anfo →
0.98-9 →
armhf → 2021-10-11 06:30:30
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| anfo 0.98-9 (armhf) Mon, 11 Oct 2021 06:11:11 +0000 |
+==============================================================================+
Package: anfo
Version: 0.98-9
Source Version: 0.98-9
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-f5f8d3a2-9557-46b9-af1b-2a82e2edf7f3' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.8 MB in 25s (1019 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'anfo' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/anfo.git
Please use:
git clone https://salsa.debian.org/med-team/anfo.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 472 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main anfo 0.98-9 (dsc) [2105 B]
Get:2 http://172.17.0.1/private bookworm-staging/main anfo 0.98-9 (tar) [462 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main anfo 0.98-9 (diff) [7952 B]
Fetched 472 kB in 0s (3655 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/anfo-IrOfIE/anfo-0.98' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/anfo-IrOfIE' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-R9BNbS/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-R9BNbS/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-R9BNbS/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-R9BNbS/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-R9BNbS/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-R9BNbS/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-R9BNbS/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-R9BNbS/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-R9BNbS/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2933 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-R9BNbS/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-R9BNbS/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 22 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-R9BNbS/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (19.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12484 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libpopt-dev, libprotobuf-dev, libelk0-dev, libelk0, zlib1g-dev, libbz2-dev, pkg-config, protobuf-compiler, d-shlibs
Filtered Build-Depends: debhelper-compat (= 13), libpopt-dev, libprotobuf-dev, libelk0-dev, libelk0, zlib1g-dev, libbz2-dev, pkg-config, protobuf-compiler, d-shlibs
dpkg-deb: building package 'sbuild-build-depends-anfo-dummy' in '/<<BUILDDIR>>/resolver-R9BNbS/apt_archive/sbuild-build-depends-anfo-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-anfo-dummy sbuild-build-depends-core-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-R9BNbS/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-R9BNbS/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-R9BNbS/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-R9BNbS/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-R9BNbS/apt_archive ./ Sources [543 B]
Get:5 copy:/<<BUILDDIR>>/resolver-R9BNbS/apt_archive ./ Packages [627 B]
Fetched 2503 B in 1s (3145 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-R9BNbS/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-R9BNbS/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install anfo build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils d-shlibs debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libbz2-dev
libdebhelper-perl libelf-dev libelf1 libelk0 libelk0-dev libffi8
libfile-stripnondeterminism-perl libglib2.0-0 libice-dev libice6 libicu67
libmagic-mgc libmagic1 libmd0 libpipeline1 libpopt-dev libpopt0
libprotobuf-dev libprotobuf-lite23 libprotobuf23 libprotoc23
libpthread-stubs0-dev libsigsegv2 libsm-dev libsm6 libsub-override-perl
libtool libuchardet0 libx11-6 libx11-data libx11-dev libxau-dev libxau6
libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxml2
libxmu-dev libxmu-headers libxmu6 libxt-dev libxt6 m4 man-db pkg-config
po-debconf protobuf-compiler sensible-utils x11-common x11proto-dev
xorg-sgml-doctools xtrans-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libice-doc libsm-doc libtool-doc
gfortran | fortran95-compiler gcj-jdk libx11-doc libxcb-doc libxext-doc
libxt-doc m4-doc apparmor less www-browser libmail-box-perl protobuf-mode-el
Recommended packages:
curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils d-shlibs debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libbz2-dev
libdebhelper-perl libelf-dev libelf1 libelk0 libelk0-dev libffi8
libfile-stripnondeterminism-perl libglib2.0-0 libice-dev libice6 libicu67
libmagic-mgc libmagic1 libmd0 libpipeline1 libpopt-dev libpopt0
libprotobuf-dev libprotobuf-lite23 libprotobuf23 libprotoc23
libpthread-stubs0-dev libsigsegv2 libsm-dev libsm6 libsub-override-perl
libtool libuchardet0 libx11-6 libx11-data libx11-dev libxau-dev libxau6
libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxml2
libxmu-dev libxmu-headers libxmu6 libxt-dev libxt6 m4 man-db pkg-config
po-debconf protobuf-compiler sbuild-build-depends-anfo-dummy sensible-utils
x11-common x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
0 upgraded, 75 newly installed, 0 to remove and 22 not upgraded.
Need to get 26.7 MB of archives.
After this operation, 99.2 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-R9BNbS/apt_archive ./ sbuild-build-depends-anfo-dummy 0.invalid.0 [916 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-1 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.4-2 [819 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf d-shlibs all 0.100 [18.1 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-1 [28.9 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.3-1 [103 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf libbz2-dev armhf 1.0.8-4 [28.0 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf libelf-dev armhf 0.185-2 [73.0 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf x11-common all 1:7.7+23 [252 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf libice6 armhf 2:1.0.10-1 [51.7 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf libxcb1 armhf 1.14-3 [136 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf libx11-data all 2:1.7.2-2 [311 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.7.2-2 [704 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libxt6 armhf 1:1.2.0-1 [159 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf libxmu6 armhf 2:1.1.2-2+b3 [52.1 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf libelk0 armhf 3.99.8-4.2+b1 [155 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf x11proto-dev all 2021.5-1 [599 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf libxau-dev armhf 1:1.0.9-1 [22.3 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf xtrans-dev all 1.4.0-1 [98.7 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf libxcb1-dev armhf 1.14-3 [171 kB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf libx11-dev armhf 2:1.7.2-2 [780 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf libxext-dev armhf 2:1.3.4-1 [102 kB]
Get:60 http://172.17.0.1/private bookworm-staging/main armhf libice-dev armhf 2:1.0.10-1 [58.7 kB]
Get:61 http://172.17.0.1/private bookworm-staging/main armhf libsm-dev armhf 2:1.2.3-1 [35.4 kB]
Get:62 http://172.17.0.1/private bookworm-staging/main armhf libxt-dev armhf 1:1.2.0-1 [372 kB]
Get:63 http://172.17.0.1/private bookworm-staging/main armhf libxmu-headers all 2:1.1.2-2 [51.9 kB]
Get:64 http://172.17.0.1/private bookworm-staging/main armhf libxmu-dev armhf 2:1.1.2-2+b3 [56.5 kB]
Get:65 http://172.17.0.1/private bookworm-staging/main armhf libelk0-dev armhf 3.99.8-4.2+b1 [177 kB]
Get:66 http://172.17.0.1/private bookworm-staging/main armhf libffi8 armhf 3.4.2-2 [21.2 kB]
Get:67 http://172.17.0.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.70.0-1 [1208 kB]
Get:68 http://172.17.0.1/private bookworm-staging/main armhf libpopt0 armhf 1.18-3 [46.9 kB]
Get:69 http://172.17.0.1/private bookworm-staging/main armhf libpopt-dev armhf 1.18-3 [51.3 kB]
Get:70 http://172.17.0.1/private bookworm-staging/main armhf libprotobuf23 armhf 3.12.4-1 [750 kB]
Get:71 http://172.17.0.1/private bookworm-staging/main armhf libprotobuf-lite23 armhf 3.12.4-1 [213 kB]
Get:72 http://172.17.0.1/private bookworm-staging/main armhf libprotobuf-dev armhf 3.12.4-1 [1104 kB]
Get:73 http://172.17.0.1/private bookworm-staging/main armhf libprotoc23 armhf 3.12.4-1 [675 kB]
Get:74 http://172.17.0.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:75 http://172.17.0.1/private bookworm-staging/main armhf protobuf-compiler armhf 3.12.4-1 [74.7 kB]
debconf: delaying package configuration, since apt-utils is not installed
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+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-9+rpi1 gcc-10_10.3.0-9+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-1 bsdutils_1:2.37.2-1 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-9+rpi1 d-shlibs_0.100 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-9+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-9+rpi1 gcc-10-base_10.3.0-9+rpi1 gcc-11-base_11.2.0-4+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 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libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libffi8_3.4.2-2 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.3.0-9+rpi1 libgcc-s1_11.2.0-4+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libglib2.0-0_2.70.0-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-4+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libice-dev_2:1.0.10-1 libice6_2:1.0.10-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.23-1 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmd0_1.0.4-1 libmount1_2.37.2-1 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-2 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-5 libpipeline1_1.5.3-1 libpopt-dev_1.18-3 libpopt0_1.18-3 libprotobuf-dev_3.12.4-1 libprotobuf-lite23_3.12.4-1 libprotobuf23_3.12.4-1 libprotoc23_3.12.4-1 libpthread-stubs0-dev_0.4-1 libreadline8_8.1-2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsm-dev_2:1.2.3-1 libsm6_2:1.2.3-1 libsmartcols1_2.37.2-1 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.9-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-1 libx11-6_2:1.7.2-2 libx11-data_2:1.7.2-2 libx11-dev_2:1.7.2-2 libxau-dev_1:1.0.9-1 libxau6_1:1.0.9-1 libxcb1_1.14-3 libxcb1-dev_1.14-3 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext-dev_2:1.3.4-1 libxext6_2:1.3.4-1 libxml2_2.9.12+dfsg-5 libxmu-dev_2:1.1.2-2+b3 libxmu-headers_2:1.1.2-2 libxmu6_2:1.1.2-2+b3 libxt-dev_1:1.2.0-1 libxt6_1:1.2.0-1 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-1 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 protobuf-compiler_3.12.4-1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-anfo-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.37.2-1 x11-common_1:7.7+23 x11proto-dev_2021.5-1 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.Hmt4CfVc/trustedkeys.kbx': General error
