fastqtl →
2.184+dfsg-6 →
armhf → 2018-07-21 05:18:20
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| fastqtl 2.184+dfsg-6 (armhf) Sat, 21 Jul 2018 04:39:56 +0000 |
+==============================================================================+
Package: fastqtl
Version: 2.184+dfsg-6
Source Version: 2.184+dfsg-6
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-0959bb1c-382d-4660-80a6-9620220bb5bd' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.9 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.7 MB]
Fetched 23.6 MB in 29s (818 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'fastqtl' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/fastqtl.git
Please use:
git clone https://salsa.debian.org/med-team/fastqtl.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 17.1 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main fastqtl 2.184+dfsg-6 (dsc) [2186 B]
Get:2 http://172.17.0.1/private buster-staging/main fastqtl 2.184+dfsg-6 (tar) [17.1 MB]
Get:3 http://172.17.0.1/private buster-staging/main fastqtl 2.184+dfsg-6 (diff) [19.2 kB]
Fetched 17.1 MB in 5s (3291 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/fastqtl-REJ1E1/fastqtl-2.184+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/fastqtl-REJ1E1' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-nlfS8V/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-nlfS8V/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-nlfS8V/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-nlfS8V/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-nlfS8V/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-nlfS8V/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-nlfS8V/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-nlfS8V/apt_archive ./ Packages [434 B]
Fetched 2110 B in 1s (3257 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core 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:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
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 50 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-nlfS8V/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15760 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libgsl-dev, r-mathlib, zlib1g-dev, libblas-dev, libeigen3-dev, libhts-dev
Filtered Build-Depends: debhelper (>= 11~), libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libgsl-dev, r-mathlib, zlib1g-dev, libblas-dev, libeigen3-dev, libhts-dev
dpkg-deb: building package 'sbuild-build-depends-fastqtl-dummy' in '/<<BUILDDIR>>/resolver-nlfS8V/apt_archive/sbuild-build-depends-fastqtl-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-fastqtl-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-nlfS8V/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-nlfS8V/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-nlfS8V/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-nlfS8V/apt_archive ./ Sources [551 B]
Get:5 copy:/<<BUILDDIR>>/resolver-nlfS8V/apt_archive ./ Packages [632 B]
Fetched 2516 B in 1s (3836 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install fastqtl 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:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libnss-systemd
libpam-systemd libsasl2-modules openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base icu-devtools intltool-debian
libarchive-zip-perl libblas-dev libblas3 libboost-dev libboost-iostreams-dev
libboost-iostreams1.62-dev libboost-iostreams1.62.0
libboost-program-options-dev libboost-program-options1.62-dev
libboost-program-options1.62.0 libboost-regex1.62-dev libboost-regex1.62.0
libboost1.62-dev libbsd0 libcroco3 libcurl3-gnutls libeigen3-dev libelf1
libfile-stripnondeterminism-perl libfreetype6 libgfortran4
libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin libglib2.0-data
libglib2.0-dev libglib2.0-dev-bin libgraphite2-3 libgraphite2-dev libgsl-dev
libgsl23 libgslcblas0 libgssapi-krb5-2 libharfbuzz-dev libharfbuzz-gobject0
libharfbuzz-icu0 libharfbuzz0b libhts-dev libhts2 libicu-dev
libicu-le-hb-dev libicu-le-hb0 libicu60 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14
libpcre16-3 libpcre3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1
libpsl5 libpython3-stdlib libpython3.6-minimal libpython3.6-stdlib librtmp1
libsigsegv2 libssh2-1 libtimedate-perl libtool libxml2 m4 man-db
mime-support pkg-config po-debconf python3 python3-distutils python3-lib2to3
python3-minimal python3.6 python3.6-minimal r-mathlib zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
liblapack-doc libboost-doc libboost1.62-doc libboost-atomic1.62-dev
libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev
libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev
libboost-filesystem1.62-dev libboost-graph1.62-dev
libboost-graph-parallel1.62-dev libboost-locale1.62-dev libboost-log1.62-dev
libboost-math1.62-dev libboost-mpi1.62-dev libboost-mpi-python1.62-dev
libboost-python1.62-dev libboost-random1.62-dev
libboost-serialization1.62-dev libboost-signals1.62-dev
libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev
libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev
libboost1.62-tools-dev libmpfrc++-dev libntl-dev libeigen3-doc libmrpt-dev
libglib2.0-doc libgraphite2-utils gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info
| gsl-ref-html krb5-doc krb5-user icu-doc liblzma-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv python3.6-venv
python3.6-doc binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl shared-mime-info xdg-user-dirs
krb5-locales publicsuffix libltdl-dev libmail-sendmail-perl r-base-core
r-base-dev
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base icu-devtools intltool-debian
libarchive-zip-perl libblas-dev libblas3 libboost-dev libboost-iostreams-dev
libboost-iostreams1.62-dev libboost-iostreams1.62.0
libboost-program-options-dev libboost-program-options1.62-dev
libboost-program-options1.62.0 libboost-regex1.62-dev libboost-regex1.62.0
