anfo →
0.98-7 →
armhf → 2018-10-25 05:08:30
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| anfo 0.98-7 (armhf) Thu, 25 Oct 2018 04:44:26 +0000 |
+==============================================================================+
Package: anfo
Version: 0.98-7
Source Version: 0.98-7
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-edeeef5e-6222-454b-94a4-2acd51173217' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.1 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.9 MB]
Fetched 24.0 MB in 30s (804 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: '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 buster-staging/main anfo 0.98-7 (dsc) [2139 B]
Get:2 http://172.17.0.1/private buster-staging/main anfo 0.98-7 (tar) [462 kB]
Get:3 http://172.17.0.1/private buster-staging/main anfo 0.98-7 (diff) [7556 B]
Fetched 472 kB in 0s (1211 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/anfo-e5qD5W/anfo-0.98' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/anfo-e5qD5W' 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-FjUpYi/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-FjUpYi/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-FjUpYi/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-FjUpYi/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-FjUpYi/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-FjUpYi/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-FjUpYi/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-FjUpYi/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (3089 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 54 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-FjUpYi/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15745 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), libpopt-dev, libprotobuf-dev, libelk0-dev, libelk0, zlib1g-dev, libbz2-dev, pkg-config, protobuf-compiler, d-shlibs (>= 0.77)
Filtered Build-Depends: debhelper (>= 11~), libpopt-dev, libprotobuf-dev, libelk0-dev, libelk0, zlib1g-dev, libbz2-dev, pkg-config, protobuf-compiler, d-shlibs (>= 0.77)
dpkg-deb: building package 'sbuild-build-depends-anfo-dummy' in '/<<BUILDDIR>>/resolver-FjUpYi/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-FjUpYi/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-FjUpYi/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-FjUpYi/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-FjUpYi/apt_archive ./ Sources [550 B]
Get:5 copy:/<<BUILDDIR>>/resolver-FjUpYi/apt_archive ./ Packages [631 B]
Fetched 2514 B in 1s (3495 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install anfo build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils d-shlibs debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3
libelf-dev libelf1 libelk0 libelk0-dev libfile-stripnondeterminism-perl
libfreetype6 libgdbm6 libglib2.0-0 libgraphite2-3 libharfbuzz0b libice-dev
libice6 libicu-le-hb0 libicu60 libmagic-mgc libmagic1 libpipeline1
libpopt-dev libpopt0 libprotobuf-dev libprotobuf-lite10 libprotobuf10
libprotoc10 libpthread-stubs0-dev libsigsegv2 libsm-dev libsm6 libtool
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 x11-common x11proto-core-dev x11proto-dev
x11proto-xext-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
gdbm-l10n 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
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 bsdmainutils d-shlibs debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3
libelf-dev libelf1 libelk0 libelk0-dev libfile-stripnondeterminism-perl
libfreetype6 libgdbm6 libglib2.0-0 libgraphite2-3 libharfbuzz0b libice-dev
libice6 libicu-le-hb0 libicu60 libmagic-mgc libmagic1 libpipeline1
libpopt-dev libpopt0 libprotobuf-dev libprotobuf-lite10 libprotobuf10
libprotoc10 libpthread-stubs0-dev libsigsegv2 libsm-dev libsm6 libtool
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 x11-common
x11proto-core-dev x11proto-dev x11proto-xext-dev xorg-sgml-doctools
xtrans-dev zlib1g-dev
0 upgraded, 77 newly installed, 0 to remove and 54 not upgraded.
Need to get 24.8 MB/26.0 MB of archives.
After this operation, 93.1 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-FjUpYi/apt_archive ./ sbuild-build-depends-anfo-dummy 0.invalid.0 [920 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libgdbm6 armhf 1.18-2 [60.1 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-2+b1 [1160 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-8 [117 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-1.1 [771 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-8 [434 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf d-shlibs all 0.82+nmu1 [19.2 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-6 [547 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.043-2 [20.2 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.043-2 [12.2 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.1-2 [1051 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.12-1 [69.1 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.9.0-1+rpi1 [877 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-8 [1220 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.4.1 [989 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-9 [27.7 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libelf-dev armhf 0.170-0.5 [69.7 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libxcb1 armhf 1.13.1-1 [132 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libx11-data all 2:1.6.7-1 [298 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libx11-6 armhf 2:1.6.7-1 [689 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libxmu6 armhf 2:1.1.2-2 [52.0 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libelk0 armhf 3.99.8-4.2+b1 [155 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf x11proto-dev all 2018.4-4 [251 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf x11proto-core-dev all 2018.4-4 [3128 B]
Get:47 http://172.17.0.1/private buster-staging/main armhf libxau-dev armhf 1:1.0.8-1+b2 [22.4 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf xtrans-dev all 1.3.5-1 [100 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libpthread-stubs0-dev armhf 0.3-4 [4042 B]
Get:51 http://172.17.0.1/private buster-staging/main armhf libxcb1-dev armhf 1.13.1-1 [169 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libx11-dev armhf 2:1.6.7-1 [760 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf x11proto-xext-dev all 2018.4-4 [3128 B]
Get:54 http://172.17.0.1/private buster-staging/main armhf libxext-dev armhf 2:1.3.3-1+b2 [102 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libice-dev armhf 2:1.0.9-2 [58.8 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libsm-dev armhf 2:1.2.2-1+b3 [33.4 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libxt-dev armhf 1:1.1.5-1 [390 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libxmu-headers all 2:1.1.2-2 [51.9 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libxmu-dev armhf 2:1.1.2-2 [56.2 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libelk0-dev armhf 3.99.8-4.2+b1 [177 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libpopt0 armhf 1.16-11 [45.9 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libpopt-dev armhf 1.16-11 [46.5 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libprotobuf10 armhf 3.0.0-9.2 [582 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libprotobuf-lite10 armhf 3.0.0-9.2 [114 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libprotobuf-dev armhf 3.0.0-9.2 [891 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libprotoc10 armhf 3.0.0-9.2 [502 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf protobuf-compiler armhf 3.0.0-9.2 [52.7 kB]
debconf: delaying package configuration, since apt-utils is not installed
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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Setting up x11-common (1:7.7+19) ...
