subread →
2.0.6+dfsg-2 →
armhf → 2023-09-21 14:52:07
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| subread 2.0.6+dfsg-2 (armhf) Thu, 21 Sep 2023 14:47:07 +0000 |
+==============================================================================+
Package: subread
Version: 2.0.6+dfsg-2
Source Version: 2.0.6+dfsg-2
Distribution: trixie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/trixie-staging-armhf-sbuild-a83d1e6d-9e62-4106-93a3-652f8340eb08' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.1 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [14.7 MB]
Fetched 28.8 MB in 10s (2914 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: '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 16.6 MB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main subread 2.0.6+dfsg-2 (dsc) [2282 B]
Get:2 http://172.17.4.1/private trixie-staging/main subread 2.0.6+dfsg-2 (tar) [16.6 MB]
Get:3 http://172.17.4.1/private trixie-staging/main subread 2.0.6+dfsg-2 (diff) [18.8 kB]
Fetched 16.6 MB in 2s (9478 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/subread-yhzPlX/subread-2.0.6+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/subread-yhzPlX' 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-8gUC6Y/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-8gUC6Y/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-8gUC6Y/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-8gUC6Y/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-8gUC6Y/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-8gUC6Y/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-8gUC6Y/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-8gUC6Y/apt_archive ./ Packages [435 B]
Fetched 2111 B in 0s (9669 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase sensible-utils sgml-base
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 55 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-8gUC6Y/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (71.9 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11771 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 riscv64 loong64 all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: bc, debhelper-compat (= 13), python3, zlib1g-dev
Filtered Build-Depends: bc, debhelper-compat (= 13), python3, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-subread-dummy' in '/<<BUILDDIR>>/resolver-8gUC6Y/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-8gUC6Y/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-8gUC6Y/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-8gUC6Y/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-8gUC6Y/apt_archive ./ Sources [516 B]
Get:5 copy:/<<BUILDDIR>>/resolver-8gUC6Y/apt_archive ./ Packages [591 B]
Fetched 2440 B in 0s (12.2 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:
krb5-locales libpam-cap netbase sgml-base util-linux-extra
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bc bsdextrautils bsdutils
debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libblkid1
libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl
libicu72 libmagic-mgc libmagic1 libmount1 libpipeline1 libpython3-stdlib
libpython3.11-minimal libpython3.11-stdlib libsmartcols1
libsub-override-perl libtool libuchardet0 libuuid1 libxml2 m4 man-db
media-types mount po-debconf python3 python3-minimal python3.11
python3.11-minimal util-linux util-linux-extra zlib1g zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff cryptsetup-bin libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser nfs-common
libmail-box-perl python3-doc python3-tk python3-venv python3.11-venv
python3.11-doc binfmt-support dosfstools kbd util-linux-locales
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libltdl-dev uuid-runtime
libmail-sendmail-perl ca-certificates
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bc bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1
libexpat1 libfile-stripnondeterminism-perl libicu72 libmagic-mgc libmagic1
libpipeline1 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib
libsub-override-perl libtool libuchardet0 libxml2 m4 man-db media-types
po-debconf python3 python3-minimal python3.11 python3.11-minimal
sbuild-build-depends-subread-dummy zlib1g-dev
The following packages will be upgraded:
bsdutils libblkid1 libmount1 libsmartcols1 libuuid1 mount util-linux
util-linux-extra zlib1g
9 upgraded, 41 newly installed, 0 to remove and 46 not upgraded.
Need to get 25.8 MB of archives.
After this operation, 92.1 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-8gUC6Y/apt_archive ./ sbuild-build-depends-subread-dummy 0.invalid.0 [880 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf bsdutils armhf 1:2.39.2-1 [85.9 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf libblkid1 armhf 2.39.2-1 [143 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf libmount1 armhf 2.39.2-1 [166 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf libsmartcols1 armhf 2.39.2-1 [101 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf util-linux-extra armhf 2.39.2-1 [136 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf util-linux armhf 2.39.2-1 [1107 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf mount armhf 2.39.2-1 [132 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-minimal armhf 3.11.5-3 [800 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-1 [77.2 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf zlib1g armhf 1:1.2.13.dfsg-3 [73.6 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf python3.11-minimal armhf 3.11.5-3 [1676 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf python3-minimal armhf 3.11.4-5 [26.2 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf media-types all 10.1.0 [26.9 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf libuuid1 armhf 2.39.2-1 [27.7 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-stdlib armhf 3.11.5-3 [1675 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf python3.11 armhf 3.11.5-3 [582 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf libpython3-stdlib armhf 3.11.4-5 [9200 B]
Get:19 http://172.17.4.1/private trixie-staging/main armhf python3 armhf 3.11.4-5 [26.2 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.22.4-10 [774 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.2-1 [80.5 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.11.2-3 [1342 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf bc armhf 1.07.1-3 [101 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-12 [156 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-3 [256 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-13 [496 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.6 [81.9 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:40 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:42 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-12 [1201 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.6 [952 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-3 [901 kB]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 11771 files and directories currently installed.)
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Setting up util-linux (2.39.2-1) ...
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Unpacking sbuild-build-depends-subread-dummy (0.invalid.0) ...
Setting up media-types (10.1.0) ...
Setting up libpipeline1:armhf (1.5.7-1) ...
Setting up libicu72:armhf (72.1-3) ...
Setting up bsdextrautils (2.39.2-1) ...
Setting up libmagic-mgc (1:5.45-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libpython3.11-stdlib:armhf (3.11.5-3) ...
Setting up libdebhelper-perl (13.11.6) ...
Setting up libmagic1:armhf (1:5.45-2) ...
Setting up bc (1.07.1-3) ...
Setting up gettext-base (0.21-12) ...
Setting up m4 (1.4.19-3) ...
Setting up file (1:5.45-2) ...
Setting up autotools-dev (20220109.1) ...
Setting up autopoint (0.21-13) ...
