nanopolish →
0.13.3-2 →
armhf → 2021-08-27 06:37:16
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| nanopolish 0.13.3-2 (armhf) Fri, 27 Aug 2021 06:06:36 +0000 |
+==============================================================================+
Package: nanopolish
Version: 0.13.3-2
Source Version: 0.13.3-2
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-28eb41c1-f676-45f9-a722-9b8e36ebbb02' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.3 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.3 MB]
Fetched 25.6 MB in 26s (1000 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: 'nanopolish' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/nanopolish.git
Please use:
git clone https://salsa.debian.org/med-team/nanopolish.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 4091 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main nanopolish 0.13.3-2 (dsc) [2095 B]
Get:2 http://172.17.0.1/private bookworm-staging/main nanopolish 0.13.3-2 (tar) [4080 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main nanopolish 0.13.3-2 (diff) [8792 B]
Fetched 4091 kB in 1s (6152 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/nanopolish-QhOb9O/nanopolish-0.13.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/nanopolish-QhOb9O' 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-fFj3PJ/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-fFj3PJ/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-fFj3PJ/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-fFj3PJ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-fFj3PJ/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-fFj3PJ/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-fFj3PJ/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-fFj3PJ/apt_archive ./ Packages [428 B]
Fetched 2104 B in 1s (2673 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 30 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-fFj3PJ/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 (22.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12488 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)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dh-python, python3, zlib1g-dev, libfast5-dev (>= 0.6.5), libhts-dev, libeigen3-dev, libminimap2-dev
Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3, zlib1g-dev, libfast5-dev (>= 0.6.5), libhts-dev, libeigen3-dev, libminimap2-dev
dpkg-deb: building package 'sbuild-build-depends-nanopolish-dummy' in '/<<BUILDDIR>>/resolver-fFj3PJ/apt_archive/sbuild-build-depends-nanopolish-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-nanopolish-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-fFj3PJ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-fFj3PJ/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-fFj3PJ/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-fFj3PJ/apt_archive ./ Sources [551 B]
Get:5 copy:/<<BUILDDIR>>/resolver-fFj3PJ/apt_archive ./ Packages [628 B]
Fetched 2512 B in 1s (3425 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install nanopolish build dependencies (apt-based resolver)
----------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
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 hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev
libdebhelper-perl libdeflate-dev libdeflate0 libeigen3-dev libelf1 libexpat1
libfast5-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0
libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102
libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libhts-dev libhts3
libicu67 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev liblzma-dev
libmagic-mgc libmagic1 libminimap2-dev libmpdec3 libnghttp2-14 libpipeline1
libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librtmp1
libsigsegv2 libssh2-1 libsub-override-perl libsz2 libtool libuchardet0
libxml2 m4 man-db media-types pkg-config po-debconf python3
python3-distutils python3-lib2to3 python3-minimal python3.9
python3.9-minimal sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev
libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev
libeigen3-doc libmpfrc++-dev libhdf5-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 python3.9-venv
python3.9-doc binfmt-support
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs publicsuffix libltdl-dev
libmail-sendmail-perl
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 hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev
libdebhelper-perl libdeflate-dev libdeflate0 libeigen3-dev libelf1 libexpat1
libfast5-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0
libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102
libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libhts-dev libhts3
libicu67 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev liblzma-dev
libmagic-mgc libmagic1 libminimap2-dev libmpdec3 libnghttp2-14 libpipeline1
libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librtmp1
libsigsegv2 libssh2-1 libsub-override-perl libsz2 libtool libuchardet0
libxml2 m4 man-db media-types pkg-config po-debconf python3
python3-distutils python3-lib2to3 python3-minimal python3.9
python3.9-minimal sbuild-build-depends-nanopolish-dummy sensible-utils
zlib1g-dev
0 upgraded, 78 newly installed, 0 to remove and 30 not upgraded.
Need to get 35.2 MB of archives.
