subread →
1.6.4+dfsg-1 →
armhf → 2019-07-13 13:51:23
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| subread 1.6.4+dfsg-1 (armhf) Sat, 13 Jul 2019 13:33:30 +0000 |
+==============================================================================+
Package: subread
Version: 1.6.4+dfsg-1
Source Version: 1.6.4+dfsg-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-af10b58b-5741-4308-90d5-fbc02846b4fa' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.4 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.0 MB]
Fetched 24.4 MB in 31s (786 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: 'subread' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/subread.git
Please use:
git clone https://salsa.debian.org/med-team/subread.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 15.8 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main subread 1.6.4+dfsg-1 (dsc) [2255 B]
Get:2 http://172.17.0.1/private bullseye-staging/main subread 1.6.4+dfsg-1 (tar) [15.8 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main subread 1.6.4+dfsg-1 (diff) [9008 B]
Fetched 15.8 MB in 6s (2694 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/subread-2udJPa/subread-1.6.4+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/subread-2udJPa' 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-mKKca6/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-mKKca6/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-mKKca6/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-mKKca6/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-mKKca6/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-mKKca6/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-mKKca6/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-mKKca6/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2749 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 20 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-mKKca6/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 (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12050 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 amd64 arm64 armel armhf i386 kfreebsd-amd64 kfreebsd-i386 ppc64el all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: bc, debhelper-compat (= 12), help2man, python, zlib1g-dev
Filtered Build-Depends: bc, debhelper-compat (= 12), help2man, python, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-subread-dummy' in '/<<BUILDDIR>>/resolver-mKKca6/apt_archive/sbuild-build-depends-subread-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-subread-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-mKKca6/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-mKKca6/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-mKKca6/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-mKKca6/apt_archive ./ Sources [513 B]
Get:5 copy:/<<BUILDDIR>>/resolver-mKKca6/apt_archive ./ Packages [593 B]
Fetched 2439 B in 1s (3226 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install subread 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 bc bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3
libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu63
libmagic-mgc libmagic1 libncurses6 libpipeline1 libpython-stdlib
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2
libssl1.1 libtinfo5 libtool libuchardet0 libxml2 m4 man-db mime-support
po-debconf python python-minimal python2 python2-minimal python2.7
python2.7-minimal sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl python-doc python-tk python2-doc python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libgpm2 libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bc bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3
libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu63
libmagic-mgc libmagic1 libncurses6 libpipeline1 libpython-stdlib
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2
libssl1.1 libtinfo5 libtool libuchardet0 libxml2 m4 man-db mime-support
po-debconf python python-minimal python2 python2-minimal python2.7
python2.7-minimal sbuild-build-depends-subread-dummy sensible-utils
zlib1g-dev
0 upgraded, 51 newly installed, 0 to remove and 20 not upgraded.
Need to get 24.0 MB of archives.
After this operation, 86.7 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-mKKca6/apt_archive ./ sbuild-build-depends-subread-dummy 0.invalid.0 [884 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.9.1-2 [104 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20181013-2 [309 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-3 [782 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.8.5-2 [1230 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-minimal armhf 2.7.16-2 [395 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf python2.7-minimal armhf 2.7.16-2 [1093 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf python2-minimal armhf 2.7.16-1 [41.4 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf python-minimal armhf 2.7.16-1 [21.0 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1c-1 [1259 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.62 [37.2 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.6-2 [77.1 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-stdlib armhf 2.7.16-2 [1844 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf python2.7 armhf 2.7.16-2 [305 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpython2-stdlib armhf 2.7.16-1 [20.8 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libpython-stdlib armhf 2.7.16-1 [20.8 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf python2 armhf 2.7.16-1 [41.6 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf python armhf 2.7.16-1 [22.8 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf bc armhf 1.07.1-2 [101 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.35-4 [242 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.35-4 [110 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.35-4 [65.3 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.58.3-2 [1077 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20181013-2 [78.6 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.1.1 [1016 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf help2man armhf 1.47.8 [176 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../24-libncurses6_6.1+20181013-2_armhf.deb ...
Unpacking libncurses6:armhf (6.1+20181013-2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../25-gettext_0.19.8.1-9_armhf.deb ...
Unpacking gettext (0.19.8.1-9) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../26-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../27-po-debconf_1.0.21_all.deb ...
Unpacking po-debconf (1.0.21) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../28-debhelper_12.1.1_all.deb ...
Unpacking debhelper (12.1.1) ...
Selecting previously unselected package help2man.
Preparing to unpack .../29-help2man_1.47.8_armhf.deb ...
Unpacking help2man (1.47.8) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../30-zlib1g-dev_1%3a1.2.11.dfsg-1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Selecting previously unselected package sbuild-build-depends-subread-dummy.
Preparing to unpack .../31-sbuild-build-depends-subread-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-subread-dummy (0.invalid.0) ...
Setting up libexpat1:armhf (2.2.6-2) ...
Setting up libpipeline1:armhf (1.5.1-2) ...
Setting up mime-support (3.62) ...
Setting up libmagic-mgc (1:5.35-4) ...
Setting up libarchive-zip-perl (1.64-1) ...
Setting up libglib2.0-0:armhf (2.58.3-2) ...
No schema files found: doing nothing.
Setting up libssl1.1:armhf (1.1.1c-1) ...
Setting up libmagic1:armhf (1:5.35-4) ...
Setting up gettext-base (0.19.8.1-9) ...
Setting up file (1:5.35-4) ...
Setting up libicu63:armhf (63.2-2) ...
Setting up libpython2.7-stdlib:armhf (2.7.16-2) ...
Setting up help2man (1.47.8) ...
Setting up autotools-dev (20180224.1) ...
Setting up libncurses6:armhf (6.1+20181013-2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up sensible-utils (0.0.12) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libbsd0:armhf (0.9.1-2) ...
Setting up libtinfo5:armhf (6.1+20181013-2) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+b1) ...
Setting up libfile-stripnondeterminism-perl (1.1.2-1) ...
Setting up python2.7 (2.7.16-2) ...
Setting up libtool (2.4.6-9) ...
Setting up libpython2-stdlib:armhf (2.7.16-1) ...
Setting up bc (1.07.1-2) ...
Setting up m4 (1.4.18-2) ...
Setting up python2 (2.7.16-1) ...
Setting up libpython-stdlib:armhf (2.7.16-1) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libcroco3:armhf (0.6.12-3) ...
Setting up autoconf (2.69-11) ...
Setting up dwz (0.12-3) ...
Setting up groff-base (1.22.4-3) ...
Setting up python (2.7.16-1) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-9) ...
Setting up man-db (2.8.5-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up po-debconf (1.0.21) ...
Setting up debhelper (12.1.1) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.1.2-1) ...
