wham-align →
0.1.5-8 →
armhf → 2021-03-01 06:32:24
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| wham-align 0.1.5-8 (armhf) Mon, 01 Mar 2021 06:24:13 +0000 |
+==============================================================================+
Package: wham-align
Version: 0.1.5-8
Source Version: 0.1.5-8
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-d177d19c-96d0-4aaf-90bf-f2273b737bed' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
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Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [12.2 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.2 MB]
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Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
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| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'wham-align' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/wham-align.git
Please use:
git clone https://salsa.debian.org/med-team/wham-align.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 130 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main wham-align 0.1.5-8 (dsc) [1987 B]
Get:2 http://172.17.0.1/private bullseye-staging/main wham-align 0.1.5-8 (tar) [120 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main wham-align 0.1.5-8 (diff) [7760 B]
Fetched 130 kB in 0s (1008 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/wham-align-pfYl82/wham-align-0.1.5' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/wham-align-pfYl82' with '<<BUILDDIR>>'
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| 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-GOEXTt/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-GOEXTt/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-GOEXTt/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-GOEXTt/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-GOEXTt/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-GOEXTt/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-GOEXTt/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-GOEXTt/apt_archive ./ Packages [430 B]
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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:
bsdextrautils krb5-locales libnss-nis libnss-nisplus libpam-cap netbase
sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 48 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-GOEXTt/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
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Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13)
Filtered Build-Depends: debhelper-compat (= 13)
dpkg-deb: building package 'sbuild-build-depends-wham-align-dummy' in '/<<BUILDDIR>>/resolver-GOEXTt/apt_archive/sbuild-build-depends-wham-align-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-wham-align-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-GOEXTt/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-GOEXTt/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-GOEXTt/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-GOEXTt/apt_archive ./ Sources [493 B]
Get:5 copy:/<<BUILDDIR>>/resolver-GOEXTt/apt_archive ./ Packages [573 B]
Fetched 2399 B in 1s (2954 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install wham-align 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 libnss-nis libnss-nisplus libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libicu67 libmagic-mgc libmagic1
libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2
m4 man-db po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libicu67 libmagic-mgc libmagic1
libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2
m4 man-db po-debconf sbuild-build-depends-wham-align-dummy
0 upgraded, 30 newly installed, 0 to remove and 48 not upgraded.
Need to get 17.3 MB of archives.
After this operation, 64.4 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-GOEXTt/apt_archive ./ sbuild-build-depends-wham-align-dummy 0.invalid.0 [856 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-6 [793 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.4-1 [1307 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3.3 [189 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.11.0-1 [15.3 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.183-1 [161 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13+20210201-1 [164 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-6 [8289 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.3.3 [1011 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up autoconf (2.69-14) ...
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Setting up dwz (0.13+20210201-1) ...
Setting up groff-base (1.22.4-6) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.9.4-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up debhelper (13.3.3) ...
Setting up sbuild-build-depends-wham-align-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-9+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.1-7+rpi1 dpkg-dev_1.20.7.1+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-9+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.9-1+rpi1
Package versions: adduser_3.118 apt_2.1.18 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1-2 binutils_2.35.1-7+rpi1 binutils-arm-linux-gnueabihf_2.35.1-7+rpi1 binutils-common_2.35.1-7+rpi1 bsdextrautils_2.36.1-6 bsdutils_1:2.36.1-6 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.74 debhelper_13.3.3 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.11.0-1 diffutils_1:3.7-5 dirmngr_2.2.20-1 dpkg_1.20.7.1+rpi1 dpkg-dev_1.20.7.1+rpi1 dwz_0.13+20210201-1 e2fsprogs_1.45.7-1 fakeroot_1.25.3-1.1 fdisk_2.36.1-6 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-6+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-2 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 krb5-locales_1.18.3-4 libacl1_2.2.53-10 libapt-pkg6.0_2.1.18 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.1-7+rpi1 libblkid1_2.36.1-6 libbz2-1.0_1.0.8-4 libc-bin_2.31-9+rpi1 libc-dev-bin_2.31-9+rpi1 libc6_2.31-9+rpi1 libc6-dev_2.31-9+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_10.2.1-6+rpi1 libcom-err2_1.45.7-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-7+rpi1 libctf0_2.35.1-7+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.256 libdebhelper-perl_13.3.3 libdpkg-perl_1.20.7.1+rpi1 libelf1_0.183-1 libext2fs2_1.45.7-1 libfakeroot_1.25.3-1.1 libfdisk1_2.36.1-6 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.11.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.0-5 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-4 libhogweed6_3.6-2 libicu67_67.1-6 libidn2-0_2.3.0-5 libisl23_0.23-1 libk5crypto3_1.18.3-4 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-4 libkrb5support0_1.18.3-4 libksba8_1.5.0-3 libldap-2.4-2_2.4.57+dfsg-1 libldap-common_2.4.57+dfsg-1 liblz4-1_1.9.3-1+rpi1 liblzma5_5.2.5-1.0 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-6 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-2 libnettle8_3.6-2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.22-1 libpam-cap_1:2.44-1 libpam-modules_1.4.0-2 libpam-modules-bin_1.4.0-2 libpam-runtime_1.4.0-2 libpam0g_1.4.0-2 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-2 libpipeline1_1.5.3-1 libreadline8_8.1-1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-2+b1 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.36.1-6 libsqlite3-0_3.34.1-1 libss2_1.45.7-1 libssl1.1_1.1.1i-3 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.2-5+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.2-5+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-6 libxml2_2.9.10+dfsg-6.3 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-1 linux-libc-dev_5.10.9-1+rpi1 login_1:4.8.1-1 logsave_1.45.7-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4 man-db_2.9.4-1 mawk_1.3.4.20200120-2 mount_2.36.1-6 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 netbase_6.2 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-2 perl-base_5.32.1-2 perl-modules-5.32_5.32.1-2 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-wham-align-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.14 sysvinit-utils_2.96-5 tar_1.32+dfsg-1+rpi1 tzdata_2021a-1 util-linux_2.36.1-6 xz-utils_5.2.5-1.0 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.yRCIitxz/trustedkeys.kbx': General error
gpgv: Signature made Fri Feb 19 07:13:34 2021 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "npatra974@gmail.com"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./wham-align_0.1.5-8.dsc
dpkg-source: info: extracting wham-align in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking wham-align_0.1.5.orig.tar.gz
dpkg-source: info: unpacking wham-align_0.1.5-8.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying makefile.patch
dpkg-source: info: applying non-x86.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying cross-build.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-d177d19c-96d0-4aaf-90bf-f2273b737bed
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package wham-align