Setting up autoconf (2.71-3) ...
Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-3) ...
Setting up mount (2.39.2-1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
Setting up libpython3-stdlib:armhf (3.11.4-5) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up python3.11 (3.11.5-3) ...
Setting up gettext (0.21-12) ...
Setting up libtool (2.4.7-7) ...
Setting up python3 (3.11.4-5) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.22.4-10) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.11.2-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.11.6) ...
Setting up sbuild-build-depends-subread-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.36-9+rpi1+deb12u1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.40-2+rpi2 dpkg-dev_1.21.22+rpi1 g++-12_12.2.0-14+rpi1 gcc-12_12.2.0-14+rpi1 libc6-dev_2.36-9+rpi1+deb12u1 libstdc++-12-dev_12.2.0-14+rpi1 libstdc++6_12.2.0-14+rpi1 linux-libc-dev_6.1.38-1+rpi1
Package versions: adduser_3.137 apt_2.6.1 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_12.4+rpi1+deb12u1 base-passwd_3.6.1 bash_5.2.15-2 bc_1.07.1-3 binutils_2.40-2+rpi2 binutils-arm-linux-gnueabihf_2.40-2+rpi2 binutils-common_2.40-2+rpi2 bsdextrautils_2.39.2-1 bsdutils_1:2.39.2-1 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:12.2.0-3+rpi1 cpp-12_12.2.0-14+rpi1 dash_0.5.12-2 debconf_1.5.82 debhelper_13.11.6 debianutils_5.7-0.4 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dirmngr_2.2.40-1.1 dpkg_1.21.22+rpi1 dpkg-dev_1.21.22+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.31-1.2 file_1:5.45-2 findutils_4.9.0-4 g++_4:12.2.0-3+rpi1 g++-12_12.2.0-14+rpi1 gcc_4:12.2.0-3+rpi1 gcc-12_12.2.0-14+rpi1 gcc-12-base_12.2.0-14+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-12 gettext-base_0.21-12 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.8-5 groff-base_1.22.4-10 gzip_1.12-1 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-3 libacl1_2.3.1-3 libapt-pkg6.0_2.6.1 libarchive-zip-perl_1.68-1 libasan8_12.2.0-14+rpi1 libassuan0_2.5.5-5 libatomic1_12.2.0-14+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.0.9-1 libbinutils_2.40-2+rpi2 libblkid1_2.39.2-1 libbz2-1.0_1.0.8-5+b2 libc-bin_2.36-9+rpi1+deb12u1 libc-dev-bin_2.36-9+rpi1+deb12u1 libc6_2.36-9+rpi1+deb12u1 libc6-dev_2.36-9+rpi1+deb12u1 libcap-ng0_0.8.3-1+b1 libcap2_1:2.66-4 libcap2-bin_1:2.66-4 libcc1-0_12.2.0-14+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.33-2 libcrypt1_1:4.4.33-2 libctf-nobfd0_2.40-2+rpi2 libctf0_2.40-2+rpi2 libdb5.3_5.3.28+dfsg2-1 libdebconfclient0_0.270 libdebhelper-perl_13.11.6 libdpkg-perl_1.21.22+rpi1 libelf1_0.188-2.1+rpi1 libexpat1_2.5.0-1 libext2fs2_1.47.0-2 libfakeroot_1.31-1.2 libffi8_3.4.4-1 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.2.0-14+rpi1 libgcc-s1_12.2.0-14+rpi1 libgcrypt20_1.10.1-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.9-2 libgomp1_12.2.0-14+rpi1 libgpg-error0_1.46-1 libgssapi-krb5-2_1.20.1-2 libhogweed6_3.8.1-2 libicu72_72.1-3 libidn2-0_2.3.3-1+b2 libisl23_0.25-1 libjansson4_2.14-2 libk5crypto3_1.20.1-2 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-2 libkrb5support0_1.20.1-2 libksba8_1.6.3-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 liblz4-1_1.9.4-1+rpi1+b1 liblzma5_5.4.1-0.2 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.0.4-2 libmount1_2.39.2-1 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libncursesw6_6.4-4 libnettle8_3.8.1-2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnumber-compare-perl_0.03-3 libp11-kit0_0.24.1-2 libpam-cap_1:2.66-4 libpam-modules_1.5.2-6 libpam-modules-bin_1.5.2-6 libpam-runtime_1.5.2-7 libpam0g_1.5.2-6 libpcre2-8-0_10.42-1 libpcre3_2:8.39-15 libperl5.36_5.36.0-7 libpipeline1_1.5.7-1 libpython3-stdlib_3.11.4-5 libpython3.11-minimal_3.11.5-3 libpython3.11-stdlib_3.11.5-3 libreadline8_8.2-1.3 libsasl2-2_2.1.28+dfsg-10 libsasl2-modules-db_2.1.28+dfsg-10 libseccomp2_2.5.4-1+rpi1+b1 libselinux1_3.4-1+b2 libsemanage-common_3.5-1 libsemanage2_3.4-1+b2 libsepol1_3.1-1 libsepol2_3.4-2.1 libsmartcols1_2.39.2-1 libsqlite3-0_3.40.1-2 libss2_1.47.0-2 libssl1.1_1.1.1o-1 libssl3_3.0.9-1 libstdc++-12-dev_12.2.0-14+rpi1 libstdc++6_12.2.0-14+rpi1 libsub-override-perl_0.09-4 libsystemd0_252.12-1~deb12u1+rpi1 libtasn1-6_4.19.0-2 libtext-glob-perl_0.11-3 libtinfo6_6.4-4 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-7 libubsan1_12.2.0-14+rpi1 libuchardet0_0.0.7-1 libudev1_252.12-1~deb12u1+rpi1 libunistring2_1.0-2 libuuid1_2.39.2-1 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.1-1 libzstd1_1.5.4+dfsg2-5 linux-libc-dev_6.1.38-1+rpi1 login_1:4.13+dfsg1-1 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-3 make_4.3-4.1 man-db_2.11.2-3 mawk_1.3.4.20200120-3.1 media-types_10.1.0 mount_2.39.2-1 nano_7.2-1 ncurses-base_6.4+20230625-2 ncurses-bin_6.4-4 netbase_6.4 passwd_1:4.13+dfsg1-1 patch_2.7.6-7 perl_5.36.0-7 perl-base_5.36.0-7 perl-modules-5.36_5.36.0-7 pinentry-curses_1.2.1-1 po-debconf_1.0.21+nmu1 python3_3.11.4-5 python3-minimal_3.11.4-5 python3.11_3.11.5-3 python3.11-minimal_3.11.5-3 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-subread-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sgml-base_1.31 sysvinit-utils_3.06-4 tar_1.34+dfsg-1.2 tzdata_2023c-10 usrmerge_37 util-linux_2.39.2-1 util-linux-extra_2.39.2-1 xz-utils_5.4.1-0.2 zlib1g_1:1.2.13.dfsg-3 zlib1g-dev_1:1.2.13.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: Signature made Wed Sep 13 12:28:29 2023 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./subread_2.0.6+dfsg-2.dsc: no acceptable signature found