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Running in chroot, ignoring request.
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Setting up autoconf (2.69-11) ...
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Processing triggers for libc-bin (2.27-6+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-6+rpi1 dpkg-dev_1.19.0.5 g++-8_8.2.0-7+rpi1 gcc-8_8.2.0-7+rpi1 libc6-dev_2.27-6+rpi1 libstdc++-8-dev_8.2.0-7+rpi1 libstdc++6_8.2.0-7+rpi1 linux-libc-dev_4.16.16-2+rpi1
Package versions: adduser_3.118 apt_1.7.0 autoconf_2.69-11 automake_1:1.16.1-1.1 autopoint_0.19.8.1-8 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-6+rpi1 binutils-arm-linux-gnueabihf_2.31.1-6+rpi1 binutils-common_2.31.1-6+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.1.0-1+rpi1 cpp-8_8.2.0-7+rpi1 d-shlibs_0.82+nmu1 dash_0.5.10.2-1 dbus_1.12.10-1 dbus-user-session_1.12.10-1 debconf_1.5.69 debhelper_11.4.1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.043-2 diffutils_1:3.6-1 dirmngr_2.2.9-1+rpi1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.4-2 e2fsprogs_1.44.4-2 e2fsprogs-l10n_1.44.4-2 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20180808-2 g++_4:8.1.0-1+rpi1 g++-8_8.2.0-7+rpi1 gcc_4:8.1.0-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-7+rpi1 gcc-8-base_8.2.0-7+rpi1 gettext_0.19.8.1-8 gettext-base_0.19.8.1-8 gnupg_2.2.9-1+rpi1 gnupg-agent_2.2.9-1+rpi1 gnupg-l10n_2.2.9-1+rpi1 gnupg-utils_2.2.9-1+rpi1 gpg_2.2.9-1+rpi1 gpg-agent_2.2.9-1+rpi1 gpg-wks-client_2.2.9-1+rpi1 gpg-wks-server_2.2.9-1+rpi1 gpgconf_2.2.9-1+rpi1 gpgsm_2.2.9-1+rpi1 gpgv_2.2.9-1+rpi1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2.1 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.54 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.13-8 libapt-pkg5.0_1.7.0 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-7+rpi1 libassuan0_2.5.1-2 libatomic1_8.2.0-7+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libbinutils_2.31.1-6+rpi1 libblkid1_2.32.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libbz2-dev_1.0.6-9 libc-bin_2.27-6+rpi1 libc-dev-bin_2.27-6+rpi1 libc6_2.27-6+rpi1 libc6-dev_2.27-6+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-7+rpi1 libcom-err2_1.44.4-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.10-1 libdebconfclient0_0.245 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.94-1+rpi1 libdrm2_2.4.94-1+rpi1 libelf-dev_0.170-0.5 libelf1_0.170-0.5 libelk0_3.99.8-4.2+b1 libelk0-dev_3.99.8-4.2+b1 libexpat1_2.2.6-1 libext2fs2_1.44.4-2 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.043-2 libfreetype6_2.8.1-2 libgcc-8-dev_8.2.0-7+rpi1 libgcc1_1:8.2.0-7+rpi1 libgcrypt20_1.8.3-1 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgdbm6_1.18-2 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.19-1 libgomp1_8.2.0-7+rpi1 libgpg-error0_1.32-1 libgraphite2-3_1.3.12-1 libharfbuzz0b_1.9.0-1+rpi1 libhogweed4_3.4-1 libice-dev_2:1.0.9-2 libice6_2:1.0.9-2 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.6.2-1.1 libisl19_0.20-2 libjson-c3_0.12.1-1.3 libklibc_2.0.4-14+rpi1 libkmod2_25-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1+20180714-1 libncurses6_6.1+20180714-1 libncursesw5_6.1+20180714-1 libncursesw6_6.1+20180714-1 libnettle6_3.4-1 libnpth0_1.6-1 libnss-systemd_239-10+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.8 libpam-modules-bin_1.1.8-3.8 libpam-runtime_1.1.8-3.8 libpam-systemd_239-10+rpi1 libpam0g_1.1.8-3.8 libpcre3_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.26_5.26.2-7 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpng16-16_1.6.34-2+rpi1 