dpkg-buildpackage: info: source version 0.1.5-8
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_auto_clean
install -d /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home
make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f wham wham-build *.o
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/wham-align.substvars debian/files
rm -fr -- debian/wham-align/ debian/tmp/
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
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
install -d /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home
dh_auto_build -a
make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>'
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings hash.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings embedhash.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings main.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings sequence.cpp
In file included from hitset.h:31,
from hash.h:29,
from embedhash.cpp:27:
pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)':
pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
265 | if (num > nError) {
| ~~~~^~~~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)':
pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable]
602 | int i, j, offset, min, tmp;
| ^~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)':
pair.h:684:15: warning: unused variable 'num' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~
pair.h:684:20: warning: unused variable 'base' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~~
pair.h:685:9: warning: unused variable 'a' [-Wunused-variable]
685 | int a;
| ^
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)':
pair.h:755:15: warning: unused variable 'num' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~
pair.h:755:20: warning: unused variable 'base' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~~
pair.h:756:9: warning: unused variable 'a' [-Wunused-variable]
756 | int a;
| ^
pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)':
pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0));
| ~~~~~~~^~~~~~~~~~
In file included from hash.h:29,
from embedhash.cpp:27:
hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)':
hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable]
86 | int size;
| ^~~~
In file included from embedhash.cpp:27:
hash.h: In function 'uint32 murmurHash(int64*, uint32)':
hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable]
86 | uint32 sum = 0;
| ^~~
In file included from hitset.h:31,
from hash.h:29,
from hash.cpp:27:
pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)':
pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
265 | if (num > nError) {
| ~~~~^~~~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)':
pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable]
602 | int i, j, offset, min, tmp;
| ^~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)':
pair.h:684:15: warning: unused variable 'num' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~
pair.h:684:20: warning: unused variable 'base' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~~
pair.h:685:9: warning: unused variable 'a' [-Wunused-variable]
685 | int a;
| ^
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)':
pair.h:755:15: warning: unused variable 'num' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~
pair.h:755:20: warning: unused variable 'base' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~~
pair.h:756:9: warning: unused variable 'a' [-Wunused-variable]
756 | int a;
| ^
pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)':
pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0));
| ~~~~~~~^~~~~~~~~~
In file included from hash.h:29,
from hash.cpp:27:
hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)':
hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable]
86 | int size;
| ^~~~
In file included from hash.cpp:27:
hash.h: In function 'uint32 murmurHash(int64*, uint32)':
hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable]
86 | uint32 sum = 0;
| ^~~
In file included from hitset.h:31,
from hash.h:29,
from aligner.h:25,
from main.cpp:34:
pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)':
pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
265 | if (num > nError) {
| ~~~~^~~~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)':
pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable]
602 | int i, j, offset, min, tmp;
| ^~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)':
pair.h:684:15: warning: unused variable 'num' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~
pair.h:684:20: warning: unused variable 'base' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~~
pair.h:685:9: warning: unused variable 'a' [-Wunused-variable]
685 | int a;
| ^
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)':
pair.h:755:15: warning: unused variable 'num' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~
pair.h:755:20: warning: unused variable 'base' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~~
pair.h:756:9: warning: unused variable 'a' [-Wunused-variable]
756 | int a;
| ^
pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)':
pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0));
| ~~~~~~~^~~~~~~~~~
In file included from hash.h:29,
from aligner.h:25,
from main.cpp:34:
hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)':
hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable]
86 | int size;
| ^~~~
In file included from aligner.h:25,
from main.cpp:34:
hash.h: In function 'uint32 murmurHash(int64*, uint32)':
hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable]
86 | uint32 sum = 0;
| ^~~
embedhash.cpp: In member function 'int EmbedHashTable::preProcessEnd()':
embedhash.cpp:137:16: warning: unused variable 'ln2' [-Wunused-variable]
137 | const double ln2 = log(2);
| ^~~
embedhash.cpp: In member function 'void EmbedHashTable::setScanThreshold(double)':
embedhash.cpp:253:9: warning: unused variable 'sum' [-Wunused-variable]
253 | int64 sum = 0;
| ^~~
embedhash.cpp:255:9: warning: unused variable 'top' [-Wunused-variable]
255 | int64 top = total - total * r;
| ^~~
embedhash.cpp: In member function 'void EmbedHashTable::insert(int64*, unsigned int)':
embedhash.cpp:369:38: warning: operation on '*(((EmbedHashTable*)this)->EmbedHashTable::overflowPool + ((sizetype)(curOverflowEntry * 4)))' may be undefined [-Wsequence-point]
369 | overflowPool[curOverflowEntry] =
embedhash.cpp:328:10: warning: unused variable 'seqOffset' [-Wunused-variable]
328 | uint32 seqOffset;
| ^~~~~~~~~
embedhash.cpp:330:10: warning: unused variable 'counter' [-Wunused-variable]
330 | uint32 counter = 0;
| ^~~~~~~
embedhash.cpp:331:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable]
331 | int64 * seqVector;
| ^~~~~~~~~
embedhash.cpp:333:11: warning: unused variable 'target' [-Wunused-variable]
333 | int64 * target = &tspace[8];
| ^~~~~~
embedhash.cpp:334:8: warning: unused variable 'isBloomFilter' [-Wunused-variable]
334 | bool isBloomFilter;
| ^~~~~~~~~~~~~
embedhash.cpp:335:12: warning: unused variable 'bloomFilter' [-Wunused-variable]
335 | uint32 * bloomFilter;
| ^~~~~~~~~~~
embedhash.cpp:336:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable]
336 | uint32 bloomFilterNum;
| ^~~~~~~~~~~~~~
embedhash.cpp: In member function 'unsigned int EmbedHashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)':
embedhash.cpp:385:7: warning: unused variable 'num' [-Wunused-variable]
385 | int num;
| ^~~
embedhash.cpp:387:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable]
387 | uint32 seqOffset, entryOffset, startOffset;
| ^~~~~~~~~~~
embedhash.cpp:389:11: warning: unused variable 'diff' [-Wunused-variable]
389 | int64 * diff = &tspace1[8], *target = &tspace2[8];
| ^~~~
embedhash.cpp:392:10: warning: unused variable 'sid' [-Wunused-variable]
392 | uint32 sid, soffset;
| ^~~
embedhash.cpp:392:15: warning: unused variable 'soffset' [-Wunused-variable]
392 | uint32 sid, soffset;
| ^~~~~~~
In file included from hitset.h:31,
from hash.h:29,
from aligner.h:25,
from sequence.cpp:30:
pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)':
pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
265 | if (num > nError) {
| ~~~~^~~~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)':
pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable]
602 | int i, j, offset, min, tmp;
| ^~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)':
pair.h:684:15: warning: unused variable 'num' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~
pair.h:684:20: warning: unused variable 'base' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~~
pair.h:685:9: warning: unused variable 'a' [-Wunused-variable]
685 | int a;
| ^
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)':
pair.h:755:15: warning: unused variable 'num' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~
pair.h:755:20: warning: unused variable 'base' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~~
pair.h:756:9: warning: unused variable 'a' [-Wunused-variable]