dpkg-source: info: extracting subread in /<<BUILDDIR>>/subread-2.0.6+dfsg
dpkg-source: info: unpacking subread_2.0.6+dfsg.orig.tar.xz
dpkg-source: info: unpacking subread_2.0.6+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 0001-src-Makefile.Linux-Do-not-set-CFLAGS-and-CXXFLAGS-to.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=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-a83d1e6d-9e62-4106-93a3-652f8340eb08
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package subread
dpkg-buildpackage: info: source version 2.0.6+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --buildsystem=makefile
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/subread-2.0.6+dfsg'
dh_auto_clean
rm -f test/subread-align/data/test-err-mut-r1.fq.gz test/subread-align/data/test-err-mut-r2.fq.gz
rm -rf bin src/longread-one/make.version
find . -name "*.o" -delete
dh_auto_clean --sourcedirectory=src -- -f Makefile.Linux
cd src && make -j4 clean -f Makefile.Linux
make[2]: Entering directory '/<<BUILDDIR>>/subread-2.0.6+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-2.0.6+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/subread-2.0.6+dfsg'
dh_autoreconf_clean -O--buildsystem=makefile
dh_clean -O--buildsystem=makefile
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 \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
debian/rules binary-arch
dh binary-arch --buildsystem=makefile
dh_update_autotools_config -a -O--buildsystem=makefile
dh_autoreconf -a -O--buildsystem=makefile
dh_auto_configure -a -O--buildsystem=makefile
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/subread-2.0.6+dfsg'
dh_auto_build --sourcedirectory=src -- -f Makefile.Linux CC=arm-linux-gnueabihf-gcc ; \
cd src && make -j4 "INSTALL=install --strip-program=true" -f Makefile.Linux CC=arm-linux-gnueabihf-gcc
make[2]: Entering directory '/<<BUILDDIR>>/subread-2.0.6+dfsg/src'
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c
core-junction.c: In function 'find_donor_receptor':
core-junction.c:2099:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
2099 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0)
| ^~
core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
2103 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){
| ^~
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c
gene-algorithms.c: In function 'miltime':
gene-algorithms.c:1395:17: warning: 'ftime' is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations]
1395 | ftime(&trp);
| ^~~~~
In file included from gene-algorithms.c:33:
/usr/include/arm-linux-gnueabihf/sys/timeb.h:29:12: note: declared here
29 | extern int ftime (struct timeb *__timebuf)
| ^~~~~
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -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:54:24: warning: implicit declaration of function 'fopen64'; did you mean 'gzopen64'? [-Wimplicit-function-declaration]
54 | return fopen64(fname, mode);
| ^~~~~~~
| gzopen64
input-files.c:54:24: warning: returning 'int' from a function with return type 'FILE *' makes pointer from integer without a cast [-Wint-conversion]
54 | return fopen64(fname, mode);
| ^~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c
gene-value-index.c: In function 'is_offset_in_chro':
gene-value-index.c:85:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
85 | if( pos < chros -> padding || pos >= ( chros->read_offsets[n] - chros->read_offsets[n-1] - chros -> padding ))
| ^~
In file included from gene-value-index.h:24,
from gene-value-index.c:25:
subread.h:143:28: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
143 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
| ^~~~~~~
gene-value-index.c:87:41: note: in expansion of macro 'SUBREADprintf'
87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos);
| ^~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c
long-hashtable.c: In function 'lnhash_create':
long-hashtable.c:46:60: 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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-blc.o input-blc.c
input-blc.c: In function 'iCache_continuous_read_lanes':
input-blc.c:579:59: warning: unused variable 'npos' [-Wunused-variable]
579 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET);
| ^~~~
input-blc.c: In function 'iCache_write_supIdx_result':
input-blc.c:1123:24: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'void *' [-Wformat=]
1123 | fprintf(ofp, "%s\t%lld\n", ky, va-NULL);
| ~^ ~~
| | |
| char * void *
| %p
input-blc.c:1123:30: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'int' [-Wformat=]
1123 | fprintf(ofp, "%s\t%lld\n", ky, va-NULL);
| ~~~^
| |
| long long int
| %d
In file included from input-blc.c:8:
input-blc.c: In function 'cacheBCL_quality_test':
input-blc.c:1419:39: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
1419 | 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:143:44: note: in definition of macro 'SUBREADprintf'
143 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
| ^~~~~~~~~~~
input-blc.c:1419:95: note: format string is defined here
1419 | 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
input-blc.c: In function 'iCache_continuous_read_lanes':
input-blc.c:489:49: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
489 | read(tfp -> cbcl_bin_fd,&btmp,1);// bits per call.