After this operation, 123 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-fFj3PJ/apt_archive ./ sbuild-build-depends-nanopolish-dummy 0.invalid.0 [920 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-1 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-6 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-minimal armhf 3.9.2-1+rpi1 [791 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libexpat1 armhf 2.2.10-2 [73.4 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf python3.9-minimal armhf 3.9.2-1+rpi1 [1625 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf media-types all 4.0.0 [30.3 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-1+rpi1 [73.4 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-stdlib armhf 3.9.2-1+rpi1 [1616 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf python3.9 armhf 3.9.2-1+rpi1 [466 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf python3 armhf 3.9.2-3 [37.9 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.14 [14.8 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.4.1 [191 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [580 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.4.1 [1039 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf python3-lib2to3 all 3.9.2-1 [77.8 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf python3-distutils all 3.9.2-1 [143 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf dh-python all 4.20201102+nmu1 [99.4 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf hdf5-helpers armhf 1.10.6+repack-2 [40.0 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf libaec0 armhf 1.0.5-2 [19.2 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libsz2 armhf 1.0.5-2 [7380 B]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf libaec-dev armhf 1.0.5-2 [17.5 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf libssh2-1 armhf 1.9.0-3 [151 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.74.0-1.3 [301 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3 [375 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf libdeflate0 armhf 1.7-2 [44.1 kB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.7-2 [40.5 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.68.4-1 [1197 kB]
Get:60 http://172.17.0.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:61 http://172.17.0.1/private bookworm-staging/main armhf libeigen3-dev all 3.3.9-2 [858 kB]
Get:62 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-103-1 armhf 1.10.6+repack-2 [1184 kB]
Get:63 http://172.17.0.1/private bookworm-staging/main armhf libgfortran5 armhf 10.2.1-6+rpi1 [232 kB]
Get:64 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-fortran-102 armhf 1.10.6+repack-2 [93.0 kB]
Get:65 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-hl-100 armhf 1.10.6+repack-2 [78.1 kB]
Get:66 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-hl-fortran-100 armhf 1.10.6+repack-2 [49.8 kB]
Get:67 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-cpp-103-1 armhf 1.10.6+repack-2 [128 kB]
Get:68 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-hl-cpp-100 armhf 1.10.6+repack-2 [36.9 kB]
Get:69 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:70 http://172.17.0.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.0.6-4 [122 kB]
Get:71 http://172.17.0.1/private bookworm-staging/main armhf libjpeg62-turbo-dev armhf 1:2.0.6-4 [240 kB]
Get:72 http://172.17.0.1/private bookworm-staging/main armhf libjpeg-dev armhf 1:2.0.6-4 [67.8 kB]
Get:73 http://172.17.0.1/private bookworm-staging/main armhf libhdf5-dev armhf 1.10.6+repack-2 [2167 kB]
Get:74 http://172.17.0.1/private bookworm-staging/main armhf libfast5-dev all 0.6.5-4 [49.8 kB]
Get:75 http://172.17.0.1/private bookworm-staging/main armhf libhts3 armhf 1.11-4 [324 kB]
Get:76 http://172.17.0.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2 [219 kB]
Get:77 http://172.17.0.1/private bookworm-staging/main armhf libhts-dev armhf 1.11-4 [3815 kB]
Get:78 http://172.17.0.1/private bookworm-staging/main armhf libminimap2-dev armhf 2.17+dfsg-12+b1 [110 kB]
debconf: delaying package configuration, since apt-utils is not installed
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
