #!/bin/sh
Package: fastdnaml
Version: 1.2.2-11
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 219
Depends: libc6 (>= 2.7)
Suggests: phylip
Section: science
Priority: optional
Homepage: ftp://ftp.bio.indiana.edu/molbio/evolve/fastdnaml/fastDNAml.html
Description: Tool for construction of phylogenetic trees of DNA sequences
fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML
(part of his PHYLIP package). Users should consult the documentation for
DNAML before using this program.
.
fastDNAml is an attempt to solve the same problem as DNAML, but to do so
faster and using less memory, so that larger trees and/or more bootstrap
replicates become tractable. Much of fastDNAml is merely a recoding of the
PHYLIP 3.3 DNAML program from PASCAL to C.
.
Note that the homepage of this program is not available any more and so
this program will probably not see any further updates.
drwxr-xr-x root/root 0 2016-01-21 05:59 ./
drwxr-xr-x root/root 0 2016-01-21 05:58 ./usr/
drwxr-xr-x root/root 0 2016-01-21 05:59 ./usr/bin/
-rwxr-xr-x root/root 50764 2016-01-21 05:59 ./usr/bin/fastDNAml
-rwxr-xr-x root/root 420 2013-09-12 08:59 ./usr/bin/fastDNAml-util
drwxr-xr-x root/root 0 2016-01-21 05:58 ./usr/lib/
drwxr-xr-x root/root 0 2016-01-21 05:58 ./usr/lib/fastdnaml/
drwxr-xr-x root/root 0 2016-01-21 05:58 ./usr/lib/fastdnaml/bin/
-rwxr-xr-x root/root 857 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/ae2dnaml
-rwxr-xr-x root/root 216 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/bootstrap
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-rwxr-xr-x root/root 140 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/categories_file
-rwxr-xr-x root/root 179 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/checkpoint_summary
-rwxr-xr-x root/root 145 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/clean_checkpoints
-rwxr-xr-x root/root 3504 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/clean_jumbles
-rwxr-xr-x root/root 183 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/dnaml_progress
-rwxr-xr-x root/root 6087 2016-01-21 05:58 ./usr/lib/fastdnaml/bin/fastDNAml_boot
-rwxr-xr-x root/root 3779 2016-01-21 05:58 ./usr/lib/fastdnaml/bin/fastDNAml_loop
-rwxr-xr-x root/root 225 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/frequencies
-rwxr-xr-x root/root 267 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/global
-rwxr-xr-x root/root 1369 2016-01-21 05:58 ./usr/lib/fastdnaml/bin/iterate_rates
-rwxr-xr-x root/root 213 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/jumble
-rwxr-xr-x root/root 172 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/min_info
-rwxr-xr-x root/root 172 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/n_categories
-rwxr-xr-x root/root 124 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/n_files
-rwxr-xr-x root/root 759 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/out.PID
-rwxr-xr-x root/root 162 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/outgroup
-rwxr-xr-x root/root 134 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/printdata
-rwxr-xr-x root/root 133 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/quickadd
-rwxr-xr-x root/root 688 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/restart
-rwxr-xr-x root/root 107 2016-01-21 05:58 ./usr/lib/fastdnaml/bin/scores
-rwxr-xr-x root/root 174 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/transition
-rwxr-xr-x root/root 272 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/treefile
-rwxr-xr-x root/root 75 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/treefile2prolog
-rwxr-xr-x root/root 370 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/trees2NEXUS
-rwxr-xr-x root/root 72 2016-01-21 05:58 ./usr/lib/fastdnaml/bin/trees2prolog
-rwxr-xr-x root/root 136 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/userlengths
-rwxr-xr-x root/root 270 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/usertree
-rwxr-xr-x root/root 270 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/usertrees
-rwxr-xr-x root/root 161 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/weights
-rwxr-xr-x root/root 187 2000-01-03 15:58 ./usr/lib/fastdnaml/bin/weights_categories
drwxr-xr-x root/root 0 2016-01-21 05:58 ./usr/share/