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:491:49: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
491 | read(tfp -> cbcl_bin_fd,&tfp -> bits_per_bitscore,1);// bits per qscore.
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:498:49: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
498 | read(tfp -> cbcl_bin_fd,&btmp,4);// Number of bins
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:501:57: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
501 | read(tfp -> cbcl_bin_fd,&fromv,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:502:57: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
502 | read(tfp -> cbcl_bin_fd,&tov,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:511:49: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
511 | read(tfp -> cbcl_bin_fd,&btmp,4);// Number of tiles (gzipped blocks) in this file
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:515:57: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
515 | read(tfp -> cbcl_bin_fd,&tile_4digit,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:516:57: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
516 | read(tfp -> cbcl_bin_fd,&reads_in_tile,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:517:57: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
517 | read(tfp -> cbcl_bin_fd,&data_size,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:518:57: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
518 | read(tfp -> cbcl_bin_fd,&compressed_size,4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-blc.c:524:49: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result]
524 | read(tfp -> cbcl_bin_fd,&btmp,1); // excluding non-FP?
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'SAM_nosort_run_once':
input-files.c:5314:37: warning: argument 1 value '4294967295' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
5314 | char * header_txt = malloc(max(1000000,pairer->BAM_l_text));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from input-files.c:24:
/usr/include/stdlib.h:553:14: note: in a call to allocation function 'malloc' declared here
553 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
| ^~~~~~
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -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
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -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
echo " " > longread-one/make.version
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -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
rm -f longread-one/*.o
cd longread-one && make
make[3]: Entering directory '/<<BUILDDIR>>/subread-2.0.6+dfsg/src/longread-one'
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMsorted-hashtable.o -c LRMsorted-hashtable.c
detection-calls.c: In function 'DTCwrite_annotations':
detection-calls.c:155:109: warning: dangling pointer 'gc_2int' to an unnamed temporary may be used [-Wdangling-pointer=]
155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0);
| ^
detection-calls.c:154:48: note: unnamed temporary defined here
154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0};
| ^
detection-calls.c:155:9: warning: dangling pointer 'gc_2int' to an unnamed temporary may be used [-Wdangling-pointer=]
155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
detection-calls.c:154:48: note: unnamed temporary defined here
154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0};
| ^
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -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
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMbase-index.o -c LRMbase-index.c
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -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
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMchro-event.o -c LRMchro-event.c
readSummary.c: In function 'scRNA_find_gene_to_umi_mark_deletee':
readSummary.c:5691:71: warning: right shift count >= width of type [-Wshift-count-overflow]
5691 | int cellno = ( key_bc_umi_p1-NULL-1 ) >> 32;
| ^~
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhelper.o -c LRMhelper.c
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -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
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMseek-zlib.o -c LRMseek-zlib.c
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -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
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -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
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMfile-io.o -c LRMfile-io.c
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhashtable.o -c LRMhashtable.c
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -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:66:31: 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:906,
from SUBindel.c:20:
In function 'sprintf',
inlined from 'load_global_context_forindel' at SUBindel.c:66:2:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 1006 bytes into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SUBindel.c: In function 'load_global_context_forindel':
SUBindel.c:77:39: 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 function 'sprintf',
inlined from 'load_global_context_forindel' at SUBindel.c:77:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SUBindel.c: In function 'load_global_context_forindel':
SUBindel.c:75:39: 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 function 'sprintf',
inlined from 'load_global_context_forindel' at SUBindel.c:75:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SUBindel.c: In function 'load_global_context_forindel':
SUBindel.c:87:40: 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');
| ^~~~
SUBindel.c:87:36: note: directive argument in the range [-2147483647, 2147483647]
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 function 'sprintf',
inlined from 'load_global_context_forindel' at SUBindel.c:87:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 1018 bytes into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SUBindel.c: In function 'load_global_context_forindel':
SUBindel.c:87:40: 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');
| ^~~~
SUBindel.c:87:36: note: directive argument in the range [-2147483647, 2147483647]
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 function 'sprintf',
inlined from 'load_global_context_forindel' at SUBindel.c:87:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 1018 bytes into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
SUBindel.c: In function 'load_indexes_forindel':
SUBindel.c:110:40: 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:110:36: 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 function 'sprintf',
inlined from 'load_indexes_forindel' at SUBindel.c:110:3:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 12 and 1018 bytes into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -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
longread-mapping.c: In function 'LRMmiltime':
longread-mapping.c:234:9: warning: 'ftime' is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations]
234 | ftime(&trp);
| ^~~~~
In file included from longread-mapping.c:33:
/usr/include/arm-linux-gnueabihf/sys/timeb.h:29:12: note: declared here
29 | extern int ftime (struct timeb *__timebuf)
| ^~~~~
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -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
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -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