756 | int a;
| ^
pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)':
pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0));
| ~~~~~~~^~~~~~~~~~
In file included from hash.h:29,
from aligner.h:25,
from sequence.cpp:30:
hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)':
hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable]
86 | int size;
| ^~~~
In file included from aligner.h:25,
from sequence.cpp:30:
hash.h: In function 'uint32 murmurHash(int64*, uint32)':
hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable]
86 | uint32 sum = 0;
| ^~~
hash.cpp: In member function 'int HashTable::preProcessEnd()':
hash.cpp:236:11: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32' {aka 'const unsigned int'} [-Wsign-compare]
236 | if (h >= nHistogram)
| ~~^~~~~~~~~~~~~
hash.cpp:285:33: warning: comparison of integer expressions of different signedness: 'uint32' {aka 'unsigned int'} and 'int' [-Wsign-compare]
285 | if (useEmbedTables() && tmp > embedShreshold) {
| ~~~~^~~~~~~~~~~~~~~~
hash.cpp: In member function 'void HashTable::setScanThreshold(double)':
hash.cpp:343:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
343 | for (int i = 0; i < nHistogram - 1; i++) {
| ~~^~~~~~~~~~~~~~~~
main.cpp: In function 'int getArguVal(char*)':
main.cpp:159:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
159 | else if (*c = 'g' || *c == 'G')
| ~~~^~~~~~~~~~~~~~~~~~
sequence.cpp: In member function 'void CompactSequence::extractFileName(char*, char*)':
sequence.cpp:97:10: warning: unused variable 'str' [-Wunused-variable]
97 | char * str;
| ^~~
sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)':
sequence.cpp:238:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
238 | for (i = 0; i < numFile; i++) {
| ~~^~~~~~~~~
hash.cpp: In member function 'void HashTable::insert(int64*, unsigned int)':
hash.cpp:460:38: warning: operation on '*(((HashTable*)this)->HashTable::overflowPool + ((sizetype)(curOverflowEntry * 4)))' may be undefined [-Wsequence-point]
460 | overflowPool[curOverflowEntry] =
hash.cpp:411:10: warning: unused variable 'seqOffset' [-Wunused-variable]
411 | uint32 seqOffset;
| ^~~~~~~~~
hash.cpp:413:10: warning: unused variable 'counter' [-Wunused-variable]
413 | uint32 counter = 0;
| ^~~~~~~
hash.cpp:414:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable]
414 | int64 * seqVector;
| ^~~~~~~~~
hash.cpp:416:11: warning: unused variable 'target' [-Wunused-variable]
416 | int64 * target = &tspace[8];
| ^~~~~~
hash.cpp:417:8: warning: unused variable 'isBloomFilter' [-Wunused-variable]
417 | bool isBloomFilter;
| ^~~~~~~~~~~~~
hash.cpp:418:12: warning: unused variable 'bloomFilter' [-Wunused-variable]
418 | uint32 * bloomFilter;
| ^~~~~~~~~~~
hash.cpp:419:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable]
419 | uint32 bloomFilterNum;
| ^~~~~~~~~~~~~~
sequence.cpp:309:13: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
309 | ( i = 0; i < nSeq; i++)
| ~~^~~~~~
sequence.cpp:324:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
324 | for (i = 0; i < numFile; i++) {
| ~~^~~~~~~~~
sequence.cpp:344:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
344 | for (j = 0; j < numError + 1; j++) {
| ~~^~~~~~~~~~~~~~
hash.cpp: In member function 'int HashTable::buildEmbedTable()':
hash.cpp:469:33: warning: unused variable 'rest' [-Wunused-variable]
469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40],
| ^~~~
hash.cpp:469:55: warning: unused variable 'rest1' [-Wunused-variable]
469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40],
| ^~~~~
hash.cpp:470:8: warning: unused variable 'rest2' [-Wunused-variable]
470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72];
| ^~~~~
hash.cpp:470:31: warning: unused variable 'noheadkey' [-Wunused-variable]
470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72];
| ^~~~~~~~~
hash.cpp:472:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable]
472 | uint32 seqOffset, entryOffset, startOffset;
| ^~~~~~~~~~~
sequence.cpp:410:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
410 | if (lenSegmentN > numError + 1) {
| ~~~~~~~~~~~~^~~~~~~~~~~~~~
sequence.cpp:429:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
429 | if (lenSegmentN > numError + 1) {
| ~~~~~~~~~~~~^~~~~~~~~~~~~~
sequence.cpp:223:16: warning: unused variable 'step' [-Wunused-variable]
223 | unsigned int step, nextstep;
| ^~~~
sequence.cpp:223:22: warning: unused variable 'nextstep' [-Wunused-variable]
223 | unsigned int step, nextstep;
| ^~~~~~~~
sequence.cpp: In member function 'int CompactSequence::filter(Aligner*, char**, int, char*)':
sequence.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
534 | for (i = 0; i < numFile; i++) {
| ~~^~~~~~~~~
sequence.cpp:599:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
599 | if (lenSegmentN > nError + 1)
| ~~~~~~~~~~~~^~~~~~~~~~~~
sequence.cpp:520:16: warning: unused variable 'step' [-Wunused-variable]
520 | unsigned int step, nextstep;
| ^~~~
sequence.cpp:520:22: warning: unused variable 'nextstep' [-Wunused-variable]
520 | unsigned int step, nextstep;
| ^~~~~~~~
hash.cpp: In member function 'void HashTable::preinsertEmbedTableEntry(int64*, int, int)':
hash.cpp:587:11: warning: unused variable 'noheadkey' [-Wunused-variable]
587 | int64 * noheadkey = &tspace[8], *rest = &tspace[24];
| ^~~~~~~~~
hash.cpp:590:8: warning: unused variable 'subkey4' [-Wunused-variable]
590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104];
| ^~~~~~~
sequence.cpp:521:9: warning: unused variable 'numFileChar' [-Wunused-variable]
521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment;
| ^~~~~~~~~~~
sequence.cpp:521:22: warning: unused variable 'numFileNSeg' [-Wunused-variable]
521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment;
| ^~~~~~~~~~~
sequence.cpp:521:35: warning: unused variable 'numFileSeq' [-Wunused-variable]
521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment;
| ^~~~~~~~~~
sequence.cpp:521:47: warning: unused variable 'nChar' [-Wunused-variable]
521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment;
| ^~~~~
sequence.cpp:521:54: warning: unused variable 'nNSegment' [-Wunused-variable]
521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment;
| ^~~~~~~~~
hash.cpp:590:32: warning: unused variable 'subkey5' [-Wunused-variable]
590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104];
| ^~~~~~~
main.cpp: In function 'int align(char*, AlignInfo*, char*, int)':
main.cpp:350:7: warning: unused variable 'i' [-Wunused-variable]
350 | int i, j, ret;
| ^
main.cpp:350:10: warning: unused variable 'j' [-Wunused-variable]
350 | int i, j, ret;
| ^
sequence.cpp: In member function 'int CompactSequence::save(char*)':
sequence.cpp:738:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare]
738 | if (ret != size) {
| ~~~~^~~~~~~
main.cpp: In function 'int main(int, char**)':
main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable]
523 | int numKeys;
| ^~~~~~~
main.cpp:526:7: warning: unused variable 'nSeq' [-Wunused-variable]
526 | int nSeq = 1;
| ^~~~
main.cpp:532:21: warning: unused variable 'sequence' [-Wunused-variable]
532 | CompactSequence * sequence;
| ^~~~~~~~
main.cpp:534:15: warning: unused variable 'threadpool' [-Wunused-variable]
534 | pthread_t * threadpool;
| ^~~~~~~~~~
main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable]
536 | int * threadid;
| ^~~~~~~~
hash.cpp: In member function 'void HashTable::insertEmbedTableEntry(int64*, uint32, int, int)':
hash.cpp:662:11: warning: unused variable 'noheadkey' [-Wunused-variable]
662 | int64 * noheadkey = &tspace[8], *rest = &tspace[24];
| ^~~~~~~~~
hash.cpp:665:8: warning: unused variable 'subkey4' [-Wunused-variable]
665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104];
| ^~~~~~~
hash.cpp:665:32: warning: unused variable 'subkey5' [-Wunused-variable]
665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104];
| ^~~~~~~
sequence.cpp: In member function 'int CompactSequence::load(char*)':
sequence.cpp:804:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare]
804 | if (ret != size) {
| ~~~~^~~~~~~
hash.cpp: In member function 'unsigned int HashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)':
hash.cpp:746:7: warning: unused variable 'num' [-Wunused-variable]
746 | int num;
| ^~~
hash.cpp:750:11: warning: unused variable 'diff' [-Wunused-variable]
750 | int64 * diff = &tspace1[8], *target = &tspace2[8];
| ^~~~
hash.cpp:753:10: warning: unused variable 'sid' [-Wunused-variable]
753 | uint32 sid, soffset;
| ^~~
hash.cpp:753:15: warning: unused variable 'soffset' [-Wunused-variable]
753 | uint32 sid, soffset;
| ^~~~~~~
hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)':
hash.cpp:962:11: warning: unused variable 'noheadkey' [-Wunused-variable]
962 | int64 * noheadkey = &tspace[8], *rest = &tspace[24];
| ^~~~~~~~~
hash.cpp:965:8: warning: unused variable 'subkey4' [-Wunused-variable]
965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104];
| ^~~~~~~
hash.cpp:965:32: warning: unused variable 'subkey5' [-Wunused-variable]