Setting up sbuild-build-depends-subread-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-10+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-16+rpi1 dpkg-dev_1.19.7 g++-8_8.3.0-6+rpi1 gcc-8_8.3.0-6+rpi1 libc6-dev_2.28-10+rpi1 libstdc++-8-dev_8.3.0-6+rpi1 libstdc++6_8.3.0-6+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.3+rpi1 base-passwd_3.5.46 bash_5.0-4 bc_1.07.1-2 binutils_2.31.1-16+rpi1 binutils-arm-linux-gnueabihf_2.31.1-16+rpi1 binutils-common_2.31.1-16+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.6 bzip2_1.0.6-9.1 coreutils_8.30-3 cpp_4:8.3.0-1+rpi2 cpp-8_8.3.0-6+rpi1 dash_0.5.10.2-5 debconf_1.5.71 debhelper_12.1.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.2-1 diffutils_1:3.7-3 dirmngr_2.2.12-1+rpi1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.12-3 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-4 findutils_4.6.0+git+20190209-2 g++_4:8.3.0-1+rpi2 g++-8_8.3.0-6+rpi1 gcc_4:8.3.0-1+rpi2 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1+b1 gcc-7-base_7.3.0-19 gcc-8_8.3.0-6+rpi1 gcc-8-base_8.3.0-6+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 help2man_1.47.8 hostname_3.21 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapt-pkg5.0_1.8.2 libarchive-zip-perl_1.64-1 libasan5_8.3.0-6+rpi1 libassuan0_2.5.2-1 libatomic1_8.3.0-6+rpi1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.4-3 libaudit1_1:2.8.4-3 libbinutils_2.31.1-16+rpi1 libblkid1_2.33.1-0.1 libbsd0_0.9.1-2 libbz2-1.0_1.0.6-9.1 libc-bin_2.28-10+rpi1 libc-dev-bin_2.28-10+rpi1 libc6_2.28-10+rpi1 libc6-dev_2.28-10+rpi1 libcap-ng0_0.7.9-2 libcc1-0_8.3.0-6+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libdb5.3_5.3.28+dfsg1-0.5 libdebconfclient0_0.249 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.6-2 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.2-1 libgcc-8-dev_8.3.0-6+rpi1 libgcc1_1:8.3.0-6+rpi1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4 libgdbm6_1.18.1-4 libglib2.0-0_2.58.3-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.7-4 libgomp1_8.3.0-6+rpi1 libgpg-error0_1.35-1 libhogweed4_3.4.1-1 libicu63_63.2-2 libidn2-0_2.0.5-1 libisl19_0.20-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-3+rpi1 libldap-common_2.4.47+dfsg-3+rpi1 liblocale-gettext-perl_1.07-3+b3 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-4 libmagic1_1:5.35-4 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses6_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libnpth0_1.6-1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libpython-stdlib_2.7.16-1 libpython2-stdlib_2.7.16-1 libpython2.7-minimal_2.7.16-2 libpython2.7-stdlib_2.7.16-2 libreadline7_7.0-5 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.27.2-3 libss2_1.44.5-1 libssl1.1_1.1.1c-1 libstdc++-8-dev_8.3.0-6+rpi1 libstdc++6_8.3.0-6+rpi1 libsystemd0_241-5+rpi1 libtasn1-6_4.13-3 libtext-charwidth-perl_0.04-7.1+b1 libtext-iconv-perl_1.7-5+b10 libtext-wrapi18n-perl_0.06-7.1 libtinfo5_6.1+20181013-2 libtinfo6_6.1+20181013-2 libtool_2.4.6-9 libubsan1_8.3.0-6+rpi1 libuchardet0_0.0.6-3 libudev1_241-5+rpi1 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.8+dfsg-3+rpi1 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2019051400+rpi1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-2 mawk_1.3.3-17 mime-support_3.62 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 netbase_5.6 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pinentry-curses_1.1.0-2 po-debconf_1.0.21 python_2.7.16-1 python-minimal_2.7.16-1 python2_2.7.16-1 python2-minimal_2.7.16-1 python2.7_2.7.16-2 python2.7-minimal_2.7.16-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-subread-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-8 tar_1.30+dfsg-6 tzdata_2019a-1 util-linux_2.33.1-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Jul 10 19:44:28 2019 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./subread_1.6.4+dfsg-1.dsc
dpkg-source: info: extracting subread in /<<BUILDDIR>>/subread-1.6.4+dfsg
dpkg-source: info: unpacking subread_1.6.4+dfsg.orig.tar.xz
dpkg-source: info: unpacking subread_1.6.4+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying typo.patch
dpkg-source: info: applying fix_ftbfs_kfreebsd.patch
dpkg-source: info: applying arch_specific_flags.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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-af10b58b-5741-4308-90d5-fbc02846b4fa
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package subread
dpkg-buildpackage: info: source version 1.6.4+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.6.4+dfsg'
cd src; make -f Makefile.Linux clean
make[2]: Entering directory '/<<BUILDDIR>>/subread-1.6.4+dfsg/src'
rm -f core featureCounts exactSNP removeDup subread-buildindex core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o
make[2]: Leaving directory '/<<BUILDDIR>>/subread-1.6.4+dfsg/src'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/subread.substvars debian/subread-data.substvars debian/files
rm -fr -- debian/subread/ debian/tmp/ debian/subread-data/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.6.4+dfsg'
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.6.4+dfsg'
cd src; make -f Makefile.Linux
make[2]: Entering directory '/<<BUILDDIR>>/subread-1.6.4+dfsg/src'
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c
input-files.c: In function 'f_subr_open':
input-files.c:50:10: warning: implicit declaration of function 'fopen64'; did you mean 'gzopen64'? [-Wimplicit-function-declaration]
return fopen64(fname, mode);
^~~~~~~
gzopen64
input-files.c:50:10: warning: returning 'int' from a function with return type 'FILE *' {aka 'struct _IO_FILE *'} makes pointer from integer without a cast [-Wint-conversion]
return fopen64(fname, mode);
^~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'SAM_nosort_run_once':
input-files.c:5258:23: warning: argument 1 value '4294967295' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
char * header_txt = malloc(max(1000000,pairer->BAM_l_text));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from input-files.c:24:
/usr/include/stdlib.h:539:14: note: in a call to allocation function 'malloc' declared here
extern void *malloc (size_t __size) __THROW __attribute_malloc__ __wur;
^~~~~~
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c
long-hashtable.c: In function 'lnhash_create':
long-hashtable.c:43:45: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '8589934592' to '0' [-Woverflow]
the_table -> key_repeated_numbers = malloc(sizeof(short) * 0x100000000llu);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o genRandomReads gen_rand_reads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o detectionCall detection-calls.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
In file included from detection-calls.c:8:
detection-calls.c: In function 'DTCprint_lentab_items':
detection-calls.c:160:16: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=]
SUBREADprintf("%s => %ld\n", (char*)key, hashed_obj - NULL);
^~~~~~~~~~~~~
subread.h:125:44: note: in definition of macro 'SUBREADprintf'
#define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
^~~~~~~~~~~
echo " " > longread-one/make.version
rm -f longread-one/*.o
cd longread-one && make
make[3]: Entering directory '/<<BUILDDIR>>/subread-1.6.4+dfsg/src/longread-one'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.4"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMsorted-hashtable.o LRMsorted-hashtable.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.4"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMbase-index.o LRMbase-index.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.4"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMchro-event.o LRMchro-event.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.4"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMhelper.o LRMhelper.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.4"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMseek-zlib.o LRMseek-zlib.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.4"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMfile-io.o LRMfile-io.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.4"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMhashtable.o LRMhashtable.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.4"\" -fmessage-length=0 -ggdb -o LRM longread-mapping.c LRMsorted-hashtable.o LRMbase-index.o LRMchro-event.o LRMhelper.o LRMseek-zlib.o LRMfile-io.o LRMhashtable.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
make[3]: Leaving directory '/<<BUILDDIR>>/subread-1.6.4+dfsg/src/longread-one'
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o txUnique tx-unique.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
SNPCalling.c: In function 'main':
SNPCalling.c:1474:32: warning: '/temp-snps-' directive writing 11 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
sprintf(temp_file_prefix, "%s/temp-snps-%06u-%s-", temp_location, getpid(), mac_rand);
^~~~~~~~~~~
SNPCalling.c:1474:29: note: using the range [0, 4294967295] for directive argument
sprintf(temp_file_prefix, "%s/temp-snps-%06u-%s-", temp_location, getpid(), mac_rand);
^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from SNPCalling.c:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 20 and 335 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
SUBindel.c: In function 'load_global_context_forindel':
SUBindel.c:66:24: warning: '.reads' directive writing 6 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.reads", context->config.index_prefix);
^~~~~~
In file included from /usr/include/stdio.h:873,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 306 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c:77:25: warning: '.00.b.tab' directive writing 9 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.00.b.tab", context->config.index_prefix);
^~~~~~~~~
In file included from /usr/include/stdio.h:873,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 309 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c:75:25: warning: '.00.c.tab' directive writing 9 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.00.c.tab", context->config.index_prefix);
^~~~~~~~~
In file included from /usr/include/stdio.h:873,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 309 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c:87:26: warning: '%02d' directive writing between 2 and 11 bytes into a region of size between 0 and 299 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.%02d.%c.tab", context->config.index_prefix, context->index_block_number, context->config.space_type == GENE_SPACE_COLOR?'c':'b');
^~~~
