fastqtl →
2.184+v7+dfsg-3 →
armhf → 2022-10-27 05:03:06
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| fastqtl 2.184+v7+dfsg-3 (armhf) Thu, 27 Oct 2022 04:42:32 +0000 |
+==============================================================================+
Package: fastqtl
Version: 2.184+v7+dfsg-3
Source Version: 2.184+v7+dfsg-3
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-95b63277-913c-4ed7-8ac2-db6b24442fde' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.4 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.2 MB]
Fetched 27.6 MB in 29s (958 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| 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 17.2 MB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main fastqtl 2.184+v7+dfsg-3 (dsc) [2366 B]
Get:2 http://172.17.4.1/private bookworm-staging/main fastqtl 2.184+v7+dfsg-3 (tar) [17.1 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main fastqtl 2.184+v7+dfsg-3 (diff) [20.8 kB]
Fetched 17.2 MB in 2s (10.7 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/fastqtl-6ihuar/fastqtl-2.184+v7+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/fastqtl-6ihuar' 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-mXmG9Q/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-mXmG9Q/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-mXmG9Q/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-mXmG9Q/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-mXmG9Q/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-mXmG9Q/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-mXmG9Q/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-mXmG9Q/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2447 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:
krb5-locales libldap-common libpam-cap netbase sensible-utils
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 24 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-mXmG9Q/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (22.0 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12907 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-compat (= 13), dh-python, python3, libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libgsl-dev, r-mathlib, zlib1g-dev, libblas-dev, libeigen3-dev, libhts-dev, libbz2-dev
Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3, libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libgsl-dev, r-mathlib, zlib1g-dev, libblas-dev, libeigen3-dev, libhts-dev, libbz2-dev
dpkg-deb: building package 'sbuild-build-depends-fastqtl-dummy' in '/<<BUILDDIR>>/resolver-mXmG9Q/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-mXmG9Q/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-mXmG9Q/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-mXmG9Q/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-mXmG9Q/apt_archive ./ Sources [572 B]
Get:5 copy:/<<BUILDDIR>>/resolver-mXmG9Q/apt_archive ./ Packages [650 B]
Fetched 2555 B in 1s (3512 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:
krb5-locales libldap-common libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext
gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl
libblas-dev libblas3 libboost-dev libboost-iostreams-dev
libboost-iostreams1.74-dev libboost-iostreams1.74.0
libboost-program-options-dev libboost-program-options1.74-dev
libboost-program-options1.74.0 libboost-regex1.74-dev libboost-regex1.74.0
libboost1.74-dev libbrotli1 libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev
libdebhelper-perl libdeflate-dev libdeflate0 libeigen3-dev libelf1 libexpat1
libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl27
libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu-dev libicu71
liblzma-dev libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libpipeline1
libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib
librtmp1 libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 m4
man-db media-types pkg-config po-debconf python3 python3-distutils
python3-lib2to3 python3-minimal python3.10 python3.10-minimal r-mathlib
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build
python3-tomli python3-installer gettext-doc libasprintf-dev libgettextpo-dev
groff liblapack-doc libboost-doc libboost1.74-doc libboost-atomic1.74-dev
libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev
libboost-contract1.74-dev libboost-coroutine1.74-dev
libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-locale1.74-dev libboost-log1.74-dev
libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev
libboost-numpy1.74-dev libboost-python1.74-dev libboost-random1.74-dev
libboost-serialization1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev
librtmp-dev libssh2-1-dev libeigen3-doc gsl-ref-psdoc | gsl-doc-pdf
| gsl-doc-info | gsl-ref-html 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 python3.10-venv
python3.10-doc binfmt-support
Recommended packages:
curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl
libglib2.0-data shared-mime-info xdg-user-dirs publicsuffix libltdl-dev
libmail-sendmail-perl r-base-core r-base-dev
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext
gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl
libblas-dev libblas3 libboost-dev libboost-iostreams-dev
libboost-iostreams1.74-dev libboost-iostreams1.74.0
libboost-program-options-dev libboost-program-options1.74-dev
libboost-program-options1.74.0 libboost-regex1.74-dev libboost-regex1.74.0
libboost1.74-dev libbrotli1 libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev
libdebhelper-perl libdeflate-dev libdeflate0 libeigen3-dev libelf1 libexpat1
libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl27
libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu-dev libicu71
liblzma-dev libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libpipeline1
libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib
librtmp1 libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 m4
man-db media-types pkg-config po-debconf python3 python3-distutils
python3-lib2to3 python3-minimal python3.10 python3.10-minimal r-mathlib
sbuild-build-depends-fastqtl-dummy zlib1g-dev
0 upgraded, 79 newly installed, 0 to remove and 24 not upgraded.