libboost1.62-dev libbsd0 libcroco3 libcurl3-gnutls libeigen3-dev libelf1
libfile-stripnondeterminism-perl libfreetype6 libgfortran4
libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin libglib2.0-data
libglib2.0-dev libglib2.0-dev-bin libgraphite2-3 libgraphite2-dev libgsl-dev
libgsl23 libgslcblas0 libgssapi-krb5-2 libharfbuzz-dev libharfbuzz-gobject0
libharfbuzz-icu0 libharfbuzz0b libhts-dev libhts2 libicu-dev
libicu-le-hb-dev libicu-le-hb0 libicu60 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14
libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpsl5
libpython3-stdlib libpython3.6-minimal libpython3.6-stdlib librtmp1
libsigsegv2 libssh2-1 libtimedate-perl libtool libxml2 m4 man-db
mime-support pkg-config po-debconf python3 python3-distutils python3-lib2to3
python3-minimal python3.6 python3.6-minimal r-mathlib
sbuild-build-depends-fastqtl-dummy zlib1g-dev
The following packages will be upgraded:
libpcre3
1 upgraded, 98 newly installed, 0 to remove and 49 not upgraded.
Need to get 60.7 MB/62.3 MB of archives.
After this operation, 309 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-nlfS8V/apt_archive ./ sbuild-build-depends-fastqtl-dummy 0.invalid.0 [920 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libpython3.6-minimal armhf 3.6.6-1 [565 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf python3.6-minimal armhf 3.6.6-1 [1383 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.6.5-3 [36.2 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.61 [37.1 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libpython3.6-stdlib armhf 3.6.6-1 [1638 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf python3.6 armhf 3.6.6-1 [234 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.6.5-3 [19.7 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.6.5-3 [24.1 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libpcre3 armhf 2:8.39-10 [313 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.33-3 [234 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.33-3 [106 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.33-3 [64.7 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.042-1 [20.1 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.042-1 [12.1 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.8.2-2 [832 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.5 [981 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libgirepository-1.0-1 armhf 1.56.1-1 [77.6 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf gir1.2-glib-2.0 armhf 1.56.1-1 [142 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-gobject0 armhf 1.8.2-2 [626 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf gir1.2-harfbuzz-0.0 armhf 1.8.2-2 [633 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 60.2-6 [166 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-19 [191 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-1 [103 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.8.0-1 [111 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-6 [7004 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.62.0.1+b8 [3918 B]
Get:54 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.62.0 armhf 1.62.0+dfsg-6 [233 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-icu0 armhf 1.8.2-2 [619 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libglib2.0-data all 2.56.1-2 [2671 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libglib2.0-bin armhf 2.56.1-2 [1694 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf python3-lib2to3 all 3.6.6-1 [79.1 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf python3-distutils all 3.6.6-1 [144 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev-bin armhf 2.56.1-2 [1733 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-10 [234 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-10 [226 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-10 [150 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-10 [561 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev armhf 2.56.1-2 [2807 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libgraphite2-dev armhf 1.3.11-2 [22.2 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-dev armhf 1.8.2-2 [919 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb-dev armhf 1.0.3+git161113-5 [28.3 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 60.2-6 [8643 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.62-dev armhf 1.62.0+dfsg-6 [327 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62.0 armhf 1.62.0+dfsg-6 [49.3 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62-dev armhf 1.62.0+dfsg-6 [58.5 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams-dev armhf 1.62.0.1+b8 [3694 B]
Get:75 http://172.17.0.1/private buster-staging/main armhf libboost-program-options1.62.0 armhf 1.62.0+dfsg-6 [137 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libboost-program-options1.62-dev armhf 1.62.0+dfsg-6 [180 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libboost-program-options-dev armhf 1.62.0.1+b8 [3716 B]
Get:78 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.32.0-1 [71.7 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-1 [52.5 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.60.0-2 [279 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libeigen3-dev all 3.3.4-4 [841 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libgslcblas0 armhf 2.5+dfsg-4 [77.6 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libgsl23 armhf 2.5+dfsg-4 [697 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libgsl-dev armhf 2.5+dfsg-4 [885 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.7-2 [259 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.7-2 [329 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf r-mathlib armhf 3.5.1-1 [1799 kB]
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up gir1.2-glib-2.0:armhf (1.56.1-1) ...