In file included from /usr/include/stdio.h:873,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 318 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c: In function 'load_indexes_forindel':
SUBindel.c:110:26: warning: '%02d' directive writing between 2 and 10 bytes into a region of size between 0 and 299 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b');
^~~~
SUBindel.c:110:22: note: directive argument in the range [0, 2147483647]
sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b');
^~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:873,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 12 and 319 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.4"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fmessage-length=0 -ggdb -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
mkdir -p ../bin/utilities
mv longread-one/LRM longread-one/sublong
mv longread-one/sublong subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/
mv detectionCall genRandomReads repair propmapped qualityScores removeDup subread-fullscan txUnique flattenGTF ../bin/utilities
###########################################################
# #
# Installation successfully completed. #
# #
# Generated executables were copied to directory ../bin/ #
# #
###########################################################
make[2]: Leaving directory '/<<BUILDDIR>>/subread-1.6.4+dfsg/src'
dh_auto_build -- CC=arm-linux-gnueabihf-gcc
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.6.4+dfsg'
rm -f debian/subread.debhelper.log
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.6.4+dfsg'
debian/tests/subread-tests /<<BUILDDIR>>/subread-1.6.4+dfsg
[2J[0;0H[30;47m
**************************************************
**************************************************
*** ***
*** This script will test the major functions ***
*** in our package, including the index build- ***
*** er, subread-align, subjunc, featureCounts ***
*** and exactSNP. ***
*** ***
*** Test will start in seconds. ***
*** ***
**************************************************
**************************************************
[13;26H[33;44m9[13;26H8[13;26H7[13;26H6[13;26H5[13;26H4[13;26H3[13;26H2[13;26H1[13;26H0[0m[2J[0,0H
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.4
//================================= setting ==================================\\
|| ||
|| Index name : small1 ||
|| Index space : base space ||
|| Index split : ns ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
|| Input files : 1 file in total ||
|| o chr901.fa ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Check the integrity of provided reference sequences ... ||
|| There were 4 notes for reference sequences. ||
|| The notes can be found in the log file, '../small1.log'. ||
|| Scan uninformative subreads in reference sequences ... ||
|| 52 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=15.1k bps/s ||
|| 16%, 0 mins elapsed, rate=28.7k bps/s ||
|| 25%, 0 mins elapsed, rate=40.7k bps/s ||
|| 33%, 0 mins elapsed, rate=51.7k bps/s ||
|| 41%, 0 mins elapsed, rate=61.9k bps/s ||
|| 50%, 0 mins elapsed, rate=71.4k bps/s ||
|| 58%, 0 mins elapsed, rate=80.2k bps/s ||
|| 66%, 0 mins elapsed, rate=86.5k bps/s ||
|| 75%, 0 mins elapsed, rate=93.5k bps/s ||
|| 83%, 0 mins elapsed, rate=100.3k bps/s ||
|| 91%, 0 mins elapsed, rate=107.6k bps/s ||
|| Save current index block... ||
|| [ 0.0% finished ] ||
|| [ 10.0% finished ] ||
|| [ 20.0% finished ] ||
|| [ 30.0% finished ] ||
|| [ 40.0% finished ] ||
|| [ 50.0% finished ] ||
|| [ 60.0% finished ] ||
|| [ 70.0% finished ] ||
|| [ 80.0% finished ] ||
|| [ 90.0% finished ] ||
|| [ 100.0% finished ] ||
|| ||
|| Total running time: 0.5 minutes. ||
|| Index ../small1 was successfully built! ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.4
//================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file : test-noerror-r1.fq ||
|| Output file : test-tmp.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 64 ||
|| Min votes : 3 / 10 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : no ||
|| Max alignments per multi-mapping read : 1 ||
|| ||
\\============================================================================//
//================ Running (13-Jul-2019 13:47:29, pid=29534) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [9,9] ||
|| Load the 1-th index block... ||
|| 33% completed, 0.1 mins elapsed, rate=10.6k reads per second ||
|| 39% completed, 0.1 mins elapsed, rate=10.6k reads per second ||
|| 46% completed, 0.1 mins elapsed, rate=10.6k reads per second ||
|| 53% completed, 0.1 mins elapsed, rate=10.6k reads per second ||
|| 60% completed, 0.1 mins elapsed, rate=10.7k reads per second ||
|| 74% completed, 0.1 mins elapsed, rate=2.3k reads per second ||
|| 83% completed, 0.1 mins elapsed, rate=2.4k reads per second ||
|| 91% completed, 0.1 mins elapsed, rate=2.5k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total reads : 19998 ||
|| Mapped : 18757 (93.8%) ||
|| Uniquely mapped : 18757 ||
|| Multi-mapping : 0 ||
|| ||
|| Unmapped : 1241 ||
|| ||
|| Indels : 3 ||
|| ||
|| Running time : 0.1 minutes ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.4
//================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file : test-noerror-r1.fq ||
|| Output file : test-tmp.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 64 ||
|| Min votes : 3 / 10 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : no ||
|| Max alignments per multi-mapping read : 1 ||
|| ||
\\============================================================================//
//================ Running (13-Jul-2019 13:47:39, pid=29538) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [9,9] ||
|| Load the 1-th index block... ||
|| 33% completed, 0.1 mins elapsed, rate=10.8k reads per second ||
|| 39% completed, 0.1 mins elapsed, rate=10.8k reads per second ||
|| 46% completed, 0.1 mins elapsed, rate=10.8k reads per second ||
|| 53% completed, 0.1 mins elapsed, rate=10.8k reads per second ||
|| 60% completed, 0.1 mins elapsed, rate=10.8k reads per second ||
|| 74% completed, 0.1 mins elapsed, rate=2.3k reads per second ||
|| 83% completed, 0.1 mins elapsed, rate=2.4k reads per second ||
|| 91% completed, 0.1 mins elapsed, rate=2.5k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total reads : 19998 ||
|| Mapped : 18757 (93.8%) ||
|| Uniquely mapped : 18757 ||
|| Multi-mapping : 0 ||
|| ||
|| Unmapped : 1241 ||
|| ||
|| Indels : 3 ||
|| ||
|| Running time : 0.1 minutes ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.4
//================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : test-noerror-r1.fq ||
|| Input file 2 : test-noerror-r2.fq ||
|| Output file : test-tmp.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 64 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : no ||
|| Max alignments per multi-mapping read : 1 ||
|| ||
\\============================================================================//
//================ Running (13-Jul-2019 13:47:49, pid=29542) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [9,9] ||
|| Load the 1-th index block... ||
|| 33% completed, 0.1 mins elapsed, rate=4.7k fragments per second ||
|| 39% completed, 0.1 mins elapsed, rate=4.7k fragments per second ||
|| 46% completed, 0.1 mins elapsed, rate=4.6k fragments per second ||
|| 53% completed, 0.1 mins elapsed, rate=4.6k fragments per second ||
|| 60% completed, 0.1 mins elapsed, rate=4.7k fragments per second ||
|| 74% completed, 0.1 mins elapsed, rate=1.7k fragments per second ||
|| 83% completed, 0.2 mins elapsed, rate=1.8k fragments per second ||
|| 91% completed, 0.2 mins elapsed, rate=1.8k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total fragments : 19998 ||
|| Mapped : 19216 (96.1%) ||
|| Uniquely mapped : 19216 ||
|| Multi-mapping : 0 ||
|| ||
|| Unmapped : 782 ||
|| ||
|| Properly paired : 18827 ||
|| Not properly paired : 389 ||
|| Singleton : 4 ||
|| Chimeric : 0 ||
|| Unexpected strandness : 0 ||
|| Unexpected fragment length : 385 ||
|| Unexpected read order : 0 ||
|| ||
|| Indels : 14 ||
|| ||
|| Running time : 0.2 minutes ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.4
//================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : test-noerror-r1.fq ||
|| Input file 2 : test-noerror-r2.fq ||
|| Output file : test-tmp.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 64 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : no ||
|| Max alignments per multi-mapping read : 1 ||
|| ||
\\============================================================================//
//================ Running (13-Jul-2019 13:48:03, pid=29571) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [9,9] ||
|| Load the 1-th index block... ||
|| 33% completed, 0.1 mins elapsed, rate=4.7k fragments per second ||
|| 39% completed, 0.1 mins elapsed, rate=4.5k fragments per second ||
|| 46% completed, 0.1 mins elapsed, rate=4.6k fragments per second ||
|| 53% completed, 0.1 mins elapsed, rate=4.6k fragments per second ||
|| 60% completed, 0.1 mins elapsed, rate=4.7k fragments per second ||
|| 74% completed, 0.2 mins elapsed, rate=1.6k fragments per second ||
|| 83% completed, 0.2 mins elapsed, rate=1.6k fragments per second ||
|| 91% completed, 0.2 mins elapsed, rate=1.6k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total fragments : 19998 ||
|| Mapped : 19216 (96.1%) ||
|| Uniquely mapped : 19216 ||
|| Multi-mapping : 0 ||
|| ||
|| Unmapped : 782 ||
|| ||
|| Properly paired : 18827 ||
|| Not properly paired : 389 ||
|| Singleton : 4 ||
|| Chimeric : 0 ||
|| Unexpected strandness : 0 ||
|| Unexpected fragment length : 385 ||
|| Unexpected read order : 0 ||
|| ||
|| Indels : 14 ||
|| ||
|| Running time : 0.2 minutes ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.4
//================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : test-error-r1.fq ||
|| Input file 2 : test-error-r2.fq ||
|| Output file : test-tmp.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 64 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : no ||
|| Max alignments per multi-mapping read : 1 ||
|| ||
\\============================================================================//
//================ Running (13-Jul-2019 13:48:18, pid=29793) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [-14,-14] ||
|| Load the 1-th index block... ||
|| 33% completed, 0.1 mins elapsed, rate=5.0k fragments per second ||
|| 39% completed, 0.1 mins elapsed, rate=5.1k fragments per second ||
|| 46% completed, 0.1 mins elapsed, rate=5.1k fragments per second ||
|| 53% completed, 0.1 mins elapsed, rate=4.9k fragments per second ||
|| 60% completed, 0.1 mins elapsed, rate=5.0k fragments per second ||
|| 74% completed, 0.1 mins elapsed, rate=1.7k fragments per second ||