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -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
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -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
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -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
arm-linux-gnueabihf-gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/subread-2.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -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
make[3]: Leaving directory '/<<BUILDDIR>>/subread-2.0.6+dfsg/src/longread-one'
readSummary.c: In function 'vote_and_add_count':
readSummary.c:4923:66: warning: 'longest_overlap_score' may be used uninitialized [-Wmaybe-uninitialized]
4923 | if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0;
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:4691:51: note: 'longest_overlap_score' was declared here
4691 | int scoring_count = 0, score_x1, longest_overlap_score;
| ^~~~~~~~~~~~~~~~~~~~~
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-2.0.6+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/subread-2.0.6+dfsg'
rm -f debian/subread.debhelper.log
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/subread-2.0.6+dfsg'
debian/tests/subread-tests /<<BUILDDIR>>/subread-2.0.6+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[0,0Hrm: cannot remove 'test-tmp.log': No such file or directory
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.6
//================================= setting ==================================\\
|| ||
|| Index name : small1 ||
|| Index space : base space ||
|| Index split : no-split ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
|| Free / total memory : 0.1GB / 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:470: 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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.6
//================================= 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 (21-Sep-2023 14:51:30, pid=4703) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [9,9] ||
|| Create the output SAM file. ||
|| Check the index. ||
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 "/<<BUILDDIR>>/subread-2.0.6+dfsg/adt_test/subread-align/readname_ora_match.py", line 83, in <module>
main()
File "/<<BUILDDIR>>/subread-2.0.6+dfsg/adt_test/subread-align/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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.6
//================================= 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 (21-Sep-2023 14:51:30, pid=4706) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [9,9] ||
|| Create the output SAM file. ||
|| Check the index. ||
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 "/<<BUILDDIR>>/subread-2.0.6+dfsg/adt_test/subread-align/readname_ora_match.py", line 83, in <module>
main()
File "/<<BUILDDIR>>/subread-2.0.6+dfsg/adt_test/subread-align/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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.6
//================================= 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 (21-Sep-2023 14:51:30, pid=4709) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [9,9] ||
|| Create the output SAM file. ||
|| Check the index. ||
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 "/<<BUILDDIR>>/subread-2.0.6+dfsg/adt_test/subread-align/readname_ora_match.py", line 83, in <module>
main()
File "/<<BUILDDIR>>/subread-2.0.6+dfsg/adt_test/subread-align/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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.6
//================================= 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 (21-Sep-2023 14:51:30, pid=4712) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [9,9] ||
|| Create the output SAM file. ||
|| Check the index. ||
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 "/<<BUILDDIR>>/subread-2.0.6+dfsg/adt_test/subread-align/readname_ora_match.py", line 83, in <module>
main()
File "/<<BUILDDIR>>/subread-2.0.6+dfsg/adt_test/subread-align/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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.6
//================================= 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 (21-Sep-2023 14:51:31, pid=4715) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [-14,-14] ||
|| Create the output SAM file. ||
|| Check the index. ||
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 "/<<BUILDDIR>>/subread-2.0.6+dfsg/adt_test/subread-align/readname_ora_match.py", line 83, in <module>
main()
File "/<<BUILDDIR>>/subread-2.0.6+dfsg/adt_test/subread-align/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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.6
//================================= 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 (21-Sep-2023 14:51:31, pid=4718) =================\\
|| ||
ERROR: unable to open file 'data/test-err-mut-r1.fq.gz'. File name might be incorrect, or you do not have the permission to read the file.
ERROR: unable to open file 'data/test-err-mut-r2.fq.gz'. File name might be incorrect, or you do not have the permission to read the file.
Traceback (most recent call last):
File "/<<BUILDDIR>>/subread-2.0.6+dfsg/adt_test/subread-align/readname_ora_match.py", line 83, in <module>
main()
File "/<<BUILDDIR>>/subread-2.0.6+dfsg/adt_test/subread-align/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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.6
//================================= setting ==================================\\
|| ||
|| Index name : small1 ||
|| Index space : base space ||
|| Memory : 3000 Mbytes ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : yes ||
|| ||
|| Free / total memory : 0.1GB / 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:470: HashTablePutReplaceEx: Assertion `key != NULL' failed.
Aborted (core dumped)
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.6
//================================= 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 (21-Sep-2023 14:51:32, pid=4725) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [2,41] ||
|| Create the output SAM file. ||
|| Check the index. ||
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.
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.6
//================================= 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 (21-Sep-2023 14:51:32, pid=4726) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [2,41] ||
|| Create the output BAM file. ||
|| Check the index. ||
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/
================================================================================
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 SAM file ||
|| ||
|| test-minimum.sam ||
|| ||
|| Output file : test-minimum.FC ||
|| Summary : test-minimum.FC.summary ||
|| Paired-end : yes ||
|| Count read pairs : no ||
|| Annotation : test-minimum.GTF (GTF) ||
|| Dir for temp files : result ||
|| ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file test-minimum.GTF ... ||
|| Features : 23 ||
|| Meta-features : 7 ||
|| Chromosomes/contigs : 3 ||
|| ||
|| Process SAM file test-minimum.sam... ||
|| Paired-end reads are included. ||
|| The reads are assigned on the single-end mode. ||
|| Total alignments : 998 ||
|| Successfully assigned alignments : 389 (39.0%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
|| 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]
mkdir: unrecognized option '--countReadPairs'
Try 'mkdir --help' for more information.