Setting up libssh2-1:armhf (1.8.0-1) ...
Setting up libglib2.0-data (2.56.1-2) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
Setting up dwz (0.12-2) ...
Setting up autotools-dev (20180224.1) ...
Setting up libpcrecpp0v5:armhf (2:8.39-10) ...
Setting up libpcre32-3:armhf (2:8.39-10) ...
Setting up libpcre16-3:armhf (2:8.39-10) ...
Setting up libboost-dev:armhf (1.62.0.1+b8) ...
Setting up liblzma-dev:armhf (5.2.2-1.3) ...
Setting up libkeyutils1:armhf (1.5.9-9.2) ...
Setting up bsdmainutils (11.1.2) ...
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 libgslcblas0:armhf (2.5+dfsg-4) ...
Setting up libglib2.0-bin (2.56.1-2) ...
Setting up libgraphite2-dev:armhf (1.3.11-2) ...
Setting up autopoint (0.19.8.1-6) ...
Setting up libmpdec2:armhf (2.4.2-2) ...
Setting up libboost-program-options-dev:armhf (1.62.0.1+b8) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (0.042-1) ...
Setting up libpython3.6-stdlib:armhf (3.6.6-1) ...
Setting up libpcre3-dev:armhf (2:8.39-10) ...
Setting up python3.6 (3.6.6-1) ...
Setting up libgsl23:armhf (2.5+dfsg-4) ...
Setting up libblas-dev:armhf (3.8.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up libgsl-dev (2.5+dfsg-4) ...
Setting up libeigen3-dev (3.3.4-4) ...
Setting up libharfbuzz0b:armhf (1.8.2-2) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.33-3) ...
Setting up libkrb5support0:armhf (1.16-2) ...
Setting up automake (1:1.15.1-3.1) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libharfbuzz-gobject0:armhf (1.8.2-2) ...
Setting up libtool (2.4.6-2.1) ...
Setting up libpython3-stdlib:armhf (3.6.5-3) ...
Setting up libk5crypto3:armhf (1.16-2) ...
Setting up python3 (3.6.5-3) ...
Setting up gir1.2-harfbuzz-0.0:armhf (1.8.2-2) ...
Setting up libkrb5-3:armhf (1.16-2) ...
Setting up python3-lib2to3 (3.6.6-1) ...
Setting up python3-distutils (3.6.6-1) ...
Setting up libglib2.0-dev-bin (2.56.1-2) ...
Setting up libglib2.0-dev:armhf (2.56.1-2) ...
Setting up libgssapi-krb5-2:armhf (1.16-2) ...
Setting up libcurl3-gnutls:armhf (7.60.0-2) ...
Setting up libhts2:armhf (1.7-2) ...
Setting up libhts-dev:armhf (1.7-2) ...
Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ...
Setting up libicu60:armhf (60.2-6) ...
Setting up libharfbuzz-icu0:armhf (1.8.2-2) ...
Setting up dh-autoreconf (19) ...
Setting up libboost-regex1.62.0:armhf (1.62.0+dfsg-6) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up dh-strip-nondeterminism (0.042-1) ...
Setting up icu-devtools (60.2-6) ...
