subread →
2.0.0+dfsg-2 →
armhf → 2020-04-22 11:15:09
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| subread 2.0.0+dfsg-2 (armhf) Wed, 22 Apr 2020 11:07:04 +0000 |
+==============================================================================+
Package: subread
Version: 2.0.0+dfsg-2
Source Version: 2.0.0+dfsg-2
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-daa49e58-c168-4f29-bbe3-7c0a47610d23' 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 [11.6 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.4 MB in 10s (2492 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 2.0.0+dfsg-2 (dsc) [2296 B]
Get:2 http://172.17.0.1/private bullseye-staging/main subread 2.0.0+dfsg-2 (tar) [15.8 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main subread 2.0.0+dfsg-2 (diff) [9992 B]
Fetched 15.8 MB in 3s (4653 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/subread-MgYbpv/subread-2.0.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/subread-MgYbpv' 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-VussyP/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-VussyP/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-VussyP/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-VussyP/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-VussyP/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-VussyP/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-VussyP/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-VussyP/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (9662 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 3 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-VussyP/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12224 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, python3, zlib1g-dev
Filtered Build-Depends: bc, debhelper-compat (= 12), help2man, python3, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-subread-dummy' in '/<<BUILDDIR>>/resolver-VussyP/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-VussyP/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-VussyP/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-VussyP/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-VussyP/apt_archive ./ Sources [512 B]
Get:5 copy:/<<BUILDDIR>>/resolver-VussyP/apt_archive ./ Packages [594 B]
Fetched 2439 B in 0s (11.2 kB/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 packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
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
libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl
libglib2.0-0 libicu63 liblocale-gettext-perl libmagic-mgc libmagic1
libmpdec2 libncurses6 libpipeline1 libpython3-stdlib libpython3.8-minimal
libpython3.8-stdlib libsigsegv2 libssl1.1 libsub-override-perl libtinfo5
libtool libuchardet0 libxml2 m4 man-db mime-support po-debconf python3
python3-minimal python3.8 python3.8-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 python3-doc python3-tk python3-venv
python3.8-venv python3.8-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
libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl
libglib2.0-0 libicu63 liblocale-gettext-perl libmagic-mgc libmagic1
libmpdec2 libncurses6 libpipeline1 libpython3-stdlib libpython3.8-minimal
libpython3.8-stdlib libsigsegv2 libssl1.1 libsub-override-perl libtinfo5
libtool libuchardet0 libxml2 m4 man-db mime-support po-debconf python3
python3-minimal python3.8 python3.8-minimal
sbuild-build-depends-subread-dummy sensible-utils zlib1g-dev
0 upgraded, 52 newly installed, 0 to remove and 3 not upgraded.
Need to get 25.2 MB of archives.
After this operation, 91.0 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-VussyP/apt_archive ./ sbuild-build-depends-subread-dummy 0.invalid.0 [884 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf liblocale-gettext-perl armhf 1.07-4 [18.1 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.2-1 [318 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.1-1 [1262 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1f-1 [1272 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-minimal armhf 3.8.2-1 [744 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3.8-minimal armhf 3.8.2-1 [1628 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.8.2-3 [37.6 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-3 [68.1 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-stdlib armhf 3.8.2-1 [1597 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf python3.8 armhf 3.8.2-1 [410 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.8.2-3 [20.8 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.8.2-3 [63.7 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2-1 [79.5 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf bc armhf 1.07.1-2+b1 [101 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-4 [262 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-4 [112 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-4 [66.9 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [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 1.4.18-4 [185 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [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 1:1.16.2-1 [775 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 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 libdebhelper-perl all 12.10 [184 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.8.0-1 [24.2 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.8.0-1 [14.8 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.1-1 [1157 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-3 [7987 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-4 [592 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.10 [1003 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf help2man armhf 1.47.13 [180 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libglib2.0-0:armhf (2.64.1-1) ...
Selecting previously unselected package libicu63:armhf.
Preparing to unpack .../24-libicu63_63.2-3_armhf.deb ...
Unpacking libicu63:armhf (63.2-3) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../25-libxml2_2.9.10+dfsg-4_armhf.deb ...
Unpacking libxml2:armhf (2.9.10+dfsg-4) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../26-libcroco3_0.6.13-1_armhf.deb ...
Unpacking libcroco3:armhf (0.6.13-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../27-gettext_0.19.8.1-10_armhf.deb ...
Unpacking gettext (0.19.8.1-10) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../28-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 .../29-po-debconf_1.0.21_all.deb ...
Unpacking po-debconf (1.0.21) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../30-debhelper_12.10_all.deb ...
Unpacking debhelper (12.10) ...
Selecting previously unselected package help2man.
Preparing to unpack .../31-help2man_1.47.13_armhf.deb ...
Unpacking help2man (1.47.13) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../32-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Selecting previously unselected package sbuild-build-depends-subread-dummy.
Preparing to unpack .../33-sbuild-build-depends-subread-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-subread-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.2-2) ...
Setting up mime-support (3.64) ...