|| 83% completed, 0.2 mins elapsed, rate=1.7k fragments per second ||
|| 91% completed, 0.2 mins elapsed, rate=1.8k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total fragments : 20000 ||
|| Mapped : 18697 (93.5%) ||
|| Uniquely mapped : 18697 ||
|| Multi-mapping : 0 ||
|| ||
|| Unmapped : 1303 ||
|| ||
|| Properly paired : 13917 ||
|| Not properly paired : 4780 ||
|| Singleton : 4502 ||
|| Chimeric : 0 ||
|| Unexpected strandness : 0 ||
|| Unexpected fragment length : 273 ||
|| Unexpected read order : 5 ||
|| ||
|| Indels : 31 ||
|| ||
|| Running time : 0.2 minutes ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.4
//================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : test-err-mut-r1.fq.gz ||
|| Input file 2 : test-err-mut-r2.fq.gz ||
|| Output file : test-tmp.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 64 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : no ||
|| Max alignments per multi-mapping read : 1 ||
|| Read group name : MyTestGroup ||
|| ||
\\============================================================================//
//================ Running (13-Jul-2019 13:48:32, pid=29797) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [-14,-14] ||
|| Load the 1-th index block... ||
|| 34% completed, 0.1 mins elapsed, rate=5.3k fragments per second ||
|| 40% completed, 0.1 mins elapsed, rate=5.4k fragments per second ||
|| 48% completed, 0.1 mins elapsed, rate=5.5k fragments per second ||
|| 53% completed, 0.1 mins elapsed, rate=5.5k fragments per second ||
|| 59% completed, 0.1 mins elapsed, rate=5.6k fragments per second ||
|| 67% completed, 0.1 mins elapsed, rate=5.6k fragments per second ||
|| 75% completed, 0.1 mins elapsed, rate=1.7k fragments per second ||
|| 83% completed, 0.1 mins elapsed, rate=1.8k fragments per second ||
|| 92% completed, 0.2 mins elapsed, rate=1.9k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total fragments : 20001 ||
|| Mapped : 18660 (93.3%) ||
|| Uniquely mapped : 18660 ||
|| Multi-mapping : 0 ||
|| ||
|| Unmapped : 1341 ||
|| ||
|| Properly paired : 13560 ||
|| Not properly paired : 5100 ||
|| Singleton : 4786 ||
|| Chimeric : 0 ||
|| Unexpected strandness : 0 ||
|| Unexpected fragment length : 309 ||
|| Unexpected read order : 5 ||
|| ||
|| Indels : 161 ||
|| ||
|| Running time : 0.2 minutes ||
|| ||
\\============================================================================//
76f6c2a84c5097b13435bbeac4a8acd8 ../small1.00.b.array
25531897eb452b012b95ae4b1ca08fd7 ../small1.00.b.tab
*************************************************
*** SINGLE-END READS NO ERROR ******
*************************************************
unmatched= 0 ; matched= 18757 ; unmapped= 1241 ; reads= 19998 ;NN= 0
accuracy= 1.0 ; sensitivity= 0.937943794379
paired_match= 0 ; paired= 0.0
*************************************************
*** SINGLE-END READS NO ERROR NO DUP ******
*************************************************
unmatched= 0 ; matched= 18757 ; unmapped= 1241 ; reads= 19998 ;NN= 0
accuracy= 1.0 ; sensitivity= 0.937943794379
paired_match= 0 ; paired= 0.0
*************************************************
*** READS WITH NO ERROR ******
*************************************************
unmatched= 0 ; matched= 38428 ; unmapped= 1568 ; reads= 39996 ;NN= 0
accuracy= 1.0 ; sensitivity= 0.960796079608
paired_match= 38424 ; paired= 0.999895909233
*************************************************
*** READS NO ERROR, NO DUPLICATED REPORT ******
*************************************************
unmatched= 0 ; matched= 38428 ; unmapped= 1568 ; reads= 39996 ;NN= 0
accuracy= 1.0 ; sensitivity= 0.960796079608
paired_match= 38424 ; paired= 0.999895909233
*************************************************
*** READS WITH ONLY SEQUENCING ERROR ******
*************************************************
unmatched= 10 ; matched= 32882 ; unmapped= 7108 ; reads= 40000 ;NN= 0
accuracy= 0.999695974705 ; sensitivity= 0.8223
paired_match= 28380 ; paired= 0.863086186972
*************************************************
*** READS WITH SEQUENCING ERROR AND MUTATION ***
*** SUBREAD IS RUN WITH LONG INDEL DETECTION ***
*************************************************
unmatched= 13 ; matched= 32519 ; unmapped= 7468 ; reads= 40002 ;NN= 0
accuracy= 0.999600393459 ; sensitivity= 0.813259337033
paired_match= 27736 ; paired= 0.852916756358
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.4
//================================= setting ==================================\\
|| ||
|| Index name : small1 ||
|| Index space : base space ||
|| Memory : 3000 Mbytes ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : yes ||
|| ||
|| Input files : 1 file in total ||
|| o chr901.fa ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Check the integrity of provided reference sequences ... ||
|| There were 4 notes for reference sequences. ||
|| The notes can be found in the log file, '../small1.log'. ||
|| Scan uninformative subreads in reference sequences ... ||
|| 2 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=32.1k bps/s ||
|| 16%, 0 mins elapsed, rate=61.6k bps/s ||
|| 25%, 0 mins elapsed, rate=88.9k bps/s ||
|| 33%, 0 mins elapsed, rate=114.1k bps/s ||
|| 41%, 0 mins elapsed, rate=137.4k bps/s ||
|| 50%, 0 mins elapsed, rate=159.0k bps/s ||
|| 58%, 0 mins elapsed, rate=179.2k bps/s ||
|| 66%, 0 mins elapsed, rate=198.3k bps/s ||
|| 75%, 0 mins elapsed, rate=216.2k bps/s ||
|| 83%, 0 mins elapsed, rate=232.9k bps/s ||
|| 91%, 0 mins elapsed, rate=249.3k bps/s ||
|| Save current index block... ||
|| [ 0.0% finished ] ||
|| [ 10.0% finished ] ||
|| [ 20.0% finished ] ||
|| [ 30.0% finished ] ||
|| [ 40.0% finished ] ||
|| [ 50.0% finished ] ||
|| [ 60.0% finished ] ||
|| [ 70.0% finished ] ||
|| [ 80.0% finished ] ||
|| [ 90.0% finished ] ||
|| [ 100.0% finished ] ||
|| ||
|| Total running time: 0.1 minutes. ||
|| Index ../small1 was successfully built! ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.4
//================================= setting ==================================\\
|| ||
|| Function : Read alignment + Junction detection (RNA-Seq) ||
|| Input file 1 : junction-reads-A.fq ||
|| Input file 2 : junction-reads-B.fq ||
|| Output file : junctions.sam (SAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 14 ||
|| Min read1 vote : 1 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : no ||
|| Max alignments per multi-mapping read : 1 ||
|| ||
\\============================================================================//
//================ Running (13-Jul-2019 13:48:53, pid=29805) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [2,41] ||
|| Load the 1-th index block... ||
|| 41% completed, 0.1 mins elapsed, rate=2.9k fragments per second ||
|| 48% completed, 0.1 mins elapsed, rate=2.9k fragments per second ||
|| 54% completed, 0.1 mins elapsed, rate=2.9k fragments per second ||
|| 61% completed, 0.1 mins elapsed, rate=2.9k fragments per second ||
|| 77% completed, 0.1 mins elapsed, rate=1.4k fragments per second ||
|| 87% completed, 0.2 mins elapsed, rate=1.5k fragments per second ||
|| 97% completed, 0.2 mins elapsed, rate=1.5k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total fragments : 16052 ||
|| Mapped : 15251 (95.0%) ||
|| Uniquely mapped : 15251 ||
|| Multi-mapping : 0 ||
|| ||
|| Unmapped : 801 ||
|| ||
|| Properly paired : 13854 ||
|| Not properly paired : 1397 ||
|| Singleton : 966 ||
|| Chimeric : 0 ||
|| Unexpected strandness : 37 ||
|| Unexpected fragment length : 332 ||
|| Unexpected read order : 62 ||
|| ||
|| Junctions : 416 ||
|| Indels : 182 ||
|| ||
|| Running time : 0.2 minutes ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.4
//================================= setting ==================================\\
|| ||
|| Function : Read alignment + Junction/Fusion detection (RNA-Seq) ||
|| Input file 1 : junction-reads-A.fq ||
|| Input file 2 : junction-reads-B.fq ||
|| Output file : junctionsNfusions.bam (BAM) ||
|| Index name : small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 28 ||
|| Min read1 vote : 1 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : no ||
|| Max alignments per multi-mapping read : 1 ||
|| ||
\\============================================================================//
//================ Running (13-Jul-2019 13:49:05, pid=29807) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [2,41] ||
|| Load the 1-th index block... ||
|| 41% completed, 0.1 mins elapsed, rate=1.7k fragments per second ||
|| 48% completed, 0.1 mins elapsed, rate=1.7k fragments per second ||
|| 54% completed, 0.1 mins elapsed, rate=1.7k fragments per second ||
|| 61% completed, 0.1 mins elapsed, rate=1.7k fragments per second ||
|| 77% completed, 0.2 mins elapsed, rate=1.2k fragments per second ||
|| 87% completed, 0.2 mins elapsed, rate=1.2k fragments per second ||
|| 97% completed, 0.2 mins elapsed, rate=1.2k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total fragments : 16052 ||
|| Mapped : 15241 (94.9%) ||
|| Uniquely mapped : 15241 ||
|| Multi-mapping : 0 ||
|| ||
|| Unmapped : 811 ||
|| ||
|| Properly paired : 13759 ||
|| Not properly paired : 1482 ||
|| Singleton : 1017 ||
|| Chimeric : 0 ||
|| Unexpected strandness : 37 ||
|| Unexpected fragment length : 366 ||
|| Unexpected read order : 62 ||
|| ||
|| Junctions : 434 ||
|| Fusions : 32 ||
|| Indels : 182 ||
|| ||
|| Running time : 0.2 minutes ||
|| ||
\\============================================================================//
================================================================================
FeatureCounts Basic Test
http://subread.sourceforge.net/
================================================================================
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.4
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 SAM file ||
|| P test-minimum.sam ||
|| ||
|| Output file : test-minimum.FC ||
|| Summary : test-minimum.FC.summary ||
|| Annotation : test-minimum.GTF (GTF) ||
|| Dir for temp files : result ||
|| ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file test-minimum.GTF ... ||
|| Features : 23 ||
|| Meta-features : 7 ||
|| Chromosomes/contigs : 3 ||
|| ||
|| Process SAM file test-minimum.sam... ||
|| Paired-end reads are included. ||
|| Assign alignments to features... ||
|| Total alignments : 998 ||
|| Successfully assigned alignments : 389 (39.0%) ||
|| Running time : 0.00 minutes ||
|| ||
|| ||
|| Summary of counting results can be found in file "result/test-minimum.FC. ||
|| summary" ||
|| ||
\\============================================================================//
================================================================================
Basic Test finished.