Setting up libharfbuzz-dev:armhf (1.8.2-2) ...
Setting up libicu-le-hb-dev:armhf (1.0.3+git161113-5) ...
Setting up gettext (0.19.8.1-6) ...
Setting up libicu-dev (60.2-6) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.20) ...
Setting up libboost-regex1.62-dev:armhf (1.62.0+dfsg-6) ...
Setting up libboost-iostreams1.62-dev:armhf (1.62.0+dfsg-6) ...
Setting up libboost-iostreams-dev:armhf (1.62.0.1+b8) ...
Setting up debhelper (11.3.5) ...
Setting up sbuild-build-depends-fastqtl-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.30-21+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-19 gcc-7_7.3.0-19 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-19 libstdc++6_8.1.0-8+rpi1 linux-libc-dev_4.16.12-1+rpi1
Package versions: adduser_3.117 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3 binutils_2.30-21+rpi1 binutils-arm-linux-gnueabihf_2.30-21+rpi1 binutils-common_2.30-21+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32-0.1 build-essential_12.5 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.3.0-3+rpi1 cpp-7_7.3.0-19 dash_0.5.8-2.10 dbus_1.12.8-3 dbus-user-session_1.12.8-3 debconf_1.5.67 debhelper_11.3.5 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dirmngr_2.2.8-1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.2-1 e2fsprogs_1.44.2-1 e2fsprogs-l10n_1.44.2-1 fakeroot_1.22-2 fdisk_2.32-0.1 file_1:5.33-3 findutils_4.6.0+git+20171230-2 g++_4:7.3.0-3+rpi1 g++-7_7.3.0-19 gcc_4:7.3.0-3+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b7 gcc-5-base_5.5.0-8 gcc-7_7.3.0-19 gcc-7-base_7.3.0-19 gcc-8-base_8.1.0-8+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gir1.2-glib-2.0_1.56.1-1 gir1.2-harfbuzz-0.0_1.8.2-2 gnupg_2.2.8-1 gnupg-agent_2.2.8-1 gnupg-l10n_2.2.8-1 gnupg-utils_2.2.8-1 gpg_2.2.8-1 gpg-agent_2.2.8-1 gpg-wks-client_2.2.8-1 gpg-wks-server_2.2.8-1 gpgconf_2.2.8-1 gpgsm_2.2.8-1 gpgv_2.2.8-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hostname_3.20 icu-devtools_60.2-6 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-4 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-2 libasan4_7.3.0-19 libassuan0_2.5.1-2 libatomic1_8.1.0-8+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.30-21+rpi1 libblas-dev_3.8.0-1 libblas3_3.8.0-1 libblkid1_2.32-0.1 libboost-dev_1.62.0.1+b8 libboost-iostreams-dev_1.62.0.1+b8 libboost-iostreams1.62-dev_1.62.0+dfsg-6 libboost-iostreams1.62.0_1.62.0+dfsg-6 libboost-program-options-dev_1.62.0.1+b8 libboost-program-options1.62-dev_1.62.0+dfsg-6 libboost-program-options1.62.0_1.62.0+dfsg-6 libboost-regex1.62-dev_1.62.0+dfsg-6 libboost-regex1.62.0_1.62.0+dfsg-6 libboost1.62-dev_1.62.0+dfsg-6 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3+rpi1 libc-dev-bin_2.27-3+rpi1 libc6_2.27-3+rpi1 libc6-dev_2.27-3+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-8+rpi1 libcilkrts5_7.3.0-19 libcom-err2_1.44.2-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.60.0-2 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.8-3 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.92-1+rpi1 libdrm2_2.4.92-1+rpi1 libeigen3-dev_3.3.4-4 libelf1_0.170-0.5 libexpat1_2.2.5-3 libext2fs2_1.44.2-1 libfakeroot_1.22-2 libfdisk1_2.32-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libfreetype6_2.8.1-2 libgcc-7-dev_7.3.0-19 libgcc1_1:8.1.0-8+rpi1 libgcrypt20_1.8.3-1 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgfortran4_7.3.0-19 libgirepository-1.0-1_1.56.1-1 libglib2.0-0_2.56.1-2 libglib2.0-bin_2.56.1-2 libglib2.0-data_2.56.1-2 libglib2.0-dev_2.56.1-2 libglib2.0-dev-bin_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8.1.0-8+rpi1 libgpg-error0_1.31-1 libgraphite2-3_1.3.11-2 libgraphite2-dev_1.3.11-2 libgsl-dev_2.5+dfsg-4 libgsl23_2.5+dfsg-4 libgslcblas0_2.5+dfsg-4 libgssapi-krb5-2_1.16-2 libharfbuzz-dev_1.8.2-2 libharfbuzz-gobject0_1.8.2-2 libharfbuzz-icu0_1.8.2-2 libharfbuzz0b_1.8.2-2 libhogweed4_3.4-1 libhts-dev_1.7-2 libhts2_1.7-2 libicu-dev_60.2-6 libicu-le-hb-dev_1.0.3+git161113-5 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl19_0.19-1 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.2 