================================================================================
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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v2.0.6
//============================= 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 (21-Sep-2023 14:51:33) ======================\\
|| ||
|| Split BAM file into result/temp-snps-005266-00163E555AE0-* ... ||
|| 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-2.0.6+dfsg'
create-stamp debian/debhelper-build-stamp
dh_testroot -a -O--buildsystem=makefile
dh_prep -a -O--buildsystem=makefile
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-2.0.6+dfsg'
find /<<BUILDDIR>>/subread-2.0.6+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \;
dh_auto_install
install -m0755 -d /<<BUILDDIR>>/subread-2.0.6\+dfsg/debian/tmp
make[1]: Leaving directory '/<<BUILDDIR>>/subread-2.0.6+dfsg'
dh_install -a -O--buildsystem=makefile
install -m0755 -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 -m0755 -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/
dh_installdocs -a -O--buildsystem=makefile
install -m0755 -d debian/subread/usr/share/doc/subread
install -m0755 -d debian/subread/usr/share/doc/subread
cp --reflink=auto -a ./README.txt debian/subread/usr/share/doc/subread
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 -O--buildsystem=makefile
install -m0755 -d debian/subread/usr/share/doc/subread
install -p -m0644 debian/.debhelper/generated/subread/dh_installchangelogs.dch.trimmed debian/subread/usr/share/doc/subread/changelog.Debian
dh_installman -a -O--buildsystem=makefile
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/exactSNP.1 debian/subread/usr/share/man/man1/exactSNP.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/featureCounts.1 debian/subread/usr/share/man/man1/featureCounts.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/flattenGTF.1 debian/subread/usr/share/man/man1/flattenGTF.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/genRandomReads.1 debian/subread/usr/share/man/man1/genRandomReads.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/propmapped.1 debian/subread/usr/share/man/man1/propmapped.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/qualityScores.1 debian/subread/usr/share/man/man1/qualityScores.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/removeDup.1 debian/subread/usr/share/man/man1/removeDup.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/repair.1 debian/subread/usr/share/man/man1/repair.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/subindel.1 debian/subread/usr/share/man/man1/subindel.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/subjunc.1 debian/subread/usr/share/man/man1/subjunc.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/sublong.1 debian/subread/usr/share/man/man1/sublong.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/subread-align.1 debian/subread/usr/share/man/man1/subread-align.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-buildindex.1
install -m0755 -d debian/subread/usr/share/man/man1/
install -p -m0644 ./debian/subread-fullscan.1 debian/subread/usr/share/man/man1/subread-fullscan.1
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/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/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
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/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
dh_installsystemduser -a -O--buildsystem=makefile
dh_perl -a -O--buildsystem=makefile
dh_link -a -O--buildsystem=makefile
dh_strip_nondeterminism -a -O--buildsystem=makefile
dh_compress -a -O--buildsystem=makefile
cd debian/subread
chmod a-x usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1
gzip -9nf usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1
cd '/<<BUILDDIR>>/subread-2.0.6+dfsg'
dh_fixperms -a -O--buildsystem=makefile
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 -O--buildsystem=makefile
dh_dwz -a -O--buildsystem=makefile
install -m0755 -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
chmod 0644 -- debian/subread/usr/lib/debug/.dwz/arm-linux-gnueabihf/subread.debug
dh_strip -a -O--buildsystem=makefile
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c2
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c2/80afd594a4b2c0f9be5f1c9b3f8744710ba46b.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c2/80afd594a4b2c0f9be5f1c9b3f8744710ba46b.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/c2/80afd594a4b2c0f9be5f1c9b3f8744710ba46b.debug debian/subread/usr/bin/subjunc
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e1
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e1/85bd0219a204009304078ab7808a1610d0dd47.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e1/85bd0219a204009304078ab7808a1610d0dd47.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/e1/85bd0219a204009304078ab7808a1610d0dd47.debug debian/subread/usr/bin/subindel
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/79
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/79/c7194ebb95f25845ec7f6ec62de3a418b6ca9c.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/79/c7194ebb95f25845ec7f6ec62de3a418b6ca9c.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/79/c7194ebb95f25845ec7f6ec62de3a418b6ca9c.debug debian/subread/usr/bin/exactSNP
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4c
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4c/7a2e00642e64b7dfdbd259f4fdf5160c9e5bcc.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4c/7a2e00642e64b7dfdbd259f4fdf5160c9e5bcc.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/4c/7a2e00642e64b7dfdbd259f4fdf5160c9e5bcc.debug debian/subread/usr/bin/sublong
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ca
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ca/cf10ad7708a34721dc693c5e73d0cfac7ace9f.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/ca/cf10ad7708a34721dc693c5e73d0cfac7ace9f.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/ca/cf10ad7708a34721dc693c5e73d0cfac7ace9f.debug debian/subread/usr/bin/featureCounts
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/14
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/14/ec74443d14a8ea3f6d24d29280990732ce7967.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/14/ec74443d14a8ea3f6d24d29280990732ce7967.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/14/ec74443d14a8ea3f6d24d29280990732ce7967.debug debian/subread/usr/bin/subread-align
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/95
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/95/24691909a9036ab644bb428f9cb7afa15ef79c.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/95/24691909a9036ab644bb428f9cb7afa15ef79c.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/95/24691909a9036ab644bb428f9cb7afa15ef79c.debug debian/subread/usr/bin/subread-buildindex
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b9
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b9/d4c9ab3aea8a5b3271b5db5a99f535c9268cc0.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/b9/d4c9ab3aea8a5b3271b5db5a99f535c9268cc0.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/b9/d4c9ab3aea8a5b3271b5db5a99f535c9268cc0.debug debian/subread/usr/lib/subread/flattenGTF
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3f