gpgv: Signature made Wed Oct 6 12:27:58 2021 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./anfo_0.98-9.dsc
dpkg-source: info: extracting anfo in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking anfo_0.98.orig.tar.gz
dpkg-source: info: unpacking anfo_0.98-9.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 01-silence-narrowing-conversion.patch
dpkg-source: info: applying 02-correct-minscore-self-initialization.patch
dpkg-source: info: applying 03-include-unistd-forF_OK.patch
dpkg-source: info: applying 04-reorder-template-for-new-scope-rules.patch
dpkg-source: info: applying 05-autoreconf.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-f5f8d3a2-9557-46b9-af1b-2a82e2edf7f3
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package anfo
dpkg-buildpackage: info: source version 0.98-9
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/anfo.substvars debian/libanfo0.substvars debian/libanfo0-dev.substvars debian/files
rm -fr -- debian/anfo/ debian/tmp/ debian/libanfo0/ debian/libanfo0-dev/
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
install -d debian/.debhelper/bucket/files
cp -an --reflink=auto config.guess debian/.debhelper/bucket/files/57cc3642a532babb5ec0db80ebefd7ad7dc2b110e85bdc438fe67221e6172a3f.tmp
mv debian/.debhelper/bucket/files/57cc3642a532babb5ec0db80ebefd7ad7dc2b110e85bdc438fe67221e6172a3f.tmp debian/.debhelper/bucket/files/57cc3642a532babb5ec0db80ebefd7ad7dc2b110e85bdc438fe67221e6172a3f
cp -f /usr/share/misc/config.guess ./config.guess
cp -an --reflink=auto config.sub debian/.debhelper/bucket/files/76dae42e342b050c73d63a4c398703beecd0915d5350e8d667abcf0f746be6e2.tmp
mv debian/.debhelper/bucket/files/76dae42e342b050c73d63a4c398703beecd0915d5350e8d667abcf0f746be6e2.tmp debian/.debhelper/bucket/files/76dae42e342b050c73d63a4c398703beecd0915d5350e8d667abcf0f746be6e2
cp -f /usr/share/misc/config.sub ./config.sub
dh_autoreconf -a
find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p
" > debian/autoreconf.before
grep -q ^XDT_ configure.ac
autoreconf -f -i
aclocal: overwriting 'm4/libtool.m4' with '/usr/share/aclocal/libtool.m4'
aclocal: overwriting 'm4/ltoptions.m4' with '/usr/share/aclocal/ltoptions.m4'
aclocal: overwriting 'm4/ltversion.m4' with '/usr/share/aclocal/ltversion.m4'
aclocal: overwriting 'm4/lt~obsolete.m4' with '/usr/share/aclocal/lt~obsolete.m4'
aclocal: overwriting 'm4/pkg.m4' with '/usr/share/aclocal/pkg.m4'
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:8: warning: The macro `AC_CONFIG_HEADER' is obsolete.
configure.ac:8: You should run autoupdate.
./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from...
configure.ac:8: the top level
configure.ac:48: warning: The macro `AC_HEADER_STDC' is obsolete.
configure.ac:48: You should run autoupdate.
./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
configure.ac:48: the top level
configure.ac:77: warning: LT_INIT was called before AM_PROG_AR
aclocal.m4:70: AM_PROG_AR is expanded from...
configure.ac:77: the top level
configure.ac:77: installing './ar-lib'
configure.ac:12: installing './compile'
configure.ac:6: installing './missing'
src/Makefile.am: installing './depcomp'
find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p
" > debian/autoreconf.after
dh_auto_configure -a
install -d /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking how to print strings... printf
checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for g++... g++
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking dependency style of g++... none
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for protoc... /usr/bin/protoc
checking for library containing exp... none required
checking for library containing log1p... none required
checking for poptGetContext in -lpopt... yes
checking for deflate in -lz... yes
checking for BZ2_bzCompress in -lbz2... yes
checking for Elk_Init in -lelk... yes
checking for popt.h... yes
checking for zlib.h... yes
checking for bzlib.h... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for protobuf >= 2.1.0... yes
checking for google/protobuf/message.h... yes
checking for elk/scheme.h... yes
checking for egrep... (cached) /bin/grep -E
checking for fcntl.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for working volatile... yes
checking for _Bool... no
checking for stdbool.h that conforms to C99... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for int32_t... yes
checking for int64_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for uint8_t... yes
checking for memset... yes
checking for munmap... yes
checking for pow... yes
checking for strerror... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating man/Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
checking the archiver (ar) interface... ar
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make all-recursive
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
protoc -I. -I/usr/include --cpp_out=. config.proto
protoc -I. -I/usr/include --cpp_out=. output.proto
[libprotobuf WARNING google/protobuf/compiler/parser.cc:648] No syntax specified for the proto file: config.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.)
[libprotobuf WARNING google/protobuf/compiler/parser.cc:648] No syntax specified for the proto file: output.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.)
[libprotobuf WARNING google/protobuf/compiler/parser.cc:648] No syntax specified for the proto file: config.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.)
make all-am
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fa2dna.o fa2dna.cc
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o align.lo align.cc
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo_common.lo anfo_common.cc
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o concurrent_stream.lo concurrent_stream.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo_common.cc -fPIC -DPIC -o .libs/anfo_common.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c align.cc -fPIC -DPIC -o .libs/align.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c concurrent_stream.cc -fPIC -DPIC -o .libs/concurrent_stream.o
In file included from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)':
compress_stream.h:395:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~~~~~~~~~~~
compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept'
In file included from stream.h:20,
from align.h:22,
from align.cc:21:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from align.cc:21:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from align.cc:21:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~~~~~~~~~~~
compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept'
In file included from stream.h:20,
from align.h:22,
from align.cc:21:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from align.cc:21:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate]
379 | else if( r < BZ_OK ) throw BzipError( r ) ;
| ^~~~~~~~~~~~~~~~~~~~
compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept'
compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)':
compress_stream.h:395:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from align.cc:21:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate]
379 | else if( r < BZ_OK ) throw BzipError( r ) ;
| ^~~~~~~~~~~~~~~~~~~~
compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept'
compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)':
compress_stream.h:395:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
concurrent_stream.cc: In member function 'virtual output::Result streams::ConcurrentStream::fetch_result()':
concurrent_stream.cc:178:2: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
178 | auto_ptr< Result > r( outgoing_[ next_out_++ ] ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
concurrent_stream.cc: In member function 'void streams::ConcurrentStream::dequeue(streams::Stream*)':
concurrent_stream.cc:212:2: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
212 | auto_ptr< Result > r( incoming_[ next_in_ ] ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c align.cc -o align.o >/dev/null 2>&1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/google/protobuf/stubs/common.h:38,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Distance = int; _Tp = Matches; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_match_lists>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/google/protobuf/stubs/common.h:38,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<compare_match_lists>]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_match_lists>]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/google/protobuf/stubs/common.h:38,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Distance = int; _Tp = Matches; _Compare = __gnu_cxx::__ops::_Iter_comp_val<compare_matches_for_heap>]':
/usr/include/c++/10/bits/stl_heap.h:134:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
134 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Distance = int; _Tp = Matches; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_matches_for_heap>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c concurrent_stream.cc -o concurrent_stream.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ducttape.lo ducttape.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c ducttape.cc -fPIC -DPIC -o .libs/ducttape.o
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/google/protobuf/stubs/common.h:38,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_match_lists>]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_match_lists>]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'int combine_seeds(PreSeeds&, uint32_t, output::Seeds*)':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stream.h:20,
from ducttape.h:21,
from ducttape.cc:21:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from ducttape.h:21,
from ducttape.cc:21:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from ducttape.h:21,
from ducttape.cc:21:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~~~~~~~~~~~
compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept'
In file included from stream.h:20,
from ducttape.h:21,
from ducttape.cc:21:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from ducttape.h:21,
from ducttape.cc:21:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from ducttape.h:21,
from ducttape.cc:21:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate]
379 | else if( r < BZ_OK ) throw BzipError( r ) ;
| ^~~~~~~~~~~~~~~~~~~~
compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept'
compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)':
compress_stream.h:395:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o index.lo index.cc
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c index.cc -fPIC -DPIC -o .libs/index.o
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.cc:21:
ducttape.h:139:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
139 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo_common.cc -o anfo_common.o >/dev/null 2>&1
In file included from /usr/include/c++/10/vector:72,
from sequence.h:25,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {streams::DuctTaper::Acc}; _Tp = streams::DuctTaper::Acc; _Alloc = std::allocator<streams::DuctTaper::Acc>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<streams::DuctTaper::Acc>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_insert_rval(std::vector<_Tp, _Alloc>::const_iterator, std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = streams::DuctTaper::Acc; _Alloc = std::allocator<streams::DuctTaper::Acc>]':
/usr/include/c++/10/bits/vector.tcc:340:5: note: parameter passing for argument of type 'std::vector<streams::DuctTaper::Acc>::const_iterator' changed in GCC 7.1
340 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:356:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<streams::DuctTaper::Acc*, std::vector<streams::DuctTaper::Acc> >' changed in GCC 7.1
356 | _M_realloc_insert(begin() + __n, std::move(__v));
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o misc_streams.lo misc_streams.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c misc_streams.cc -fPIC -DPIC -o .libs/misc_streams.o
In file included from /usr/include/c++/10/vector:67,
from sequence.h:25,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void streams::DuctTaper::put_result_ancient(const output::Result&)':
/usr/include/c++/10/bits/stl_vector.h:1294:30: note: parameter passing for argument of type 'std::vector<streams::DuctTaper::Acc>::const_iterator' changed in GCC 7.1
1294 | { return _M_insert_rval(__position, std::move(__x)); }
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1294:30: note: parameter passing for argument of type 'std::vector<streams::DuctTaper::Acc>::const_iterator' changed in GCC 7.1
1294 | { return _M_insert_rval(__position, std::move(__x)); }
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void streams::DuctTaper::put_result_recent(const output::Result&)':
/usr/include/c++/10/bits/stl_vector.h:1294:30: note: parameter passing for argument of type 'std::vector<streams::DuctTaper::Acc>::const_iterator' changed in GCC 7.1
1294 | { return _M_insert_rval(__position, std::move(__x)); }
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1294:30: note: parameter passing for argument of type 'std::vector<streams::DuctTaper::Acc>::const_iterator' changed in GCC 7.1
1294 | { return _M_insert_rval(__position, std::move(__x)); }
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~~~~~~~~~~~
compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept'
In file included from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate]
379 | else if( r < BZ_OK ) throw BzipError( r ) ;
| ^~~~~~~~~~~~~~~~~~~~
compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept'
compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)':
compress_stream.h:395:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c ducttape.cc -o ducttape.o >/dev/null 2>&1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/google/protobuf/stubs/common.h:44,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from index.cc:21:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Matches}; _Tp = Matches; _Alloc = std::allocator<Matches>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Matches>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'unsigned int FixedIndex::lookup1(Oligo, PreSeeds&, const FixedIndex::LookupParams&, int32_t, int*) const':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
misc_streams.cc: In constructor 'streams::RegionFilter::RegionFilter(const std::pair<std::basic_istream<char>*, std::__cxx11::basic_string<char> >&)':
misc_streams.cc:489:2: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
489 | auto_ptr< istream > deffile( p.first ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c index.cc -o index.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o output_streams.lo output_streams.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c output_streams.cc -fPIC -DPIC -o .libs/output_streams.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c misc_streams.cc -o misc_streams.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence.lo sequence.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c sequence.cc -fPIC -DPIC -o .libs/sequence.o
In file included from stream.h:20,
from output_streams.h:21,
from output_streams.cc:21:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from output_streams.h:21,
from output_streams.cc:21:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from output_streams.h:21,
from output_streams.cc:21:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~~~~~~~~~~~
compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept'
In file included from stream.h:20,
from output_streams.h:21,
from output_streams.cc:21:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from output_streams.h:21,
from output_streams.cc:21:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from output_streams.h:21,
from output_streams.cc:21:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate]
379 | else if( r < BZ_OK ) throw BzipError( r ) ;
| ^~~~~~~~~~~~~~~~~~~~
compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept'
compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)':
compress_stream.h:395:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.cc:21:
output_streams.h:45:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
45 | auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.cc:21:
output_streams.h:72:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
72 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.cc:21:
output_streams.h:123:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
123 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.cc:21:
output_streams.h:138:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
138 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.cc:21:
output_streams.h:149:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
149 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.cc:21:
output_streams.h:176:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
176 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from sequence.cc:23:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from sequence.cc:23:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from sequence.cc:23:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~~~~~~~~~~~
compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept'
In file included from stream.h:20,
from sequence.cc:23:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from sequence.cc:23:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from sequence.cc:23:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate]
379 | else if( r < BZ_OK ) throw BzipError( r ) ;
| ^~~~~~~~~~~~~~~~~~~~
compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept'
compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)':
compress_stream.h:395:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stream.lo stream.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c stream.cc -fPIC -DPIC -o .libs/stream.o
In file included from stream.cc:21:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.cc:21:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.cc:21:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~~~~~~~~~~~
compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept'
In file included from stream.cc:21:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.cc:21:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.cc:21:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate]
379 | else if( r < BZ_OK ) throw BzipError( r ) ;
| ^~~~~~~~~~~~~~~~~~~~
compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept'
compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)':
compress_stream.h:395:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c sequence.cc -o sequence.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c output_streams.cc -o output_streams.o >/dev/null 2>&1
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc:81:30: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
81 | AnfoReader::AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc: In member function 'virtual void streams::ChunkedWriter::put_result(const output::Result&)':
stream.cc:344:27: warning: 'int google::protobuf::MessageLite::ByteSize() const' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations]
344 | flush_buffer( r.ByteSize() ) ;
| ^
In file included from /usr/include/google/protobuf/generated_enum_util.h:36,
from /usr/include/google/protobuf/map.h:49,
from /usr/include/google/protobuf/generated_message_table_driven.h:34,
from output.pb.h:26,
from stream.h:22,
from misc_streams.h:4,
from stream.cc:22:
/usr/include/google/protobuf/message_lite.h:408:7: note: declared here
408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); }
| ^~~~~~~~
stream.cc: At global scope:
stream.cc:421:36: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
421 | ChunkedReader::ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc:1093:9: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
1093 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc:1114:29: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
1114 | StreamWithProgress( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, int64_t total )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc:1149:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
1149 | StreamHolder make_input_stream_( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, bool solexa_scores, char origin, const string& genome )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc: In function 'streams::StreamHolder streams::{anonymous}::make_input_stream_(std::auto_ptr<google::protobuf::io::ZeroCopyInputStream>, const string&, bool, char, const string&)':
stream.cc:1179:9: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
1179 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > bs( new BunzipStream( is ) ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc:1189:9: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
1189 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > zs( new InflateStream( is ) ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc: In member function 'virtual output::Header streams::UniversalReader::fetch_header()':
stream.cc:1233:9: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
1233 | std::auto_ptr< google::protobuf::io::FileInputStream > s( new google::protobuf::io::FileInputStream( fd ) ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc:1238:12: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
1238 | std::auto_ptr<google::protobuf::io::ZeroCopyInputStream>(s), name_, st.st_size ) ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc: At global scope:
stream.cc:1378:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
1378 | BamReader::BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h: In instantiation of 'void streams::write_delimited_message(google::protobuf::io::CodedOutputStream&, int, const Msg&) [with Msg = output::Header]':
stream.h:102:25: required from 'void streams::write_delimited_message(google::protobuf::io::ZeroCopyOutputStream*, int, const Msg&) [with Msg = output::Header]'
stream.cc:322:44: required from here
stream.h:88:30: warning: 'int google::protobuf::MessageLite::ByteSize() const' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations]
88 | os.WriteVarint32( m.ByteSize() ) ;
| ~~~~~~~~~~^~
In file included from /usr/include/google/protobuf/generated_enum_util.h:36,
from /usr/include/google/protobuf/map.h:49,
from /usr/include/google/protobuf/generated_message_table_driven.h:34,
from output.pb.h:26,
from stream.h:22,
from misc_streams.h:4,
from stream.cc:22:
/usr/include/google/protobuf/message_lite.h:408:7: note: declared here
408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); }
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h: In instantiation of 'void streams::write_delimited_message(google::protobuf::io::CodedOutputStream&, int, const Msg&) [with Msg = output::Footer]':
stream.h:102:25: required from 'void streams::write_delimited_message(google::protobuf::io::ZeroCopyOutputStream*, int, const Msg&) [with Msg = output::Footer]'
stream.cc:331:44: required from here
stream.h:88:30: warning: 'int google::protobuf::MessageLite::ByteSize() const' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations]
88 | os.WriteVarint32( m.ByteSize() ) ;
| ~~~~~~~~~~^~
In file included from /usr/include/google/protobuf/generated_enum_util.h:36,
from /usr/include/google/protobuf/map.h:49,
from /usr/include/google/protobuf/generated_message_table_driven.h:34,
from output.pb.h:26,
from stream.h:22,
from misc_streams.h:4,
from stream.cc:22:
/usr/include/google/protobuf/message_lite.h:408:7: note: declared here
408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); }
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h: In instantiation of 'void streams::write_delimited_message(google::protobuf::io::CodedOutputStream&, int, const Msg&) [with Msg = output::Result]':
stream.h:102:25: required from 'void streams::write_delimited_message(google::protobuf::io::ZeroCopyOutputStream*, int, const Msg&) [with Msg = output::Result]'
stream.cc:345:44: required from here
stream.h:88:30: warning: 'int google::protobuf::MessageLite::ByteSize() const' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations]
88 | os.WriteVarint32( m.ByteSize() ) ;
| ~~~~~~~~~~^~
In file included from /usr/include/google/protobuf/generated_enum_util.h:36,
from /usr/include/google/protobuf/map.h:49,
from /usr/include/google/protobuf/generated_message_table_driven.h:34,
from output.pb.h:26,
from stream.h:22,
from misc_streams.h:4,
from stream.cc:22:
/usr/include/google/protobuf/message_lite.h:408:7: note: declared here
408 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); }
| ^~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo util.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c util.cc -fPIC -DPIC -o .libs/util.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo-elk.lo anfo-elk.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo-elk.cc -fPIC -DPIC -o .libs/anfo-elk.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c util.cc -o util.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fastlz.lo fastlz.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c fastlz.c -fPIC -DPIC -o .libs/fastlz.o
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~~~~~~~~~~~
compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept'
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c fastlz.c -o fastlz.o >/dev/null 2>&1
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate]
379 | else if( r < BZ_OK ) throw BzipError( r ) ;
| ^~~~~~~~~~~~~~~~~~~~
compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept'
compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)':
compress_stream.h:395:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o config.pb.lo config.pb.cc
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c config.pb.cc -fPIC -DPIC -o .libs/config.pb.o
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-elk.cc:28:
ducttape.h:139:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
139 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o output.pb.lo output.pb.cc
In file included from anfo-elk.cc:31:
output_streams.h:45:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
45 | auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-elk.cc:31:
output_streams.h:72:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
72 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c output.pb.cc -fPIC -DPIC -o .libs/output.pb.o
In file included from anfo-elk.cc:31:
output_streams.h:123:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
123 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-elk.cc:31:
output_streams.h:138:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
138 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-elk.cc:31:
output_streams.h:149:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
149 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-elk.cc:31:
output_streams.h:176:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
176 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-elk.cc:30:
misc_streams.h: In instantiation of 'void streams::SortingStream<Comp>::put_result(const output::Result&) [with Comp = streams::by_seqid]':
misc_streams.h:282:16: required from here
misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations]
284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from output.pb.h:31,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/google/protobuf/message.h:299:7: note: declared here
299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); }
| ^~~~~~~~~
In file included from anfo-elk.cc:30:
misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations]
284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from output.pb.h:31,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/google/protobuf/message.h:299:7: note: declared here
299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); }
| ^~~~~~~~~
In file included from anfo-elk.cc:30:
misc_streams.h: In instantiation of 'void streams::SortingStream<Comp>::put_result(const output::Result&) [with Comp = streams::by_genome_coordinate]':
misc_streams.h:282:16: required from here
misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations]
284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from output.pb.h:31,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/google/protobuf/message.h:299:7: note: declared here
299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); }
| ^~~~~~~~~
In file included from anfo-elk.cc:30:
misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations]
284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from output.pb.h:31,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/google/protobuf/message.h:299:7: note: declared here
299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); }
| ^~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c stream.cc -o stream.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c config.pb.cc -o config.pb.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c output.pb.cc -o output.pb.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo-elk.cc -o anfo-elk.o >/dev/null 2>&1
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o dnaindex.o dnaindex.cc
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo-tool.o anfo-tool.cc
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo.o anfo.cc
In file included from anfo-tool.cc:21:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:21:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:21:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~~~~~~~~~~~
compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept'
In file included from anfo-tool.cc:21:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:21:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:21:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate]
379 | else if( r < BZ_OK ) throw BzipError( r ) ;
| ^~~~~~~~~~~~~~~~~~~~
compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept'
compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)':
compress_stream.h:395:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:22:
ducttape.h:139:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
139 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:24:
output_streams.h:45:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
45 | auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:24:
output_streams.h:72:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
72 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:24:
output_streams.h:123:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
123 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:24:
output_streams.h:138:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
138 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:24:
output_streams.h:149:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
149 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:24:
output_streams.h:176:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
176 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~~~~~~~~~~~
compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept'
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate]
379 | else if( r < BZ_OK ) throw BzipError( r ) ;
| ^~~~~~~~~~~~~~~~~~~~
compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept'
compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)':
compress_stream.h:395:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:23:
misc_streams.h: In instantiation of 'void streams::SortingStream<Comp>::put_result(const output::Result&) [with Comp = streams::by_seqid]':
misc_streams.h:282:16: required from here
misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations]
284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from output.pb.h:31,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from anfo-tool.cc:22:
/usr/include/google/protobuf/message.h:299:7: note: declared here
299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); }
| ^~~~~~~~~
In file included from anfo-tool.cc:23:
misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations]
284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from output.pb.h:31,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from anfo-tool.cc:22:
/usr/include/google/protobuf/message.h:299:7: note: declared here
299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); }
| ^~~~~~~~~
In file included from anfo-tool.cc:23:
misc_streams.h: In instantiation of 'void streams::SortingStream<Comp>::put_result(const output::Result&) [with Comp = streams::by_genome_coordinate]':
misc_streams.h:282:16: required from here
misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations]
284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from output.pb.h:31,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from anfo-tool.cc:22:
/usr/include/google/protobuf/message.h:299:7: note: declared here
299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); }
| ^~~~~~~~~
In file included from anfo-tool.cc:23:
misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations]
284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from output.pb.h:31,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from anfo-tool.cc:22:
/usr/include/google/protobuf/message.h:299:7: note: declared here
299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); }
| ^~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o index-test.o index-test.cc
In file included from index-test.cc:27:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:27:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:27:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~~~~~~~~~~~
compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept'
In file included from index-test.cc:27:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:27:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:27:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate]
379 | else if( r < BZ_OK ) throw BzipError( r ) ;
| ^~~~~~~~~~~~~~~~~~~~
compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept'
compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)':
compress_stream.h:395:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o file-info.o file-info.cc
In file included from index-test.cc:30:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/google/protobuf/stubs/common.h:38,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Distance = int; _Tp = Matches; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_match_lists>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/google/protobuf/stubs/common.h:38,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<compare_match_lists>]':
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1824 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_match_lists>]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/google/protobuf/stubs/common.h:38,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Distance = int; _Tp = Matches; _Compare = __gnu_cxx::__ops::_Iter_comp_val<compare_matches_for_heap>]':
/usr/include/c++/10/bits/stl_heap.h:134:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
134 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Distance = int; _Tp = Matches; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_matches_for_heap>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/google/protobuf/stubs/common.h:38,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_match_lists>]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1667:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_match_lists>]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1964:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stream.h:20,
from file-info.cc:25:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from file-info.cc:25:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from file-info.cc:25:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:26: warning: 'throw' will always call 'terminate' [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~~~~~~~~~~~
compress_stream.h:198:26: note: in C++11 destructors default to 'noexcept'
In file included from stream.h:20,
from file-info.cc:25:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from file-info.cc:25:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from file-info.cc:25:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:26: warning: 'throw' will always call 'terminate' [-Wterminate]
379 | else if( r < BZ_OK ) throw BzipError( r ) ;
| ^~~~~~~~~~~~~~~~~~~~
compress_stream.h:379:26: note: in C++11 destructors default to 'noexcept'
compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)':
compress_stream.h:395:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'int combine_seeds(PreSeeds&, uint32_t, output::Seeds*)':
/usr/include/c++/10/bits/stl_algo.h:1979:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from file-info.cc:25:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
echo "; DO NOT EDIT THIS FILE! EDIT anfo.scm.in AND RUN MAKE INSTEAD!" > anfo.scm
sed -e "s#__LIBDIR__#/usr/lib/arm-linux-gnueabihf#g" < ./anfo.scm.in >> anfo.scm
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libanfo.la -rpath /usr/lib/arm-linux-gnueabihf align.lo anfo_common.lo concurrent_stream.lo ducttape.lo index.lo misc_streams.lo output_streams.lo sequence.lo stream.lo util.lo anfo-elk.lo fastlz.lo config.pb.lo output.pb.lo -lprotobuf -lpthread -lelk -lbz2 -lz -lpopt
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/10/crtbeginS.o .libs/align.o .libs/anfo_common.o .libs/concurrent_stream.o .libs/ducttape.o .libs/index.o .libs/misc_streams.o .libs/output_streams.o .libs/sequence.o .libs/stream.o .libs/util.o .libs/anfo-elk.o .libs/fastlz.o .libs/config.pb.o .libs/output.pb.o -lprotobuf -lpthread -lelk -lbz2 -lz -lpopt -L/usr/lib/gcc/arm-linux-gnueabihf/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/10/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crtn.o -pthread -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -Wl,-soname -Wl,libanfo.so.0 -o .libs/libanfo.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libanfo.so.0" && ln -s "libanfo.so.0.0.0" "libanfo.so.0")
libtool: link: (cd ".libs" && rm -f "libanfo.so" && ln -s "libanfo.so.0.0.0" "libanfo.so")
libtool: link: ar cr .libs/libanfo.a align.o anfo_common.o concurrent_stream.o ducttape.o index.o misc_streams.o output_streams.o sequence.o stream.o util.o anfo-elk.o fastlz.o config.pb.o output.pb.o
libtool: link: ranlib .libs/libanfo.a
libtool: link: ( cd ".libs" && rm -f "libanfo.la" && ln -s "../libanfo.la" "libanfo.la" )
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o dnaindex dnaindex.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fa2dna fa2dna.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o anfo anfo.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt
libtool: link: g++ -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/dnaindex dnaindex.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread
libtool: link: g++ -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/anfo anfo.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread
libtool: link: g++ -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/fa2dna fa2dna.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o index-test index-test.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o file-info file-info.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o anfo-tool anfo-tool.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt
libtool: link: g++ -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/index-test index-test.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread
libtool: link: g++ -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/file-info file-info.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread
libtool: link: g++ -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/anfo-tool anfo-tool.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making all in man
make[3]: Entering directory '/<<PKGBUILDDIR>>/man'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/man'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 check VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making check in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make check-am
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Nothing to be done for 'check-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making check in man
make[2]: Entering directory '/<<PKGBUILDDIR>>/man'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/man'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
rm -fr -- /tmp/dh-xdg-rundir-_s5R96Dg
create-stamp debian/debhelper-build-stamp
dh_prep -a
rm -f -- debian/anfo.substvars debian/libanfo0.substvars debian/libanfo0-dev.substvars
rm -fr -- debian/.debhelper/generated/anfo/ debian/anfo/ debian/tmp/ debian/.debhelper/generated/libanfo0/ debian/libanfo0/ debian/.debhelper/generated/libanfo0-dev/ debian/libanfo0-dev/
dh_auto_install -a
install -d /<<PKGBUILDDIR>>/debian/tmp
make -j1 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making install in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make install-am
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
/bin/bash ../libtool --mode=install /usr/bin/install -c libanfo.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/libanfo.so.0.0.0 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libanfo.so.0.0.0 libanfo.so.0 || { rm -f libanfo.so.0 && ln -s libanfo.so.0.0.0 libanfo.so.0; }; })
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libanfo.so.0.0.0 libanfo.so || { rm -f libanfo.so && ln -s libanfo.so.0.0.0 libanfo.so; }; })
libtool: install: /usr/bin/install -c .libs/libanfo.lai /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.la
libtool: install: /usr/bin/install -c .libs/libanfo.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.a
libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/bin/bash ../libtool --mode=install /usr/bin/install -c fa2dna dnaindex anfo-tool anfo '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/fa2dna /<<PKGBUILDDIR>>/debian/tmp/usr/bin/fa2dna
libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/dnaindex /<<PKGBUILDDIR>>/debian/tmp/usr/bin/dnaindex
libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/anfo-tool /<<PKGBUILDDIR>>/debian/tmp/usr/bin/anfo-tool
libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/anfo /<<PKGBUILDDIR>>/debian/tmp/usr/bin/anfo
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/libexec'
/bin/bash ../libtool --mode=install /usr/bin/install -c index-test file-info '/<<PKGBUILDDIR>>/debian/tmp/usr/libexec'
libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/index-test /<<PKGBUILDDIR>>/debian/tmp/usr/libexec/index-test
libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/file-info /<<PKGBUILDDIR>>/debian/tmp/usr/libexec/file-info
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/anfo'
/usr/bin/install -c -m 644 config.proto output.proto '/<<PKGBUILDDIR>>/debian/tmp/usr/share/anfo'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/elk'
/usr/bin/install -c srfi-88.scm srfi-89.scm '/<<PKGBUILDDIR>>/debian/tmp/usr/share/elk'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/include/anfo'
