anfo →
0.98-4+b3 →
armhf → 2016-09-01 16:49:12
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on testwandboard
+==============================================================================+
| anfo 0.98-4+b3 (armhf) 01 Sep 2016 16:20 |
+==============================================================================+
Package: anfo
Version: 0.98-4+b3
Source Version: 0.98-4
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/anfo-zMZ4Bl/anfo-0.98' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/anfo-zMZ4Bl' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-2139fd5e-497a-47ba-8135-02b7f9c7a0c5' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9258 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.2 MB]
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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 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/anfo/trunk/
Need to get 472 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main anfo 0.98-4 (dsc) [2132 B]
Get:2 http://172.17.0.1/private stretch-staging/main anfo 0.98-4 (tar) [462 kB]
Get:3 http://172.17.0.1/private stretch-staging/main anfo 0.98-4 (diff) [7204 B]
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Download complete and in download only mode
Check architectures
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Check dependencies
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-t0xd1N/apt_archive/sbuild-build-depends-core-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Get:1 file:/<<BUILDDIR>>/resolver-t0xd1N/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-t0xd1N/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-t0xd1N/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-t0xd1N/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-t0xd1N/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-t0xd1N/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-t0xd1N/apt_archive ./ Sources [194 B]
Get:5 file:/<<BUILDDIR>>/resolver-t0xd1N/apt_archive ./ Packages [509 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-t0xd1N/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
Reading package lists...
+------------------------------------------------------------------------------+
| Install core build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 25 not upgraded.
Need to get 0 B/768 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-t0xd1N/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
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(Reading database ... 13951 files and directories currently installed.)
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W: No sandbox user '_apt' on the system, can not drop privileges
Merged Build-Depends: debhelper (>= 9), libpopt-dev, libprotobuf-dev, libelk0-dev, libelk0, zlib1g-dev, libbz2-dev, pkg-config, protobuf-compiler, dh-autoreconf, d-shlibs
Filtered Build-Depends: debhelper (>= 9), libpopt-dev, libprotobuf-dev, libelk0-dev, libelk0, zlib1g-dev, libbz2-dev, pkg-config, protobuf-compiler, dh-autoreconf, d-shlibs
dpkg-deb: building package 'sbuild-build-depends-anfo-dummy' in '/<<BUILDDIR>>/resolver-7mTTd2/apt_archive/sbuild-build-depends-anfo-dummy.deb'.
Warning: apt-key output should not be parsed (stdout is not a terminal)
OK
Get:1 file:/<<BUILDDIR>>/resolver-7mTTd2/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-7mTTd2/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-7mTTd2/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-7mTTd2/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-7mTTd2/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-7mTTd2/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-7mTTd2/apt_archive ./ Sources [253 B]
Get:5 file:/<<BUILDDIR>>/resolver-7mTTd2/apt_archive ./ Packages [573 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-7mTTd2/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
Reading package lists...
+------------------------------------------------------------------------------+
| Install anfo build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils d-shlibs debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3 libelfg0
libelfg0-dev libelk0 libelk0-dev libffi6 libfile-stripnondeterminism-perl
libglib2.0-0 libice-dev libice6 libicu57 libmagic-mgc libmagic1 libpipeline1
libpopt-dev libpopt0 libprotobuf-dev libprotobuf-lite10 libprotobuf10
libprotoc10 libpthread-stubs0-dev libsigsegv2 libsm-dev libsm6
libtimedate-perl libtool libunistring0 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-input-dev x11proto-kb-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
libice-doc libsm-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
libxcb-doc libxext-doc libxt-doc less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur bzip2-doc libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libx11-doc xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils d-shlibs debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3 libelfg0
libelfg0-dev libelk0 libelk0-dev libffi6 libfile-stripnondeterminism-perl
libglib2.0-0 libice-dev libice6 libicu57 libmagic-mgc libmagic1 libpipeline1
libpopt-dev libpopt0 libprotobuf-dev libprotobuf-lite10 libprotobuf10
libprotoc10 libpthread-stubs0-dev libsigsegv2 libsm-dev libsm6
libtimedate-perl libtool libunistring0 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-input-dev x11proto-kb-dev x11proto-xext-dev xorg-sgml-doctools
xtrans-dev zlib1g-dev
0 upgraded, 75 newly installed, 0 to remove and 25 not upgraded.