965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104];
| ^~~~~~~
hash.cpp:973:11: warning: unused variable 'seqVector' [-Wunused-variable]
973 | int64 * seqVector = sequence->getSequence();
| ^~~~~~~~~
hash.cpp: In member function 'bool HashTable::lookup(int64*, uint32)':
hash.cpp:1052:7: warning: unused variable 'num' [-Wunused-variable]
1052 | int num;
| ^~~
hash.cpp:1056:11: warning: unused variable 'diff' [-Wunused-variable]
1056 | int64 * diff = &tspace1[8], *target = &tspace2[8];
| ^~~~
hash.cpp:1056:32: warning: unused variable 'target' [-Wunused-variable]
1056 | int64 * diff = &tspace1[8], *target = &tspace2[8];
| ^~~~~~
hash.cpp:1057:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable]
1057 | int64 * seqVector;
| ^~~~~~~~~
hash.cpp:1059:10: warning: unused variable 'sid' [-Wunused-variable]
1059 | uint32 sid, soffset;
| ^~~
hash.cpp:1059:15: warning: unused variable 'soffset' [-Wunused-variable]
1059 | uint32 sid, soffset;
| ^~~~~~~
hash.cpp: In member function 'uint32 HashTable::printOverflowList(uint32, uint32, int64*)':
hash.cpp:1184:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare]
1184 | for (int i = 0; i < keyOffset / BITS_PER_BASE; i++)
hash.cpp:1188:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare]
1188 | for (int i = 0; i < (lenSeq - keyOffset - lenKey) / BITS_PER_BASE; i++)
hash.cpp:1247:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
1247 | for (int j = 0; j < strlen(set[i].str); j++)
| ~~^~~~~~~~~~~~~~~~~~~~
hash.cpp:1254:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
1254 | for (int j = 0; j < strlen(set[i].str); j++)
| ~~^~~~~~~~~~~~~~~~~~~~
hash.cpp:1137:11: warning: unused variable 'diff' [-Wunused-variable]
1137 | int64 * diff = &tspace1[8], *target = &tspace2[8];
| ^~~~
hash.cpp: In member function 'int HashTable::sortList()':
hash.cpp:1430:14: warning: variable 'pool' set but not used [-Wunused-but-set-variable]
1430 | uint32 * pool;
| ^~~~
hash.cpp:1321:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable]
1321 | uint32 entryOffset, seqOffset, offset;
| ^~~~~~
hash.cpp: In member function 'void HashTable::checkRepeat(uint32)':
hash.cpp:1673:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable]
1673 | uint32 entryOffset, seqOffset, offset;
| ^~~~~~
hash.cpp:1690:5: warning: label 'restart' defined but not used [-Wunused-label]
1690 | restart: if (buckets[bucketId] == HASH_EMPTY
| ^~~~~~~
In file included from embedhash.cpp:32:
edit_distance.h: At global scope:
edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable]
25 | static score_mat obj_score_mat = { 1, 1, 1, 1 };
| ^~~~~~~~~~~~~
In file included from pair.h:26,
from hitset.h:31,
from hash.h:29,
from embedhash.cpp:27:
rdtsc.h: In function 'long long unsigned int curtick()':
rdtsc.h:32:10: warning: 'tick' is used uninitialized in this function [-Wuninitialized]
32 | return tick;
| ^~~~
In file included from main.cpp:38:
edit_distance.h: At global scope:
edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable]
25 | static score_mat obj_score_mat = { 1, 1, 1, 1 };
| ^~~~~~~~~~~~~
hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)':
hash.cpp:1049:1: warning: control reaches end of non-void function [-Wreturn-type]
1049 | }
| ^
In file included from hash.cpp:31:
edit_distance.h: At global scope:
edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable]
25 | static score_mat obj_score_mat = { 1, 1, 1, 1 };
| ^~~~~~~~~~~~~
In file included from pair.h:26,
from hitset.h:31,
from hash.h:29,
from hash.cpp:27:
rdtsc.h: In function 'long long unsigned int curtick()':
rdtsc.h:32:10: warning: 'tick' is used uninitialized in this function [-Wuninitialized]
32 | return tick;
| ^~~~
sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)':
sequence.cpp:506:15: warning: 'offsetInOrgSeq' may be used uninitialized in this function [-Wmaybe-uninitialized]
506 | itree->flush(offsetInCmptSeq, 0, curSeq, offsetInOrgSeq);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp: In function 'void mergeFiles(std::string)':
main.cpp:269:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=]
269 | sprintf(buf, ".t%d ", i);
| ^~
main.cpp:269:18: note: directive argument in the range [0, 2147483647]
269 | sprintf(buf, ".t%d ", i);
| ^~~~~~~
main.cpp:269:12: note: 'sprintf' output between 5 and 14 bytes into a destination of size 10
269 | sprintf(buf, ".t%d ", i);
| ~~~~~~~^~~~~~~~~~~~~~~~~
main.cpp:276:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=]
276 | sprintf(buf, ".t%d", i);
| ^~
main.cpp:276:18: note: directive argument in the range [0, 2147483647]
276 | sprintf(buf, ".t%d", i);
| ^~~~~~
main.cpp:276:12: note: 'sprintf' output between 4 and 13 bytes into a destination of size 10
276 | sprintf(buf, ".t%d", i);
| ~~~~~~~^~~~~~~~~~~~~~~~
sequence.cpp: In static member function 'static void CompactSequence::compose(char*, int, int64*)':
sequence.cpp:672:19: warning: 'code' may be used uninitialized in this function [-Wmaybe-uninitialized]
672 | | (code >> (forward_offset + BITS_PER_BASE - BITS_PER_LONGWORD));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings aligner.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings interval.cpp
In file included from hitset.h:31,
from hash.h:29,
from aligner.h:25,
from aligner.cpp:25:
pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)':
pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
265 | if (num > nError) {
| ~~~~^~~~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)':
pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable]
602 | int i, j, offset, min, tmp;
| ^~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)':
pair.h:684:15: warning: unused variable 'num' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~
pair.h:684:20: warning: unused variable 'base' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~~
pair.h:685:9: warning: unused variable 'a' [-Wunused-variable]
685 | int a;
| ^
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)':
pair.h:755:15: warning: unused variable 'num' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~
pair.h:755:20: warning: unused variable 'base' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~~
pair.h:756:9: warning: unused variable 'a' [-Wunused-variable]
756 | int a;
| ^
pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)':
pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0));
| ~~~~~~~^~~~~~~~~~
In file included from hash.h:29,
from aligner.h:25,
from aligner.cpp:25:
hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)':
hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable]
86 | int size;
| ^~~~
In file included from aligner.h:25,
from aligner.cpp:25:
hash.h: In function 'uint32 murmurHash(int64*, uint32)':
hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable]
86 | uint32 sum = 0;
| ^~~
interval.cpp: In constructor 'IntervalTree::IntervalTree(uint32, uint32)':
interval.cpp:67:21: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare]
67 | for (int i = 0; i < numLevel - 1; i++) {
| ~~^~~~~~~~~~~~~~
interval.cpp: In member function 'int IntervalTree::save(char*)':
interval.cpp:304:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare]
304 | if (ret != numLEntry) {
| ~~~~^~~~~~~~~~~~
interval.cpp:310:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare]
310 | if (ret != numIEntry) {
| ~~~~^~~~~~~~~~~~
interval.cpp: In member function 'int IntervalTree::load(char*)':
interval.cpp:359:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare]
359 | if (ret != numLEntry) {
| ~~~~^~~~~~~~~~~~
interval.cpp:370:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare]
370 | if (ret != numIEntry) {
| ~~~~^~~~~~~~~~~~
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings edit_distance.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings error.cpp
error.cpp: In function 'void elog(int, char*, ...)':
error.cpp:31:9: warning: unused variable 'filename' [-Wunused-variable]
31 | char *filename = __FILE__;
| ^~~~~~~~
error.cpp:32:7: warning: unused variable 'lineno' [-Wunused-variable]
32 | int lineno = __LINE__;
| ^~~~~~
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings short.cpp
aligner.cpp: In member function 'int Aligner::initLookupArray()':
aligner.cpp:365:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
365 | if ((indexBits[i] >> j) & 0x1 == 1) {
| ~~~~^~~~
aligner.cpp:371:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
371 | if ((indexBits[i] >> j) & 0x1 == 1) {
| ~~~~^~~~
aligner.cpp: In member function 'int Aligner::preProcessHashTables()':
aligner.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
534 | for (i = 0; i < nHashTable; i++) {
| ~~^~~~~~~~~~~~
aligner.cpp:712:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
712 | for (i = 0; i < nHashTable; i++) {
| ~~^~~~~~~~~~~~
aligner.cpp: In member function 'int Aligner::build(char*)':
aligner.cpp:724:16: warning: unused variable 'i' [-Wunused-variable]
724 | unsigned int i, j;
| ^
aligner.cpp:724:19: warning: unused variable 'j' [-Wunused-variable]
724 | unsigned int i, j;
| ^
aligner.cpp: In member function 'int Aligner::buildHashTables(char*)':