/usr/bin/install -c -m 644 align.h align_fwd.h anfo_common.h compress_stream.h concurrent_stream.h conffile.h ducttape.h index.h logdom.h misc_streams.h output_streams.h sequence.h stream.h trim.h util.h '/<<PKGBUILDDIR>>/debian/tmp/usr/include/anfo'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/elk'
/usr/bin/install -c anfo.scm '/<<PKGBUILDDIR>>/debian/tmp/usr/share/elk'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making install in man
make[2]: Entering directory '/<<PKGBUILDDIR>>/man'
make[3]: Entering directory '/<<PKGBUILDDIR>>/man'
make[3]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1'
/usr/bin/install -c -m 644 fa2dna.1 dnaindex.1 anfo-sge.1 anfo-tool.1 file-info.1 '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/man'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/man'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/anfo'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/anfo/example'
/usr/bin/install -c -m 644 example/ancient.cfg example/default.cfg example/split-anfo.scm example/threebam.scm '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/anfo/example'
/usr/bin/install -c -m 644 README '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/anfo/.'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
d-shlibmove --commit \
--multiarch \
--movedev debian/tmp/usr/include/* usr/include \
debian/tmp/usr/lib/*/libanfo.so
Library package automatic movement utility
--> libbz2-dev package exists.
--> libelk0-dev package exists.
--> libprotobuf-dev package exists.
--> zlib1g-dev package exists.
set -e
install -d -m 755 debian/libanfo0-dev/usr/lib/arm-linux-gnueabihf
install -d -m 755 debian/libanfo0/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.a debian/libanfo0-dev/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.la debian/libanfo0-dev/usr/lib/arm-linux-gnueabihf || true
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.so debian/libanfo0-dev/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.so.0 debian/libanfo0/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0 debian/libanfo0/usr/lib/arm-linux-gnueabihf
PKGDEV=libanfo0-dev
PKGSHL=libanfo0
install -d -m 755 debian/libanfo0-dev/usr/include
mv debian/tmp/usr/include/anfo debian/libanfo0-dev/usr/include
find debian -name "lib*.la" -delete
dh_install
install -d debian/anfo/usr
cp --reflink=auto -a debian/tmp/usr/bin debian/tmp/usr/share debian/anfo/usr/
install -d debian/anfo/usr/lib/anfo
cp --reflink=auto -a debian/tmp/usr/libexec/file-info debian/tmp/usr/libexec/index-test debian/anfo/usr/lib/anfo/
install -d debian/.debhelper/generated/anfo
install -d debian/.debhelper/generated/libanfo0
install -d debian/.debhelper/generated/libanfo0-dev
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
install -p -m0644 debian/README.Debian debian/anfo/usr/share/doc/anfo/README.Debian
install -p -m0644 debian/copyright debian/anfo/usr/share/doc/anfo/copyright
install -d debian/libanfo0/usr/share/doc/libanfo0
install -p -m0644 debian/copyright debian/libanfo0/usr/share/doc/libanfo0/copyright
install -d debian/libanfo0-dev/usr/share/doc/libanfo0-dev
install -p -m0644 debian/copyright debian/libanfo0-dev/usr/share/doc/libanfo0-dev/copyright
dh_installchangelogs -a
install -p -m0644 debian/changelog debian/libanfo0/usr/share/doc/libanfo0/changelog.Debian
install -p -m0644 debian/changelog debian/anfo/usr/share/doc/anfo/changelog.Debian
install -p -m0644 debian/changelog debian/libanfo0-dev/usr/share/doc/libanfo0-dev/changelog.Debian
rm -f debian/anfo.debhelper.log debian/libanfo0-dev.debhelper.log debian/libanfo0.debhelper.log
debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installman
install -p -m0644 ./debian/anfo.1 debian/anfo/usr/share/man/man1/anfo.1
man-recode --to-code UTF-8 --suffix .dh-new debian/anfo/usr/share/man/man1/anfo-sge.1 debian/anfo/usr/share/man/man1/anfo-tool.1
man-recode --to-code UTF-8 --suffix .dh-new debian/anfo/usr/share/man/man1/anfo.1 debian/anfo/usr/share/man/man1/dnaindex.1
man-recode --to-code UTF-8 --suffix .dh-new debian/anfo/usr/share/man/man1/fa2dna.1 debian/anfo/usr/share/man/man1/file-info.1
mv debian/anfo/usr/share/man/man1/anfo.1.dh-new debian/anfo/usr/share/man/man1/anfo.1
mv debian/anfo/usr/share/man/man1/dnaindex.1.dh-new debian/anfo/usr/share/man/man1/dnaindex.1
chmod 0644 -- debian/anfo/usr/share/man/man1/anfo.1 debian/anfo/usr/share/man/man1/dnaindex.1
mv debian/anfo/usr/share/man/man1/anfo-sge.1.dh-new debian/anfo/usr/share/man/man1/anfo-sge.1
mv debian/anfo/usr/share/man/man1/anfo-tool.1.dh-new debian/anfo/usr/share/man/man1/anfo-tool.1
chmod 0644 -- debian/anfo/usr/share/man/man1/anfo-sge.1 debian/anfo/usr/share/man/man1/anfo-tool.1
mv debian/anfo/usr/share/man/man1/fa2dna.1.dh-new debian/anfo/usr/share/man/man1/fa2dna.1
mv debian/anfo/usr/share/man/man1/file-info.1.dh-new debian/anfo/usr/share/man/man1/file-info.1
chmod 0644 -- debian/anfo/usr/share/man/man1/fa2dna.1 debian/anfo/usr/share/man/man1/file-info.1
# delete unused manpage
find debian/anfo -name anfo-sge.1 -delete
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_perl -a
dh_link -a
rm -f debian/libanfo0/usr/lib/arm-linux-gnueabihf/libanfo.so.0
ln -s libanfo.so.0.0.0 debian/libanfo0/usr/lib/arm-linux-gnueabihf/libanfo.so.0
rm -f debian/libanfo0-dev/usr/lib/arm-linux-gnueabihf/libanfo.so
ln -s libanfo.so.0.0.0 debian/libanfo0-dev/usr/lib/arm-linux-gnueabihf/libanfo.so
dh_strip_nondeterminism -a
dh_compress -a
cd debian/anfo
cd debian/libanfo0
cd debian/libanfo0-dev
chmod a-x usr/share/doc/libanfo0/changelog.Debian
chmod a-x usr/share/doc/libanfo0-dev/changelog.Debian
chmod a-x usr/share/doc/anfo/README usr/share/doc/anfo/changelog.Debian usr/share/man/man1/anfo-tool.1 usr/share/man/man1/anfo.1 usr/share/man/man1/dnaindex.1 usr/share/man/man1/fa2dna.1 usr/share/man/man1/file-info.1
gzip -9nf usr/share/doc/libanfo0/changelog.Debian
gzip -9nf usr/share/doc/libanfo0-dev/changelog.Debian
gzip -9nf usr/share/doc/anfo/README usr/share/doc/anfo/changelog.Debian usr/share/man/man1/anfo-tool.1 usr/share/man/man1/anfo.1 usr/share/man/man1/dnaindex.1 usr/share/man/man1/fa2dna.1 usr/share/man/man1/file-info.1
cd '/<<PKGBUILDDIR>>'
cd '/<<PKGBUILDDIR>>'
cd '/<<PKGBUILDDIR>>'
rm -f debian/anfo.debhelper.log debian/libanfo0-dev.debhelper.log debian/libanfo0.debhelper.log
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_fixperms
find debian/anfo ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/libanfo0 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/libanfo0-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/libanfo0/usr/share/doc -type f -a -true -a ! -regex 'debian/libanfo0/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libanfo0-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libanfo0-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libanfo0/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/libanfo0-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/anfo/usr/share/doc -type f -a -true -a ! -regex 'debian/anfo/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libanfo0-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/anfo/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/libanfo0 -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/libanfo0-dev -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/anfo/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libanfo0/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
find debian/libanfo0-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
find debian/anfo -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/anfo/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
find debian/anfo/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
find debian/anfo -perm -5 -type f \( -name '*.scm' \) -print0 2>/dev/null | xargs -0r chmod 644
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_missing -a
dh_dwz -a
dwz -- debian/libanfo0/usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0
install -d debian/anfo/usr/lib/debug/.dwz/arm-linux-gnueabihf
dwz -mdebian/anfo/usr/lib/debug/.dwz/arm-linux-gnueabihf/anfo.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/anfo.debug -- debian/anfo/usr/bin/anfo debian/anfo/usr/bin/anfo-tool debian/anfo/usr/bin/dnaindex debian/anfo/usr/bin/fa2dna debian/anfo/usr/lib/anfo/file-info debian/anfo/usr/lib/anfo/index-test
objcopy --compress-debug-sections debian/anfo/usr/lib/debug/.dwz/arm-linux-gnueabihf/anfo.debug
dh_strip -a
strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives -R .gnu.lto_\* -R .gnu.debuglto_\* -N __gnu_lto_slim -N __gnu_lto_v1 debian/libanfo0-dev/usr/lib/arm-linux-gnueabihf/libanfo.a
install -d debian/.debhelper/libanfo0/dbgsym-root/usr/lib/debug/.build-id/df
objcopy --only-keep-debug --compress-debug-sections debian/libanfo0/usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0 debian/.debhelper/libanfo0/dbgsym-root/usr/lib/debug/.build-id/df/8fb6f19ceee3f2e6a1664319759a0a79e65f8f.debug
install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/ef
objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/bin/anfo debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/ef/c221f1e24cbfe070dbbbf1d5a1d8edc49def15.debug
chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/ef/c221f1e24cbfe070dbbbf1d5a1d8edc49def15.debug
strip --remove-section=.comment --remove-section=.note debian/anfo/usr/bin/anfo
objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/ef/c221f1e24cbfe070dbbbf1d5a1d8edc49def15.debug debian/anfo/usr/bin/anfo
install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/6e
objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/bin/anfo-tool debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/6e/f85b092e689057cb8a3c3d4c4610bfb04ebd24.debug
chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/6e/f85b092e689057cb8a3c3d4c4610bfb04ebd24.debug
strip --remove-section=.comment --remove-section=.note debian/anfo/usr/bin/anfo-tool
objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/6e/f85b092e689057cb8a3c3d4c4610bfb04ebd24.debug debian/anfo/usr/bin/anfo-tool
install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/79
objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/bin/dnaindex debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/79/84d7e1e975aad22884e530432d14b56938ded4.debug
chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/79/84d7e1e975aad22884e530432d14b56938ded4.debug
strip --remove-section=.comment --remove-section=.note debian/anfo/usr/bin/dnaindex
objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/79/84d7e1e975aad22884e530432d14b56938ded4.debug debian/anfo/usr/bin/dnaindex
install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/9e
objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/bin/fa2dna debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/9e/aa53dd556e90e194ce8c65d9d341aa8c3f16dc.debug
chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/9e/aa53dd556e90e194ce8c65d9d341aa8c3f16dc.debug
strip --remove-section=.comment --remove-section=.note debian/anfo/usr/bin/fa2dna
objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/9e/aa53dd556e90e194ce8c65d9d341aa8c3f16dc.debug debian/anfo/usr/bin/fa2dna
install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/36
objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/lib/anfo/file-info debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/36/d47664c018744f1c56d1e39cf60376a77eb245.debug
chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/36/d47664c018744f1c56d1e39cf60376a77eb245.debug
strip --remove-section=.comment --remove-section=.note debian/anfo/usr/lib/anfo/file-info
objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/36/d47664c018744f1c56d1e39cf60376a77eb245.debug debian/anfo/usr/lib/anfo/file-info
install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/c4
objcopy --only-keep-debug --compress-debug-sections debian/anfo/usr/lib/anfo/index-test debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/c4/c8b3d48fce424906aab3479b9aafd74ce6560e.debug
chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/c4/c8b3d48fce424906aab3479b9aafd74ce6560e.debug
strip --remove-section=.comment --remove-section=.note debian/anfo/usr/lib/anfo/index-test
objcopy --add-gnu-debuglink debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.build-id/c4/c8b3d48fce424906aab3479b9aafd74ce6560e.debug debian/anfo/usr/lib/anfo/index-test
install -d debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.dwz
cp --reflink=auto -a debian/anfo/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/anfo/dbgsym-root/usr/lib/debug/.dwz
rm -fr debian/anfo/usr/lib/debug/.dwz
rmdir -p --ignore-fail-on-non-empty debian/anfo/usr/lib/debug
install -d debian/.debhelper/anfo/dbgsym-root/usr/share/doc
ln -s anfo debian/.debhelper/anfo/dbgsym-root/usr/share/doc/anfo-dbgsym
chmod 0644 -- debian/.debhelper/libanfo0/dbgsym-root/usr/lib/debug/.build-id/df/8fb6f19ceee3f2e6a1664319759a0a79e65f8f.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libanfo0/usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0
objcopy --add-gnu-debuglink debian/.debhelper/libanfo0/dbgsym-root/usr/lib/debug/.build-id/df/8fb6f19ceee3f2e6a1664319759a0a79e65f8f.debug debian/libanfo0/usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0
install -d debian/.debhelper/libanfo0/dbgsym-root/usr/share/doc
ln -s libanfo0 debian/.debhelper/libanfo0/dbgsym-root/usr/share/doc/libanfo0-dbgsym
dh_makeshlibs -a
rm -f debian/anfo/DEBIAN/shlibs
rm -f debian/libanfo0/DEBIAN/shlibs
install -d debian/libanfo0/DEBIAN
echo "libanfo 0 libanfo0 (>= 0.98)" >> debian/libanfo0/DEBIAN/shlibs
chmod 0644 -- debian/libanfo0/DEBIAN/shlibs
mv debian/.debhelper/generated/libanfo0/triggers.new debian/.debhelper/generated/libanfo0/triggers
rm -f debian/libanfo0-dev/DEBIAN/shlibs
dh_shlibdeps -a
dpkg-shlibdeps -Tdebian/libanfo0.substvars debian/libanfo0/usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0
install -d debian/anfo/DEBIAN
dpkg-shlibdeps -Tdebian/anfo.substvars debian/anfo/usr/bin/anfo debian/anfo/usr/bin/anfo-tool debian/anfo/usr/bin/dnaindex debian/anfo/usr/bin/fa2dna debian/anfo/usr/lib/anfo/file-info debian/anfo/usr/lib/anfo/index-test
dpkg-shlibdeps: warning: debian/anfo/usr/lib/anfo/index-test contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/anfo/usr/bin/anfo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/anfo/usr/bin/dnaindex contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libanfo0/usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0 found in none of the libraries
dpkg-shlibdeps: warning: debian/anfo/usr/bin/fa2dna contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/anfo/usr/lib/anfo/file-info contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/anfo/usr/bin/anfo-tool 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/anfo/usr/bin/anfo debian/anfo/usr/bin/anfo-tool were not linked against libelk.so.0 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/anfo/usr/lib/anfo/index-test debian/anfo/usr/bin/anfo debian/anfo/usr/bin/dnaindex debian/anfo/usr/bin/fa2dna debian/anfo/usr/lib/anfo/file-info debian/anfo/usr/bin/anfo-tool were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
install -p -m0644 debian/.debhelper/generated/libanfo0/triggers debian/libanfo0/DEBIAN/triggers
install -d debian/libanfo0-dev/DEBIAN
dh_gencontrol -a
echo misc:Depends= >> debian/libanfo0-dev.substvars
echo misc:Pre-Depends= >> debian/libanfo0-dev.substvars
dpkg-gencontrol -plibanfo0-dev -ldebian/changelog -Tdebian/libanfo0-dev.substvars -Pdebian/libanfo0-dev
echo misc:Depends= >> debian/anfo.substvars
echo misc:Pre-Depends= >> debian/anfo.substvars
install -d debian/.debhelper/anfo/dbgsym-root/DEBIAN
dpkg-gencontrol -panfo -ldebian/changelog -Tdebian/anfo.substvars -Pdebian/.debhelper/anfo/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=anfo-dbgsym "-DDepends=anfo (= \${binary:Version})" "-DDescription=debug symbols for anfo" "-DBuild-Ids=36d47664c018744f1c56d1e39cf60376a77eb245 6ef85b092e689057cb8a3c3d4c4610bfb04ebd24 7984d7e1e975aad22884e530432d14b56938ded4 9eaa53dd556e90e194ce8c65d9d341aa8c3f16dc c4c8b3d48fce424906aab3479b9aafd74ce6560e efc221f1e24cbfe070dbbbf1d5a1d8edc49def15" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
echo misc:Depends= >> debian/libanfo0.substvars
echo misc:Pre-Depends= >> debian/libanfo0.substvars
install -d debian/.debhelper/libanfo0/dbgsym-root/DEBIAN
dpkg-gencontrol -plibanfo0 -ldebian/changelog -Tdebian/libanfo0.substvars -Pdebian/.debhelper/libanfo0/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=libanfo0-dbgsym "-DDepends=libanfo0 (= \${binary:Version})" "-DDescription=debug symbols for libanfo0" -DBuild-Ids=df8fb6f19ceee3f2e6a1664319759a0a79e65f8f -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/libanfo0/dbgsym-root/DEBIAN/control
dpkg-gencontrol -plibanfo0 -ldebian/changelog -Tdebian/libanfo0.substvars -Pdebian/libanfo0
chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/DEBIAN/control
dpkg-gencontrol -panfo -ldebian/changelog -Tdebian/anfo.substvars -Pdebian/anfo
chmod 0644 -- debian/libanfo0-dev/DEBIAN/control
chmod 0644 -- debian/anfo/DEBIAN/control
chmod 0644 -- debian/libanfo0/DEBIAN/control
dh_md5sums -a
cd debian/libanfo0 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/libanfo0-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/anfo >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/libanfo0/DEBIAN/md5sums
chmod 0644 -- debian/anfo/DEBIAN/md5sums
cd debian/.debhelper/libanfo0/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/.debhelper/anfo/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/libanfo0-dev/DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/libanfo0/dbgsym-root/DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/anfo/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --root-owner-group --build debian/anfo ..
dpkg-deb --root-owner-group --build debian/libanfo0 ..
dpkg-deb --root-owner-group --build debian/libanfo0-dev ..
dpkg-deb: building package 'libanfo0' in '../libanfo0_0.98-9_armhf.deb'.
dpkg-deb: building package 'libanfo0-dev' in '../libanfo0-dev_0.98-9_armhf.deb'.
dpkg-deb: building package 'anfo' in '../anfo_0.98-9_armhf.deb'.
dpkg-deb --root-owner-group --build debian/.debhelper/anfo/dbgsym-root ..
dpkg-deb: building package 'anfo-dbgsym' in '../anfo-dbgsym_0.98-9_armhf.deb'.
dpkg-deb --root-owner-group --build debian/.debhelper/libanfo0/dbgsym-root ..
dpkg-deb: building package 'libanfo0-dbgsym' in '../libanfo0-dbgsym_0.98-9_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../anfo_0.98-9_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 2021-10-11T06:30:22Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
anfo_0.98-9_armhf.changes:
--------------------------
Format: 1.8
Date: Wed, 06 Oct 2021 14:24:46 +0200
Source: anfo
Binary: anfo anfo-dbgsym libanfo0 libanfo0-dbgsym libanfo0-dev
Architecture: armhf
Version: 0.98-9
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
anfo - Short Read Aligner/Mapper from MPG
libanfo0 - Library for Short Read Aligner/Mapper from MPG
libanfo0-dev - Development files for Short Read Aligner/Mapper from MPG
Changes:
anfo (0.98-9) unstable; urgency=medium
.
* uscan can't fetch latest upstream since https certificate became invalid
thus silencing the uscan error by providing a fake watch file
* Remove Tim Booth from Uploaders (thanks for all your previous work Tim)
* Standards-Version: 4.6.0 (routine-update)
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Files:
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d7828332332e6602625346955520d913 307184 libdevel optional libanfo0-dev_0.98-9_armhf.deb
7758cd961fe2b86cf079c75ddf774716 235544 libs optional libanfo0_0.98-9_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
anfo-dbgsym_0.98-9_armhf.deb
----------------------------
new Debian package, version 2.0.
size 1039456 bytes: control archive=848 bytes.
562 bytes, 12 lines control
720 bytes, 7 lines md5sums
Package: anfo-dbgsym
Source: anfo
Version: 0.98-9
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1120
Depends: anfo (= 0.98-9)
Section: debug
Priority: optional
Description: debug symbols for anfo
Build-Ids: 36d47664c018744f1c56d1e39cf60376a77eb245 6ef85b092e689057cb8a3c3d4c4610bfb04ebd24 7984d7e1e975aad22884e530432d14b56938ded4 9eaa53dd556e90e194ce8c65d9d341aa8c3f16dc c4c8b3d48fce424906aab3479b9aafd74ce6560e efc221f1e24cbfe070dbbbf1d5a1d8edc49def15
drwxr-xr-x root/root 0 2021-10-06 12:24 ./
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/debug/.build-id/36/
-rw-r--r-- root/root 76492 2021-10-06 12:24 ./usr/lib/debug/.build-id/36/d47664c018744f1c56d1e39cf60376a77eb245.debug
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/debug/.build-id/6e/
-rw-r--r-- root/root 472956 2021-10-06 12:24 ./usr/lib/debug/.build-id/6e/f85b092e689057cb8a3c3d4c4610bfb04ebd24.debug
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/debug/.build-id/79/
-rw-r--r-- root/root 108344 2021-10-06 12:24 ./usr/lib/debug/.build-id/79/84d7e1e975aad22884e530432d14b56938ded4.debug
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/debug/.build-id/9e/
-rw-r--r-- root/root 71012 2021-10-06 12:24 ./usr/lib/debug/.build-id/9e/aa53dd556e90e194ce8c65d9d341aa8c3f16dc.debug
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/debug/.build-id/c4/
-rw-r--r-- root/root 110772 2021-10-06 12:24 ./usr/lib/debug/.build-id/c4/c8b3d48fce424906aab3479b9aafd74ce6560e.debug
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/debug/.build-id/ef/
-rw-r--r-- root/root 182872 2021-10-06 12:24 ./usr/lib/debug/.build-id/ef/c221f1e24cbfe070dbbbf1d5a1d8edc49def15.debug
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 103480 2021-10-06 12:24 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/anfo.debug
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/share/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-10-06 12:24 ./usr/share/doc/anfo-dbgsym -> anfo
anfo_0.98-9_armhf.deb
---------------------
new Debian package, version 2.0.
size 101096 bytes: control archive=1500 bytes.