libpopt-dev_1.16-11 libpopt0_1.16-11 libprocps7_2:3.3.15-2 libprotobuf-dev_3.0.0-9.2 libprotobuf-lite10_3.0.0-9.2 libprotobuf10_3.0.0-9.2 libprotoc10_3.0.0-9.2 libpthread-stubs0-dev_0.3-4 libreadline7_7.0-5 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsm-dev_2:1.2.2-1+b3 libsm6_2:1.2.2-1+b3 libsmartcols1_2.32.1-0.1 libsqlite3-0_3.25.2-1 libss2_1.44.4-2 libssl1.1_1.1.0h-4 libstdc++-8-dev_8.2.0-7+rpi1 libstdc++6_8.2.0-7+rpi1 libsystemd0_239-10+rpi1 libtasn1-6_4.13-3 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libtinfo5_6.1+20180714-1 libtinfo6_6.1+20180714-1 libtool_2.4.6-6 libubsan1_8.2.0-7+rpi1 libudev1_239-10+rpi1 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32.1-0.1 libx11-6_2:1.6.7-1 libx11-data_2:1.6.7-1 libx11-dev_2:1.6.7-1 libxau-dev_1:1.0.8-1+b2 libxau6_1:1.0.8-1+b2 libxcb1_1.13.1-1 libxcb1-dev_1.13.1-1 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext-dev_2:1.3.3-1+b2 libxext6_2:1.3.3-1+b2 libxml2_2.9.4+dfsg1-7 libxmu-dev_2:1.1.2-2 libxmu-headers_2:1.1.2-2 libxmu6_2:1.1.2-2 libxt-dev_1:1.1.5-1 libxt6_1:1.1.5-1 libzstd1_1.3.5+dfsg-1+rpi1 linux-base_4.5 linux-libc-dev_4.16.16-2+rpi1 login_1:4.5-1.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.4-2+b1 mawk_1.3.3-17 mount_2.32.1-0.1 multiarch-support_2.27-6+rpi1 nano_3.1-1 ncurses-base_6.1+20180714-1 ncurses-bin_6.1+20180714-1 netbase_5.4 openssl_1.1.0h-4 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.26.2-7 perl-base_5.26.2-7 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-7 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 protobuf-compiler_3.0.0-9.2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-anfo-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 systemd_239-10+rpi1 systemd-sysv_239-10+rpi1 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 udev_239-10+rpi1 util-linux_2.32.1-0.1 x11-common_1:7.7+19 x11proto-core-dev_2018.4-4 x11proto-dev_2018.4-4 x11proto-xext-dev_2018.4-4 xorg-sgml-doctools_1:1.11-1 xtrans-dev_1.3.5-1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Oct 15 14:55:48 2018 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_0.98-7.dsc
dpkg-source: info: extracting anfo in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking anfo_0.98.orig.tar.gz
dpkg-source: info: unpacking anfo_0.98-7.debian.tar.xz
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=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-edeeef5e-6222-454b-94a4-2acd51173217
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package anfo
dpkg-buildpackage: info: source version 0.98-7
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build anfo-0.98
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
configure.ac:77: warning: LT_INIT was called before AM_PROG_AR
/usr/share/aclocal-1.16/ar-lib.m4:13: AM_PROG_AR is expanded from...
configure.ac:77: the top level
configure.ac:77: warning: LT_INIT was called before AM_PROG_AR
/usr/share/aclocal-1.16/ar-lib.m4:13: AM_PROG_AR is expanded from...
configure.ac:77: the top level
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'
configure.ac:77: warning: LT_INIT was called before AM_PROG_AR
/usr/share/aclocal-1.16/ar-lib.m4:13: AM_PROG_AR is expanded from...
configure.ac:77: 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
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:77: warning: LT_INIT was called before AM_PROG_AR
/usr/share/aclocal-1.16/ar-lib.m4:13: AM_PROG_AR is expanded from...
configure.ac:77: the top level
configure.ac:77: warning: LT_INIT was called before AM_PROG_AR
/usr/share/aclocal-1.16/ar-lib.m4:13: AM_PROG_AR is expanded from...