Need to get 26.6 MB/26.7 MB of archives.
After this operation, 92.7 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-7mTTd2/apt_archive ./ sbuild-build-depends-anfo-dummy 0.invalid.0 [832 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libelfg0 armhf 0.8.13-5 [55.7 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libxdmcp6 armhf 1:1.1.2-1.1 [24.9 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libxcb1 armhf 1.11.1-1.1 [41.3 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libx11-data all 2:1.6.3-1 [128 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.28-4 [210 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-4 [104 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-4 [62.7 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-3 [7408 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-1+b1 [803 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf d-shlibs all 0.75 [18.0 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.1-3 [2547 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.023-2 [13.4 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.023-2 [8202 B]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160814 [800 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libbz2-dev armhf 1.0.6-8 [27.8 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libelfg0-dev armhf 0.8.13-5 [63.2 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf x11-common all 1:7.7+16 [251 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libice6 armhf 2:1.0.9-1+b1 [51.9 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libsm6 armhf 2:1.2.2-1+b1 [31.2 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libxt6 armhf 1:1.1.5-1 [155 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libxmu6 armhf 2:1.1.2-2 [52.0 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libelk0 armhf 3.99.8-2.1 [194 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf x11proto-core-dev all 7.0.29-1 [728 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libxau-dev armhf 1:1.0.8-1 [23.0 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libxdmcp-dev armhf 1:1.1.2-1.1 [40.8 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf x11proto-input-dev all 2.3.2-1 [158 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf x11proto-kb-dev all 1.0.7-1 [233 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf xtrans-dev all 1.3.5-1 [100 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libpthread-stubs0-dev armhf 0.3-4 [4042 B]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libxcb1-dev armhf 1.11.1-1.1 [76.2 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libx11-dev armhf 2:1.6.3-1 [749 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf x11proto-xext-dev all 7.3.0-1 [212 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libxext-dev armhf 2:1.3.3-1 [102 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libice-dev armhf 2:1.0.9-1+b1 [59.0 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libsm-dev armhf 2:1.2.2-1+b1 [33.5 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libxt-dev armhf 1:1.1.5-1 [390 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libxmu-headers all 2:1.1.2-2 [51.9 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libxmu-dev armhf 2:1.1.2-2 [56.2 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libelk0-dev armhf 3.99.8-2.1 [234 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libpopt-dev armhf 1.16-10 [47.0 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libprotobuf10 armhf 3.0.0-6 [585 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libprotobuf-lite10 armhf 3.0.0-6 [114 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libprotobuf-dev armhf 3.0.0-6 [893 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libprotoc10 armhf 3.0.0-6 [516 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf protobuf-compiler armhf 3.0.0-6 [52.1 kB]
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Processing triggers for libc-bin (2.23-4) ...
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W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.5.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26.1-1 dpkg-dev_1.18.10 g++-6_6.1.1-11+rpi1 gcc-6_6.1.1-11+rpi1 libc6-dev_2.23-4 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3~pre3 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-15 binutils_2.26.1-1 bsdmainutils_9.0.10 bsdutils_1:2.28-6 build-essential_12.2 bzip2_1.0.6-8 console-setup_1.147 console-setup-linux_1.147 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.1.1-11+rpi1 d-shlibs_0.75 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_9.20160814 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.023-2 diffutils_1:3.3-3 dmsetup_2:1.02.130-1 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.1-1 e2fsprogs_1.43.1-1 fakeroot_1.21-1 file_1:5.28-4 findutils_4.6.0+git+20160703-2 fuse2fs_1.43.1-1 g++_4:6.1.1-1 g++-6_6.1.1-11+rpi1 gcc_4:6.1.1-1 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_4.9.3-14 gcc-5-base_5.4.0-4 gcc-6_6.1.1-11+rpi1 gcc-6-base_6.1.1-11+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_1.4.20-6 gpgv_1.4.20-6 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libelk0-dev_3.99.8-2.1 libfakeroot_1.21-1 libfdisk1_2.28-6 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.023-2 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.1.1-11+rpi1 