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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_2.35.2-2+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-13+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.2.4 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11.1+rpi1 base-passwd_3.5.51 bash_5.1-2 binutils_2.35.2-2+rpi1 binutils-arm-linux-gnueabihf_2.35.2-2+rpi1 binutils-common_2.35.2-2+rpi1 bsdextrautils_2.37.2-1 bsdutils_1:2.36.1-8 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.77 debhelper_13.4.1 debianutils_4.11.2 dh-autoreconf_20 dh-python_4.20201102+nmu1 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.2-2 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.3.0-22+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-4 hdf5-helpers_1.10.6+repack-2 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10 libaec-dev_1.0.5-2 libaec0_1.0.5-2 libapt-pkg6.0_2.2.4 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.2-2+rpi1 libblkid1_2.36.1-8 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.31-13+rpi1 libc-dev-bin_2.31-13+rpi1 libc6_2.31-13+rpi1 libc6-dev_2.31-13+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_10.2.1-6+rpi1 libcom-err2_1.46.2-2 libcrypt-dev_1:4.4.18-4 libcrypt1_1:4.4.18-4 libctf-nobfd0_2.35.2-2+rpi1 libctf0_2.35.2-2+rpi1 libcurl3-gnutls_7.74.0-1.3 libcurl4-gnutls-dev_7.74.0-1.3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.4.1 libdeflate-dev_1.7-2 libdeflate0_1.7-2 libdpkg-perl_1.20.9+rpi1 libeigen3-dev_3.3.9-2 libelf1_0.185-2 libexpat1_2.2.10-2 libext2fs2_1.46.2-2 libfakeroot_1.25.3-1.1 libfast5-dev_0.6.5-4 libffi7_3.3-6 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-6 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgfortran5_10.2.1-6+rpi1 libglib2.0-0_2.68.4-1 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.1-5 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-6 libhdf5-103-1_1.10.6+repack-2 libhdf5-cpp-103-1_1.10.6+repack-2 libhdf5-dev_1.10.6+repack-2 libhdf5-fortran-102_1.10.6+repack-2 libhdf5-hl-100_1.10.6+repack-2 libhdf5-hl-cpp-100_1.10.6+repack-2 libhdf5-hl-fortran-100_1.10.6+repack-2 libhogweed6_3.7.3-1 libhts-dev_1.11-4 libhts3_1.11-4 libicu67_67.1-7 libidn2-0_2.3.0-5 libisl23_0.23-1 libjpeg-dev_1:2.0.6-4 libjpeg62-turbo_1:2.0.6-4 libjpeg62-turbo-dev_1:2.0.6-4 libk5crypto3_1.18.3-6 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-6 libkrb5support0_1.18.3-6 libksba8_1.5.0-3 libldap-2.4-2_2.4.57+dfsg-3 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libminimap2-dev_2.17+dfsg-12+b1 libmount1_2.36.1-8 libmpc3_1.2.0-1 libmpdec3_2.5.1-1+rpi1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-2 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.23.22-1 libpam-modules_1.4.0-9 libpam-modules-bin_1.4.0-9 libpam-runtime_1.4.0-9 libpam0g_1.4.0-9 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-4+deb11u1 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.2 libpython3-stdlib_3.9.2-3 libpython3.9-minimal_3.9.2-1+rpi1 libpython3.9-stdlib_3.9.2-1+rpi1 libreadline8_8.1-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.36.1-8 libsqlite3-0_3.34.1-3 libss2_1.46.2-2 libssh2-1_1.9.0-3 libssl1.1_1.1.1k-1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.3-6+rpi1 libsz2_1.0.5-2 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.3-6+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-8 libxml2_2.9.10+dfsg-6.7 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.2-2 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.36.1-8 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-4+deb11u1 perl-base_5.32.1-4+deb11u1 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 python3_3.9.2-3 python3-distutils_3.9.2-1 python3-lib2to3_3.9.2-1 python3-minimal_3.9.2-3 python3.9_3.9.2-1+rpi1 python3.9-minimal_3.9.2-1+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-nanopolish-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.14 sysvinit-utils_2.96-7 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.36.1-8 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.lT0lPwJc/trustedkeys.kbx': General error
gpgv: Signature made Tue Aug 24 20:24:49 2021 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "npatra974@gmail.com"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./nanopolish_0.13.3-2.dsc
dpkg-source: info: extracting nanopolish in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking nanopolish_0.13.3.orig.tar.gz
dpkg-source: info: unpacking nanopolish_0.13.3-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying add-shebang-to-script.patch
dpkg-source: info: applying reproducible.patch
dpkg-source: info: applying fix_remaining_python_interpreters.patch
dpkg-source: info: applying staticMinimap2Library.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-28eb41c1-f676-45f9-a722-9b8e36ebbb02
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package nanopolish