configure.ac:77: 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: 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: 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'
dh_auto_configure -a
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe 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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... 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... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.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 we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
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 popt.h usability... yes
checking popt.h presence... yes
checking for popt.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking bzlib.h usability... yes
checking bzlib.h presence... 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... yes
checking google/protobuf/message.h usability... yes
checking google/protobuf/message.h presence... yes
checking for google/protobuf/message.h... yes
checking elk/scheme.h usability... yes
checking elk/scheme.h presence... yes
checking for elk/scheme.h... yes
checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
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 stdbool.h that conforms to C99... no
checking for _Bool... no
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
configure: WARNING: unrecognized options: --disable-maintainer-mode
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:547] 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:547] 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:547] 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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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]
std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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:198:36: warning: throw will always call terminate() [-Wterminate]
else if( r != Z_OK ) throw zs_.msg ;
^~~
compress_stream.h:198:36: 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_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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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:379:45: warning: throw will always call terminate() [-Wterminate]
else if( r < BZ_OK ) throw BzipError( r ) ;
^
compress_stream.h:379:45: 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]
std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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:198:36: warning: throw will always call terminate() [-Wterminate]
else if( r != Z_OK ) throw zs_.msg ;
^~~
compress_stream.h:198:36: 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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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:379:45: warning: throw will always call terminate() [-Wterminate]
else if( r < BZ_OK ) throw BzipError( r ) ;
^
compress_stream.h:379:45: 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]
std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
auto_ptr< Result > r( outgoing_[ next_out_++ ] ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
auto_ptr< Result > r( incoming_[ next_in_ ] ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
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]
std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
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]
BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c align.cc -o align.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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c ducttape.cc -fPIC -DPIC -o .libs/ducttape.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c concurrent_stream.cc -o concurrent_stream.o >/dev/null 2>&1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from index.h:24,
from align.h:21,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/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++/8/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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:198:36: warning: throw will always call terminate() [-Wterminate]
else if( r != Z_OK ) throw zs_.msg ;
^~~
compress_stream.h:198:36: 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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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:379:45: warning: throw will always call terminate() [-Wterminate]
else if( r < BZ_OK ) throw BzipError( r ) ;
^
compress_stream.h:379:45: 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]
std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from index.h:24,
from align.h:21,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from index.h:24,
from align.h:21,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/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++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from ducttape.cc:21:
ducttape.h:139:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from index.h:24,
from align.h:21,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o index.lo index.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c index.cc -fPIC -DPIC -o .libs/index.o
/usr/include/c++/8/bits/stl_algo.h: In member function 'virtual void streams::Indexer::put_result(const output::Result&)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o misc_streams.lo misc_streams.cc
In file included from /usr/include/c++/8/vector:69,
from sequence.h:25,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<streams::DuctTaper::Acc>::iterator' {aka '__gnu_cxx::__normal_iterator<streams::DuctTaper::Acc*, std::vector<streams::DuctTaper::Acc> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c misc_streams.cc -fPIC -DPIC -o .libs/misc_streams.o
/usr/include/c++/8/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++/8/bits/vector.tcc:327:5: note: parameter passing for argument of type 'std::vector<streams::DuctTaper::Acc>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const streams::DuctTaper::Acc*, std::vector<streams::DuctTaper::Acc> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:343:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<streams::DuctTaper::Acc*, std::vector<streams::DuctTaper::Acc> >' changed in GCC 7.1
_M_realloc_insert(begin() + __n, std::move(__v));
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from sequence.h:25,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void streams::DuctTaper::put_result_ancient(const output::Result&)':
/usr/include/c++/8/bits/stl_vector.h:1181:57: note: parameter passing for argument of type 'std::vector<streams::DuctTaper::Acc>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const streams::DuctTaper::Acc*, std::vector<streams::DuctTaper::Acc> >'} changed in GCC 7.1
{ return _M_insert_rval(__position, std::move(__x)); }
^
/usr/include/c++/8/bits/stl_vector.h:1181:57: note: parameter passing for argument of type 'std::vector<streams::DuctTaper::Acc>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const streams::DuctTaper::Acc*, std::vector<streams::DuctTaper::Acc> >'} changed in GCC 7.1
{ 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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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:198:36: warning: throw will always call terminate() [-Wterminate]
else if( r != Z_OK ) throw zs_.msg ;
^~~
compress_stream.h:198:36: 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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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:379:45: warning: throw will always call terminate() [-Wterminate]
else if( r < BZ_OK ) throw BzipError( r ) ;
^
compress_stream.h:379:45: 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]
std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo_common.cc -o anfo_common.o >/dev/null 2>&1
/usr/include/c++/8/bits/stl_vector.h: In member function 'void streams::DuctTaper::put_result_recent(const output::Result&)':
/usr/include/c++/8/bits/stl_vector.h:1181:57: note: parameter passing for argument of type 'std::vector<streams::DuctTaper::Acc>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const streams::DuctTaper::Acc*, std::vector<streams::DuctTaper::Acc> >'} changed in GCC 7.1
{ return _M_insert_rval(__position, std::move(__x)); }
^
/usr/include/c++/8/bits/stl_vector.h:1181:57: note: parameter passing for argument of type 'std::vector<streams::DuctTaper::Acc>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const streams::DuctTaper::Acc*, std::vector<streams::DuctTaper::Acc> >'} changed in GCC 7.1