The results are in result/test-minimum.FC
================================================================================
================================================================================
FeatureCounts Chromosome Name Aliases Tests
http://subread.sourceforge.net/
================================================================================
Testing chromosome aliases ... [[32mPASS[0m]
================================================================================
FeatureCounts Chromosome Name Inference Tests
http://subread.sourceforge.net/
================================================================================
Testing automatic inference of chromosome names ... [[32mPASS[0m]
================================================================================
FeatureCounts Corner Case Tests
http://subread.sourceforge.net/
================================================================================
Testing indel reads ... [[32mPASS[0m]
Testing junction reads ... [[32mPASS[0m]
Testing paired-end reads (fragment counting) ... [[32mPASS[0m]
Testing paired-end reads (fragment counting, both ends mapped) ... [[32mPASS[0m]
Testing multi-overlapping reads ... [[32mPASS[0m]
Testing feature-level summarization ... [[32mPASS[0m]
Testing gene-level summarization ... [[32mPASS[0m]
Testing multi-mapping reads ... [[32mPASS[0m]
Testing multi-mapping reads (primary only) ... [[32mPASS[0m]
Testing both ends mapped ... [[32mPASS[0m]
Testing disallowing chimeric fragments ... [[32mPASS[0m]
Testing Allowing multi-mapped reads ... [[32mPASS[0m]
Testing not sorting input file ... [[32mPASS[0m]
Testing minimum overlapping length ... [[32mPASS[0m]
Testing minimum overlapping fraction ... [[32mPASS[0m]
Testing Largest Overlapping ... [[32mPASS[0m]
Testing paired-end distance ... [[32mPASS[0m]
Testing Read to position (5' end) ... [[32mPASS[0m]
Testing Read to position (3' end) ... [[32mPASS[0m]
Testing Read extension to the 3' end ... [[32mPASS[0m]
Testing Read extension to the 5' end ... [[32mPASS[0m]
Testing Low maxOPs value ... [[32mPASS[0m]
Testing minimum mapping quality ... [[32mPASS[0m]
Testing Ignoring duplicated reads ... [[32mPASS[0m]
Testing Fraction counting ... [[32mPASS[0m]
Testing Advanced fractions ... [[32mPASS[0m]
Testing Junction counting ... [[32mPASS[0m,[32mPASS[0m]
Skipping Junction counting (with genome).
Testing GTF format annotations ... [[32mPASS[0m]
Testing SAF format annotations ... [[32mPASS[0m]
Testing SAM format input ... [[32mPASS[0m]
Testing BAM format input ... [[32mPASS[0m]
Testing unstranded read summarization ... [[32mPASS[0m]
Testing stranded read summarization ... [[32mPASS[0m]
Testing reversely stranded read summarization ... [[32mPASS[0m]
Testing Ignoring duplicate fragments ... [[32mPASS[0m]
Testing Junction reads only ... [[32mPASS[0m]
Testing Exonic reads only ... [[32mPASS[0m]
Testing intron_between ... [[32mPASS[0m]
Testing intron_between ... [[32mPASS[0m]
Testing intron_between ... [[32mPASS[0m]
Testing intron_between ... [[32mPASS[0m]
Testing across_genes ... [[32mPASS[0m]
Testing across_genes ... [[32mPASS[0m]
Testing across_genes ... [[32mPASS[0m]
Testing across_genes ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
../../bin/exactSNP -g ../chr901.fa -o result/test-out.VCF -i data/test-in.BAM -b
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.4
//============================= exactSNP setting =============================\\
|| ||
|| Input file : test-in.BAM (BAM) ||
|| Output file : test-out.VCF ||
|| Reference genome : chr901.fa ||
|| Temp path : ||
|| ||
|| Threads : 1 ||
|| Min supporting reads : 1 ||
|| Min pct. of supporting reads : 0.0% ||
|| Min base quality score : 13 ||
|| Number of trimmed bases : 3 ||
|| ||
|| Q value cutoff : 10E-12.0 ||
|| P value upper bound : 0.00500 ||
|| Flanking windows size : 5 ||
|| ||
\\============================================================================//
//====================== Running (13-Jul-2019 13:49:24) ======================\\
|| ||
|| Split BAM file into result/temp-snps-030346-001F7BB4051E-* ... ||
|| processed block chr901@999950 by thread 1/1 [block number=1/1] ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed reads : 50204 ||
|| Reported SNPs : 415 ||
|| Reported indels : 21 ||
|| ||
|| Running time : 0.1 minutes ||
|| ||
\\============================================================================//
[30;47m
**************************************************
**************************************************
*** ***
*** Test finished. ***
*** ***
*** Should there be any error, please visit ***
*** [34mhttp://subread.sourceforge.net/[0;30;47m for more ***
*** information. ***
*** ***
**************************************************
**************************************************
[0m
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.6.4+dfsg'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
rm -f -- debian/subread.substvars
rm -fr -- debian/.debhelper/generated/subread/ debian/subread/ debian/tmp/
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.6.4+dfsg'
find /<<BUILDDIR>>/subread-1.6.4+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \;
mkdir -p /<<BUILDDIR>>/subread-1.6.4+dfsg/debian/subread/usr/share/man/man1
help2man --no-info --help-option="''" --no-discard-stderr --name='an accurate and efficient aligner for mapping both genomic \
DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \
/<<BUILDDIR>>/subread-1.6.4+dfsg/bin/subread-align | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.4+dfsg/debian/subread/usr/share/man/man1/subread-align.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='builds an base-space or color-space index using the reference sequences' \
/<<BUILDDIR>>/subread-1.6.4+dfsg/bin/subread-buildindex | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.4+dfsg/debian/subread/usr/share/man/man1/subread-buildindex.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='an RNA-seq aligner suitable for all purposes of RNA-seq analyses' \
/<<BUILDDIR>>/subread-1.6.4+dfsg/bin/subjunc | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.4+dfsg/debian/subread/usr/share/man/man1/subjunc.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='a highly efficient and accurate read summarization program' \
/<<BUILDDIR>>/subread-1.6.4+dfsg/bin/featureCounts | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.4+dfsg/debian/subread/usr/share/man/man1/featureCounts.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='a SNP caller that discovers SNPs by testing signals against local background noises' \
/<<BUILDDIR>>/subread-1.6.4+dfsg/bin/exactSNP | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.4+dfsg/debian/subread/usr/share/man/man1/exactSNP.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='detect short and long indels' \
/<<BUILDDIR>>/subread-1.6.4+dfsg/bin/subindel | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.4+dfsg/debian/subread/usr/share/man/man1/subindel.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='long-read aligner that is designed based on seed-and-vote' \
/<<BUILDDIR>>/subread-1.6.4+dfsg/bin/sublong| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.4+dfsg/debian/subread/usr/share/man/man1/sublong.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='scans the entire genome and reports all matches of a specified sequence' \
/<<BUILDDIR>>/subread-1.6.4+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.4+dfsg/debian/subread/usr/share/man/man1/subread-fullscan.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='calculate the proportion of mapped reads/fragments' \
/<<BUILDDIR>>/subread-1.6.4+dfsg/bin/utilities/propmapped | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.4+dfsg/debian/subread/usr/share/man/man1/propmapped.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='retrieve Phred score for read bases' \
/<<BUILDDIR>>/subread-1.6.4+dfsg/bin/utilities/qualityScores| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.4+dfsg/debian/subread/usr/share/man/man1/qualityScores.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='Find reads that are from the same pair in the input and then place them next \
to each other in the output. A dummy read is added for each singleton read that does not have a pair. \
The output file is compatible with featureCounts program' \
/<<BUILDDIR>>/subread-1.6.4+dfsg/bin/utilities/repair| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.4+dfsg/debian/subread/usr/share/man/man1/repair.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='Remove duplicated reads' \
/<<BUILDDIR>>/subread-1.6.4+dfsg/bin/utilities/removeDup| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.4+dfsg/debian/subread/usr/share/man/man1/removeDup.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='Flatten features included in a GTF annotation and save the modified annotation \
to a SAF format file.' \
/<<BUILDDIR>>/subread-1.6.4+dfsg/bin/utilities/flattenGTF| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.4+dfsg/debian/subread/usr/share/man/man1/flattenGTF.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='helper tool from subread suite' \
/<<BUILDDIR>>/subread-1.6.4+dfsg/bin/utilities/genRandomReads| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.4+dfsg/debian/subread/usr/share/man/man1/genRandomReads.1;
dh_auto_install
install -d /<<BUILDDIR>>/subread-1.6.4\+dfsg/debian/tmp
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.6.4+dfsg'
dh_install -a
install -d debian/subread/usr/bin