dpkg-buildpackage: info: source version 0.13.3-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --with python3
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
sed -i~ 's/^.depend: .*/.depend:/' Makefile
touch .depend
/usr/bin/make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f nanopolish nanopolish_test src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/io/nanopolish_fast5_io.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_processor.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_detect_polyi.o src/nanopolish_extract.o src/nanopolish_fast5_check.o src/nanopolish_getmodel.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_polya_estimator.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/nanopolish_vcf2fasta.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/training_core.o src/thirdparty/fet.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/stdaln.o \
src/main/nanopolish.o src/test/nanopolish_test.o
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f .depend
mv Makefile~ Makefile
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
dh_auto_build
make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f ./.depend
g++ -o src/main/nanopolish.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/main/nanopolish.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -MM src/alignment/nanopolish_alignment_db.cpp src/alignment/nanopolish_anchor.cpp src/alignment/nanopolish_eventalign.cpp src/common/fs_support.cpp src/common/logsum.cpp src/common/nanopolish_alphabet.cpp src/common/nanopolish_bam_processor.cpp src/common/nanopolish_bam_utils.cpp src/common/nanopolish_common.cpp src/common/nanopolish_iupac.cpp src/common/nanopolish_klcs.cpp src/common/nanopolish_variant.cpp src/hmm/nanopolish_duration_model.cpp src/hmm/nanopolish_profile_hmm.cpp src/hmm/nanopolish_profile_hmm_r7.cpp src/hmm/nanopolish_profile_hmm_r9.cpp src/hmm/nanopolish_transition_parameters.cpp src/io/nanopolish_fast5_io.cpp src/io/nanopolish_fast5_loader.cpp src/io/nanopolish_fast5_processor.cpp src/nanopolish_call_methylation.cpp src/nanopolish_call_variants.cpp src/nanopolish_detect_polyi.cpp src/nanopolish_extract.cpp src/nanopolish_fast5_check.cpp src/nanopolish_getmodel.cpp src/nanopolish_haplotype.cpp src/nanopolish_index.cpp src/nanopolish_methyltrain.cpp src/nanopolish_phase_reads.cpp src/nanopolish_polya_estimator.cpp src/nanopolish_raw_loader.cpp src/nanopolish_read_db.cpp src/nanopolish_scorereads.cpp src/nanopolish_squiggle_read.cpp src/nanopolish_train_poremodel_from_basecalls.cpp src/nanopolish_variant_db.cpp src/nanopolish_vcf2fasta.cpp src/pore_model/nanopolish_model_names.cpp src/pore_model/nanopolish_pore_model_set.cpp src/pore_model/nanopolish_poremodel.cpp src/training_core.cpp src/thirdparty/fet.c src/thirdparty/scrappie/event_detection.c src/thirdparty/scrappie/scrappie_common.c src/thirdparty/stdaln.c > ./.depend;
g++ -o src/alignment/nanopolish_alignment_db.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/alignment/nanopolish_alignment_db.cpp
g++ -o src/alignment/nanopolish_anchor.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/alignment/nanopolish_anchor.cpp
g++ -o src/alignment/nanopolish_eventalign.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/alignment/nanopolish_eventalign.cpp
g++ -o src/common/fs_support.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/common/fs_support.cpp
g++ -o src/common/logsum.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/common/logsum.cpp
g++ -o src/common/nanopolish_alphabet.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/common/nanopolish_alphabet.cpp
g++ -o src/common/nanopolish_bam_processor.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/common/nanopolish_bam_processor.cpp
g++ -o src/common/nanopolish_bam_utils.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/common/nanopolish_bam_utils.cpp
g++ -o src/common/nanopolish_common.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/common/nanopolish_common.cpp
g++ -o src/common/nanopolish_iupac.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/common/nanopolish_iupac.cpp
g++ -o src/common/nanopolish_klcs.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/common/nanopolish_klcs.cpp
g++ -o src/common/nanopolish_variant.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/common/nanopolish_variant.cpp
g++ -o src/hmm/nanopolish_duration_model.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/hmm/nanopolish_duration_model.cpp