{ return _M_insert_rval(__position, std::move(__x)); }
^
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c ducttape.cc -o ducttape.o >/dev/null 2>&1
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]
auto_ptr< istream > deffile( p.first ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /usr/include/google/protobuf/unknown_field_set.h:43,
from /usr/include/google/protobuf/metadata.h:43,
from config.pb.h:25,
from index.h:20,
from index.cc:21:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<Matches>::iterator' {aka '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'unsigned int FixedIndex::lookup1(Oligo, PreSeeds&, const FixedIndex::LookupParams&, int32_t, int*) const':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c index.cc -o index.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c output_streams.cc -fPIC -DPIC -o .libs/output_streams.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-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 -fdebug-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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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:198:36: warning: throw will always call terminate() [-Wterminate]
else if( r != Z_OK ) throw zs_.msg ;
^~~
compress_stream.h:198:36: 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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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:379:45: warning: throw will always call terminate() [-Wterminate]
else if( r < BZ_OK ) throw BzipError( r ) ;
^
compress_stream.h:379:45: 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]
std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from config.pb.h:26,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c stream.cc -fPIC -DPIC -o .libs/stream.o
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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:198:36: warning: throw will always call terminate() [-Wterminate]
else if( r != Z_OK ) throw zs_.msg ;
^~~
compress_stream.h:198:36: 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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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:379:45: warning: throw will always call terminate() [-Wterminate]
else if( r < BZ_OK ) throw BzipError( r ) ;
^
compress_stream.h:379:45: 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]
std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from sequence.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.cc:21:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.cc:21:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate]
else if( r != Z_OK ) throw zs_.msg ;
^~~
compress_stream.h:198:36: 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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.cc:21:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate]
else if( r < BZ_OK ) throw BzipError( r ) ;
^
compress_stream.h:379:45: 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]
std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
stream.cc:81:30: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
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++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
stream.cc:421:36: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
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++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
stream.cc:1093:9: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
stream.cc:1114:29: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
StreamWithProgress( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, int64_t total )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
stream.cc:1149:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
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++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > bs( new BunzipStream( is ) ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
stream.cc:1189:9: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > zs( new InflateStream( is ) ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::FileInputStream > s( new google::protobuf::io::FileInputStream( fd ) ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
stream.cc:1238:12: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<google::protobuf::io::ZeroCopyInputStream>(s), name_, st.st_size ) ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BamReader::BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from stream.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c output_streams.cc -o output_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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c util.cc -fPIC -DPIC -o .libs/util.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c util.cc -o util.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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo-elk.cc -fPIC -DPIC -o .libs/anfo-elk.o
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c fastlz.c -fPIC -DPIC -o .libs/fastlz.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c fastlz.c -o fastlz.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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o config.pb.lo config.pb.cc
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o output.pb.lo output.pb.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c config.pb.cc -fPIC -DPIC -o .libs/config.pb.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-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 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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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:198:36: warning: throw will always call terminate() [-Wterminate]
else if( r != Z_OK ) throw zs_.msg ;
^~~
compress_stream.h:198:36: 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-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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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:379:45: warning: throw will always call terminate() [-Wterminate]
else if( r < BZ_OK ) throw BzipError( r ) ;
^
compress_stream.h:379:45: 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]
std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-elk.cc:31:
output_streams.h:45:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-elk.cc:31:
output_streams.h:123:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
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/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c output.pb.cc -o output.pb.o >/dev/null 2>&1
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o dnaindex.o dnaindex.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo-tool.o anfo-tool.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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-tool.cc:21:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate]
else if( r != Z_OK ) throw zs_.msg ;
^~~
compress_stream.h:198:36: 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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-tool.cc:21:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate]
else if( r < BZ_OK ) throw BzipError( r ) ;
^
compress_stream.h:379:45: 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]
std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo.o anfo.cc
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< std::ostream > out_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from anfo-tool.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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:198:36: warning: throw will always call terminate() [-Wterminate]
else if( r != Z_OK ) throw zs_.msg ;
^~~
compress_stream.h:198:36: 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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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:379:45: warning: throw will always call terminate() [-Wterminate]
else if( r < BZ_OK ) throw BzipError( r ) ;
^
compress_stream.h:379:45: 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]
std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:27:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate]
else if( r != Z_OK ) throw zs_.msg ;
^~~
compress_stream.h:198:36: 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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:27:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate]
else if( r < BZ_OK ) throw BzipError( r ) ;
^
compress_stream.h:379:45: 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]