aligner.cpp:807:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
807 | for (i = 0; i < nHashTable; i++) {
| ~~^~~~~~~~~~~~
aligner.cpp:844:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
844 | for (i1 = 0; i1 < lenPartition * (nPartition - 1); i1 += lenPartition) {
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:864:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
864 | for (i1 = 0; i1 < lenPartition * (nPartition - 2); i1 += lenPartition) {
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:871:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
871 | for (i2 = i1; i2 < lenPartition * (nPartition - 2);
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:894:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
894 | for (i1 = 0; i1 < lenPartition * (nPartition - 3); i1 += lenPartition) {
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:901:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
901 | for (i2 = i1; i2 < lenPartition * (nPartition - 3);
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:909:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
909 | for (i3 = i2; i3 < lenPartition * (nPartition - 3);
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:928:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
928 | for (i1 = 0; i1 < lenPartition * (nPartition - 4); i1 += lenPartition) {
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:930:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
930 | for (i2 = i1; i2 < lenPartition * (nPartition - 4);
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:933:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
933 | for (i3 = i2; i3 < lenPartition * (nPartition - 4);
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:936:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
936 | for (i4 = i3; i4 < lenPartition * (nPartition - 4); i4 +=
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:951:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
951 | for (i1 = 0; i1 < lenPartition * (nPartition - 5); i1 += lenPartition) {
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:953:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
953 | for (i2 = i1; i2 < lenPartition * (nPartition - 5);
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:956:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
956 | for (i3 = i2; i3 < lenPartition * (nPartition - 5);
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:959:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
959 | for (i4 = i3; i4 < lenPartition * (nPartition - 5); i4 +=
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:962:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
962 | for (i5 = i4; i5 < lenPartition * (nPartition - 5); i5 +=
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aligner.cpp:983:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
983 | for (i = 0; i < nHashTable; i++) {
| ~~^~~~~~~~~~~~
aligner.cpp:1006:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
1006 | for (i = 0; i < nHashTable; i++) {
| ~~^~~~~~~~~~~~
aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)':
aligner.cpp:1035:10: warning: unused variable 'offset' [-Wunused-variable]
1035 | uint32 offset;
| ^~~~~~
aligner.cpp:1039:7: warning: unused variable 'nHit' [-Wunused-variable]
1039 | int nHit = 0;
| ^~~~
aligner.cpp: In member function 'unsigned int Aligner::align(int64*, char*, strand, int, HitSet*, bool, bool)':
aligner.cpp:1119:10: warning: variable 'offset' set but not used [-Wunused-but-set-variable]
1119 | uint32 offset;
| ^~~~~~
aligner.cpp:1123:7: warning: variable 'nHit' set but not used [-Wunused-but-set-variable]
1123 | int nHit = 0;
| ^~~~
aligner.cpp: In member function 'int Aligner::check(int)':
aligner.cpp:1436:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
1436 | for (i = 0; i < num; i++) {
| ~~^~~~~
aligner.cpp:1452:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
1452 | for (j = 0; j < nError; j++) {
| ~~^~~~~~~~
aligner.cpp:1426:7: warning: unused variable 'ret' [-Wunused-variable]
1426 | int ret;
| ^~~
aligner.cpp: In member function 'AlignRes Aligner::alignSingleEnd(AlignInfo*, char*)':
aligner.cpp:1541:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
1541 | for (i = 0; i < nHashTable; i++) {
| ~~^~~~~~~~~~~~
aligner.cpp:1547:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
1547 | for (i = 0; i < res.nRead; i++) {
| ~~^~~~~~~~~~~
aligner.cpp:1629:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
1629 | delete writer;
| ^~~~~~~~~~~~~
aligner.cpp:1502:10: warning: unused variable 'file' [-Wunused-variable]
1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL;
| ^~~~
aligner.cpp:1502:24: warning: unused variable 'alfile' [-Wunused-variable]
1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL;
| ^~~~~~
aligner.cpp:1502:40: warning: unused variable 'unfile' [-Wunused-variable]
1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL;
| ^~~~~~
aligner.cpp:1505:7: warning: unused variable 'strand' [-Wunused-variable]
1505 | int strand;
| ^~~~~~
aligner.cpp:1508:9: warning: unused variable 'ratio' [-Wunused-variable]
1508 | float ratio;
| ^~~~~
aligner.cpp:1514:31: warning: unused variable 'strata' [-Wunused-variable]
1514 | bool sorted = info->sorted, strata = info->strata;
| ^~~~~~
aligner.cpp: In member function 'AlignRes Aligner::alignPairEnd(AlignInfo*, char*)':
aligner.cpp:1685:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
1685 | for (i = 0; i < res.nRead; i++) {
| ~~^~~~~~~~~~~
aligner.cpp:1754:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
1754 | delete writer;
| ^~~~~~~~~~~~~
aligner.cpp:1637:8: warning: unused variable 'success' [-Wunused-variable]
1637 | bool success;
| ^~~~~~~
aligner.cpp:1638:16: warning: unused variable 'nSuccessRead' [-Wunused-variable]
1638 | unsigned int nSuccessRead = 0;
| ^~~~~~~~~~~~
aligner.cpp:1639:10: warning: unused variable 'file' [-Wunused-variable]
1639 | FILE * file = NULL;
| ^~~~
aligner.cpp:1646:8: warning: unused variable 'mateFilename' [-Wunused-variable]
1646 | char mateFilename[256];
| ^~~~~~~~~~~~
aligner.cpp:1652:31: warning: unused variable 'strata' [-Wunused-variable]
1652 | bool sorted = info->sorted, strata = info->strata;
| ^~~~~~
aligner.cpp: In member function 'AlignRes Aligner::mergeSingleEnd(AlignInfo*, int, char*)':
aligner.cpp:1851:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
1851 | delete writer;
| ^~~~~~~~~~~~~
aligner.cpp:1775:10: warning: unused variable 'ret' [-Wunused-variable]
1775 | int i, ret;
| ^~~
aligner.cpp: In member function 'AlignRes Aligner::mergePairEnd(AlignInfo*, int, char*)':
aligner.cpp:1989:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
1989 | delete writer;
| ^~~~~~~~~~~~~
aligner.cpp:1874:10: warning: unused variable 'ret' [-Wunused-variable]
1874 | int i, ret;
| ^~~
short.cpp: In member function 'int ShortRead::preProcess(int)':
short.cpp:212:16: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
212 | while (len = readLine(file, str, 256)) {
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
short.cpp: In member function 'ShortRead** ShortRead::split(int)':
short.cpp:483:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
483 | if (szPartition <= nRead - curRead)
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
edit_distance.cpp: In function 'scoreinfo edit_distance(char*, char*, int, int, char*, char*, int)':
edit_distance.cpp:61:7: warning: unused variable 'i' [-Wunused-variable]
61 | int i;
| ^
edit_distance.cpp: In function 'scoreinfo edit_distance_align(int**, char**, char*, char*, int, int, char*, char*, int)':
edit_distance.cpp:181:10: warning: unused variable 'tmp_trace' [-Wunused-variable]
181 | char tmp_trace = traceback[i][j];
| ^~~~~~~~~
edit_distance.cpp:132:14: warning: unused variable 'x' [-Wunused-variable]
132 | int k = 0, x = 0, y = 0;
| ^
edit_distance.cpp:132:21: warning: unused variable 'y' [-Wunused-variable]
132 | int k = 0, x = 0, y = 0;
| ^
edit_distance.cpp:178:7: warning: unused variable 'kk' [-Wunused-variable]
178 | int kk = 0;
| ^~
short.cpp: In member function 'int ShortRead::load(int)':
short.cpp:436:34: warning: 'code' may be used uninitialized in this function [-Wmaybe-uninitialized]
436 | | (reverse[code] << backward_offset);
| ~~~~~~~~~~~~^
short.cpp: In member function 'ShortRead** ShortRead::split(int)':
short.cpp:503:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=]
503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i);
| ^~
short.cpp:503:42: note: directive argument in the range [0, 536870910]
503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i);
| ^~~~~~~~
short.cpp:503:14: note: 'sprintf' output between 4 and 267 bytes into a destination of size 256
503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
short.cpp:510:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=]
510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i);
| ^~
short.cpp:510:42: note: directive argument in the range [0, 536870910]
510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i);