Setting up libmagic-mgc (1:5.38-4) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.64.1-1) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (12.10) ...
Setting up libmagic1:armhf (1:5.38-4) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-4) ...
Setting up libicu63:armhf (63.2-3) ...
Setting up autotools-dev (20180224.1) ...
Setting up libncurses6:armhf (6.2-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libmpdec2:armhf (2.4.2-3) ...
Setting up libpython3.8-stdlib:armhf (3.8.2-1) ...
Setting up python3.8 (3.8.2-1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.2-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.10+dfsg-4) ...
Setting up liblocale-gettext-perl (1.07-4) ...
Setting up libpython3-stdlib:armhf (3.8.2-3) ...
Setting up libfile-stripnondeterminism-perl (1.8.0-1) ...
Setting up libtool (2.4.6-14) ...
Setting up bc (1.07.1-2+b1) ...
Setting up m4 (1.4.18-4) ...
Setting up python3 (3.8.2-3) ...
Setting up help2man (1.47.13) ...
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 (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.8.0-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-4) ...
Setting up automake (1:1.16.2-1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up man-db (2.9.1-1) ...
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 dh-autoreconf (19) ...
Setting up debhelper (12.10) ...
Setting up sbuild-build-depends-subread-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.30-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.34-5+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-10+rpi1 gcc-9_9.3.0-10+rpi1 libc6-dev_2.30-4+rpi1 libstdc++-9-dev_9.3.0-10+rpi1 libstdc++6_10-20200324-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.0.2 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 bc_1.07.1-2+b1 binutils_2.34-5+rpi1 binutils-arm-linux-gnueabihf_2.34-5+rpi1 binutils-common_2.34-5+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-10+rpi1 dash_0.5.10.2-7 debconf_1.5.73 debhelper_12.10 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.8.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-10+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10-20200324-1+rpi1 gcc-9_9.3.0-10+rpi1 gcc-9-base_9.3.0-10+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-2 help2man_1.47.13 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-6 libapt-pkg6.0_2.0.2 libarchive-zip-perl_1.68-1 libasan5_9.3.0-10+rpi1 libassuan0_2.5.3-7 libatomic1_10-20200324-1+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-5+rpi1 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-4+rpi1 libc-dev-bin_2.30-4+rpi1 libc6_2.30-4+rpi1 libc6-dev_2.30-4+rpi1 libcap-ng0_0.7.9-2.1+b1 libcap2_1:2.33-1 libcap2-bin_1:2.33-1 libcc1-0_10-20200324-1+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-5+rpi1 libctf0_2.34-5+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_12.10 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.0-1 libgcc-9-dev_9.3.0-10+rpi1 libgcc-s1_10-20200324-1+rpi1 libgcc1_1:10-20200324-1+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.1-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10-20200324-1+rpi1 libgpg-error0_1.37-1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.49+dfsg-2 libldap-common_2.4.49+dfsg-3 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-3 libmpfr6_4.0.2-1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libp11-kit0_0.23.20-1 libpam-cap_1:2.33-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libpython3-stdlib_3.8.2-3 libpython3.8-minimal_3.8.2-1 libpython3.8-stdlib_3.8.2-1 libreadline7_7.0-5 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.1-4 libss2_1.45.6-1 libssl1.1_1.1.1f-1 libstdc++-9-dev_9.3.0-10+rpi1 libstdc++6_10-20200324-1+rpi1 libsub-override-perl_0.09-2 libsystemd0_244.3-1+rpi1 libtasn1-6_4.16.0-2 libtinfo5_6.2-1 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10-20200324-1+rpi1 libuchardet0_0.0.6-3 libudev1_244.3-1+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.10+dfsg-4 libzstd1_1.4.4+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 python3_3.8.2-3 python3-minimal_3.8.2-3 python3.8_3.8.2-1 python3.8-minimal_3.8.2-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 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+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Apr 18 17:10:00 2020 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./subread_2.0.0+dfsg-2.dsc
dpkg-source: info: extracting subread in /<<BUILDDIR>>/subread-2.0.0+dfsg
dpkg-source: info: unpacking subread_2.0.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking subread_2.0.0+dfsg-2.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
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying gcc10.patch
Check disk 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=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-daa49e58-c168-4f29-bbe3-7c0a47610d23
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package subread
dpkg-buildpackage: info: source version 2.0.0+dfsg-2
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-2.0.0+dfsg'
cd src; make -f Makefile.Linux clean
make[2]: Entering directory '/<<BUILDDIR>>/subread-2.0.0+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 input-blc.o
make[2]: Leaving directory '/<<BUILDDIR>>/subread-2.0.0+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-2.0.0+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-2.0.0+dfsg'
cd src; make -f Makefile.Linux
make[2]: Entering directory '/<<BUILDDIR>>/subread-2.0.0+dfsg/src'
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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-2.0.0+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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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-2.0.0+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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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-2.0.0+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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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-2.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c
In file included from /usr/include/string.h:495,
from sambam-file.c:30:
In function 'strncpy',
inlined from 'PBam_chunk_headers' at sambam-file.c:560:6:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 100 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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-2.0.0+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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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-2.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c
In file included from /usr/include/string.h:495,
from gene-algorithms.c:26:
In function 'strncpy',
inlined from 'bad_reverse_cigar' at gene-algorithms.c:2583:4:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 99 bytes from a string of length 102 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncat',