src/common/nanopolish_variant.cpp: In function 'void score_variant_group(VariantGroup&, Haplotype, const std::vector<HMMInputData>&, int, int, bool, uint32_t, const std::vector<std::__cxx11::basic_string<char> >&)':
src/common/nanopolish_variant.cpp:209:56: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
209 | fprintf(stderr, "Number of variants in span (%lu) would exceed max-haplotypes. Variants may be missed. Consider running with a higher value of max-haplotypes!\n", num_variants);
| ~~^ ~~~~~~~~~~~~
| | |
| long unsigned int size_t {aka unsigned int}
| %u
g++ -o src/hmm/nanopolish_profile_hmm.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/hmm/nanopolish_profile_hmm.cpp
g++ -o src/hmm/nanopolish_profile_hmm_r7.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/hmm/nanopolish_profile_hmm_r7.cpp
g++ -o src/hmm/nanopolish_profile_hmm_r9.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/hmm/nanopolish_profile_hmm_r9.cpp
g++ -o src/hmm/nanopolish_transition_parameters.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/hmm/nanopolish_transition_parameters.cpp
g++ -o src/io/nanopolish_fast5_io.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/io/nanopolish_fast5_io.cpp
g++ -o src/io/nanopolish_fast5_loader.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/io/nanopolish_fast5_loader.cpp
src/io/nanopolish_fast5_io.cpp: In function 'raw_table fast5_get_raw_samples(fast5_file&, const string&, fast5_raw_scaling)':
src/io/nanopolish_fast5_io.cpp:162:28: warning: narrowing conversion of 'nsample' from 'hsize_t' {aka 'long long unsigned int'} to 'size_t' {aka 'unsigned int'} [-Wnarrowing]
162 | rawtbl = (raw_table) { nsample, 0, nsample, rawptr };
| ^~~~~~~
src/io/nanopolish_fast5_io.cpp:162:40: warning: narrowing conversion of 'nsample' from 'hsize_t' {aka 'long long unsigned int'} to 'size_t' {aka 'unsigned int'} [-Wnarrowing]
162 | rawtbl = (raw_table) { nsample, 0, nsample, rawptr };
| ^~~~~~~
g++ -o src/io/nanopolish_fast5_processor.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/io/nanopolish_fast5_processor.cpp
g++ -o src/nanopolish_call_methylation.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/nanopolish_call_methylation.cpp
g++ -o src/nanopolish_call_variants.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/nanopolish_call_variants.cpp
g++ -o src/nanopolish_detect_polyi.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/nanopolish_detect_polyi.cpp
src/nanopolish_call_methylation.cpp: In member function 'void WatchStatus::update(const string&)':
src/nanopolish_call_methylation.cpp:120:73: warning: format '%d' expects argument of type 'int', but argument 4 has type 'double' [-Wformat=]
120 | fprintf(stderr, "\33[2K\r[call-methylation] fast5 progress: %d/%d %.2lfs/fast5 [%s]", processed_fast5s, seconds_per_file, total_fast5s, message.c_str());
| ~^ ~~~~~~~~~~~~~~~~
| | |
| int double
| %f
src/nanopolish_call_methylation.cpp:120:79: warning: format '%lf' expects argument of type 'double', but argument 5 has type 'int' [-Wformat=]
120 | fprintf(stderr, "\33[2K\r[call-methylation] fast5 progress: %d/%d %.2lfs/fast5 [%s]", processed_fast5s, seconds_per_file, total_fast5s, message.c_str());
| ~~~~^ ~~~~~~~~~~~~
| | |
| double int
| %.2d
src/nanopolish_call_variants.cpp: In function 'Haplotype fix_homopolymers(const Haplotype&, const AlignmentDB&)':
src/nanopolish_call_variants.cpp:680:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
680 | fprintf(stderr, "SUM_VAR\t%zu\t%zu\t%d\t%d\t%lu\t%.5lf\t%.2lf\n", ref_hp_start, hp_length, var_sequence_length, call_window, variant_offset_end - variant_offset_start, sum_duration, log_gamma);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int size_t {aka unsigned int}
| %u
g++ -o src/nanopolish_extract.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/nanopolish_extract.cpp
src/nanopolish_detect_polyi.cpp: In function 'void dpi_estimate_polya_for_single_read(const ReadDB&, const faidx_t*, FILE*, const bam_hdr_t*, const bam1_t*, size_t, int, int)':
src/nanopolish_detect_polyi.cpp:1040:40: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'long long int' [-Wformat=]
1040 | fprintf(out_fp, "%s\t%s\t%zu\t-1.0\t-1.0\t-1.0\t-1.0\t-1.00\t-1.00\tREAD_FAILED_LOAD\n",
| ~~^
| |
| unsigned int
| %llu
1041 | read_name.c_str(), ref_name.c_str(), record->core.pos);
| ~~~~~~~~~~~~~~~~
| |
| long long int
src/nanopolish_detect_polyi.cpp:1105:36: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'long long int' [-Wformat=]
1105 | fprintf(out_fp, "%s\t%s\t%zu\t%.1lf\t%.1lf\t%.1lf\t%.1lf\t%.2lf\t%.2lf\t%s\t%s\n",