cp --reflink=auto -a ./bin/exactSNP ./bin/featureCounts ./bin/subindel ./bin/subjunc ./bin/sublong ./bin/subread-align ./bin/subread-buildindex debian/subread/usr/bin/
install -d debian/subread/usr/lib/subread
cp --reflink=auto -a ./bin/utilities/flattenGTF ./bin/utilities/genRandomReads ./bin/utilities/propmapped ./bin/utilities/qualityScores ./bin/utilities/removeDup ./bin/utilities/repair ./bin/utilities/subread-fullscan ./bin/utilities/txUnique debian/subread/usr/lib/subread/
install -d debian/.debhelper/generated/subread
install -d debian/.debhelper/generated/subread-data
dh_installdocs -a
install -d debian/subread/usr/share/doc/subread
cp --reflink=auto -a ./README.txt debian/subread/usr/share/doc/subread
chown -R 0:0 debian/subread/usr/share/doc
chmod -R u\+rw,go=rX debian/subread/usr/share/doc
install -p -m0644 debian/README.Debian debian/subread/usr/share/doc/subread/README.Debian
install -p -m0644 debian/copyright debian/subread/usr/share/doc/subread/copyright
dh_installchangelogs -a
install -p -m0644 debian/changelog debian/subread/usr/share/doc/subread/changelog.Debian
dh_installman -a
man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/subread-align.1 > debian/subread/usr/share/man/man1/subread-align.1.dh-new
man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/exactSNP.1 > debian/subread/usr/share/man/man1/exactSNP.1.dh-new
man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/propmapped.1 > debian/subread/usr/share/man/man1/propmapped.1.dh-new
man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/flattenGTF.1 > debian/subread/usr/share/man/man1/flattenGTF.1.dh-new
mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1
man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/genRandomReads.1 > debian/subread/usr/share/man/man1/genRandomReads.1.dh-new
mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1
man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/qualityScores.1 > debian/subread/usr/share/man/man1/qualityScores.1.dh-new
mv debian/subread/usr/share/man/man1/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1
man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/subread-buildindex.1 > debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new
mv debian/subread/usr/share/man/man1/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.1
man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/subindel.1 > debian/subread/usr/share/man/man1/subindel.1.dh-new
mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1
man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/sublong.1 > debian/subread/usr/share/man/man1/sublong.1.dh-new
mv debian/subread/usr/share/man/man1/genRandomReads.1.dh-new debian/subread/usr/share/man/man1/genRandomReads.1
chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1
mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.1
man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/subjunc.1 > debian/subread/usr/share/man/man1/subjunc.1.dh-new
mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1
man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/repair.1 > debian/subread/usr/share/man/man1/repair.1.dh-new
mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1
man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/featureCounts.1 > debian/subread/usr/share/man/man1/featureCounts.1.dh-new
mv debian/subread/usr/share/man/man1/repair.1.dh-new debian/subread/usr/share/man/man1/repair.1
man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/removeDup.1 > debian/subread/usr/share/man/man1/removeDup.1.dh-new
mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1
man -l --recode UTF-8 ./debian/subread/usr/share/man/man1/subread-fullscan.1 > debian/subread/usr/share/man/man1/subread-fullscan.1.dh-new
mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1
chmod 0644 -- debian/subread/usr/share/man/man1/subread-align.1 debian/subread/usr/share/man/man1/subread-buildindex.1 debian/subread/usr/share/man/man1/subjunc.1 debian/subread/usr/share/man/man1/featureCounts.1
mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.1
chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 debian/subread/usr/share/man/man1/repair.1 debian/subread/usr/share/man/man1/removeDup.1
mv debian/subread/usr/share/man/man1/subread-fullscan.1.dh-new debian/subread/usr/share/man/man1/subread-fullscan.1
chmod 0644 -- debian/subread/usr/share/man/man1/exactSNP.1 debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-fullscan.1
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
cd debian/subread
chmod a-x usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1
gzip -9nf usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1
cd '/<<BUILDDIR>>/subread-1.6.4+dfsg'
dh_fixperms -a
find debian/subread -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/subread ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/subread/usr/share/doc -type f -a -true -a ! -regex 'debian/subread/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/subread/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/subread/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/subread -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/subread/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
find debian/subread/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
dh_missing -a
dh_dwz -a
install -d debian/subread/usr/lib/debug/.dwz/arm-linux-gnueabihf
dwz -q -mdebian/subread/usr/lib/debug/.dwz/arm-linux-gnueabihf/subread.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/subread.debug -- debian/subread/usr/bin/exactSNP debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/bin/sublong debian/subread/usr/bin/subread-align debian/subread/usr/bin/subread-buildindex debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/txUnique
objcopy --compress-debug-sections debian/subread/usr/lib/debug/.dwz/arm-linux-gnueabihf/subread.debug
dh_strip -a
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/53
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/53/3cd1a08b435a7cc582dfccc96d9a1342278d80.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/53/3cd1a08b435a7cc582dfccc96d9a1342278d80.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/53/3cd1a08b435a7cc582dfccc96d9a1342278d80.debug
strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/exactSNP
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/53/3cd1a08b435a7cc582dfccc96d9a1342278d80.debug debian/subread/usr/bin/exactSNP
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ec
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ec/9ec6b612e381ee8d416977d38b265478c18e1f.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ec/9ec6b612e381ee8d416977d38b265478c18e1f.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ec/9ec6b612e381ee8d416977d38b265478c18e1f.debug
strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/featureCounts
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ec/9ec6b612e381ee8d416977d38b265478c18e1f.debug debian/subread/usr/bin/featureCounts
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70/7093d3cf5ab3ba0c5f522985376ca98bab1f4f.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70/7093d3cf5ab3ba0c5f522985376ca98bab1f4f.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70/7093d3cf5ab3ba0c5f522985376ca98bab1f4f.debug
strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subindel
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70/7093d3cf5ab3ba0c5f522985376ca98bab1f4f.debug debian/subread/usr/bin/subindel
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8a
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8a/196b5ebc78a7acbc2c82a378baf9f0b82157ad.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8a/196b5ebc78a7acbc2c82a378baf9f0b82157ad.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8a/196b5ebc78a7acbc2c82a378baf9f0b82157ad.debug
strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subjunc
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8a/196b5ebc78a7acbc2c82a378baf9f0b82157ad.debug debian/subread/usr/bin/subjunc
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/90
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/90/442afaa4f82f6af3a703a7e275ca9f832dcfc5.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/90/442afaa4f82f6af3a703a7e275ca9f832dcfc5.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/90/442afaa4f82f6af3a703a7e275ca9f832dcfc5.debug
strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/sublong
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/90/442afaa4f82f6af3a703a7e275ca9f832dcfc5.debug debian/subread/usr/bin/sublong
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70/e9b32cb13888ba1c99374b46d2f9b77798d8f2.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70/e9b32cb13888ba1c99374b46d2f9b77798d8f2.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70/e9b32cb13888ba1c99374b46d2f9b77798d8f2.debug
strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-align
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/70/e9b32cb13888ba1c99374b46d2f9b77798d8f2.debug debian/subread/usr/bin/subread-align
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e1
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e1/9522470afddcc73ea92c2c9d7edb446fab3e08.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e1/9522470afddcc73ea92c2c9d7edb446fab3e08.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e1/9522470afddcc73ea92c2c9d7edb446fab3e08.debug
strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-buildindex