Need to get 54.9 MB of archives.
After this operation, 334 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-mXmG9Q/apt_archive ./ sbuild-build-depends-fastqtl-dummy 0.invalid.0 [940 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-minimal armhf 3.10.7-2 [769 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.9-1 [83.3 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf python3.10-minimal armhf 3.10.7-2 [1477 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.10.6-1 [38.7 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf media-types all 8.0.0 [33.4 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-stdlib armhf 3.10.7-2 [1597 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf python3.10 armhf 3.10.7-2 [502 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.10.6-1 [21.7 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.10.6-1 [38.2 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-1.1 [78.2 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-3 [34.3 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.0-1 [1299 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-9 [171 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-9 [510 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.10 [79.8 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-9 [1220 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.10 [940 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.10.7-1 [79.9 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.10.7-1 [141 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf dh-python all 5.20220819+rpi1 [114 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf icu-devtools armhf 71.1-3 [177 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.10.1-2 [109 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libblas-dev armhf 3.10.1-2 [114 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-17 [9534 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libboost-dev armhf 1.74.0.3+b4 [4824 B]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libboost-regex1.74.0 armhf 1.74.0-17 [444 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libicu-dev armhf 71.1-3 [9799 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libboost-regex1.74-dev armhf 1.74.0-17 [550 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libboost-iostreams1.74.0 armhf 1.74.0-17 [260 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libboost-iostreams1.74-dev armhf 1.74.0-17 [270 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libboost-iostreams-dev armhf 1.74.0.3+b4 [4592 B]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libboost-program-options1.74.0 armhf 1.74.0-17 [332 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libboost-program-options1.74-dev armhf 1.74.0-17 [370 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libboost-program-options-dev armhf 1.74.0.3+b4 [4616 B]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libbz2-dev armhf 1.0.8-5+b2 [26.8 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.50.0-1 [65.0 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.85.0-1 [320 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.85.0-1 [397 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.14-1 [50.9 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.14-1 [48.1 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.74.0-3 [1211 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libeigen3-dev all 3.4.0-4 [1041 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libgslcblas0 armhf 2.7.1+dfsg-3 [81.4 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libgsl27 armhf 2.7.1+dfsg-3 [758 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libgsl-dev armhf 2.7.1+dfsg-3 [958 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.3.0-4 [59.5 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libhts3 armhf 1.16+ds-3 [367 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2.1 [218 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4.1 [183 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libhts-dev armhf 1.16+ds-3 [1479 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf r-mathlib armhf 4.2.1-3 [2220 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libpython3.10-minimal:armhf.
(Reading database ... 12907 files and directories currently installed.)
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Setting up libexpat1:armhf (2.4.9-1) ...
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(Reading database ... 13210 files and directories currently installed.)
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W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.39-6+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-3+rpi1 gcc-12_12.2.0-3+rpi1 libc6-dev_2.35-2+rpi1 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 linux-libc-dev_5.19.6-1+rpi1