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3f/5c14f331d872ccbc455050bdd8651423a6492a.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3f/5c14f331d872ccbc455050bdd8651423a6492a.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/3f/5c14f331d872ccbc455050bdd8651423a6492a.debug debian/subread/usr/lib/subread/genRandomReads
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e9
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e9/e48044960f0b8b4edfc2e4ab63f8cd2048d940.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/e9/e48044960f0b8b4edfc2e4ab63f8cd2048d940.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/e9/e48044960f0b8b4edfc2e4ab63f8cd2048d940.debug debian/subread/usr/lib/subread/propmapped
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9e
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9e/8641c462fb94ea122b2ed492bd2953754c6788.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/9e/8641c462fb94ea122b2ed492bd2953754c6788.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/9e/8641c462fb94ea122b2ed492bd2953754c6788.debug debian/subread/usr/lib/subread/qualityScores
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/19
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/19/2fd8555bf5d604053be38fe8c06762b37b06a5.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/19/2fd8555bf5d604053be38fe8c06762b37b06a5.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/19/2fd8555bf5d604053be38fe8c06762b37b06a5.debug debian/subread/usr/lib/subread/removeDup
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c8
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c8/ebdceff3ce5bd609c5756c04c9c1e4057df44f.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/c8/ebdceff3ce5bd609c5756c04c9c1e4057df44f.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/c8/ebdceff3ce5bd609c5756c04c9c1e4057df44f.debug debian/subread/usr/lib/subread/repair
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3f
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3f/14d1a83d34cc6ca955040d0d29b405bb49230b.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/3f/14d1a83d34cc6ca955040d0d29b405bb49230b.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/3f/14d1a83d34cc6ca955040d0d29b405bb49230b.debug debian/subread/usr/lib/subread/subread-fullscan
install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/5c
objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/5c/d5979676f5713aabab4c890eb00cf3b620ced0.debug
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/5c/d5979676f5713aabab4c890eb00cf3b620ced0.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/5c/d5979676f5713aabab4c890eb00cf3b620ced0.debug debian/subread/usr/lib/subread/txUnique
install -m0755 -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 -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/share/doc
ln -s subread debian/.debhelper/subread/dbgsym-root/usr/share/doc/subread-dbgsym
install -m0755 -d debian/.debhelper/subread
dh_makeshlibs -a -O--buildsystem=makefile
rm -f debian/subread/DEBIAN/shlibs
dh_shlibdeps -a -O--buildsystem=makefile
install -m0755 -d debian/subread/DEBIAN
dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/bin/subjunc debian/subread/usr/bin/subindel debian/subread/usr/bin/exactSNP debian/subread/usr/bin/sublong debian/subread/usr/bin/featureCounts 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/subjunc debian/subread/usr/bin/subindel debian/subread/usr/lib/subread/repair debian/subread/usr/bin/subread-align debian/subread/usr/lib/subread/qualityScores debian/subread/usr/bin/exactSNP debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/bin/featureCounts debian/subread/usr/bin/sublong debian/subread/usr/bin/subread-buildindex debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/propmapped were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a -O--buildsystem=makefile
install -m0755 -d debian/subread/DEBIAN
dh_gencontrol -a -O--buildsystem=makefile
install -m0755 -d debian/subread/DEBIAN
echo misc:Depends= >> debian/subread.substvars
echo misc:Pre-Depends= >> debian/subread.substvars
install -m0755 -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 -UProtected -DPackage=subread-dbgsym "-DDepends=subread (= \${binary:Version})" "-DDescription=debug symbols for subread" "-DBuild-Ids=14ec74443d14a8ea3f6d24d29280990732ce7967 192fd8555bf5d604053be38fe8c06762b37b06a5 3f14d1a83d34cc6ca955040d0d29b405bb49230b 3f5c14f331d872ccbc455050bdd8651423a6492a 4c7a2e00642e64b7dfdbd259f4fdf5160c9e5bcc 5cd5979676f5713aabab4c890eb00cf3b620ced0 79c7194ebb95f25845ec7f6ec62de3a418b6ca9c 9524691909a9036ab644bb428f9cb7afa15ef79c 9e8641c462fb94ea122b2ed492bd2953754c6788 b9d4c9ab3aea8a5b3271b5db5a99f535c9268cc0 c280afd594a4b2c0f9be5f1c9b3f8744710ba46b c8ebdceff3ce5bd609c5756c04c9c1e4057df44f cacf10ad7708a34721dc693c5e73d0cfac7ace9f e185bd0219a204009304078ab7808a1610d0dd47 e9e48044960f0b8b4edfc2e4ab63f8cd2048d940" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/control
dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -Pdebian/subread
chmod 0644 -- debian/subread/DEBIAN/control
dh_md5sums -a -O--buildsystem=makefile
install -m0755 -d debian/subread/DEBIAN
cd debian/subread >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/subread/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/subread/dbgsym-root/DEBIAN
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
dh_builddeb -a -O--buildsystem=makefile
dpkg-deb --root-owner-group --build debian/subread ..
dpkg-deb --root-owner-group --build debian/.debhelper/subread/dbgsym-root ..
dpkg-deb: building package 'subread' in '../subread_2.0.6+dfsg-2_armhf.deb'.
dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.6+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=any -O../subread_2.0.6+dfsg-2_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../subread_2.0.6+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 2023-09-21T14:52:03Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
subread_2.0.6+dfsg-2_armhf.changes:
-----------------------------------
Format: 1.8
Date: Wed, 13 Sep 2023 14:21:47 +0200
Source: subread
Binary: subread subread-dbgsym
Architecture: armhf
Version: 2.0.6+dfsg-2
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Michael R. Crusoe <crusoe@debian.org>
Description:
subread - toolkit for processing next-gen sequencing data
Closes: 1033089
Changes:
subread (2.0.6+dfsg-2) unstable; urgency=medium
.
* Team upload.
* d/control: build on riscv64 as well.
* d/patches/0001-src-Makefile.Linux-Do-not-set-CFLAGS-and-CXXFLAGS-
to.patch: fix embedded build path in various binaries.
Thanks to Vagrant Cascadian <vagrant@reproducible-builds.org>.
Closes: #1033089.
Checksums-Sha1:
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7a144d4801d7e656a082815016fa7a0dea877783 562936 subread_2.0.6+dfsg-2_armhf.deb
Checksums-Sha256:
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Files:
9aef6e6a7551657dd1159d24f67039af 9697924 debug optional subread-dbgsym_2.0.6+dfsg-2_armhf.deb
1169ba3d76fd6bd75cdf1d13bbc8b17a 5574 science optional subread_2.0.6+dfsg-2_armhf.buildinfo
5e288c120690dbb566aaff9e3cd8a2df 562936 science optional subread_2.0.6+dfsg-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
subread-dbgsym_2.0.6+dfsg-2_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 9697924 bytes: control archive=1308 bytes.