| ~~^
| |
| unsigned int
| %llu
1106 | read_name.c_str(), ref_name.c_str(), record->core.pos,
| ~~~~~~~~~~~~~~~~
| |
| long long int
g++ -o src/nanopolish_fast5_check.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/nanopolish_fast5_check.cpp
g++ -o src/nanopolish_getmodel.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/nanopolish_getmodel.cpp
g++ -o src/nanopolish_haplotype.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/nanopolish_haplotype.cpp
src/nanopolish_haplotype.cpp: In member function 'void Haplotype::print_debug_info() const':
src/nanopolish_haplotype.cpp:172:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'unsigned int' [-Wformat=]
172 | fprintf(stderr, "[haplotype-debug] ctg: %s, position: %lu\n", m_ref_name.c_str(), m_ref_position);
| ~~^ ~~~~~~~~~~~~~~
| | |
| long unsigned int unsigned int
| %u
g++ -o src/nanopolish_index.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/nanopolish_index.cpp
g++ -o src/nanopolish_methyltrain.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/nanopolish_methyltrain.cpp
g++ -o src/nanopolish_phase_reads.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/nanopolish_phase_reads.cpp
g++ -o src/nanopolish_polya_estimator.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/nanopolish_polya_estimator.cpp
g++ -o src/nanopolish_raw_loader.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/nanopolish_raw_loader.cpp
src/nanopolish_polya_estimator.cpp: In function 'void estimate_polya_for_single_read(const ReadDB&, const faidx_t*, FILE*, const bam_hdr_t*, const bam1_t*, size_t, int, int)':
src/nanopolish_polya_estimator.cpp:765:40: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'long long int' [-Wformat=]
765 | fprintf(out_fp, "%s\t%s\t%zu\t-1.0\t-1.0\t-1.0\t-1.0\t-1.00\t-1.00\tREAD_FAILED_LOAD\n",
| ~~^
| |
| unsigned int
| %llu
766 | read_name.c_str(), ref_name.c_str(), record->core.pos);
| ~~~~~~~~~~~~~~~~
| |
| long long int
src/nanopolish_polya_estimator.cpp:823:36: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'long long int' [-Wformat=]
823 | fprintf(out_fp, "%s\t%s\t%zu\t%.1lf\t%.1lf\t%.1lf\t%.1lf\t%.2lf\t%.2lf\t%s\n",
| ~~^
| |
| unsigned int
| %llu
824 | read_name.c_str(), ref_name.c_str(), record->core.pos,
| ~~~~~~~~~~~~~~~~
| |
| long long int
g++ -o src/nanopolish_read_db.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/nanopolish_read_db.cpp
g++ -o src/nanopolish_scorereads.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/nanopolish_scorereads.cpp
g++ -o src/nanopolish_squiggle_read.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/nanopolish_squiggle_read.cpp
g++ -o src/nanopolish_train_poremodel_from_basecalls.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/nanopolish_train_poremodel_from_basecalls.cpp
g++ -o src/nanopolish_variant_db.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/nanopolish_variant_db.cpp
g++ -o src/nanopolish_vcf2fasta.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/nanopolish_vcf2fasta.cpp
g++ -o src/pore_model/nanopolish_model_names.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/pore_model/nanopolish_model_names.cpp
g++ -o src/pore_model/nanopolish_pore_model_set.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/pore_model/nanopolish_pore_model_set.cpp
g++ -o src/pore_model/nanopolish_poremodel.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/pore_model/nanopolish_poremodel.cpp
g++ -o src/training_core.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/training_core.cpp
cc -o src/thirdparty/fet.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/thirdparty/fet.c
cc -o src/thirdparty/scrappie/event_detection.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/thirdparty/scrappie/event_detection.c
cc -o src/thirdparty/scrappie/scrappie_common.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/thirdparty/scrappie/scrappie_common.c
cc -o src/thirdparty/stdaln.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/thirdparty/stdaln.c
g++ -o nanopolish -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/main/nanopolish.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/io/nanopolish_fast5_io.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_processor.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_detect_polyi.o src/nanopolish_extract.o src/nanopolish_fast5_check.o src/nanopolish_getmodel.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_polya_estimator.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/nanopolish_vcf2fasta.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/training_core.o src/thirdparty/fet.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/stdaln.o -lz -lrt -lhdf5 -lhts -lminimap2 -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