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 liblz4-1_1.8.2-1+rpi1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-3 libmagic1_1:5.33-3 libmount1_2.32-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-1 libncurses5_6.1+20180210-4 libncurses6_6.1+20180210-4 libncursesw5_6.1+20180210-4 libncursesw6_6.1+20180210-4 libnettle6_3.4-1 libnghttp2-14_1.32.0-1 libnpth0_1.5-4 libnss-systemd_238-4 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-4 libpam0g_1.1.8-3.7 libpcre16-3_2:8.39-10 libpcre3_2:8.39-10 libpcre3-dev_2:8.39-10 libpcre32-3_2:8.39-10 libpcrecpp0v5_2:8.39-10 libperl5.24_5.24.1-7 libperl5.26_5.26.2-6 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpng16-16_1.6.34-1 libprocps7_2:3.3.15-2 libpsl5_0.20.2-1 libpython3-stdlib_3.6.5-3 libpython3.6-minimal_3.6.6-1 libpython3.6-stdlib_3.6.6-1 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-2 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32-0.1 libsqlite3-0_3.24.0-1 libss2_1.44.2-1 libssh2-1_1.8.0-1 libssl1.1_1.1.0h-4 libstdc++-7-dev_7.3.0-19 libstdc++6_8.1.0-8+rpi1 libsystemd0_238-4 libtasn1-6_4.13-3 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-4 libtinfo6_6.1+20180210-4 libtool_2.4.6-2.1 libubsan0_7.3.0-19 libudev1_238-4 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32-0.1 libxml2_2.9.4+dfsg1-7 libzstd1_1.3.4+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.16.12-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.3-2 mawk_1.3.3-17 mime-support_3.61 mount_2.32-0.1 multiarch-support_2.27-3+rpi1 nano_2.9.8-1 ncurses-base_6.1+20180210-4 ncurses-bin_6.1+20180210-4 netbase_5.4 openssl_1.1.0h-4 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-6 perl-base_5.26.2-6 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-6 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 python3_3.6.5-3 python3-distutils_3.6.6-1 python3-lib2to3_3.6.6-1 python3-minimal_3.6.5-3 python3.6_3.6.6-1 python3.6-minimal_3.6.6-1 r-mathlib_3.5.1-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-fastqtl-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-4 systemd-sysv_238-4 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 udev_238-4 util-linux_2.32-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Jul 18 19:00:13 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./fastqtl_2.184+dfsg-6.dsc
dpkg-source: info: extracting fastqtl in /<<BUILDDIR>>/fastqtl-2.184+dfsg
dpkg-source: info: unpacking fastqtl_2.184+dfsg.orig.tar.xz
dpkg-source: info: unpacking fastqtl_2.184+dfsg-6.debian.tar.xz
dpkg-source: info: applying 01_Makefile_dynamic_hardenings.patch
dpkg-source: info: applying 02_Replace_libtabix_by_libhts.patch
dpkg-source: info: applying 03_Reproducible_builds.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-0959bb1c-382d-4660-80a6-9620220bb5bd
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package fastqtl
dpkg-buildpackage: info: source version 2.184+dfsg-6
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build fastqtl-2.184+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/fastqtl-2.184+dfsg'
rm -f obj/*.o bin/fastQTL
make[1]: Leaving directory '/<<BUILDDIR>>/fastqtl-2.184+dfsg'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/fastqtl-2.184+dfsg'
mkdir -p /<<BUILDDIR>>/fastqtl-2.184+dfsg/obj/
mkdir -p /<<BUILDDIR>>/fastqtl-2.184+dfsg/bin/
/usr/bin/make CXXFLAGS='-g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security'
make[2]: Entering directory '/<<BUILDDIR>>/fastqtl-2.184+dfsg'
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisMapping.o -c src/analysisMapping.cpp -Isrc
In file included from src/analysisMapping.cpp:17:0:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:170:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:171:2: note: here
case 2: sum0 += vec1[i+1] * vec2[i+1];
^~~~
src/data.h:171:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:172:2: note: here
case 1: sum0 += vec1[i+0] * vec2[i+0];
^~~~
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisNominal.o -c src/analysisNominal.cpp -Isrc