| ^~~~~~~~
short.cpp:510:14: note: 'sprintf' output between 4 and 267 bytes into a destination of size 256
510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings hitset.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings perfcounters.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings model.cpp
In file included from hitset.h:31,
from hitset.cpp:1:
pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)':
pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
265 | if (num > nError) {
| ~~~~^~~~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)':
pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable]
602 | int i, j, offset, min, tmp;
| ^~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)':
pair.h:684:15: warning: unused variable 'num' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~
pair.h:684:20: warning: unused variable 'base' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~~
pair.h:685:9: warning: unused variable 'a' [-Wunused-variable]
685 | int a;
| ^
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)':
pair.h:755:15: warning: unused variable 'num' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~
pair.h:755:20: warning: unused variable 'base' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~~
pair.h:756:9: warning: unused variable 'a' [-Wunused-variable]
756 | int a;
| ^
pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)':
pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0));
| ~~~~~~~^~~~~~~~~~
In file included from hitset.cpp:1:
hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)':
hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable]
86 | int size;
| ^~~~
hitset.cpp: In member function 'int HitPairSet::build(HitSet*, HitSet*, uint32, uint32, bool (*)[2], bool)':
hitset.cpp:90:8: warning: unused variable 'pairMatch' [-Wunused-variable]
90 | bool pairMatch = false;
| ^~~~~~~~~
model.cpp: In static member function 'static int AlignerModel::estimateNumPartition(unsigned int, int, int, bool)':
model.cpp:76:16: warning: variable 'nIndex' set but not used [-Wunused-but-set-variable]
76 | unsigned int nIndex, nLookup, nBucket;
| ^~~~~~
model.cpp: In static member function 'static unsigned int AlignerModel::getFreeMemory()':
model.cpp:166:28: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=]
166 | fscanf(file, "MemTotal: %d kB\n", &memTotal);
| ~^ ~~~~~~~~~
| | |
| int* unsigned int*
| %d
model.cpp:167:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=]
167 | fscanf(file, "MemFree: %d kB\n", &memFree);
| ~^ ~~~~~~~~
| | |
| int* unsigned int*
| %d
model.cpp:168:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=]
168 | fscanf(file, "Buffers: %d kB\n", &memBuffer);
| ~^ ~~~~~~~~~~
| | |
| int* unsigned int*
| %d
model.cpp:169:26: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=]
169 | fscanf(file, "Cached: %d kB\n", &memCache);
| ~^ ~~~~~~~~~
| | |
| int* unsigned int*
| %d
model.cpp: In static member function 'static unsigned int AlignerModel::estimateHashtableSpace(unsigned int, int, int, int)':
model.cpp:198:26: warning: variable 'p2' set but not used [-Wunused-but-set-variable]
198 | double nSpace, p0, p1, p2;
| ^~
In file included from aligner.h:25,
from aligner.cpp:25:
hash.h: In member function 'int Aligner::initLookupArray()':
hash.h:353:18: warning: 'keySpan' may be used uninitialized in this function [-Wmaybe-uninitialized]
353 | widthKeySpan = keySpan;
| ~~~~~~~~~~~~~^~~~~~~~~
aligner.cpp:360:7: note: 'keySpan' was declared here
360 | int keySpan;
| ^~~~~~~
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings writer.cpp
g++ -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings builder.cpp
In file included from hitset.h:31,
from writer.h:26,
from writer.cpp:21:
pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)':
pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
265 | if (num > nError) {
| ~~~~^~~~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)':
pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable]
602 | int i, j, offset, min, tmp;
| ^~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)':
pair.h:684:15: warning: unused variable 'num' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~
pair.h:684:20: warning: unused variable 'base' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~~
pair.h:685:9: warning: unused variable 'a' [-Wunused-variable]
685 | int a;
| ^
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)':
pair.h:755:15: warning: unused variable 'num' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~
pair.h:755:20: warning: unused variable 'base' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~~
pair.h:756:9: warning: unused variable 'a' [-Wunused-variable]
756 | int a;
| ^
pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)':
pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0));
| ~~~~~~~^~~~~~~~~~
In file included from writer.h:26,
from writer.cpp:21:
hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)':
hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable]
86 | int size;
| ^~~~
writer.cpp: In member function 'void SimpleWriter::writeField(int64*, int64*, strand)':
writer.cpp:154:27: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
154 | j = BITS_PER_LONGWORD - (length * BITS_PER_BASE) & BITS_LONGWORD_MASK;
writer.cpp:148:10: warning: unused variable 'sid' [-Wunused-variable]
148 | uint32 sid = 0, soffset = 0;
| ^~~
writer.cpp:148:19: warning: unused variable 'soffset' [-Wunused-variable]
148 | uint32 sid = 0, soffset = 0;
| ^~~~~~~
writer.cpp: In member function 'void SamWriter::writeValidAlignment(int, HitSet*)':
writer.cpp:271:7: warning: unused variable 'i' [-Wunused-variable]
271 | int i, j, k, h, lastDiff;
| ^
writer.cpp:271:10: warning: unused variable 'j' [-Wunused-variable]
271 | int i, j, k, h, lastDiff;
| ^
writer.cpp:271:13: warning: unused variable 'k' [-Wunused-variable]
271 | int i, j, k, h, lastDiff;
| ^
writer.cpp:271:19: warning: unused variable 'lastDiff' [-Wunused-variable]
271 | int i, j, k, h, lastDiff;
| ^~~~~~~~
writer.cpp:272:9: warning: unused variable 'code1' [-Wunused-variable]
272 | int64 code1, code2;
| ^~~~~
writer.cpp:272:16: warning: unused variable 'code2' [-Wunused-variable]
272 | int64 code1, code2;
| ^~~~~
writer.cpp:278:10: warning: unused variable 'p' [-Wunused-variable]
278 | double p, sump;
| ^
writer.cpp:278:13: warning: unused variable 'sump' [-Wunused-variable]
278 | double p, sump;
| ^~~~
writer.cpp:279:30: warning: unused variable 'tag' [-Wunused-variable]
279 | char qseq[128], rseq[128], tag[128];
| ^~~
writer.cpp:281:8: warning: unused variable 'shortread' [-Wunused-variable]
281 | char shortread[256];
| ^~~~~~~~~
writer.cpp: In member function 'void SamWriter::getCIGAR(char*, char*, char*, ErrorVector)':
writer.cpp:382:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
382 | for (i = 0, j = 0; i < strlen(query); i++, j++) {
| ~~^~~~~~~~~~~~~~~
writer.cpp: In member function 'void SamWriter::getMDfield(char*, char*, char*, ErrorVector)':
writer.cpp:431:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
431 | for (i = 0, j = 0; i < strlen(query); i++, j++) {
| ~~^~~~~~~~~~~~~~~
writer.cpp: In member function 'void SamPairWriter::writeValidAlignment(int, HitSet*)':
writer.cpp:619:47: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
619 | if (!mate1Unmatch && !mate2Unmatch & sid1 == sid2) {
| ~~~~~^~~~~~~
In file included from hitset.h:31,
from hash.h:29,
from aligner.h:25,
from builder.cpp:31:
pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)':
pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
265 | if (num > nError) {
| ~~~~^~~~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)':
pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable]
602 | int i, j, offset, min, tmp;
| ^~~~~~
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)':
pair.h:684:15: warning: unused variable 'num' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~
pair.h:684:20: warning: unused variable 'base' [-Wunused-variable]
684 | int i, p, num, base, Cscore;
| ^~~~
pair.h:685:9: warning: unused variable 'a' [-Wunused-variable]
685 | int a;
| ^
pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)':
pair.h:755:15: warning: unused variable 'num' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~
pair.h:755:20: warning: unused variable 'base' [-Wunused-variable]
755 | int i, p, num, base, Cscore;
| ^~~~
pair.h:756:9: warning: unused variable 'a' [-Wunused-variable]
756 | int a;
| ^
pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)':
pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0));
| ~~~~~~~^~~~~~~~~~
In file included from hash.h:29,
from aligner.h:25,
from builder.cpp:31:
hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)':
hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable]
86 | int size;
| ^~~~
In file included from aligner.h:25,
from builder.cpp:31:
hash.h: In function 'uint32 murmurHash(int64*, uint32)':
hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable]
86 | uint32 sum = 0;