/usr/bin/make nanopolish_test
make[2]: Entering directory '/<<PKGBUILDDIR>>'
g++ -o src/test/nanopolish_test.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/test/nanopolish_test.cpp
g++ -o nanopolish_test -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -fPIC src/test/nanopolish_test.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/io/nanopolish_fast5_io.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_processor.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_detect_polyi.o src/nanopolish_extract.o src/nanopolish_fast5_check.o src/nanopolish_getmodel.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_polya_estimator.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/nanopolish_vcf2fasta.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/training_core.o src/thirdparty/fet.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/stdaln.o -lz -lrt -lhdf5 -lhts -lminimap2 -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
echo "Since we need the executable created inside build time test in autopkgtest this is enforced in dh_auto_build to circumvent nocheck."
Since we need the executable created inside build time test in autopkgtest this is enforced in dh_auto_build to circumvent nocheck.
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_auto_install -a
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
for pl in `find debian -name "*.pl"` ; do \
sed -i '1s?^#!/usr/bin/env.*perl?#!/usr/bin/perl?' ${pl} ; \
done
for pl in `grep -Rl '#![[:space:]]*/usr/bin/env *python' debian/*/usr/*` ; do \
sed -i '1s?^#!.*python.*?#!/usr/bin/python3?' ${pl} ; \
done
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_python3 -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_fixperms
find debian -name *.fast5 -exec chmod -x \{\} \;
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_missing -a
dh_dwz -a -a
dh_strip -a -a
dh_makeshlibs -a -a
dh_shlibdeps -a -a
dpkg-shlibdeps: warning: debian/nanopolish/usr/bin/nanopolish contains an unresolvable reference to symbol __aeabi_atexit@GLIBC_2.4: it's probably a plugin
dpkg-shlibdeps: warning: debian/nanopolish/usr/lib/nanopolish/nanopolish_test contains an unresolvable reference to symbol __aeabi_atexit@GLIBC_2.4: it's probably a plugin
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'nanopolish-dbgsym' in '../nanopolish-dbgsym_0.13.3-2_armhf.deb'.
dpkg-deb: building package 'nanopolish' in '../nanopolish_0.13.3-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../nanopolish_0.13.3-2_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 2021-08-27T06:37:08Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
nanopolish_0.13.3-2_armhf.changes:
----------------------------------
Format: 1.8
Date: Wed, 25 Aug 2021 01:51:10 +0530
Source: nanopolish
Binary: nanopolish nanopolish-dbgsym
Architecture: armhf
Version: 0.13.3-2
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Description:
nanopolish - consensus caller for nanopore sequencing data
Closes: 983767
Changes:
nanopolish (0.13.3-2) unstable; urgency=medium
.
* Team Upload.
* d/rules: Explicitly call $(MAKE) on nanopolish_test so as to
vendor the same even when nocheck is enabled (Closes: #983767)
* Bump Standards-Version to 4.6.0 (no changes needed)
* Bump debhelper compatibility level to 13
* Bump watch file version to 4
Checksums-Sha1:
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17067dae9265e7cc82d76970d6db94d7527dabe5 6725 nanopolish_0.13.3-2_armhf.buildinfo
4505e13a5398e9747ece216deef61ef61c045773 2183000 nanopolish_0.13.3-2_armhf.deb
Checksums-Sha256:
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d3f6b0feab5594b265997de36f2d996402fc3ba599b057cf0bd59ed34bf9cdbf 6725 nanopolish_0.13.3-2_armhf.buildinfo
8bce48515cf8f853e1a89157ca347ed091da6e47389d8cefa4c0c6bd345cb438 2183000 nanopolish_0.13.3-2_armhf.deb
Files:
ea867afe8f5285abe97c2738eff92e74 8167080 debug optional nanopolish-dbgsym_0.13.3-2_armhf.deb
8ede047e9507943fc6423b572ada29bd 6725 science optional nanopolish_0.13.3-2_armhf.buildinfo
7abde607662c87c9ba8b373db100c724 2183000 science optional nanopolish_0.13.3-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
nanopolish-dbgsym_0.13.3-2_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 8167080 bytes: control archive=652 bytes.