std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h:47,
from /usr/include/google/protobuf/io/zero_copy_stream_impl.h:46,
from compress_stream.h:23,
from index-test.cc:27:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from index.h:24,
from index-test.cc:29:
/usr/include/c++/8/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++/8/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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:198:36: warning: throw will always call terminate() [-Wterminate]
else if( r != Z_OK ) throw zs_.msg ;
^~~
compress_stream.h:198:36: 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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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:379:45: warning: throw will always call terminate() [-Wterminate]
else if( r < BZ_OK ) throw BzipError( r ) ;
^
compress_stream.h:379:45: 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]
std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from file-info.cc:25:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
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]
BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from index.h:24,
from index-test.cc:29:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from file-info.cc:25:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
^~~~~~~~
In file included from /usr/include/c++/8/memory:80,
from /usr/include/google/protobuf/descriptor.h:57,
from /usr/include/google/protobuf/message.h:122,
from output.pb.h:26,
from sequence.h:32,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/8/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from index.h:24,
from index-test.cc:29:
/usr/include/c++/8/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++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from index.h:24,
from index-test.cc:29:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'int main_(int, const char**)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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 -fdebug-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 -pthread -lpthread -lpthread -lelk -lbz2 -lz -lpopt
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/8/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/8/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/8 -L/usr/lib/gcc/arm-linux-gnueabihf/8/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/8/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/8/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/8/../../../arm-linux-gnueabihf/crtn.o -pthread -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -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 cru .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
ar: `u' modifier ignored since `D' is the default (see `U')
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fa2dna fa2dna.o libanfo.la -lprotobuf -pthread -lpthread -lelk -lbz2 -lz -lpopt
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o dnaindex dnaindex.o libanfo.la -lprotobuf -pthread -lpthread -lelk -lbz2 -lz -lpopt
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o anfo anfo.o libanfo.la -lprotobuf -pthread -lpthread -lelk -lbz2 -lz -lpopt
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-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 -pthread -lpthread -lelk -lbz2 -lz -lpopt
libtool: link: g++ -pthread -g -O2 -fdebug-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 -pthread ./.libs/libanfo.so -lprotobuf -lpthread -lelk -lbz2 -lz -lpopt -pthread
libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/anfo anfo.o -pthread ./.libs/libanfo.so -lprotobuf -lpthread -lelk -lbz2 -lz -lpopt -pthread
libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/fa2dna fa2dna.o -pthread ./.libs/libanfo.so -lprotobuf -lpthread -lelk -lbz2 -lz -lpopt -pthread
libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/dnaindex dnaindex.o -pthread ./.libs/libanfo.so -lprotobuf -lpthread -lelk -lbz2 -lz -lpopt -pthread
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-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 -pthread -lpthread -lelk -lbz2 -lz -lpopt
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-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 -pthread -lpthread -lelk -lbz2 -lz -lpopt
libtool: link: g++ -pthread -g -O2 -fdebug-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 -pthread ./.libs/libanfo.so -lprotobuf -lpthread -lelk -lbz2 -lz -lpopt -pthread
libtool: link: g++ -pthread -g -O2 -fdebug-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 -pthread ./.libs/libanfo.so -lprotobuf -lpthread -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>>'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
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/lib/arm-linux-gnueabihf'
/bin/bash ../libtool --mode=install /usr/bin/install -c index-test file-info '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
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/lib/arm-linux-gnueabihf/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/lib/arm-linux-gnueabihf/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'
/usr/bin/install -c -m 644 README '/<<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'
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>>'
rm `find debian/tmp -name '*.la'`
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.
--> libpopt-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
mv: cannot stat 'debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.la': No such file or directory
dh_install
mv debian/anfo/usr/lib/* debian/anfo/usr/lib/anfo
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installman
# delete unused manpage
find debian/anfo -name anfo-sge.1 -delete
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_fixperms
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_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
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/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/libanfo0/usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0 was not linked against libpopt.so.0 (it uses none of the library's symbols)
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: 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/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/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/fa2dna 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-tool debian/anfo/usr/bin/dnaindex debian/anfo/usr/bin/anfo debian/anfo/usr/lib/anfo/file-info debian/anfo/usr/lib/anfo/index-test debian/anfo/usr/bin/fa2dna were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/anfo/usr/bin/anfo-tool debian/anfo/usr/bin/dnaindex debian/anfo/usr/bin/anfo debian/anfo/usr/lib/anfo/file-info debian/anfo/usr/lib/anfo/index-test debian/anfo/usr/bin/fa2dna were not linked against libbz2.so.1.0 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'anfo' in '../anfo_0.98-7_armhf.deb'.
dpkg-deb: building package 'libanfo0' in '../libanfo0_0.98-7_armhf.deb'.
dpkg-deb: building package 'libanfo0-dev' in '../libanfo0-dev_0.98-7_armhf.deb'.
dpkg-deb: building package 'anfo-dbgsym' in '../anfo-dbgsym_0.98-7_armhf.deb'.
dpkg-deb: building package 'libanfo0-dbgsym' in '../libanfo0-dbgsym_0.98-7_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../anfo_0.98-7_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build anfo-0.98
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-10-25T05:08:21Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
anfo_0.98-7_armhf.changes:
--------------------------
Format: 1.8
Date: Mon, 15 Oct 2018 15:41:57 +0200
Source: anfo
Binary: anfo libanfo0 libanfo0-dev
Architecture: armhf
Version: 0.98-7
Distribution: buster-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 (0.98-7) unstable; urgency=medium
.
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
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Files:
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da1f6367d23b3e8c4261a39567859715 7617 science optional anfo_0.98-7_armhf.buildinfo
6d8349e60d141881b66802a9f9d3c114 103796 science optional anfo_0.98-7_armhf.deb
b86289ab164228237c9ce8dd2bad9c0d 3264936 debug optional libanfo0-dbgsym_0.98-7_armhf.deb
f39fb2681da82a1bdda889c0fac9e3b2 309148 libdevel optional libanfo0-dev_0.98-7_armhf.deb
8fa6d3a516881f3caff1352e5f565a36 230740 libs optional libanfo0_0.98-7_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
anfo-dbgsym_0.98-7_armhf.deb
----------------------------
new Debian package, version 2.0.
size 1278948 bytes: control archive=804 bytes.