inlined from 'bad_reverse_cigar' at gene-algorithms.c:2575:4:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:10: warning: '__builtin___strncat_chk' output may be truncated copying 99 bytes from a string of length 99 [-Wstringop-truncation]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncpy',
inlined from 'bad_reverse_cigar' at gene-algorithms.c:2576:4:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 99 bytes from a string of length 102 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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-2.0.0+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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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-2.0.0+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:54:10: warning: implicit declaration of function 'fopen64'; did you mean 'gzopen64'? [-Wimplicit-function-declaration]
54 | return fopen64(fname, mode);
| ^~~~~~~
| gzopen64
input-files.c:54:10: warning: returning 'int' from a function with return type 'FILE *' {aka 'struct _IO_FILE *'} makes pointer from integer without a cast [-Wint-conversion]
54 | return fopen64(fname, mode);
| ^~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'SAM_nosort_run_once':
input-files.c:5243:23: warning: argument 1 value '4294967295' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
5243 | 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
539 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
| ^~~~~~
input-files.c: In function 'is_SAM_unsorted':
input-files.c:6213:33: warning: 'read_name[0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
6213 | for(field_cursor = 0; read_name[field_cursor] ; field_cursor++)
| ~~~~~~~~~^~~~~~~~~~~~~~
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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-2.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c
In file included from sorted-hashtable.h:25,
from sorted-hashtable.c:20:
sorted-hashtable.c: In function 'gehash_load':
sorted-hashtable.c:1677:19: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1677 | SUBREADprintf("Error: the index cannot be fully loaded : %p > %p + %ld. It may contain format errors or file '%s' may be truncated.\n",curr_ptr, the_table -> malloc_ptr, rdbytes , fname);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~
| |
| size_t {aka unsigned int}
subread.h:132:44: note: in definition of macro 'SUBREADprintf'
132 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
| ^~~~~~~~~~~
sorted-hashtable.c:1677:74: note: format string is defined here
1677 | SUBREADprintf("Error: the index cannot be fully loaded : %p > %p + %ld. It may contain format errors or file '%s' may be truncated.\n",curr_ptr, the_table -> malloc_ptr, rdbytes , fname);
| ~~^
| |
| long int
| %d
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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-2.0.0+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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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-2.0.0+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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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-2.0.0+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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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-2.0.0+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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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-2.0.0+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:46:46: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '8589934592' to '0' [-Woverflow]
46 | the_table -> key_repeated_numbers = malloc(sizeof(short) * 0x100000000llu);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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-2.0.0+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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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-2.0.0+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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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-2.0.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-blc.o input-blc.c
In file included from input-blc.c:7:
input-blc.c: In function 'cacheBCL_quality_test':
input-blc.c:910:18: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
910 | SUBREADprintf("ERROR: the cell barcodes have different lengths (%d!=%ld at %d). The program cannot process the cell barcodes.\n", known_cell_barcode_length, strlen(bcbstr),xx1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~
| |
| size_t {aka unsigned int}
subread.h:132:44: note: in definition of macro 'SUBREADprintf'
132 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
| ^~~~~~~~~~~
input-blc.c:910:74: note: format string is defined here
910 | SUBREADprintf("ERROR: the cell barcodes have different lengths (%d!=%ld at %d). The program cannot process the cell barcodes.\n", known_cell_barcode_length, strlen(bcbstr),xx1);
| ~~^
| |
| long int
| %d
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 input-blc.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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
In file included from /usr/include/string.h:495,
from detection-calls.c:4:
In function 'strncpy',
inlined from 'DTCdo_add_feature' at detection-calls.c:52:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncpy',
inlined from 'DTCdo_add_feature' at detection-calls.c:53:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 200 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
echo " " > longread-one/make.version
rm -f longread-one/*.o
cd longread-one && make
make[3]: Entering directory '/<<BUILDDIR>>/subread-2.0.0+dfsg/src/longread-one'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 -DSUBREAD_VERSION=\""2.0.0"\" -fmessage-length=0 -ggdb -o LRMsorted-hashtable.o -c LRMsorted-hashtable.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 -DSUBREAD_VERSION=\""2.0.0"\" -fmessage-length=0 -ggdb -o LRMbase-index.o -c LRMbase-index.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 -DSUBREAD_VERSION=\""2.0.0"\" -fmessage-length=0 -ggdb -o LRMchro-event.o -c LRMchro-event.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 -DSUBREAD_VERSION=\""2.0.0"\" -fmessage-length=0 -ggdb -o LRMhelper.o -c LRMhelper.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 -DSUBREAD_VERSION=\""2.0.0"\" -fmessage-length=0 -ggdb -o LRMseek-zlib.o -c LRMseek-zlib.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 -DSUBREAD_VERSION=\""2.0.0"\" -fmessage-length=0 -ggdb -o LRMfile-io.o -c LRMfile-io.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 -DSUBREAD_VERSION=\""2.0.0"\" -fmessage-length=0 -ggdb -o LRMhashtable.o -c LRMhashtable.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 -DSUBREAD_VERSION=\""2.0.0"\" -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-2.0.0+dfsg/src/longread-one'
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 input-blc.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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 input-blc.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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