Package versions: adduser_3.129 apt_2.5.3 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-9 autotools-dev_20220109.1 base-files_12.3+rpi1 base-passwd_3.6.1 bash_5.2~rc2-2 binutils_2.39-6+rpi1 binutils-arm-linux-gnueabihf_2.39-6+rpi1 binutils-common_2.39-6+rpi1 bsdextrautils_2.38.1-1.1 bsdutils_1:2.38.1-1.1 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-3+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.10 debianutils_5.7-0.3 dh-autoreconf_20 dh-python_5.20220819+rpi1 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dirmngr_2.2.39-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-3+rpi1 gcc_4:12.2.0-1+rpi1 gcc-10-base_10.4.0-5+rpi1 gcc-12_12.2.0-3+rpi1 gcc-12-base_12.2.0-3+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-9 gettext-base_0.21-9 gnupg_2.2.39-1 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libpython3.10-minimal_3.10.7-2 libpython3.10-stdlib_3.10.7-2 libreadline8_8.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-8 libsasl2-modules-db_2.1.28+dfsg-8 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol2_3.4-2 libsmartcols1_2.38.1-1.1 libsqlite3-0_3.39.4-1 libss2_1.46.6~rc1-1 libssh2-1_1.10.0-3+b1 libssl1.1_1.1.1o-1 libssl3_3.0.5-4 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 libsub-override-perl_0.09-4 libsystemd0_251.5-1+rpi1 libtasn1-6_4.19.0-2 libtext-charwidth-perl_0.04-10+b2 libtext-iconv-perl_1.7-7+b2 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-4 libubsan1_12.2.0-3+rpi1 libuchardet0_0.0.7-1 libudev1_251.5-1+rpi1 libunistring2_1.0-2 libuuid1_2.38.1-1.1 libxml2_2.9.14+dfsg-1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.6-1+rpi1 login_1:4.12.3+dfsg1-1 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 m4_1.4.19-1 make_4.3-4.1 man-db_2.11.0-1 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mount_2.38.1-1.1 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 netbase_6.3 passwd_1:4.12.3+dfsg1-1 patch_2.7.6-7 perl_5.34.0-5 perl-base_5.34.0-5 perl-modules-5.34_5.34.0-5 pinentry-curses_1.2.0-2 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 python3_3.10.6-1 python3-distutils_3.10.7-1 python3-lib2to3_3.10.7-1 python3-minimal_3.10.6-1 python3.10_3.10.7-2 python3.10-minimal_3.10.7-2 r-mathlib_4.2.1-3 raspbian-archive-keyring_20120528.2 readline-common_8.2-1 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-fastqtl-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.31 sysvinit-utils_3.05-6 tar_1.34+dfsg-1 tzdata_2022d-1 util-linux_2.38.1-1.1 util-linux-extra_2.38.1-1.1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.cDr1Gmlp/trustedkeys.kbx': General error
gpgv: Signature made Sat Oct 22 12:02:48 2022 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./fastqtl_2.184+v7+dfsg-3.dsc
dpkg-source: info: extracting fastqtl in /<<BUILDDIR>>/fastqtl-2.184+v7+dfsg
dpkg-source: info: unpacking fastqtl_2.184+v7+dfsg.orig.tar.xz
dpkg-source: info: unpacking fastqtl_2.184+v7+dfsg-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
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
dpkg-source: info: applying cross.patch
dpkg-source: info: applying set_path.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=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-95b63277-913c-4ed7-8ac2-db6b24442fde
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package fastqtl
dpkg-buildpackage: info: source version 2.184+v7+dfsg-3
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --with python3
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg'
rm -f obj/*.o bin/fastQTL
make[1]: Leaving directory '/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg'
dh_clean
debian/rules binary-arch
dh binary-arch --with python3
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+v7+dfsg'
mkdir -p /<<BUILDDIR>>/fastqtl-2.184+v7+dfsg/obj/
mkdir -p /<<BUILDDIR>>/fastqtl-2.184+v7+dfsg/bin/
dh_auto_build -- CXXFLAGS='-g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14'
make -j4 "INSTALL=install --strip-program=true" "CXXFLAGS=-g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14"
make[2]: Entering directory '/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg'
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisMapping.o -c src/analysisMapping.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisNominal.o -c src/analysisNominal.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisNominalBest.o -c src/analysisNominalBest.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisPermutation.o -c src/analysisPermutation.cpp -Isrc
In file included from src/analysisNominalBest.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
In file included from src/analysisPermutation.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
In file included from src/analysisMapping.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
In file included from src/analysisNominal.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
In file included from /usr/include/c++/12/vector:70,
from src/utils/utils.h:46,
from src/data.h:25:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void data::runPermutation(std::string, std::vector<int>)' at src/analysisPermutation.cpp:83:31:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void data::runPermutation(std::string, std::vector<int>)' at src/analysisPermutation.cpp:104:79:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisPermutationInteraction.o -c src/analysisPermutationInteraction.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisPermutationPerGroup.o -c src/analysisPermutationPerGroup.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisPermutationSequence.o -c src/analysisPermutationSequence.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/commands.o -c src/commands.cpp -Isrc
In file included from src/analysisPermutationInteraction.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
In file included from src/analysisPermutationPerGroup.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