562 bytes, 12 lines control
636 bytes, 6 lines md5sums
Package: anfo-dbgsym
Source: anfo
Version: 0.98-7
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1353
Depends: anfo (= 0.98-7)
Section: debug
Priority: optional
Description: debug symbols for anfo
Build-Ids: 4af78b83eeb8d565e8ff52c780ad44043e731891 6e66893b58ffd9199ecba95deedfd56ee13a670a 87073efde8f5a4b538d24929e6a7580292d70ca5 8d38ce3d0c941808b29c297283f1e65ad88b5ba8 9aa65269579e76c9d61dde61e731c571eb5452a9 a74eb76a899df715b389f016f0a0449ee85e10f9
drwxr-xr-x root/root 0 2018-10-15 13:41 ./
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/.build-id/4a/
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-rw-r--r-- root/root 162348 2018-10-15 13:41 ./usr/lib/debug/.build-id/6e/66893b58ffd9199ecba95deedfd56ee13a670a.debug
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/.build-id/87/
-rw-r--r-- root/root 529604 2018-10-15 13:41 ./usr/lib/debug/.build-id/87/073efde8f5a4b538d24929e6a7580292d70ca5.debug
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drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/.build-id/9a/
-rw-r--r-- root/root 256640 2018-10-15 13:41 ./usr/lib/debug/.build-id/9a/a65269579e76c9d61dde61e731c571eb5452a9.debug
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/.build-id/a7/
-rw-r--r-- root/root 109028 2018-10-15 13:41 ./usr/lib/debug/.build-id/a7/4eb76a899df715b389f016f0a0449ee85e10f9.debug
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-10-15 13:41 ./usr/share/doc/anfo-dbgsym -> anfo
anfo_0.98-7_armhf.deb
---------------------
new Debian package, version 2.0.
size 103796 bytes: control archive=1496 bytes.
868 bytes, 16 lines control
1508 bytes, 24 lines md5sums
Package: anfo
Version: 0.98-7
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 347
Depends: libanfo0, libbz2-1.0, libc6 (>= 2.27), libelk0, libgcc1 (>= 1:3.5), libpopt0 (>= 1.14), libprotobuf10, libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4)
Section: science
Priority: optional
Homepage: http://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 2018-10-15 13:41 ./
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/bin/
-rwxr-xr-x root/root 34320 2018-10-15 13:41 ./usr/bin/anfo
-rwxr-xr-x root/root 112144 2018-10-15 13:41 ./usr/bin/anfo-tool
-rwxr-xr-x root/root 42512 2018-10-15 13:41 ./usr/bin/dnaindex
-rwxr-xr-x root/root 30224 2018-10-15 13:41 ./usr/bin/fa2dna
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/anfo/
-rwxr-xr-x root/root 17936 2018-10-15 13:41 ./usr/lib/anfo/file-info
-rwxr-xr-x root/root 26128 2018-10-15 13:41 ./usr/lib/anfo/index-test
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/anfo/
-rw-r--r-- root/root 6784 2018-10-15 13:41 ./usr/share/anfo/config.proto
-rw-r--r-- root/root 14546 2018-10-15 13:41 ./usr/share/anfo/output.proto
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/anfo/
-rw-r--r-- root/root 909 2018-10-15 13:41 ./usr/share/doc/anfo/README.Debian
-rw-r--r-- root/root 2441 2018-10-15 13:41 ./usr/share/doc/anfo/README.gz
-rw-r--r-- root/root 1006 2018-10-15 13:41 ./usr/share/doc/anfo/changelog.Debian.gz
-rw-r--r-- root/root 2550 2018-10-15 13:41 ./usr/share/doc/anfo/copyright
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/anfo/example/
-rw-r--r-- root/root 1807 2018-10-15 13:41 ./usr/share/doc/anfo/example/ancient.cfg
-rw-r--r-- root/root 2056 2018-10-15 13:41 ./usr/share/doc/anfo/example/default.cfg
-rw-r--r-- root/root 521 2018-10-15 13:41 ./usr/share/doc/anfo/example/split-anfo.scm
-rw-r--r-- root/root 567 2018-10-15 13:41 ./usr/share/doc/anfo/example/threebam.scm
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/elk/
-rw-r--r-- root/root 9717 2018-10-15 13:41 ./usr/share/elk/anfo.scm
-rw-r--r-- root/root 2593 2018-10-15 13:41 ./usr/share/elk/srfi-88.scm
-rw-r--r-- root/root 12138 2018-10-15 13:41 ./usr/share/elk/srfi-89.scm
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/man/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/man/man1/
-rw-r--r-- root/root 4029 2018-10-15 13:41 ./usr/share/man/man1/anfo-tool.1.gz
-rw-r--r-- root/root 1616 2018-10-15 13:41 ./usr/share/man/man1/anfo.1.gz
-rw-r--r-- root/root 1684 2018-10-15 13:41 ./usr/share/man/man1/dnaindex.1.gz
-rw-r--r-- root/root 1202 2018-10-15 13:41 ./usr/share/man/man1/fa2dna.1.gz
-rw-r--r-- root/root 634 2018-10-15 13:41 ./usr/share/man/man1/file-info.1.gz
libanfo0-dbgsym_0.98-7_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 3264936 bytes: control archive=536 bytes.