readSummary.c: In function 'fc_thread_start_threads':
readSummary.c:4956:28: warning: '%s' directive writing up to 1019 bytes into a region of size between 100 and 1099 [-Wformat-overflow=]
4956 | sprintf(tmp_fname2, "%s/%s", applied_detail_path, modified_fname);
| ^~
In file included from /usr/include/stdio.h:867,
from readSummary.c:23:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 2 and 2020 bytes into a destination of size 1100
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 input-blc.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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 input-blc.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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 input-blc.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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 input-blc.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 1000 [-Wformat-overflow=]
66 | sprintf(tmp_fname, "%s.reads", context->config.index_prefix);
| ^~~~~~
In file included from /usr/include/stdio.h:867,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 1006 bytes into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __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 1000 [-Wformat-overflow=]
77 | sprintf(tmp_fname, "%s.00.b.tab", context->config.index_prefix);
| ^~~~~~~~~
In file included from /usr/include/stdio.h:867,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __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 1000 [-Wformat-overflow=]
75 | sprintf(tmp_fname, "%s.00.c.tab", context->config.index_prefix);
| ^~~~~~~~~
In file included from /usr/include/stdio.h:867,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __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 999 [-Wformat-overflow=]
87 | 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:867,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 1018 bytes into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c: In function 'load_indexes_forindel':
SUBindel.c:110:26: warning: '%02d' directive writing between 2 and 9 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
110 | 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, 134217728]
110 | 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:867,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 12 and 1018 bytes into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 input-blc.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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 input-blc.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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 input-blc.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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 input-blc.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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 input-blc.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=\""2.0.0"\" -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-2.0.0+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 input-blc.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-2.0.0+dfsg/src'
dh_auto_build -- CC=arm-linux-gnueabihf-gcc
make[1]: Leaving directory '/<<BUILDDIR>>/subread-2.0.0+dfsg'
rm -f debian/subread.debhelper.log
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/subread-2.0.0+dfsg'
debian/tests/subread-tests /<<BUILDDIR>>/subread-2.0.0+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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.0
//================================= setting ==================================\\
|| ||
|| Index name : small1 ||
|| Index space : base space ||
|| Index split : no-split ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
|| Free / total memory : 0.5GB / 0.0GB ||
|| ||
|| Input files : 1 file in total ||
|| o chr901.fa ||
|| ||
|| ||
|| WARNING: the free memory is lower than 3.0GB. ||
|| the program may run very slow or crash. ||
|| ||
\\============================================================================//
//================================= 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 ... ||
subread-buildindex: hashtable.c:422: HashTablePutReplaceEx: Assertion `key != NULL' failed.
Aborted (core dumped)
md5sum: ../small1.00.b.array: No such file or directory
md5sum: ../small1.00.b.tab: No such file or directory
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.0
//================================= 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 (22-Apr-2020 11:14:29, pid=17554) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [9,9] ||
Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix.
Traceback (most recent call last):
File "readname_ora_match.py", line 83, in <module>
main()
File "readname_ora_match.py", line 80, in main
print("accuracy=",(matched*1.)/(matched+unmatched)," ; sensitivity=",(matched+unmatched)*1./(line-NN))
ZeroDivisionError: float division by zero
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.0
//================================= 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 (22-Apr-2020 11:14:29, pid=17557) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [9,9] ||
Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix.
Traceback (most recent call last):
File "readname_ora_match.py", line 83, in <module>
main()
File "readname_ora_match.py", line 80, in main
print("accuracy=",(matched*1.)/(matched+unmatched)," ; sensitivity=",(matched+unmatched)*1./(line-NN))
ZeroDivisionError: float division by zero
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.0
//================================= 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 (22-Apr-2020 11:14:29, pid=17560) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [9,9] ||
Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix.
Traceback (most recent call last):
File "readname_ora_match.py", line 83, in <module>
main()
File "readname_ora_match.py", line 80, in main
print("accuracy=",(matched*1.)/(matched+unmatched)," ; sensitivity=",(matched+unmatched)*1./(line-NN))
ZeroDivisionError: float division by zero
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.0
//================================= 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 (22-Apr-2020 11:14:29, pid=17563) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [9,9] ||
Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix.
Traceback (most recent call last):
File "readname_ora_match.py", line 83, in <module>
main()
File "readname_ora_match.py", line 80, in main
print("accuracy=",(matched*1.)/(matched+unmatched)," ; sensitivity=",(matched+unmatched)*1./(line-NN))
ZeroDivisionError: float division by zero
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.0
//================================= 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 (22-Apr-2020 11:14:29, pid=17566) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [-14,-14] ||
Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix.