drwxr-xr-x root/root 0 2016-01-21 05:58 ./usr/share/doc-base/
-rw-r--r-- root/root 350 2013-09-12 08:59 ./usr/share/doc-base/fastdnaml
-rw-r--r-- root/root 526 2013-09-12 08:59 ./usr/share/doc-base/fastdnaml-scripts
drwxr-xr-x root/root 0 2016-01-21 05:58 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-01-21 05:59 ./usr/share/doc/fastdnaml/
-rw-r--r-- root/root 619 2013-09-12 08:59 ./usr/share/doc/fastdnaml/README.Debian
-rw-r--r-- root/root 2153 2016-01-09 17:35 ./usr/share/doc/fastdnaml/changelog.Debian.gz
-rw-r--r-- root/root 1272 2016-01-09 17:29 ./usr/share/doc/fastdnaml/copyright
drwxr-xr-x root/root 0 2016-01-21 05:59 ./usr/share/doc/fastdnaml/examples/
-rw-r--r-- root/root 2139 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5.out
-rw-r--r-- root/root 708 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5.phy
-rw-r--r-- root/root 2189 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5B.out
-rw-r--r-- root/root 717 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5B.phy
-rw-r--r-- root/root 2554 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5C.out
-rw-r--r-- root/root 903 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5C.phy
-rw-r--r-- root/root 2092 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5GRT.out
-rw-r--r-- root/root 796 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5GRT.phy
-rw-r--r-- root/root 2139 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5I.out
-rw-r--r-- root/root 710 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5I.phy
-rw-r--r-- root/root 2139 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5I2.out
-rw-r--r-- root/root 800 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5I2.phy
-rw-r--r-- root/root 2172 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5J.out
-rw-r--r-- root/root 717 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5J.phy
-rw-r--r-- root/root 2370 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5R.out
-rw-r--r-- root/root 780 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5R.phy
-rw-r--r-- root/root 2161 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5TF.out
-rw-r--r-- root/root 743 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5TF.phy
-rw-r--r-- root/root 1297 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5U.out.gz
-rw-r--r-- root/root 941 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5U.phy
-rw-r--r-- root/root 2157 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5W.out
-rw-r--r-- root/root 851 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5W.phy
-rw-r--r-- root/root 2503 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5WC.out
-rw-r--r-- root/root 1045 2000-01-03 15:58 ./usr/share/doc/fastdnaml/examples/test5WC.phy
drwxr-xr-x root/root 0 2011-12-06 11:04 ./usr/share/doc/fastdnaml/examples/tests/
-rw-r--r-- root/root 635 2013-09-12 08:59 ./usr/share/doc/fastdnaml/examples/tests/Makefile
-rw-r--r-- root/root 1246 2013-09-12 08:59 ./usr/share/doc/fastdnaml/examples/tests/fastdnaml.data
lrwxrwxrwx root/root 0 2016-01-21 05:59 ./usr/share/doc/fastdnaml/fastDNAml_doc_1.2.txt -> ../../fastdnaml/fastdnaml_help
-rw-r--r-- root/root 6980 2000-01-03 15:58 ./usr/share/doc/fastdnaml/fastDNAml_scripts.txt.gz
drwxr-xr-x root/root 0 2016-01-21 05:58 ./usr/share/fastdnaml/
-rw-r--r-- root/root 34150 2000-01-03 15:58 ./usr/share/fastdnaml/fastdnaml_help
drwxr-xr-x root/root 0 2016-01-21 05:58 ./usr/share/man/
drwxr-xr-x root/root 0 2016-01-21 05:59 ./usr/share/man/man1/
lrwxrwxrwx root/root 0 2016-01-21 05:59 ./usr/share/man/man1/fastDNAml-util.1.gz -> fastDNAml.1.gz
-rw-r--r-- root/root 742 2016-01-21 05:58 ./usr/share/man/man1/fastDNAml.1.gz
drwxr-xr-x root/root 0 2016-01-21 05:58 ./usr/share/menu/
-rw-r--r-- root/root 191 2013-09-12 08:59 ./usr/share/menu/fastdnaml
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 1376
Build-Time: 40
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 171
Job: fastdnaml_1.2.2-11
Machine Architecture: armhf
Package: fastdnaml
Package-Time: 253
Source-Version: 1.2.2-11
Space: 1376
Status: successful
Version: 1.2.2-11
────────────────────────────────────────────────────────────────────────────────
Finished at 20160121-0559
Build needed 00:04:13, 1376k disc space