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e1/9522470afddcc73ea92c2c9d7edb446fab3e08.debug debian/subread/usr/bin/subread-buildindex
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2d
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2d/0c028847b8b9860f07ecf279013af90f411a9e.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2d/0c028847b8b9860f07ecf279013af90f411a9e.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2d/0c028847b8b9860f07ecf279013af90f411a9e.debug
strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/flattenGTF
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2d/0c028847b8b9860f07ecf279013af90f411a9e.debug debian/subread/usr/lib/subread/flattenGTF
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6/b4506d718de5cbc50b00621a063dc741dc400d.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6/b4506d718de5cbc50b00621a063dc741dc400d.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6/b4506d718de5cbc50b00621a063dc741dc400d.debug
strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/genRandomReads
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c6/b4506d718de5cbc50b00621a063dc741dc400d.debug debian/subread/usr/lib/subread/genRandomReads
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/56
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/56/e599f3450d54d1000c0013e0bd691513c6084b.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/56/e599f3450d54d1000c0013e0bd691513c6084b.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/56/e599f3450d54d1000c0013e0bd691513c6084b.debug
strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/propmapped
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/56/e599f3450d54d1000c0013e0bd691513c6084b.debug debian/subread/usr/lib/subread/propmapped
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3f
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3f/954e31bdfc9f0f5c461b2a717193b55033017b.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3f/954e31bdfc9f0f5c461b2a717193b55033017b.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3f/954e31bdfc9f0f5c461b2a717193b55033017b.debug
strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/qualityScores
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3f/954e31bdfc9f0f5c461b2a717193b55033017b.debug debian/subread/usr/lib/subread/qualityScores
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e9
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e9/49507f4d2c39b217c6b42474a3aa2b1bbe499b.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e9/49507f4d2c39b217c6b42474a3aa2b1bbe499b.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e9/49507f4d2c39b217c6b42474a3aa2b1bbe499b.debug
strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/removeDup
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e9/49507f4d2c39b217c6b42474a3aa2b1bbe499b.debug debian/subread/usr/lib/subread/removeDup
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/63
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/63/0ea95798472840345b8c14bb9d3e302ff23f5e.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/63/0ea95798472840345b8c14bb9d3e302ff23f5e.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/63/0ea95798472840345b8c14bb9d3e302ff23f5e.debug
strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/repair
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/63/0ea95798472840345b8c14bb9d3e302ff23f5e.debug debian/subread/usr/lib/subread/repair
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/db
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/db/05699c8d4daffcf61d83f1e47bc73e45353c78.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/db/05699c8d4daffcf61d83f1e47bc73e45353c78.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/db/05699c8d4daffcf61d83f1e47bc73e45353c78.debug
strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/subread-fullscan
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/db/05699c8d4daffcf61d83f1e47bc73e45353c78.debug debian/subread/usr/lib/subread/subread-fullscan
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0b
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0b/ef33c5721b704e3a8ced928412f9d2e02a4512.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0b/ef33c5721b704e3a8ced928412f9d2e02a4512.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0b/ef33c5721b704e3a8ced928412f9d2e02a4512.debug
strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/txUnique
objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0b/ef33c5721b704e3a8ced928412f9d2e02a4512.debug debian/subread/usr/lib/subread/txUnique
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz
cp --reflink=auto -a debian/subread/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz
rm -fr debian/subread/usr/lib/debug/.dwz
rmdir -p --ignore-fail-on-non-empty debian/subread/usr/lib/debug
install -d debian/.debhelper/subread/dbgsym-root/usr/share/doc
ln -s subread debian/.debhelper/subread/dbgsym-root/usr/share/doc/subread-dbgsym
dh_makeshlibs -a
rm -f debian/subread/DEBIAN/shlibs
dh_shlibdeps -a
install -d debian/subread/DEBIAN
dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/bin/exactSNP debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/bin/sublong debian/subread/usr/bin/subread-align debian/subread/usr/bin/subread-buildindex debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/txUnique
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/bin/featureCounts debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/repair debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/subjunc debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/bin/subindel debian/subread/usr/lib/subread/removeDup debian/subread/usr/bin/exactSNP debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/bin/subread-align debian/subread/usr/bin/sublong debian/subread/usr/lib/subread/txUnique were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
echo misc:Depends= >> debian/subread.substvars
echo misc:Pre-Depends= >> debian/subread.substvars
install -d debian/.debhelper/subread/dbgsym-root/DEBIAN
dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -Pdebian/.debhelper/subread/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=subread-dbgsym "-DDepends=subread (= \${binary:Version})" "-DDescription=debug symbols for subread" "-DBuild-Ids=0bef33c5721b704e3a8ced928412f9d2e02a4512 2d0c028847b8b9860f07ecf279013af90f411a9e 3f954e31bdfc9f0f5c461b2a717193b55033017b 533cd1a08b435a7cc582dfccc96d9a1342278d80 56e599f3450d54d1000c0013e0bd691513c6084b 630ea95798472840345b8c14bb9d3e302ff23f5e 707093d3cf5ab3ba0c5f522985376ca98bab1f4f 70e9b32cb13888ba1c99374b46d2f9b77798d8f2 8a196b5ebc78a7acbc2c82a378baf9f0b82157ad 90442afaa4f82f6af3a703a7e275ca9f832dcfc5 c6b4506d718de5cbc50b00621a063dc741dc400d db05699c8d4daffcf61d83f1e47bc73e45353c78 e19522470afddcc73ea92c2c9d7edb446fab3e08 e949507f4d2c39b217c6b42474a3aa2b1bbe499b ec9ec6b612e381ee8d416977d38b265478c18e1f" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/control
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/control
dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -Pdebian/subread -UMulti-Arch
chmod 0644 -- debian/subread/DEBIAN/control
chown 0:0 -- debian/subread/DEBIAN/control
dh_md5sums -a
cd debian/subread >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/subread/DEBIAN/md5sums
chown 0:0 -- debian/subread/DEBIAN/md5sums
cd debian/.debhelper/subread/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/md5sums
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --build debian/subread ..
dpkg-deb --build debian/.debhelper/subread/dbgsym-root ..
dpkg-deb: building package 'subread' in '../subread_1.6.4+dfsg-1_armhf.deb'.
dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_1.6.4+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../subread_1.6.4+dfsg-1_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 2019-07-13T13:51:09Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
subread_1.6.4+dfsg-1_armhf.changes:
-----------------------------------
Format: 1.8
Date: Tue, 30 Apr 2019 10:58:08 +0200
Source: subread
Binary: subread subread-dbgsym
Architecture: armhf
Version: 1.6.4+dfsg-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Alexandre Mestiashvili <mestia@debian.org>
Description:
subread - toolkit for processing next-gen sequencing data
Changes:
subread (1.6.4+dfsg-1) unstable; urgency=medium
.
* Update d/watch, add uversionmangle to remove -source suffix
* New upstream version 1.6.4+dfsg
* Refresh patches, update typo.patch
* Switch to debhelper-compat, drop d/compat
* Install genRandomReads binary and generate man page
Checksums-Sha1:
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1c71aa11ced4abbaf26a68cf7fbc4b4d735d96c2 5030 subread_1.6.4+dfsg-1_armhf.buildinfo
f5d8dc6d31febe2a9829fdf03347c547e0d632d0 450652 subread_1.6.4+dfsg-1_armhf.deb
Checksums-Sha256:
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e27b14dc75add6bd5f3d40b202d92dbb0e8fba85fb1ce8f5ca89ce55519580ae 5030 subread_1.6.4+dfsg-1_armhf.buildinfo
a956d7620ab3572430c611b413c08e05864f3cb80c3b0ae65ef57802eac00602 450652 subread_1.6.4+dfsg-1_armhf.deb
Files:
4080aafd5c6038e03d00f79d65d6640d 7305236 debug optional subread-dbgsym_1.6.4+dfsg-1_armhf.deb
c0a27c72bd1d6bd9652de69e4ae71684 5030 science optional subread_1.6.4+dfsg-1_armhf.buildinfo
535977de4c29693e56e294f214cc728b 450652 science optional subread_1.6.4+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
subread-dbgsym_1.6.4+dfsg-1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 7305236 bytes: control archive=1284 bytes.