Traceback (most recent call last):
File "readname_ora_match.py", line 83, in <module>
main()
File "readname_ora_match.py", line 80, in main
print("accuracy=",(matched*1.)/(matched+unmatched)," ; sensitivity=",(matched+unmatched)*1./(line-NN))
ZeroDivisionError: float division by zero
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.0
//================================= 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 (22-Apr-2020 11:14:29, pid=17569) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [-14,-14] ||
Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix.
Traceback (most recent call last):
File "readname_ora_match.py", line 83, in <module>
main()
File "readname_ora_match.py", line 80, in main
print("accuracy=",(matched*1.)/(matched+unmatched)," ; sensitivity=",(matched+unmatched)*1./(line-NN))
ZeroDivisionError: float division by zero
*************************************************
*** SINGLE-END READS NO ERROR ******
*************************************************
unmatched= 0 ; matched= 0 ; unmapped= 0 ; reads= 0 ;NN= 0
*************************************************
*** SINGLE-END READS NO ERROR NO DUP ******
*************************************************
unmatched= 0 ; matched= 0 ; unmapped= 0 ; reads= 0 ;NN= 0
*************************************************
*** READS WITH NO ERROR ******
*************************************************
unmatched= 0 ; matched= 0 ; unmapped= 0 ; reads= 0 ;NN= 0
*************************************************
*** READS NO ERROR, NO DUPLICATED REPORT ******
*************************************************
unmatched= 0 ; matched= 0 ; unmapped= 0 ; reads= 0 ;NN= 0
*************************************************
*** READS WITH ONLY SEQUENCING ERROR ******
*************************************************
unmatched= 0 ; matched= 0 ; unmapped= 0 ; reads= 0 ;NN= 0
*************************************************
*** READS WITH SEQUENCING ERROR AND MUTATION ***
*** SUBREAD IS RUN WITH LONG INDEL DETECTION ***
*************************************************
unmatched= 0 ; matched= 0 ; unmapped= 0 ; reads= 0 ;NN= 0
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.0
//================================= setting ==================================\\
|| ||
|| Index name : small1 ||
|| Index space : base space ||
|| Memory : 3000 Mbytes ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : yes ||
|| ||
|| Free / total memory : 0.5GB / 0.0GB ||
|| ||
|| Input files : 1 file in total ||
|| o chr901.fa ||
|| ||
|| ||
|| WARNING: the free memory is lower than 3.0GB. ||
|| the program may run very slow or crash. ||
|| ||
\\============================================================================//
//================================= 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 ... ||
subread-buildindex: hashtable.c:422: HashTablePutReplaceEx: Assertion `key != NULL' failed.
Aborted (core dumped)
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.0
//================================= 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 (22-Apr-2020 11:14:31, pid=17576) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [2,41] ||
Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix.
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.0
//================================= 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 (22-Apr-2020 11:14:31, pid=17577) =================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [2,41] ||
Unable top open index '../small1'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix.
================================================================================
FeatureCounts Basic Test
http://subread.sourceforge.net/
================================================================================
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.0
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 SAM file ||
|| o 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... ||
|| WARNING: Paired-end reads were found. ||
|| 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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.0
//============================= 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 (22-Apr-2020 11:14:32) ======================\\
|| ||
|| Split BAM file into result/temp-snps-018115-00163E7BF7E6-* ... ||
|| processed block chr901@999950 by thread 1/1 [block number=1/1] ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed reads : 50204 ||
|| Reported SNPs : 416 ||
|| Reported indels : 22 ||
|| ||
|| 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-2.0.0+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-2.0.0+dfsg'
find /<<BUILDDIR>>/subread-2.0.0+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \;
mkdir -p /<<BUILDDIR>>/subread-2.0.0+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-2.0.0+dfsg/bin/subread-align | debian/filter.pl > /<<BUILDDIR>>/subread-2.0.0+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-2.0.0+dfsg/bin/subread-buildindex | debian/filter.pl > /<<BUILDDIR>>/subread-2.0.0+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-2.0.0+dfsg/bin/subjunc | debian/filter.pl > /<<BUILDDIR>>/subread-2.0.0+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-2.0.0+dfsg/bin/featureCounts | debian/filter.pl > /<<BUILDDIR>>/subread-2.0.0+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-2.0.0+dfsg/bin/exactSNP | debian/filter.pl > /<<BUILDDIR>>/subread-2.0.0+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-2.0.0+dfsg/bin/subindel | debian/filter.pl > /<<BUILDDIR>>/subread-2.0.0+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-2.0.0+dfsg/bin/sublong| debian/filter.pl > /<<BUILDDIR>>/subread-2.0.0+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-2.0.0+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /<<BUILDDIR>>/subread-2.0.0+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-2.0.0+dfsg/bin/utilities/propmapped | debian/filter.pl > /<<BUILDDIR>>/subread-2.0.0+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-2.0.0+dfsg/bin/utilities/qualityScores| debian/filter.pl > /<<BUILDDIR>>/subread-2.0.0+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-2.0.0+dfsg/bin/utilities/repair| debian/filter.pl > /<<BUILDDIR>>/subread-2.0.0+dfsg/debian/subread/usr/share/man/man1/repair.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='Remove duplicated reads' \