In file included from src/analysisPermutationSequence.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
In file included from /usr/include/c++/12/vector:70,
from src/utils/utils.h:46,
from src/data.h:25:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:70,
from src/utils/utils.h:46,
from src/data.h:25:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void data::runPermutationPerGroup(std::string, std::vector<int>)' at src/analysisPermutationPerGroup.cpp:107:22:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void data::runPermutationPerGroup(std::string, std::vector<int>)' at src/analysisPermutationPerGroup.cpp:128:70:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void data::runPermutation(std::string, std::string)' at src/analysisPermutationSequence.cpp:89:22:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void data::runPermutation(std::string, std::string)' at src/analysisPermutationSequence.cpp:105:70:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/df.o -c src/df.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/fastQTL.o -c src/fastQTL.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/management.o -c src/management.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/mle.o -c src/mle.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readCovariates.o -c src/readCovariates.cpp -Isrc
In file included from src/management.cpp:20:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readGenotypes.o -c src/readGenotypes.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readGroups.o -c src/readGroups.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readInclusionsExclusions.o -c src/readInclusionsExclusions.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readInteractions.o -c src/readInteractions.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readPhenotypes.o -c src/readPhenotypes.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readThresholds.o -c src/readThresholds.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/residualizer.o -c src/residualizer.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -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::string&)':
src/utils/tabix.cpp:17:22: warning: 'int bgzf_is_bgzf(const char*)' is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
17 | if ( bgzf_is_bgzf(cfilename)!=1 )
| ~~~~~~~~~~~~^~~~~~~~~~~
In file included from src/utils/tabix.hpp:12,
from src/utils/tabix.cpp:6:
/usr/include/htslib/bgzf.h:270:9: note: declared here
270 | int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
| ^~~~~~~~~~~~
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/utils.o -c src/utils/utils.cpp -Isrc
g++ -std=c++11 -O3 -Wl,-z,relro -Wl,-z,now obj/analysisMapping.o obj/analysisNominal.o obj/analysisNominalBest.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 -lRmath -lhts -lm -lz -lbz2 -lboost_iostreams -lboost_program_options -lgslcblas -lgsl -lblas -o bin/fastQTL
make[2]: Leaving directory '/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg'
cd /<<BUILDDIR>>/fastqtl-2.184+v7+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+v7+dfsg'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_auto_install -a
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_python3 -a
I: dh_python3 tools:114: replacing shebang in debian/fastqtl/usr/bin/annotate_outputs.py
I: dh_python3 tools:114: replacing shebang in debian/fastqtl/usr/bin/merge_chunks.py
I: dh_python3 tools:114: replacing shebang in debian/fastqtl/usr/bin/run_FastQTL_threaded.py
I: dh_python3 tools:114: replacing shebang in debian/fastqtl/usr/bin/run_chunk.py
I: dh_python3 tools:114: replacing shebang in debian/fastqtl/usr/bin/sort_index_pairs.py
dh_lintian -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
debian/rules execute_after_dh_fixperms-arch
make[1]: Entering directory '/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg'
chmod -x debian/*/usr/share/fastqtl/*.R
make[1]: Leaving directory '/<<BUILDDIR>>/fastqtl-2.184+v7+dfsg'
dh_missing -a
dh_dwz -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)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'fastqtl-dbgsym' in '../fastqtl-dbgsym_2.184+v7+dfsg-3_armhf.deb'.
dpkg-deb: building package 'fastqtl' in '../fastqtl_2.184+v7+dfsg-3_armhf.deb'.
dpkg-genbuildinfo --build=any -O../fastqtl_2.184+v7+dfsg-3_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> -O../fastqtl_2.184+v7+dfsg-3_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2022-10-27T05:02:24Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
fastqtl_2.184+v7+dfsg-3_armhf.changes:
--------------------------------------
Format: 1.8
Date: Sat, 22 Oct 2022 13:50:04 +0200
Source: fastqtl
Binary: fastqtl fastqtl-dbgsym
Architecture: armhf
Version: 2.184+v7+dfsg-3
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
fastqtl - Quantitative Trait Loci (QTL) mapper in cis for molecular phenoty
Closes: 1021994 1021995
Changes:
fastqtl (2.184+v7+dfsg-3) unstable; urgency=medium
.
* Team upload.
* d/rules: only fix permissions for arch-any builds. (Closes: #1021994)
* d/t/fastqtl_expected_output.txt: update to match behavior of v7.
(Closes: #1021995)
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
fastqtl-dbgsym_2.184+v7+dfsg-3_armhf.deb
----------------------------------------
new Debian package, version 2.0.
size 5361296 bytes: control archive=544 bytes.