In file included from src/analysisNominal.cpp:17:0:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:170:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:171:2: note: here
case 2: sum0 += vec1[i+1] * vec2[i+1];
^~~~
src/data.h:171:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:172:2: note: here
case 1: sum0 += vec1[i+0] * vec2[i+0];
^~~~
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisPermutation.o -c src/analysisPermutation.cpp -Isrc
In file included from src/analysisPermutation.cpp:17:0:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:170:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:171:2: note: here
case 2: sum0 += vec1[i+1] * vec2[i+1];
^~~~
src/data.h:171:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:172:2: note: here
case 1: sum0 += vec1[i+0] * vec2[i+0];
^~~~
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisPermutationInteraction.o -c src/analysisPermutationInteraction.cpp -Isrc
In file included from src/analysisPermutationInteraction.cpp:17:0:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:170:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:171:2: note: here
case 2: sum0 += vec1[i+1] * vec2[i+1];
^~~~
src/data.h:171:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:172:2: note: here
case 1: sum0 += vec1[i+0] * vec2[i+0];
^~~~
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisPermutationPerGroup.o -c src/analysisPermutationPerGroup.cpp -Isrc
In file included from src/analysisPermutationPerGroup.cpp:17:0:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:170:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:171:2: note: here
case 2: sum0 += vec1[i+1] * vec2[i+1];
^~~~
src/data.h:171:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:172:2: note: here
case 1: sum0 += vec1[i+0] * vec2[i+0];
^~~~
In file included from /usr/include/c++/7/vector:69:0,
from src/utils/utils.h:46,
from src/data.h:25,
from src/analysisPermutationPerGroup.cpp:17:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
/usr/include/c++/7/bits/vector.tcc: In member function 'void data::runPermutationPerGroup(std::__cxx11::string, std::vector<int>)':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisPermutationSequence.o -c src/analysisPermutationSequence.cpp -Isrc
In file included from src/analysisPermutationSequence.cpp:17:0:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:170:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:171:2: note: here
case 2: sum0 += vec1[i+1] * vec2[i+1];
^~~~
src/data.h:171:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:172:2: note: here
case 1: sum0 += vec1[i+0] * vec2[i+0];
^~~~
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/commands.o -c src/commands.cpp -Isrc
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/df.o -c src/df.cpp -Isrc
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/fastQTL.o -c src/fastQTL.cpp -Isrc
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/management.o -c src/management.cpp -Isrc
In file included from src/management.cpp:20:0:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:170:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:171:2: note: here
case 2: sum0 += vec1[i+1] * vec2[i+1];
^~~~
src/data.h:171:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:172:2: note: here
case 1: sum0 += vec1[i+0] * vec2[i+0];
^~~~
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/mle.o -c src/mle.cpp -Isrc
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readCovariates.o -c src/readCovariates.cpp -Isrc
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readGenotypes.o -c src/readGenotypes.cpp -Isrc
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readGroups.o -c src/readGroups.cpp -Isrc
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readInclusionsExclusions.o -c src/readInclusionsExclusions.cpp -Isrc
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readInteractions.o -c src/readInteractions.cpp -Isrc
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readPhenotypes.o -c src/readPhenotypes.cpp -Isrc