| ^~~
builder.cpp: In function 'int getArguVal(char*)':
builder.cpp:115:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
115 | else if (*c = 'g' || *c == 'G')
| ~~~^~~~~~~~~~~~~~~~~~
builder.cpp: In function 'int main(int, char**)':
builder.cpp:159:7: warning: unused variable 'build_mode' [-Wunused-variable]
159 | int build_mode = BUILD_MODE_ALL;
| ^~~~~~~~~~
builder.cpp:277:7: warning: unused variable 'nChar' [-Wunused-variable]
277 | int nChar = sequence->getNum();
| ^~~~~
In file included from builder.cpp:34:
edit_distance.h: At global scope:
edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable]
25 | static score_mat obj_score_mat = { 1, 1, 1, 1 };
| ^~~~~~~~~~~~~
aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)':
aligner.cpp:1097:3: warning: 'ret' may be used uninitialized in this function [-Wmaybe-uninitialized]
1097 | if (ret == MSG_HITSETFULL)
| ^~
g++ -o wham sequence.o hash.o embedhash.o main.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o -lpthread
g++ -o wham-build sequence.o hash.o embedhash.o builder.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o -lpthread
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
rm -fr -- /tmp/dh-xdg-rundir-Y5zMkSlA
create-stamp debian/debhelper-build-stamp
dh_prep -a
rm -f -- debian/wham-align.substvars
rm -fr -- debian/.debhelper/generated/wham-align/ debian/wham-align/ debian/tmp/
dh_auto_install -a
install -d /<<PKGBUILDDIR>>/debian/wham-align
dh_install -a
install -d debian/wham-align/usr/bin
cp --reflink=auto -a ./wham ./wham-build debian/wham-align/usr/bin/
install -d debian/.debhelper/generated/wham-align
dh_installdocs -a
install -d debian/wham-align/usr/share/doc/wham-align
cp --reflink=auto -a ./MANUAL debian/wham-align/usr/share/doc/wham-align
cd './reads/..' && find 'reads' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /<<PKGBUILDDIR>>/debian/wham-align/usr/share/doc/wham-align
cd './sequences/..' && find 'sequences' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /<<PKGBUILDDIR>>/debian/wham-align/usr/share/doc/wham-align
cp --reflink=auto -a ./debian/README.test debian/wham-align/usr/share/doc/wham-align
cp --reflink=auto -a ./debian/tests/ref/README.test_data debian/wham-align/usr/share/doc/wham-align
chmod -R u\+rw,go=rX debian/wham-align/usr/share/doc
install -p -m0644 debian/copyright debian/wham-align/usr/share/doc/wham-align/copyright
install -d debian/wham-align/usr/share/doc-base/
install -p -m0644 debian/wham-align.doc-base debian/wham-align/usr/share/doc-base/wham
dh_installchangelogs -a
install -p -m0644 debian/changelog debian/wham-align/usr/share/doc/wham-align/changelog.Debian
dh_installexamples -a
install -d debian/wham-align/usr/share/doc/wham-align/examples
cp --reflink=auto -a ./reads debian/wham-align/usr/share/doc/wham-align/examples
cp --reflink=auto -a ./sequences debian/wham-align/usr/share/doc/wham-align/examples
cp --reflink=auto -a ./debian/tests/ref debian/wham-align/usr/share/doc/wham-align/examples
dh_installman -a
install -d debian/wham-align/usr/share/man/man1/
install -p -m0644 ./debian/wham-build.1 debian/wham-align/usr/share/man/man1/wham-build.1
install -p -m0644 ./debian/wham.1 debian/wham-align/usr/share/man/man1/wham.1
man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham-build.1
man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham.1
mv debian/wham-align/usr/share/man/man1/wham.1.dh-new debian/wham-align/usr/share/man/man1/wham.1
chmod 0644 -- debian/wham-align/usr/share/man/man1/wham.1
mv debian/wham-align/usr/share/man/man1/wham-build.1.dh-new debian/wham-align/usr/share/man/man1/wham-build.1
chmod 0644 -- debian/wham-align/usr/share/man/man1/wham-build.1
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
cd debian/wham-align
chmod a-x usr/share/doc/wham-align/MANUAL usr/share/doc/wham-align/changelog.Debian usr/share/doc/wham-align/sequences/chr1_100k.fa usr/share/man/man1/wham-build.1 usr/share/man/man1/wham.1
gzip -9nf usr/share/doc/wham-align/MANUAL usr/share/doc/wham-align/changelog.Debian usr/share/doc/wham-align/sequences/chr1_100k.fa usr/share/man/man1/wham-build.1 usr/share/man/man1/wham.1
cd '/<<PKGBUILDDIR>>'
dh_fixperms -a
find debian/wham-align ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/wham-align/usr/share/doc -type f -a -true -a ! -regex 'debian/wham-align/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/wham-align/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/wham-align/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/wham-align -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/wham-align/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
dh_missing -a
dh_dwz -a -a
install -d debian/wham-align/usr/lib/debug/.dwz/arm-linux-gnueabihf
dwz -mdebian/wham-align/usr/lib/debug/.dwz/arm-linux-gnueabihf/wham-align.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/wham-align.debug -- debian/wham-align/usr/bin/wham debian/wham-align/usr/bin/wham-build
objcopy --compress-debug-sections debian/wham-align/usr/lib/debug/.dwz/arm-linux-gnueabihf/wham-align.debug
dh_strip -a -a
install -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/c1
objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/c1/0876b11defdd20f4e384e6be16f6aad9e2e027.debug
chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/c1/0876b11defdd20f4e384e6be16f6aad9e2e027.debug
strip --remove-section=.comment --remove-section=.note debian/wham-align/usr/bin/wham
objcopy --add-gnu-debuglink debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/c1/0876b11defdd20f4e384e6be16f6aad9e2e027.debug debian/wham-align/usr/bin/wham
install -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/d4
objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham-build debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/d4/770b4b79b3a270f1e09eb9b7c99c87c0c95004.debug
chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/d4/770b4b79b3a270f1e09eb9b7c99c87c0c95004.debug
strip --remove-section=.comment --remove-section=.note debian/wham-align/usr/bin/wham-build
objcopy --add-gnu-debuglink debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/d4/770b4b79b3a270f1e09eb9b7c99c87c0c95004.debug debian/wham-align/usr/bin/wham-build
install -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.dwz
cp --reflink=auto -a debian/wham-align/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.dwz
rm -fr debian/wham-align/usr/lib/debug/.dwz
rmdir -p --ignore-fail-on-non-empty debian/wham-align/usr/lib/debug
install -d debian/.debhelper/wham-align/dbgsym-root/usr/share/doc
ln -s wham-align debian/.debhelper/wham-align/dbgsym-root/usr/share/doc/wham-align-dbgsym
dh_makeshlibs -a -a
rm -f debian/wham-align/DEBIAN/shlibs
dh_shlibdeps -a -a
install -d debian/wham-align/DEBIAN
dpkg-shlibdeps -Tdebian/wham-align.substvars debian/wham-align/usr/bin/wham debian/wham-align/usr/bin/wham-build
dpkg-shlibdeps: warning: debian/wham-align/usr/bin/wham-build contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/wham-align/usr/bin/wham contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/wham-align/usr/bin/wham-build debian/wham-align/usr/bin/wham were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
echo misc:Depends= >> debian/wham-align.substvars
echo misc:Pre-Depends= >> debian/wham-align.substvars
install -d debian/.debhelper/wham-align/dbgsym-root/DEBIAN
dpkg-gencontrol -pwham-align -ldebian/changelog -Tdebian/wham-align.substvars -Pdebian/.debhelper/wham-align/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=wham-align-dbgsym "-DDepends=wham-align (= \${binary:Version})" "-DDescription=debug symbols for wham-align" "-DBuild-Ids=c10876b11defdd20f4e384e6be16f6aad9e2e027 d4770b4b79b3a270f1e09eb9b7c99c87c0c95004" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/DEBIAN/control
dpkg-gencontrol -pwham-align -ldebian/changelog -Tdebian/wham-align.substvars -Pdebian/wham-align
chmod 0644 -- debian/wham-align/DEBIAN/control
dh_md5sums -a
cd debian/wham-align >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/wham-align/DEBIAN/md5sums
cd debian/.debhelper/wham-align/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --root-owner-group --build debian/wham-align ..
dpkg-deb --root-owner-group --build debian/.debhelper/wham-align/dbgsym-root ..
dpkg-deb: building package 'wham-align' in '../wham-align_0.1.5-8_armhf.deb'.
dpkg-deb: building package 'wham-align-dbgsym' in '../wham-align-dbgsym_0.1.5-8_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../wham-align_0.1.5-8_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-03-01T06:32:08Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
wham-align_0.1.5-8_armhf.changes:
---------------------------------
Format: 1.8
Date: Fri, 19 Feb 2021 12:34:48 +0530
Source: wham-align
Binary: wham-align wham-align-dbgsym
Architecture: armhf
Version: 0.1.5-8
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Nilesh Patra <npatra974@gmail.com>
Description:
wham-align - Wisconsin's High-Throughput Alignment Method
Changes:
wham-align (0.1.5-8) unstable; urgency=medium
.