387 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: fastqtl-dbgsym
Source: fastqtl
Version: 2.184+v7+dfsg-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5432
Depends: fastqtl (= 2.184+v7+dfsg-3)
Section: debug
Priority: optional
Description: debug symbols for fastqtl
Build-Ids: b93034ce6819774103000691ca69cf507ce03396
drwxr-xr-x root/root 0 2022-10-22 11:50 ./
drwxr-xr-x root/root 0 2022-10-22 11:50 ./usr/
drwxr-xr-x root/root 0 2022-10-22 11:50 ./usr/lib/
drwxr-xr-x root/root 0 2022-10-22 11:50 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-10-22 11:50 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-10-22 11:50 ./usr/lib/debug/.build-id/b9/
-rw-r--r-- root/root 5551884 2022-10-22 11:50 ./usr/lib/debug/.build-id/b9/3034ce6819774103000691ca69cf507ce03396.debug
drwxr-xr-x root/root 0 2022-10-22 11:50 ./usr/share/
drwxr-xr-x root/root 0 2022-10-22 11:50 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-10-22 11:50 ./usr/share/doc/fastqtl-dbgsym -> fastqtl
fastqtl_2.184+v7+dfsg-3_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 173020 bytes: control archive=1640 bytes.
1169 bytes, 20 lines control
714 bytes, 11 lines md5sums
261 bytes, 12 lines * postinst #!/bin/sh
374 bytes, 12 lines * prerm #!/bin/sh
Package: fastqtl
Version: 2.184+v7+dfsg-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 595
Depends: libblas3 | libblas.so.3, libboost-iostreams1.74.0 (>= 1.74.0), libboost-program-options1.74.0 (>= 1.74.0), libc6 (>= 2.34), libgcc-s1 (>= 3.5), libgsl27 (>= 2.7.1), libhts3 (>= 1.10), libstdc++6 (>= 11), r-mathlib, python3:any, python3
Recommends: r-cran-qvalue, r-cran-tools, r-cran-argparser
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 2022-10-22 11:50 ./
drwxr-xr-x root/root 0 2022-10-22 11:50 ./usr/
drwxr-xr-x root/root 0 2022-10-22 11:50 ./usr/bin/
-rwxr-xr-x root/root 6497 2022-10-22 11:50 ./usr/bin/annotate_outputs.py
-rwxr-xr-x root/root 525836 2022-10-22 11:50 ./usr/bin/fastQTL
-rwxr-xr-x root/root 2968 2022-10-22 11:50 ./usr/bin/merge_chunks.py
-rwxr-xr-x root/root 5981 2022-10-22 11:50 ./usr/bin/run_FastQTL_threaded.py
-rwxr-xr-x root/root 3093 2022-10-22 11:50 ./usr/bin/run_chunk.py
-rwxr-xr-x root/root 1210 2022-10-22 11:50 ./usr/bin/sort_index_pairs.py
drwxr-xr-x root/root 0 2022-10-22 11:50 ./usr/share/
drwxr-xr-x root/root 0 2022-10-22 11:50 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-10-22 11:50 ./usr/share/doc/fastqtl/
-rw-r--r-- root/root 957 2022-10-22 11:50 ./usr/share/doc/fastqtl/changelog.Debian.gz
-rw-r--r-- root/root 38490 2022-10-22 11:50 ./usr/share/doc/fastqtl/copyright
drwxr-xr-x root/root 0 2022-10-22 11:50 ./usr/share/fastqtl/
-rw-r--r-- root/root 2607 2017-11-29 03:09 ./usr/share/fastqtl/calculateSignificanceFastQTL.R
drwxr-xr-x root/root 0 2022-10-22 11:50 ./usr/share/lintian/
drwxr-xr-x root/root 0 2022-10-22 11:50 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 294 2022-10-22 11:50 ./usr/share/lintian/overrides/fastqtl
drwxr-xr-x root/root 0 2022-10-22 11:50 ./usr/share/man/
drwxr-xr-x root/root 0 2022-10-22 11:50 ./usr/share/man/man1/
-rw-r--r-- root/root 1573 2022-10-22 11:50 ./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: 107400
Build-Time: 608
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 523
Job: fastqtl_2.184+v7+dfsg-3
Machine Architecture: armhf
Package: fastqtl
Package-Time: 1192
Source-Version: 2.184+v7+dfsg-3
Space: 107400
Status: successful
Version: 2.184+v7+dfsg-3
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Finished at 2022-10-27T05:02:24Z
Build needed 00:19:52, 107400k disc space