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readThresholds.o -c src/readThresholds.cpp -Isrc
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/residualizer.o -c src/residualizer.cpp -Isrc
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/tabix.o -c src/utils/tabix.cpp -Isrc
src/utils/tabix.cpp: In constructor 'Tabix::Tabix(std::__cxx11::string&)':
src/utils/tabix.cpp:17:32: warning: 'int bgzf_is_bgzf(const char*)' is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
if ( bgzf_is_bgzf(cfilename)!=1 )
^
In file included from src/utils/tabix.hpp:12:0,
from src/utils/tabix.cpp:6:
/usr/include/htslib/bgzf.h:243:9: note: declared here
int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
^~~~~~~~~~~~
g++ -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -fdebug-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/utils.o -c src/utils/utils.cpp -Isrc
src/utils/utils.cpp: In function 'bool futils::isFile(std::__cxx11::string)':
src/utils/utils.cpp:469:35: warning: enum constant in boolean context [-Wint-in-bool-context]
inp.open(f.c_str(), ifstream::in);
^
g++ -O3 -Wl,-z,relro -Wl,-z,now obj/analysisMapping.o obj/analysisNominal.o obj/analysisPermutation.o obj/analysisPermutationInteraction.o obj/analysisPermutationPerGroup.o obj/analysisPermutationSequence.o obj/commands.o obj/df.o obj/fastQTL.o obj/management.o obj/mle.o obj/readCovariates.o obj/readGenotypes.o obj/readGroups.o obj/readInclusionsExclusions.o obj/readInteractions.o obj/readPhenotypes.o obj/readThresholds.o obj/residualizer.o obj/tabix.o obj/utils.o /usr/lib/arm-linux-gnueabihf/libhts.so -lRmath -lhts -lm -lz -lboost_iostreams -lboost_program_options -lgsl -lblas -o bin/fastQTL
make[2]: Leaving directory '/<<BUILDDIR>>/fastqtl-2.184+dfsg'
cd /<<BUILDDIR>>/fastqtl-2.184+dfsg/example/ && \
tar Jcvf examples.tar.xz * --sort=name --mode=go=rX,u+rw,a-s --owner=root --group=root --numeric-owner
covariates.txt.gz
genotypes.vcf.gz
genotypes.vcf.gz.tbi
interaction.txt
phenotypes.bed.gz
phenotypes.bed.gz.tbi
make[1]: Leaving directory '/<<BUILDDIR>>/fastqtl-2.184+dfsg'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_lintian -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/fastqtl/usr/bin/fastQTL contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/fastqtl/usr/bin/fastQTL was not linked against libblas.so.3 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/fastqtl/usr/bin/fastQTL was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/fastqtl/usr/bin/fastQTL was not linked against libz.so.1 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'fastqtl-dbgsym' in '../fastqtl-dbgsym_2.184+dfsg-6_armhf.deb'.
dpkg-deb: building package 'fastqtl' in '../fastqtl_2.184+dfsg-6_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../fastqtl_2.184+dfsg-6_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build fastqtl-2.184+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-07-21T05:18:09Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
fastqtl_2.184+dfsg-6_armhf.changes:
-----------------------------------
Format: 1.8
Date: Wed, 18 Jul 2018 20:55:22 +0200
Source: fastqtl
Binary: fastqtl fastqtl-doc
Architecture: armhf
Version: 2.184+dfsg-6
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
fastqtl - Quantitative Trait Loci (QTL) mapper in cis for molecular phenoty
fastqtl-doc - QTL mapper in cis for molecular phenotypes - documentation
Changes:
fastqtl (2.184+dfsg-6) unstable; urgency=medium
.
* Team upload
.
[ Dylan Aïssi ]
* Mark fastqtl-doc as Multi-Arch: foreign.
* Add OMICtools ref (Dylan) and declared others as
missing (Steffen Moeller)
* Remove unnecessary "Testsuite: autopkgtest" from d/control.
* Switch to secure URI in d/copyright.
.
[ Andreas Tille ]
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.5
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ade08a344c3421d04e307cdf64d35c13 7061 science optional fastqtl_2.184+dfsg-6_armhf.buildinfo
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
fastqtl-dbgsym_2.184+dfsg-6_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 4518852 bytes: control archive=540 bytes.