* Team Upload.
* Append -fsignedchar in CXXFLAFS for autopkgtests fix
Checksums-Sha1:
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75135beb9b869908a54b8672d03ba47e742b9a40 4851 wham-align_0.1.5-8_armhf.buildinfo
54c7a826e9131dc72f1814402e660c51ae29c78e 176548 wham-align_0.1.5-8_armhf.deb
Checksums-Sha256:
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ccbaa2b936d9f8541a40fbc36b0f207c67d753d0ae827dd7aa8137eb8fb1208a 4851 wham-align_0.1.5-8_armhf.buildinfo
8910e7b442ee9c134e2046cdf28fb1db14bded998ad9d5ad08bdad8b4166e120 176548 wham-align_0.1.5-8_armhf.deb
Files:
0fda247583e6be57c7a0f22b728a1e9b 480452 debug optional wham-align-dbgsym_0.1.5-8_armhf.deb
840e687dbb6e9415be0cbb8f28fec4b3 4851 science optional wham-align_0.1.5-8_armhf.buildinfo
d42d388a578f7264db70cf4a31bd7fb6 176548 science optional wham-align_0.1.5-8_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
wham-align-dbgsym_0.1.5-8_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 480452 bytes: control archive=652 bytes.
423 bytes, 12 lines control
302 bytes, 3 lines md5sums
Package: wham-align-dbgsym
Source: wham-align
Version: 0.1.5-8
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 521
Depends: wham-align (= 0.1.5-8)
Section: debug
Priority: optional
Description: debug symbols for wham-align
Build-Ids: c10876b11defdd20f4e384e6be16f6aad9e2e027 d4770b4b79b3a270f1e09eb9b7c99c87c0c95004
drwxr-xr-x root/root 0 2021-02-19 07:04 ./
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/lib/
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/lib/debug/.build-id/c1/
-rw-r--r-- root/root 266368 2021-02-19 07:04 ./usr/lib/debug/.build-id/c1/0876b11defdd20f4e384e6be16f6aad9e2e027.debug
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/lib/debug/.build-id/d4/
-rw-r--r-- root/root 218796 2021-02-19 07:04 ./usr/lib/debug/.build-id/d4/770b4b79b3a270f1e09eb9b7c99c87c0c95004.debug
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 32800 2021-02-19 07:04 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/wham-align.debug
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/share/
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-02-19 07:04 ./usr/share/doc/wham-align-dbgsym -> wham-align
wham-align_0.1.5-8_armhf.deb
----------------------------
new Debian package, version 2.0.
size 176548 bytes: control archive=1252 bytes.
522 bytes, 13 lines control
1984 bytes, 26 lines md5sums
Package: wham-align
Version: 0.1.5-8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 627
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libstdc++6 (>= 5.2)
Section: science
Priority: optional
Homepage: http://research.cs.wisc.edu/wham
Description: Wisconsin's High-Throughput Alignment Method
This package provides functionality analogous to BWA or
bowtie in aligning reads from next-generation DNA sequencing
machines against a reference genome.
drwxr-xr-x root/root 0 2021-02-19 07:04 ./
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/bin/
-rwxr-xr-x root/root 239684 2021-02-19 07:04 ./usr/bin/wham
-rwxr-xr-x root/root 227272 2021-02-19 07:04 ./usr/bin/wham-build
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/share/
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/share/doc-base/
-rw-r--r-- root/root 273 2021-02-16 17:56 ./usr/share/doc-base/wham
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/share/doc/wham-align/
-rw-r--r-- root/root 2483 2021-02-19 07:04 ./usr/share/doc/wham-align/MANUAL.gz
-rw-r--r-- root/root 278 2021-02-16 17:56 ./usr/share/doc/wham-align/README.test
-rw-r--r-- root/root 150 2021-02-16 17:56 ./usr/share/doc/wham-align/README.test_data
-rw-r--r-- root/root 902 2021-02-19 07:04 ./usr/share/doc/wham-align/changelog.Debian.gz
-rw-r--r-- root/root 1297 2021-02-16 17:56 ./usr/share/doc/wham-align/copyright
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/share/doc/wham-align/examples/
drwxr-xr-x root/root 0 2012-11-26 20:40 ./usr/share/doc/wham-align/examples/reads/
-rw-r--r-- root/root 898 2011-03-18 21:47 ./usr/share/doc/wham-align/examples/reads/sample.fq
-rw-r--r-- root/root 878 2011-04-17 03:34 ./usr/share/doc/wham-align/examples/reads/sample_pair_1.fq
-rw-r--r-- root/root 878 2011-04-17 03:34 ./usr/share/doc/wham-align/examples/reads/sample_pair_2.fq
drwxr-xr-x root/root 0 2021-02-16 17:56 ./usr/share/doc/wham-align/examples/ref/
-rw-r--r-- root/root 150 2021-02-16 17:56 ./usr/share/doc/wham-align/examples/ref/README.test_data
-rw-r--r-- root/root 231 2021-02-16 17:56 ./usr/share/doc/wham-align/examples/ref/output1
-rw-r--r-- root/root 719 2021-02-16 17:56 ./usr/share/doc/wham-align/examples/ref/output2
-rw-r--r-- root/root 244 2021-02-16 17:56 ./usr/share/doc/wham-align/examples/ref/output3
-rw-r--r-- root/root 326 2021-02-16 17:56 ./usr/share/doc/wham-align/examples/ref/output4
-rw-r--r-- root/root 0 2021-02-16 17:56 ./usr/share/doc/wham-align/examples/ref/output5
-rw-r--r-- root/root 463 2021-02-16 17:56 ./usr/share/doc/wham-align/examples/ref/output6
-rw-r--r-- root/root 231 2021-02-16 17:56 ./usr/share/doc/wham-align/examples/ref/output7
drwxr-xr-x root/root 0 2012-11-26 20:40 ./usr/share/doc/wham-align/examples/sequences/
-rw-r--r-- root/root 101955 2011-02-08 11:01 ./usr/share/doc/wham-align/examples/sequences/chr1_100k.fa
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/share/doc/wham-align/reads/
-rw-r--r-- root/root 898 2011-03-18 21:47 ./usr/share/doc/wham-align/reads/sample.fq
-rw-r--r-- root/root 878 2011-04-17 03:34 ./usr/share/doc/wham-align/reads/sample_pair_1.fq
-rw-r--r-- root/root 878 2011-04-17 03:34 ./usr/share/doc/wham-align/reads/sample_pair_2.fq
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/share/doc/wham-align/sequences/
-rw-r--r-- root/root 29876 2011-02-08 11:01 ./usr/share/doc/wham-align/sequences/chr1_100k.fa.gz
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/share/man/
drwxr-xr-x root/root 0 2021-02-19 07:04 ./usr/share/man/man1/
-rw-r--r-- root/root 689 2021-02-19 07:04 ./usr/share/man/man1/wham-build.1.gz
-rw-r--r-- root/root 993 2021-02-19 07:04 ./usr/share/man/man1/wham.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 6748
Build-Time: 123
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 299
Job: wham-align_0.1.5-8
Machine Architecture: armhf
Package: wham-align
Package-Time: 475
Source-Version: 0.1.5-8
Space: 6748
Status: successful
Version: 0.1.5-8
--------------------------------------------------------------------------------
Finished at 2021-03-01T06:32:08Z
Build needed 00:07:55, 6748k disc space