956 bytes, 12 lines control
1677 bytes, 16 lines md5sums
Package: subread-dbgsym
Source: subread
Version: 2.0.6+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 11439
Depends: subread (= 2.0.6+dfsg-2)
Section: debug
Priority: optional
Description: debug symbols for subread
Build-Ids: 14ec74443d14a8ea3f6d24d29280990732ce7967 192fd8555bf5d604053be38fe8c06762b37b06a5 3f14d1a83d34cc6ca955040d0d29b405bb49230b 3f5c14f331d872ccbc455050bdd8651423a6492a 4c7a2e00642e64b7dfdbd259f4fdf5160c9e5bcc 5cd5979676f5713aabab4c890eb00cf3b620ced0 79c7194ebb95f25845ec7f6ec62de3a418b6ca9c 9524691909a9036ab644bb428f9cb7afa15ef79c 9e8641c462fb94ea122b2ed492bd2953754c6788 b9d4c9ab3aea8a5b3271b5db5a99f535c9268cc0 c280afd594a4b2c0f9be5f1c9b3f8744710ba46b c8ebdceff3ce5bd609c5756c04c9c1e4057df44f cacf10ad7708a34721dc693c5e73d0cfac7ace9f e185bd0219a204009304078ab7808a1610d0dd47 e9e48044960f0b8b4edfc2e4ab63f8cd2048d940
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drwxr-xr-x root/root 0 2023-09-13 12:21 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2023-09-13 12:21 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 60076 2023-09-13 12:21 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/subread.debug
drwxr-xr-x root/root 0 2023-09-13 12:21 ./usr/share/
drwxr-xr-x root/root 0 2023-09-13 12:21 ./usr/share/doc/
lrwxrwxrwx root/root 0 2023-09-13 12:21 ./usr/share/doc/subread-dbgsym -> subread
subread_2.0.6+dfsg-2_armhf.deb
------------------------------
new Debian package, version 2.0.
size 562936 bytes: control archive=1572 bytes.
623 bytes, 14 lines control
2126 bytes, 33 lines md5sums
Package: subread
Version: 2.0.6+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7437
Depends: libc6 (>= 2.34), zlib1g (>= 1:1.2.3.3)
Section: science
Priority: optional
Homepage: http://sourceforge.net/projects/subread/
Description: toolkit for processing next-gen sequencing data
Subread aligner can be used to align both gDNA-seq and RNA-seq reads.
Subjunc aligner was specified designed for the detection of exon-exon
junction. For the mapping of RNA-seq reads, Subread performs local
alignments and Subjunc performs global alignments.
drwxr-xr-x root/root 0 2023-09-13 12:21 ./
drwxr-xr-x root/root 0 2023-09-13 12:21 ./usr/
drwxr-xr-x root/root 0 2023-09-13 12:21 ./usr/bin/
-rwxr-xr-x root/root 543148 2023-09-13 12:21 ./usr/bin/exactSNP
-rwxr-xr-x root/root 666540 2023-09-13 12:21 ./usr/bin/featureCounts
-rwxr-xr-x root/root 518588 2023-09-13 12:21 ./usr/bin/subindel
-rwxr-xr-x root/root 531820 2023-09-13 12:21 ./usr/bin/subjunc
-rwxr-xr-x root/root 71296 2023-09-13 12:21 ./usr/bin/sublong
-rwxr-xr-x root/root 531804 2023-09-13 12:21 ./usr/bin/subread-align
-rwxr-xr-x root/root 534924 2023-09-13 12:21 ./usr/bin/subread-buildindex
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-rwxr-xr-x root/root 518540 2023-09-13 12:21 ./usr/lib/subread/removeDup
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-rwxr-xr-x root/root 518540 2023-09-13 12:21 ./usr/lib/subread/subread-fullscan
-rwxr-xr-x root/root 518540 2023-09-13 12:21 ./usr/lib/subread/txUnique
drwxr-xr-x root/root 0 2023-09-13 12:21 ./usr/share/
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drwxr-xr-x root/root 0 2023-09-13 12:21 ./usr/share/doc/subread/
-rw-r--r-- root/root 692 2023-09-13 11:24 ./usr/share/doc/subread/README.Debian
-rw-r--r-- root/root 3257 2023-02-23 21:28 ./usr/share/doc/subread/README.txt
-rw-r--r-- root/root 1270 2023-09-13 12:21 ./usr/share/doc/subread/changelog.Debian.gz
-rw-r--r-- root/root 1268 2023-09-13 12:20 ./usr/share/doc/subread/copyright
drwxr-xr-x root/root 0 2023-09-13 12:21 ./usr/share/man/
drwxr-xr-x root/root 0 2023-09-13 12:21 ./usr/share/man/man1/
-rw-r--r-- root/root 1259 2023-09-13 12:21 ./usr/share/man/man1/exactSNP.1.gz
-rw-r--r-- root/root 3633 2023-09-13 12:21 ./usr/share/man/man1/featureCounts.1.gz
-rw-r--r-- root/root 634 2023-09-13 12:21 ./usr/share/man/man1/flattenGTF.1.gz
-rw-r--r-- root/root 1247 2023-09-13 12:21 ./usr/share/man/man1/genRandomReads.1.gz
-rw-r--r-- root/root 590 2023-09-13 12:21 ./usr/share/man/man1/propmapped.1.gz
-rw-r--r-- root/root 698 2023-09-13 12:21 ./usr/share/man/man1/qualityScores.1.gz
-rw-r--r-- root/root 623 2023-09-13 12:21 ./usr/share/man/man1/removeDup.1.gz
-rw-r--r-- root/root 693 2023-09-13 12:21 ./usr/share/man/man1/repair.1.gz
-rw-r--r-- root/root 472 2023-09-13 12:21 ./usr/share/man/man1/subindel.1.gz
-rw-r--r-- root/root 2391 2023-09-13 12:21 ./usr/share/man/man1/subjunc.1.gz
-rw-r--r-- root/root 689 2023-09-13 12:21 ./usr/share/man/man1/sublong.1.gz
-rw-r--r-- root/root 2430 2023-09-13 12:21 ./usr/share/man/man1/subread-align.1.gz
-rw-r--r-- root/root 866 2023-09-13 12:21 ./usr/share/man/man1/subread-buildindex.1.gz
-rw-r--r-- root/root 519 2023-09-13 12:21 ./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: 155776
Build-Time: 93
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 181
Job: subread_2.0.6+dfsg-2
Machine Architecture: armhf
Package: subread
Package-Time: 296
Source-Version: 2.0.6+dfsg-2
Space: 155776
Status: successful
Version: 2.0.6+dfsg-2
--------------------------------------------------------------------------------
Finished at 2023-09-21T14:52:03Z
Build needed 00:04:56, 155776k disk space