/<<BUILDDIR>>/subread-2.0.0+dfsg/bin/utilities/removeDup| debian/filter.pl > /<<BUILDDIR>>/subread-2.0.0+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-2.0.0+dfsg/bin/utilities/flattenGTF| debian/filter.pl > /<<BUILDDIR>>/subread-2.0.0+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-2.0.0+dfsg/bin/utilities/genRandomReads| debian/filter.pl > /<<BUILDDIR>>/subread-2.0.0+dfsg/debian/subread/usr/share/man/man1/genRandomReads.1;
dh_auto_install
install -d /<<BUILDDIR>>/subread-2.0.0\+dfsg/debian/tmp
make[1]: Leaving directory '/<<BUILDDIR>>/subread-2.0.0+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-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 debian/subread/usr/share/man/man1/flattenGTF.1 debian/subread/usr/share/man/man1/genRandomReads.1
man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/propmapped.1 debian/subread/usr/share/man/man1/qualityScores.1 debian/subread/usr/share/man/man1/removeDup.1 debian/subread/usr/share/man/man1/repair.1
man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1
man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1
mv debian/subread/usr/share/man/man1/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.1
mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1
mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1
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/exactSNP.1 debian/subread/usr/share/man/man1/featureCounts.1 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
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/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-fullscan.1
mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1
mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1
mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1
mv debian/subread/usr/share/man/man1/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1
chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 debian/subread/usr/share/man/man1/subjunc.1 debian/subread/usr/share/man/man1/sublong.1 debian/subread/usr/share/man/man1/subread-align.1
mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1
mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1
mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.1
mv debian/subread/usr/share/man/man1/repair.1.dh-new debian/subread/usr/share/man/man1/repair.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/removeDup.1 debian/subread/usr/share/man/man1/repair.1
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
cd debian/subread
chmod a-x usr/share/doc/subread/README.txt 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/README.txt 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-2.0.0+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 -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/1e
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1e/effe6f81c76f2ec3d472890ec81716ec1ec686.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1e/effe6f81c76f2ec3d472890ec81716ec1ec686.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1e/effe6f81c76f2ec3d472890ec81716ec1ec686.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/1e/effe6f81c76f2ec3d472890ec81716ec1ec686.debug debian/subread/usr/bin/exactSNP
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a6
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a6/f32f26f4904db9be39ee3221b499bbc3d5d58e.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a6/f32f26f4904db9be39ee3221b499bbc3d5d58e.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a6/f32f26f4904db9be39ee3221b499bbc3d5d58e.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/a6/f32f26f4904db9be39ee3221b499bbc3d5d58e.debug debian/subread/usr/bin/featureCounts
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8f
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8f/dcff9c14601cfd0910ac24a58706dbc78507a2.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8f/dcff9c14601cfd0910ac24a58706dbc78507a2.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/8f/dcff9c14601cfd0910ac24a58706dbc78507a2.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/8f/dcff9c14601cfd0910ac24a58706dbc78507a2.debug debian/subread/usr/bin/subindel
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/20
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/20/77298ef5676dfbcc1bb8b921ed243fe3d41053.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/20/77298ef5676dfbcc1bb8b921ed243fe3d41053.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/20/77298ef5676dfbcc1bb8b921ed243fe3d41053.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/20/77298ef5676dfbcc1bb8b921ed243fe3d41053.debug debian/subread/usr/bin/subjunc
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6e
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6e/634fa2a3238f0c84b8819fbffa9411a1f11d55.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6e/634fa2a3238f0c84b8819fbffa9411a1f11d55.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6e/634fa2a3238f0c84b8819fbffa9411a1f11d55.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/6e/634fa2a3238f0c84b8819fbffa9411a1f11d55.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/1e/265846243b657cad387bc98aad31d6a0e20db0.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1e/265846243b657cad387bc98aad31d6a0e20db0.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/1e/265846243b657cad387bc98aad31d6a0e20db0.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/1e/265846243b657cad387bc98aad31d6a0e20db0.debug debian/subread/usr/bin/subread-align
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f3