426 bytes, 12 lines control
302 bytes, 3 lines md5sums
Package: nanopolish-dbgsym
Source: nanopolish
Version: 0.13.3-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8541
Depends: nanopolish (= 0.13.3-2)
Section: debug
Priority: optional
Description: debug symbols for nanopolish
Build-Ids: 0869e34c47ae376c3d77c46fa06ab0e53a00472f c9932c6d773129df96f3dc1f9f9aa3124282218c
drwxr-xr-x root/root 0 2021-08-24 20:21 ./
drwxr-xr-x root/root 0 2021-08-24 20:21 ./usr/
drwxr-xr-x root/root 0 2021-08-24 20:21 ./usr/lib/
drwxr-xr-x root/root 0 2021-08-24 20:21 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-08-24 20:21 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-08-24 20:21 ./usr/lib/debug/.build-id/08/
-rw-r--r-- root/root 2981456 2021-08-24 20:21 ./usr/lib/debug/.build-id/08/69e34c47ae376c3d77c46fa06ab0e53a00472f.debug
drwxr-xr-x root/root 0 2021-08-24 20:21 ./usr/lib/debug/.build-id/c9/
-rw-r--r-- root/root 2570424 2021-08-24 20:21 ./usr/lib/debug/.build-id/c9/932c6d773129df96f3dc1f9f9aa3124282218c.debug
drwxr-xr-x root/root 0 2021-08-24 20:21 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-08-24 20:21 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 3179188 2021-08-24 20:21 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/nanopolish.debug
drwxr-xr-x root/root 0 2021-08-24 20:21 ./usr/share/
drwxr-xr-x root/root 0 2021-08-24 20:21 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-08-24 20:21 ./usr/share/doc/nanopolish-dbgsym -> nanopolish
nanopolish_0.13.3-2_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 2183000 bytes: control archive=2120 bytes.
894 bytes, 18 lines control
2320 bytes, 30 lines md5sums
283 bytes, 12 lines * postinst #!/bin/sh
394 bytes, 12 lines * prerm #!/bin/sh
Package: nanopolish
Version: 0.13.3-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 9385
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libhdf5-103-1, libhts3 (>= 1.10), libstdc++6 (>= 9), zlib1g (>= 1:1.1.4), python3:any, perl:any
Recommends: python3-biopython, python3-pysam
Suggests: perl, make
Section: science
Priority: optional
Homepage: https://github.com/jts/nanopolish
Description: consensus caller for nanopore sequencing data
Nanopolish uses a signal-level hidden Markov model for consensus calling
of nanopore genome sequencing data. It can perform signal-level analysis
of Oxford Nanopore sequencing data. Nanopolish can calculate an improved
consensus sequence for a draft genome assembly, detect base
modifications, call SNPs and indels with respect to a reference genome
and more.
drwxr-xr-x root/root 0 2021-08-24 20:21 ./
drwxr-xr-x root/root 0 2021-08-24 20:21 ./usr/
drwxr-xr-x root/root 0 2021-08-24 20:21 ./usr/bin/
-rwxr-xr-x root/root 3987816 2021-08-24 20:21 ./usr/bin/nanopolish
-rwxr-xr-x root/root 75 2021-04-22 19:08 ./usr/bin/nanopolish_makerange
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 164364
Build-Time: 1364
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 417
Job: nanopolish_0.13.3-2
Machine Architecture: armhf
Package: nanopolish
Package-Time: 1832
Source-Version: 0.13.3-2
Space: 164364
Status: successful
Version: 0.13.3-2
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Finished at 2021-08-27T06:37:08Z
Build needed 00:30:32, 164364k disc space