369 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: libanfo0-dbgsym
Source: anfo
Version: 0.98-7
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3377
Depends: libanfo0 (= 0.98-7)
Section: debug
Priority: optional
Description: debug symbols for libanfo0
Build-Ids: 1e038d13a959e368dafe8649750768cc16905d3b
drwxr-xr-x root/root 0 2018-10-15 13:41 ./
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/.build-id/1e/
-rw-r--r-- root/root 3447452 2018-10-15 13:41 ./usr/lib/debug/.build-id/1e/038d13a959e368dafe8649750768cc16905d3b.debug
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-10-15 13:41 ./usr/share/doc/libanfo0-dbgsym -> libanfo0
libanfo0-dev_0.98-7_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 309148 bytes: control archive=1408 bytes.
1007 bytes, 22 lines control
1166 bytes, 18 lines md5sums
Package: libanfo0-dev
Source: anfo
Version: 0.98-7
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1751
Depends: libanfo0 (= 0.98-7), libbz2-dev, libelk0-dev, libpopt-dev, libprotobuf-dev, zlib1g-dev
Conflicts: libanfo-dev
Provides: libanfo-dev
Section: libdevel
Priority: optional
Homepage: http://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 2018-10-15 13:41 ./
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/include/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/include/anfo/
-rw-r--r-- root/root 14361 2018-10-15 13:41 ./usr/include/anfo/align.h
-rw-r--r-- root/root 2595 2018-10-15 13:41 ./usr/include/anfo/align_fwd.h
-rw-r--r-- root/root 3399 2018-10-15 13:41 ./usr/include/anfo/anfo_common.h
-rw-r--r-- root/root 11973 2018-10-15 13:41 ./usr/include/anfo/compress_stream.h
-rw-r--r-- root/root 4906 2018-10-15 13:41 ./usr/include/anfo/concurrent_stream.h
-rw-r--r-- root/root 2979 2018-10-15 13:41 ./usr/include/anfo/conffile.h
-rw-r--r-- root/root 5051 2018-10-15 13:41 ./usr/include/anfo/ducttape.h
-rw-r--r-- root/root 17630 2018-10-15 13:41 ./usr/include/anfo/index.h
-rw-r--r-- root/root 5881 2018-10-15 13:41 ./usr/include/anfo/logdom.h
-rw-r--r-- root/root 22028 2018-10-15 13:41 ./usr/include/anfo/misc_streams.h
-rw-r--r-- root/root 5942 2018-10-15 13:41 ./usr/include/anfo/output_streams.h
-rw-r--r-- root/root 14774 2018-10-15 13:41 ./usr/include/anfo/sequence.h
-rw-r--r-- root/root 30889 2018-10-15 13:41 ./usr/include/anfo/stream.h
-rw-r--r-- root/root 5292 2018-10-15 13:41 ./usr/include/anfo/trim.h
-rw-r--r-- root/root 9473 2018-10-15 13:41 ./usr/include/anfo/util.h
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 1612380 2018-10-15 13:41 ./usr/lib/arm-linux-gnueabihf/libanfo.a
lrwxrwxrwx root/root 0 2018-10-15 13:41 ./usr/lib/arm-linux-gnueabihf/libanfo.so -> libanfo.so.0.0.0
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/libanfo0-dev/
-rw-r--r-- root/root 1006 2018-10-15 13:41 ./usr/share/doc/libanfo0-dev/changelog.Debian.gz
-rw-r--r-- root/root 2550 2018-10-15 13:41 ./usr/share/doc/libanfo0-dev/copyright
libanfo0_0.98-7_armhf.deb
-------------------------
new Debian package, version 2.0.
size 230740 bytes: control archive=1080 bytes.
953 bytes, 19 lines control
223 bytes, 3 lines md5sums
19 bytes, 1 lines shlibs
67 bytes, 2 lines triggers
Package: libanfo0
Source: anfo
Version: 0.98-7
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 781
Depends: libbz2-1.0, libc6 (>= 2.27), libelk0, libgcc1 (>= 1:3.5), libpopt0 (>= 1.14), libprotobuf10, libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.0)
Section: libs
Priority: optional
Homepage: http://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 2018-10-15 13:41 ./
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2018-10-15 13:41 ./usr/lib/arm-linux-gnueabihf/libanfo.so.0 -> libanfo.so.0.0.0
-rw-r--r-- root/root 783952 2018-10-15 13:41 ./usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/libanfo0/
-rw-r--r-- root/root 1006 2018-10-15 13:41 ./usr/share/doc/libanfo0/changelog.Debian.gz
-rw-r--r-- root/root 2550 2018-10-15 13:41 ./usr/share/doc/libanfo0/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 101720
Build-Time: 597
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 784
Job: anfo_0.98-7
Machine Architecture: armhf
Package: anfo
Package-Time: 1435
Source-Version: 0.98-7
Space: 101720
Status: successful
Version: 0.98-7
--------------------------------------------------------------------------------
Finished at 2018-10-25T05:08:21Z
Build needed 00:23:55, 101720k disc space