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f3/7b0e161390812cc79c9e6ea3a6c954af4706b4.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f3/7b0e161390812cc79c9e6ea3a6c954af4706b4.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f3/7b0e161390812cc79c9e6ea3a6c954af4706b4.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/f3/7b0e161390812cc79c9e6ea3a6c954af4706b4.debug debian/subread/usr/bin/subread-buildindex
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/23
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/23/e2030f6801d390fa8c55f147e72f2fee1c7762.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/23/e2030f6801d390fa8c55f147e72f2fee1c7762.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/23/e2030f6801d390fa8c55f147e72f2fee1c7762.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/23/e2030f6801d390fa8c55f147e72f2fee1c7762.debug debian/subread/usr/lib/subread/flattenGTF
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df/336a5e9af991b4e49ed46a2dda2c475e95a4d5.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df/336a5e9af991b4e49ed46a2dda2c475e95a4d5.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/df/336a5e9af991b4e49ed46a2dda2c475e95a4d5.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/df/336a5e9af991b4e49ed46a2dda2c475e95a4d5.debug debian/subread/usr/lib/subread/genRandomReads
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/76
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/76/f03dda88dd2e69f9a9ee5f1d55ead65ef8ca85.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/76/f03dda88dd2e69f9a9ee5f1d55ead65ef8ca85.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/76/f03dda88dd2e69f9a9ee5f1d55ead65ef8ca85.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/76/f03dda88dd2e69f9a9ee5f1d55ead65ef8ca85.debug debian/subread/usr/lib/subread/propmapped
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d3
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d3/fe5c027e352fc10eec507dfe43474b2e9a25a9.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d3/fe5c027e352fc10eec507dfe43474b2e9a25a9.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/d3/fe5c027e352fc10eec507dfe43474b2e9a25a9.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/d3/fe5c027e352fc10eec507dfe43474b2e9a25a9.debug debian/subread/usr/lib/subread/qualityScores
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/65
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/65/0866eda6fbfeae0b7e408aada03ff89915161c.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/65/0866eda6fbfeae0b7e408aada03ff89915161c.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/65/0866eda6fbfeae0b7e408aada03ff89915161c.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/65/0866eda6fbfeae0b7e408aada03ff89915161c.debug debian/subread/usr/lib/subread/removeDup
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9b
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9b/aaab7ff8ce46d71ed47c4ab2200894f6cc910d.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9b/aaab7ff8ce46d71ed47c4ab2200894f6cc910d.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9b/aaab7ff8ce46d71ed47c4ab2200894f6cc910d.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/9b/aaab7ff8ce46d71ed47c4ab2200894f6cc910d.debug debian/subread/usr/lib/subread/repair
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/17
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/17/a4aa4d1a45e97032e533b56da3b2c273d83f90.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/17/a4aa4d1a45e97032e533b56da3b2c273d83f90.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/17/a4aa4d1a45e97032e533b56da3b2c273d83f90.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/17/a4aa4d1a45e97032e533b56da3b2c273d83f90.debug debian/subread/usr/lib/subread/subread-fullscan
install -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7/05c444cae752ee87d85f570851dcb02ad71638.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7/05c444cae752ee87d85f570851dcb02ad71638.debug
chown 0:0 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7/05c444cae752ee87d85f570851dcb02ad71638.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/f7/05c444cae752ee87d85f570851dcb02ad71638.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/bin/subread-buildindex debian/subread/usr/bin/featureCounts debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/removeDup debian/subread/usr/bin/exactSNP debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/lib/subread/propmapped debian/subread/usr/bin/sublong debian/subread/usr/lib/subread/qualityScores debian/subread/usr/bin/subread-align 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 -UBuilt-Using -DAuto-Built-Package=debug-symbols -DPackage=subread-dbgsym "-DDepends=subread (= \${binary:Version})" "-DDescription=debug symbols for subread" "-DBuild-Ids=17a4aa4d1a45e97032e533b56da3b2c273d83f90 1e265846243b657cad387bc98aad31d6a0e20db0 1eeffe6f81c76f2ec3d472890ec81716ec1ec686 2077298ef5676dfbcc1bb8b921ed243fe3d41053 23e2030f6801d390fa8c55f147e72f2fee1c7762 650866eda6fbfeae0b7e408aada03ff89915161c 6e634fa2a3238f0c84b8819fbffa9411a1f11d55 76f03dda88dd2e69f9a9ee5f1d55ead65ef8ca85 8fdcff9c14601cfd0910ac24a58706dbc78507a2 9baaab7ff8ce46d71ed47c4ab2200894f6cc910d a6f32f26f4904db9be39ee3221b499bbc3d5d58e d3fe5c027e352fc10eec507dfe43474b2e9a25a9 df336a5e9af991b4e49ed46a2dda2c475e95a4d5 f37b0e161390812cc79c9e6ea3a6c954af4706b4 f705c444cae752ee87d85f570851dcb02ad71638" -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_2.0.0+dfsg-2_armhf.deb'.
dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.0+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../subread_2.0.0+dfsg-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-04-22T11:15:06Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
subread_2.0.0+dfsg-2_armhf.changes:
-----------------------------------
Format: 1.8
Date: Sat, 18 Apr 2020 21:55:06 +0530
Source: subread
Binary: subread subread-dbgsym
Architecture: armhf
Version: 2.0.0+dfsg-2
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Nilesh Patra <npatra974@gmail.com>
Description:
subread - toolkit for processing next-gen sequencing data
Closes: 957846
Changes:
subread (2.0.0+dfsg-2) unstable; urgency=medium
.