955 bytes, 12 lines control
1677 bytes, 16 lines md5sums
Package: subread-dbgsym
Source: subread
Version: 1.6.4+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8679
Depends: subread (= 1.6.4+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for subread
Build-Ids: 0bef33c5721b704e3a8ced928412f9d2e02a4512 2d0c028847b8b9860f07ecf279013af90f411a9e 3f954e31bdfc9f0f5c461b2a717193b55033017b 533cd1a08b435a7cc582dfccc96d9a1342278d80 56e599f3450d54d1000c0013e0bd691513c6084b 630ea95798472840345b8c14bb9d3e302ff23f5e 707093d3cf5ab3ba0c5f522985376ca98bab1f4f 70e9b32cb13888ba1c99374b46d2f9b77798d8f2 8a196b5ebc78a7acbc2c82a378baf9f0b82157ad 90442afaa4f82f6af3a703a7e275ca9f832dcfc5 c6b4506d718de5cbc50b00621a063dc741dc400d db05699c8d4daffcf61d83f1e47bc73e45353c78 e19522470afddcc73ea92c2c9d7edb446fab3e08 e949507f4d2c39b217c6b42474a3aa2b1bbe499b ec9ec6b612e381ee8d416977d38b265478c18e1f
drwxr-xr-x root/root 0 2019-04-30 08:58 ./
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/debug/.build-id/0b/
-rw-r--r-- root/root 608568 2019-04-30 08:58 ./usr/lib/debug/.build-id/0b/ef33c5721b704e3a8ced928412f9d2e02a4512.debug
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/debug/.build-id/2d/
-rw-r--r-- root/root 603560 2019-04-30 08:58 ./usr/lib/debug/.build-id/2d/0c028847b8b9860f07ecf279013af90f411a9e.debug
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/debug/.build-id/3f/
-rw-r--r-- root/root 605880 2019-04-30 08:58 ./usr/lib/debug/.build-id/3f/954e31bdfc9f0f5c461b2a717193b55033017b.debug
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/debug/.build-id/53/
-rw-r--r-- root/root 642864 2019-04-30 08:58 ./usr/lib/debug/.build-id/53/3cd1a08b435a7cc582dfccc96d9a1342278d80.debug
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/debug/.build-id/56/
-rw-r--r-- root/root 606600 2019-04-30 08:58 ./usr/lib/debug/.build-id/56/e599f3450d54d1000c0013e0bd691513c6084b.debug
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/debug/.build-id/63/
-rw-r--r-- root/root 601892 2019-04-30 08:58 ./usr/lib/debug/.build-id/63/0ea95798472840345b8c14bb9d3e302ff23f5e.debug
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/debug/.build-id/70/
-rw-r--r-- root/root 603332 2019-04-30 08:58 ./usr/lib/debug/.build-id/70/7093d3cf5ab3ba0c5f522985376ca98bab1f4f.debug
-rw-r--r-- root/root 609064 2019-04-30 08:58 ./usr/lib/debug/.build-id/70/e9b32cb13888ba1c99374b46d2f9b77798d8f2.debug
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/debug/.build-id/8a/
-rw-r--r-- root/root 609112 2019-04-30 08:58 ./usr/lib/debug/.build-id/8a/196b5ebc78a7acbc2c82a378baf9f0b82157ad.debug
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/debug/.build-id/90/
-rw-r--r-- root/root 106620 2019-04-30 08:58 ./usr/lib/debug/.build-id/90/442afaa4f82f6af3a703a7e275ca9f832dcfc5.debug
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/debug/.build-id/c6/
-rw-r--r-- root/root 621620 2019-04-30 08:58 ./usr/lib/debug/.build-id/c6/b4506d718de5cbc50b00621a063dc741dc400d.debug
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/debug/.build-id/db/
-rw-r--r-- root/root 602392 2019-04-30 08:58 ./usr/lib/debug/.build-id/db/05699c8d4daffcf61d83f1e47bc73e45353c78.debug
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/debug/.build-id/e1/
-rw-r--r-- root/root 626028 2019-04-30 08:58 ./usr/lib/debug/.build-id/e1/9522470afddcc73ea92c2c9d7edb446fab3e08.debug
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/debug/.build-id/e9/
-rw-r--r-- root/root 608064 2019-04-30 08:58 ./usr/lib/debug/.build-id/e9/49507f4d2c39b217c6b42474a3aa2b1bbe499b.debug
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/debug/.build-id/ec/
-rw-r--r-- root/root 751808 2019-04-30 08:58 ./usr/lib/debug/.build-id/ec/9ec6b612e381ee8d416977d38b265478c18e1f.debug
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 45312 2019-04-30 08:58 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/subread.debug
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/share/
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-04-30 08:58 ./usr/share/doc/subread-dbgsym -> subread
subread_1.6.4+dfsg-1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 450652 bytes: control archive=1568 bytes.
622 bytes, 14 lines control
2126 bytes, 33 lines md5sums
Package: subread
Version: 1.6.4+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5413
Depends: libc6 (>= 2.7), zlib1g (>= 1:1.2.3.3)
Section: science
Priority: optional
Homepage: http://sourceforge.net/projects/subread/
Description: toolkit for processing next-gen sequencing data
Subread aligner can be used to align both gDNA-seq and RNA-seq reads.
Subjunc aligner was specified designed for the detection of exon-exon
junction. For the mapping of RNA-seq reads, Subread performs local
alignments and Subjunc performs global alignments.
drwxr-xr-x root/root 0 2019-04-30 08:58 ./
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/bin/
-rwxr-xr-x root/root 403884 2019-04-30 08:58 ./usr/bin/exactSNP
-rwxr-xr-x root/root 478060 2019-04-30 08:58 ./usr/bin/featureCounts
-rwxr-xr-x root/root 375228 2019-04-30 08:58 ./usr/bin/subindel
-rwxr-xr-x root/root 384332 2019-04-30 08:58 ./usr/bin/subjunc
-rwxr-xr-x root/root 63104 2019-04-30 08:58 ./usr/bin/sublong
-rwxr-xr-x root/root 384284 2019-04-30 08:58 ./usr/bin/subread-align
-rwxr-xr-x root/root 391572 2019-04-30 08:58 ./usr/bin/subread-buildindex
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/lib/subread/
-rwxr-xr-x root/root 375180 2019-04-30 08:58 ./usr/lib/subread/flattenGTF
-rwxr-xr-x root/root 387756 2019-04-30 08:58 ./usr/lib/subread/genRandomReads
-rwxr-xr-x root/root 375228 2019-04-30 08:58 ./usr/lib/subread/propmapped
-rwxr-xr-x root/root 375340 2019-04-30 08:58 ./usr/lib/subread/qualityScores
-rwxr-xr-x root/root 375180 2019-04-30 08:58 ./usr/lib/subread/removeDup
-rwxr-xr-x root/root 375180 2019-04-30 08:58 ./usr/lib/subread/repair
-rwxr-xr-x root/root 371084 2019-04-30 08:58 ./usr/lib/subread/subread-fullscan
-rwxr-xr-x root/root 375180 2019-04-30 08:58 ./usr/lib/subread/txUnique
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/share/
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/share/doc/subread/
-rw-r--r-- root/root 692 2019-04-30 08:58 ./usr/share/doc/subread/README.Debian
-rw-r--r-- root/root 3850 2019-03-11 01:26 ./usr/share/doc/subread/README.txt
-rw-r--r-- root/root 2841 2019-04-30 08:58 ./usr/share/doc/subread/changelog.Debian.gz
-rw-r--r-- root/root 1130 2019-04-30 08:58 ./usr/share/doc/subread/copyright
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/share/man/
drwxr-xr-x root/root 0 2019-04-30 08:58 ./usr/share/man/man1/
-rw-r--r-- root/root 1189 2019-04-30 08:58 ./usr/share/man/man1/exactSNP.1.gz
-rw-r--r-- root/root 3420 2019-04-30 08:58 ./usr/share/man/man1/featureCounts.1.gz
-rw-r--r-- root/root 457 2019-04-30 08:58 ./usr/share/man/man1/flattenGTF.1.gz
-rw-r--r-- root/root 1019 2019-04-30 08:58 ./usr/share/man/man1/genRandomReads.1.gz
-rw-r--r-- root/root 472 2019-04-30 08:58 ./usr/share/man/man1/propmapped.1.gz
-rw-r--r-- root/root 577 2019-04-30 08:58 ./usr/share/man/man1/qualityScores.1.gz
-rw-r--r-- root/root 519 2019-04-30 08:58 ./usr/share/man/man1/removeDup.1.gz
-rw-r--r-- root/root 602 2019-04-30 08:58 ./usr/share/man/man1/repair.1.gz
-rw-r--r-- root/root 367 2019-04-30 08:58 ./usr/share/man/man1/subindel.1.gz
-rw-r--r-- root/root 2308 2019-04-30 08:58 ./usr/share/man/man1/subjunc.1.gz
-rw-r--r-- root/root 577 2019-04-30 08:58 ./usr/share/man/man1/sublong.1.gz
-rw-r--r-- root/root 2384 2019-04-30 08:58 ./usr/share/man/man1/subread-align.1.gz
-rw-r--r-- root/root 716 2019-04-30 08:58 ./usr/share/man/man1/subread-buildindex.1.gz
-rw-r--r-- root/root 369 2019-04-30 08:58 ./usr/share/man/man1/subread-fullscan.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 128820
Build-Time: 532
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 458
Job: subread_1.6.4+dfsg-1
Machine Architecture: armhf
Package: subread
Package-Time: 1059
Source-Version: 1.6.4+dfsg-1
Space: 128820
Status: successful
Version: 1.6.4+dfsg-1
--------------------------------------------------------------------------------
Finished at 2019-07-13T13:51:09Z
Build needed 00:17:39, 128820k disc space