381 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: fastqtl-dbgsym
Source: fastqtl
Version: 2.184+dfsg-6
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4635
Depends: fastqtl (= 2.184+dfsg-6)
Section: debug
Priority: optional
Description: debug symbols for fastqtl
Build-Ids: 0c9e18c5328bece27590b98f82681fbc79d7a814
drwxr-xr-x root/root 0 2018-07-18 18:55 ./
drwxr-xr-x root/root 0 2018-07-18 18:55 ./usr/
drwxr-xr-x root/root 0 2018-07-18 18:55 ./usr/lib/
drwxr-xr-x root/root 0 2018-07-18 18:55 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-07-18 18:55 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-07-18 18:55 ./usr/lib/debug/.build-id/0c/
-rw-r--r-- root/root 4735892 2018-07-18 18:55 ./usr/lib/debug/.build-id/0c/9e18c5328bece27590b98f82681fbc79d7a814.debug
drwxr-xr-x root/root 0 2018-07-18 18:55 ./usr/share/
drwxr-xr-x root/root 0 2018-07-18 18:55 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-07-18 18:55 ./usr/share/doc/fastqtl-dbgsym -> fastqtl
fastqtl_2.184+dfsg-6_armhf.deb
------------------------------
new Debian package, version 2.0.
size 146836 bytes: control archive=1088 bytes.
1080 bytes, 19 lines control
328 bytes, 5 lines md5sums
Package: fastqtl
Version: 2.184+dfsg-6
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 491
Depends: libblas3 | libblas.so.3, libboost-iostreams1.62.0, libboost-program-options1.62.0, libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgsl23 (>= 2.5), libhts2 (>= 1.0), libstdc++6 (>= 5.2), r-mathlib, zlib1g (>= 1:1.1.4)
Suggests: fastqtl-doc
Section: science
Priority: optional
Homepage: http://fastqtl.sourceforge.net/
Description: Quantitative Trait Loci (QTL) mapper in cis for molecular phenotypes
The goal of FastQTL is to identify single-nucleotide polymorphisms (SNPs)
which are significantly associated with various molecular phenotypes
(i.e. expression of known genes, cytosine methylation levels, etc).
It performs scans for all possible phenotype-variant pairs in cis
(i.e. variants located within a specific window around a phenotype).
FastQTL implements a new permutation scheme (Beta approximation) to accurately
and rapidly correct for multiple-testing at both the genotype and phenotype
levels.
drwxr-xr-x root/root 0 2018-07-18 18:55 ./
drwxr-xr-x root/root 0 2018-07-18 18:55 ./usr/
drwxr-xr-x root/root 0 2018-07-18 18:55 ./usr/bin/
-rwxr-xr-x root/root 448012 2018-07-18 18:55 ./usr/bin/fastQTL
drwxr-xr-x root/root 0 2018-07-18 18:55 ./usr/share/
drwxr-xr-x root/root 0 2018-07-18 18:55 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-07-18 18:55 ./usr/share/doc/fastqtl/
-rw-r--r-- root/root 723 2018-07-18 18:55 ./usr/share/doc/fastqtl/changelog.Debian.gz
-rw-r--r-- root/root 38452 2018-07-18 18:55 ./usr/share/doc/fastqtl/copyright
drwxr-xr-x root/root 0 2018-07-18 18:55 ./usr/share/lintian/
drwxr-xr-x root/root 0 2018-07-18 18:55 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 190 2018-07-18 18:55 ./usr/share/lintian/overrides/fastqtl
drwxr-xr-x root/root 0 2018-07-18 18:55 ./usr/share/man/
drwxr-xr-x root/root 0 2018-07-18 18:55 ./usr/share/man/man1/
-rw-r--r-- root/root 1573 2018-07-18 18:55 ./usr/share/man/man1/fastQTL.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 91668
Build-Time: 1007
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 1226
Job: fastqtl_2.184+dfsg-6
Machine Architecture: armhf
Package: fastqtl
Package-Time: 2293
Source-Version: 2.184+dfsg-6
Space: 91668
Status: successful
Version: 2.184+dfsg-6
--------------------------------------------------------------------------------
Finished at 2018-07-21T05:18:09Z
Build needed 00:38:13, 91668k disc space