* Add patch to build with gcc-10
Closes: #957846
Checksums-Sha1:
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9f092a635649530333a1878bd4e23858fe7a6826 5239 subread_2.0.0+dfsg-2_armhf.buildinfo
6139c7b92d0a4964cd2d58a25e8b18e83eb0e333 482680 subread_2.0.0+dfsg-2_armhf.deb
Checksums-Sha256:
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cfe1784da6afbbe12ab3b58e40c855799549ecce0444dfa482b986311b6a850d 5239 subread_2.0.0+dfsg-2_armhf.buildinfo
ebebc3a21ab176d6379678276ce127af0696518e7a251aa5233ed189f2457af8 482680 subread_2.0.0+dfsg-2_armhf.deb
Files:
c95255224cdff353bda52bcd2fb18682 7388452 debug optional subread-dbgsym_2.0.0+dfsg-2_armhf.deb
09d06c27ece6c01454cb4df7537ab008 5239 science optional subread_2.0.0+dfsg-2_armhf.buildinfo
be9cafd21cc78c820bdbf313bb9f7a5e 482680 science optional subread_2.0.0+dfsg-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
subread-dbgsym_2.0.0+dfsg-2_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 7388452 bytes: control archive=1300 bytes.
955 bytes, 12 lines control
1677 bytes, 16 lines md5sums
Package: subread-dbgsym
Source: subread
Version: 2.0.0+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 9026
Depends: subread (= 2.0.0+dfsg-2)
Section: debug
Priority: optional
Description: debug symbols for subread
Build-Ids: 17a4aa4d1a45e97032e533b56da3b2c273d83f90 1e265846243b657cad387bc98aad31d6a0e20db0 1eeffe6f81c76f2ec3d472890ec81716ec1ec686 2077298ef5676dfbcc1bb8b921ed243fe3d41053 23e2030f6801d390fa8c55f147e72f2fee1c7762 650866eda6fbfeae0b7e408aada03ff89915161c 6e634fa2a3238f0c84b8819fbffa9411a1f11d55 76f03dda88dd2e69f9a9ee5f1d55ead65ef8ca85 8fdcff9c14601cfd0910ac24a58706dbc78507a2 9baaab7ff8ce46d71ed47c4ab2200894f6cc910d a6f32f26f4904db9be39ee3221b499bbc3d5d58e d3fe5c027e352fc10eec507dfe43474b2e9a25a9 df336a5e9af991b4e49ed46a2dda2c475e95a4d5 f37b0e161390812cc79c9e6ea3a6c954af4706b4 f705c444cae752ee87d85f570851dcb02ad71638
drwxr-xr-x root/root 0 2020-04-18 16:25 ./
drwxr-xr-x root/root 0 2020-04-18 16:25 ./usr/
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subread_2.0.0+dfsg-2_armhf.deb
------------------------------
new Debian package, version 2.0.
size 482680 bytes: control archive=1568 bytes.
623 bytes, 14 lines control
2129 bytes, 33 lines md5sums
Package: subread
Version: 2.0.0+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5780
Depends: libc6 (>= 2.29), 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.
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-rwxr-xr-x root/root 399804 2020-04-18 16:25 ./usr/bin/subindel
-rwxr-xr-x root/root 413020 2020-04-18 16:25 ./usr/bin/subjunc
-rwxr-xr-x root/root 71296 2020-04-18 16:25 ./usr/bin/sublong
-rwxr-xr-x root/root 412972 2020-04-18 16:25 ./usr/bin/subread-align
-rwxr-xr-x root/root 416140 2020-04-18 16:25 ./usr/bin/subread-buildindex
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-rwxr-xr-x root/root 412348 2020-04-18 16:25 ./usr/lib/subread/genRandomReads
-rwxr-xr-x root/root 399804 2020-04-18 16:25 ./usr/lib/subread/propmapped
-rwxr-xr-x root/root 404012 2020-04-18 16:25 ./usr/lib/subread/qualityScores
-rwxr-xr-x root/root 399756 2020-04-18 16:25 ./usr/lib/subread/removeDup
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-rwxr-xr-x root/root 399756 2020-04-18 16:25 ./usr/lib/subread/subread-fullscan
-rwxr-xr-x root/root 399756 2020-04-18 16:25 ./usr/lib/subread/txUnique
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-rw-r--r-- root/root 1130 2020-04-18 16:25 ./usr/share/doc/subread/copyright
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drwxr-xr-x root/root 0 2020-04-18 16:25 ./usr/share/man/man1/
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-rw-r--r-- root/root 589 2020-04-18 16:25 ./usr/share/man/man1/sublong.1.gz
-rw-r--r-- root/root 2397 2020-04-18 16:25 ./usr/share/man/man1/subread-align.1.gz
-rw-r--r-- root/root 717 2020-04-18 16:25 ./usr/share/man/man1/subread-buildindex.1.gz
-rw-r--r-- root/root 378 2020-04-18 16:25 ./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: 132428
Build-Time: 139
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 319
Job: subread_2.0.0+dfsg-2
Machine Architecture: armhf
Package: subread
Package-Time: 482
Source-Version: 2.0.0+dfsg-2
Space: 132428
Status: successful
Version: 2.0.0+dfsg-2
--------------------------------------------------------------------------------
Finished at 2020-04-22T11:15:06Z
Build needed 00:08:02, 132428k disk space