877 bytes, 16 lines control
1508 bytes, 24 lines md5sums
Package: anfo
Version: 0.98-9
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 336
Depends: libanfo0 (>= 0.98), libc6 (>= 2.29), libelk0, libgcc-s1 (>= 3.5), libpopt0 (>= 1.14), libprotobuf23 (>= 3.12.4), libstdc++6 (>= 9), zlib1g (>= 1:1.1.4)
Section: science
Priority: optional
Homepage: https://bioinf.eva.mpg.de/anfo/
Description: Short Read Aligner/Mapper from MPG
Anfo is a mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes
more after BLAST/BLAT. It's most useful for the alignment of sequencing reads
where the DNA sequence is somehow modified (think ancient DNA or bisulphite
treatment) and/or there is more divergence between sample and reference than
what fast mappers will handle gracefully (say the reference genome is missing
and a related species is used instead).
drwxr-xr-x root/root 0 2021-10-06 12:24 ./
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/bin/
-rwxr-xr-x root/root 34444 2021-10-06 12:24 ./usr/bin/anfo
-rwxr-xr-x root/root 116364 2021-10-06 12:24 ./usr/bin/anfo-tool
-rwxr-xr-x root/root 30348 2021-10-06 12:24 ./usr/bin/dnaindex
-rwxr-xr-x root/root 26252 2021-10-06 12:24 ./usr/bin/fa2dna
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/anfo/
-rwxr-xr-x root/root 18060 2021-10-06 12:24 ./usr/lib/anfo/file-info
-rwxr-xr-x root/root 26252 2021-10-06 12:24 ./usr/lib/anfo/index-test
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/share/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/share/anfo/
-rw-r--r-- root/root 6784 2021-10-06 12:24 ./usr/share/anfo/config.proto
-rw-r--r-- root/root 14546 2021-10-06 12:24 ./usr/share/anfo/output.proto
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/share/doc/anfo/
-rw-r--r-- root/root 909 2021-10-06 12:24 ./usr/share/doc/anfo/README.Debian
-rw-r--r-- root/root 2441 2021-10-06 12:24 ./usr/share/doc/anfo/README.gz
-rw-r--r-- root/root 1336 2021-10-06 12:24 ./usr/share/doc/anfo/changelog.Debian.gz
-rw-r--r-- root/root 2550 2021-10-06 12:24 ./usr/share/doc/anfo/copyright
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/share/doc/anfo/example/
-rw-r--r-- root/root 1807 2021-10-06 12:24 ./usr/share/doc/anfo/example/ancient.cfg
-rw-r--r-- root/root 2056 2021-10-06 12:24 ./usr/share/doc/anfo/example/default.cfg
-rw-r--r-- root/root 521 2021-10-06 12:24 ./usr/share/doc/anfo/example/split-anfo.scm
-rw-r--r-- root/root 567 2021-10-06 12:24 ./usr/share/doc/anfo/example/threebam.scm
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/share/elk/
-rw-r--r-- root/root 9717 2021-10-06 12:24 ./usr/share/elk/anfo.scm
-rw-r--r-- root/root 2593 2021-10-06 12:24 ./usr/share/elk/srfi-88.scm
-rw-r--r-- root/root 12138 2021-10-06 12:24 ./usr/share/elk/srfi-89.scm
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/share/man/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/share/man/man1/
-rw-r--r-- root/root 4029 2021-10-06 12:24 ./usr/share/man/man1/anfo-tool.1.gz
-rw-r--r-- root/root 1616 2021-10-06 12:24 ./usr/share/man/man1/anfo.1.gz
-rw-r--r-- root/root 1684 2021-10-06 12:24 ./usr/share/man/man1/dnaindex.1.gz
-rw-r--r-- root/root 1202 2021-10-06 12:24 ./usr/share/man/man1/fa2dna.1.gz
-rw-r--r-- root/root 634 2021-10-06 12:24 ./usr/share/man/man1/file-info.1.gz
libanfo0-dbgsym_0.98-9_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 3374484 bytes: control archive=540 bytes.
369 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: libanfo0-dbgsym
Source: anfo
Version: 0.98-9
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3468
Depends: libanfo0 (= 0.98-9)
Section: debug
Priority: optional
Description: debug symbols for libanfo0
Build-Ids: df8fb6f19ceee3f2e6a1664319759a0a79e65f8f
drwxr-xr-x root/root 0 2021-10-06 12:24 ./
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/debug/.build-id/df/
-rw-r--r-- root/root 3540108 2021-10-06 12:24 ./usr/lib/debug/.build-id/df/8fb6f19ceee3f2e6a1664319759a0a79e65f8f.debug
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/share/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-10-06 12:24 ./usr/share/doc/libanfo0-dbgsym -> libanfo0
libanfo0-dev_0.98-9_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 307184 bytes: control archive=1404 bytes.
995 bytes, 22 lines control
1166 bytes, 18 lines md5sums
Package: libanfo0-dev
Source: anfo
Version: 0.98-9
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1655
Depends: libanfo0 (= 0.98-9), libbz2-dev, libelk0-dev, libprotobuf-dev, zlib1g-dev
Conflicts: libanfo-dev
Provides: libanfo-dev
Section: libdevel
Priority: optional
Homepage: https://bioinf.eva.mpg.de/anfo/
Description: Development files for Short Read Aligner/Mapper from MPG
Anfo is a mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes
more after BLAST/BLAT. It's most useful for the alignment of sequencing reads
where the DNA sequence is somehow modified (think ancient DNA or bisulphite
treatment) and/or there is more divergence between sample and reference than
what fast mappers will handle gracefully (say the reference genome is missing
and a related species is used instead).
.
This package contains the development files that might be used in connection
with the anfo binaries.
drwxr-xr-x root/root 0 2021-10-06 12:24 ./
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/include/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/include/anfo/
-rw-r--r-- root/root 14361 2021-10-06 12:24 ./usr/include/anfo/align.h
-rw-r--r-- root/root 2595 2021-10-06 12:24 ./usr/include/anfo/align_fwd.h
-rw-r--r-- root/root 3399 2021-10-06 12:24 ./usr/include/anfo/anfo_common.h
-rw-r--r-- root/root 11973 2021-10-06 12:24 ./usr/include/anfo/compress_stream.h
-rw-r--r-- root/root 4906 2021-10-06 12:24 ./usr/include/anfo/concurrent_stream.h
-rw-r--r-- root/root 2979 2021-10-06 12:24 ./usr/include/anfo/conffile.h
-rw-r--r-- root/root 5051 2021-10-06 12:24 ./usr/include/anfo/ducttape.h
-rw-r--r-- root/root 17630 2021-10-06 12:24 ./usr/include/anfo/index.h
-rw-r--r-- root/root 5881 2021-10-06 12:24 ./usr/include/anfo/logdom.h
-rw-r--r-- root/root 22028 2021-10-06 12:24 ./usr/include/anfo/misc_streams.h
-rw-r--r-- root/root 5942 2021-10-06 12:24 ./usr/include/anfo/output_streams.h
-rw-r--r-- root/root 14774 2021-10-06 12:24 ./usr/include/anfo/sequence.h
-rw-r--r-- root/root 30889 2021-10-06 12:24 ./usr/include/anfo/stream.h
-rw-r--r-- root/root 5292 2021-10-06 12:24 ./usr/include/anfo/trim.h
-rw-r--r-- root/root 9473 2021-10-06 12:24 ./usr/include/anfo/util.h
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 1512962 2021-10-06 12:24 ./usr/lib/arm-linux-gnueabihf/libanfo.a
lrwxrwxrwx root/root 0 2021-10-06 12:24 ./usr/lib/arm-linux-gnueabihf/libanfo.so -> libanfo.so.0.0.0
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/share/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/share/doc/libanfo0-dev/
-rw-r--r-- root/root 1336 2021-10-06 12:24 ./usr/share/doc/libanfo0-dev/changelog.Debian.gz
-rw-r--r-- root/root 2550 2021-10-06 12:24 ./usr/share/doc/libanfo0-dev/copyright
libanfo0_0.98-9_armhf.deb
-------------------------
new Debian package, version 2.0.
size 235544 bytes: control archive=1092 bytes.
944 bytes, 19 lines control
223 bytes, 3 lines md5sums
29 bytes, 1 lines shlibs
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Package: libanfo0
Source: anfo
Version: 0.98-9
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 790
Depends: libbz2-1.0, libc6 (>= 2.29), libelk0, libgcc-s1 (>= 3.5), libprotobuf23 (>= 3.12.4), libstdc++6 (>= 9), zlib1g (>= 1:1.2.0)
Section: libs
Priority: optional
Homepage: https://bioinf.eva.mpg.de/anfo/
Description: Library for Short Read Aligner/Mapper from MPG
Anfo is a mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes
more after BLAST/BLAT. It's most useful for the alignment of sequencing reads
where the DNA sequence is somehow modified (think ancient DNA or bisulphite
treatment) and/or there is more divergence between sample and reference than
what fast mappers will handle gracefully (say the reference genome is missing
and a related species is used instead).
.
This package contains the dynamic library for the anfo binaries.
drwxr-xr-x root/root 0 2021-10-06 12:24 ./
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2021-10-06 12:24 ./usr/lib/arm-linux-gnueabihf/libanfo.so.0 -> libanfo.so.0.0.0
-rw-r--r-- root/root 792516 2021-10-06 12:24 ./usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/share/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-06 12:24 ./usr/share/doc/libanfo0/
-rw-r--r-- root/root 1336 2021-10-06 12:24 ./usr/share/doc/libanfo0/changelog.Debian.gz
-rw-r--r-- root/root 2550 2021-10-06 12:24 ./usr/share/doc/libanfo0/copyright
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Build Architecture: armhf
Build-Space: 112220
Build-Time: 638
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 467
Job: anfo_0.98-9
Machine Architecture: armhf
Package: anfo
Package-Time: 1151
Source-Version: 0.98-9
Space: 112220
Status: successful
Version: 0.98-9
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Finished at 2021-10-11T06:30:22Z
Build needed 00:19:11, 112220k disc space