libgcc1_1:6.1.1-11+rpi1 libgcrypt20_1.7.2-2 libgdbm3_1.8.3-14 libglib2.0-0_2.48.1-3 libgmp10_2:6.1.1+dfsg-1 libgomp1_6.1.1-11+rpi1 libgpg-error0_1.24-1 libice-dev_2:1.0.9-1+b1 libice6_2:1.0.9-1+b1 libicu57_57.1-3 libidn11_1.33-1 libisl15_0.17.1-1 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 liblocale-gettext-perl_1.07-3 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmount1_2.28-6 libmpc3_1.0.3-1 libmpfr4_3.1.4-2 libncurses5_6.0+20160625-1 libncursesw5_6.0+20160625-1 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpcre3_2:8.39-1 libperl5.22_5.22.2-3 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng12-0_1.2.54-6 libpopt-dev_1.16-10 libpopt0_1.16-10 libprocps6_2:3.3.12-2 libprotobuf-dev_3.0.0-6 libprotobuf-lite10_3.0.0-6 libprotobuf10_3.0.0-6 libprotoc10_3.0.0-6 libpthread-stubs0-dev_0.3-4 libreadline6_6.3-8+b3 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsm-dev_2:1.2.2-1+b1 libsm6_2:1.2.2-1+b1 libsmartcols1_2.28-6 libss2_1.43.1-1 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 libsystemd0_230-7+b1 libtext-charwidth-perl_0.04-7+b6 libtext-iconv-perl_1.7-5+b7 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1 libtool_2.4.6-2 libubsan0_6.1.1-11+rpi1 libudev1_230-7+b1 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28-6 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libx11-dev_2:1.6.3-1 libxau-dev_1:1.0.8-1 libxau6_1:1.0.8-1 libxcb1_1.11.1-1.1 libxcb1-dev_1.11.1-1.1 libxdmcp-dev_1:1.1.2-1.1 libxdmcp6_1:1.1.2-1.1 libxext-dev_2:1.3.3-1 libxext6_2:1.3.3-1 libxml2_2.9.4+dfsg1-1+b1 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 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.07-1 mawk_1.3.3-17 mount_2.28-6 multiarch-support_2.23-4 ncurses-base_6.0+20160625-1 ncurses-bin_6.0+20160625-1 netbase_5.3 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-3 perl-base_5.22.2-3 perl-modules-5.22_5.22.2-3 pkg-config_0.29-4 po-debconf_1.0.19 procps_2:3.3.12-2 protobuf-compiler_3.0.0-6 psmisc_22.21-2.1 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-anfo-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_230-7+b1 systemd-sysv_230-7+b1 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016f-1 udev_230-7+b1 util-linux_2.28-6 x11-common_1:7.7+16 x11proto-core-dev_7.0.29-1 x11proto-input-dev_2.3.2-1 x11proto-kb-dev_1.0.7-1 x11proto-xext-dev_7.3.0-1 xkb-data_2.17-1 xorg-sgml-doctools_1:1.11-1 xtrans-dev_1.3.5-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sat Feb 8 07:45:40 2014 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./anfo_0.98-4.dsc
dpkg-source: info: extracting anfo in anfo-0.98
dpkg-source: info: unpacking anfo_0.98.orig.tar.gz
dpkg-source: info: unpacking anfo_0.98-4.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
Hack binNMU version
-------------------
Created changelog entry for binNMU version 0.98-4+b3
User Environment
----------------
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-2139fd5e-497a-47ba-8135-02b7f9c7a0c5
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package anfo
dpkg-buildpackage: info: source version 0.98-4+b3
dpkg-buildpackage: info: source distribution stretch-staging
dpkg-source --before-build anfo-0.98
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with autoreconf
dh_testdir
dh_auto_clean
dh_autoreconf_clean
dh_clean
debian/rules build-arch
dh build-arch --with autoreconf
dh_testdir -a
dh_update_autotools_config -a
dh_autoreconf -a
configure.ac:77: warning: LT_INIT was called before AM_PROG_AR
/usr/share/aclocal-1.15/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-1.15/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-1.15/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-1.15/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-1.15/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 --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 for style of include used by make... GNU
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 -j1
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
[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.)
protoc -I. -I/usr/include --cpp_out=. output.proto
[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'
/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
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
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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 /usr/include/c++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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 anfo_common.lo anfo_common.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
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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
/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 concurrent_stream.cc -fPIC -DPIC -o .libs/concurrent_stream.o
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from concurrent_stream.h:23:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from concurrent_stream.h:23:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from concurrent_stream.h:23:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from concurrent_stream.h:23:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from concurrent_stream.h:23:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from concurrent_stream.h:23:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from concurrent_stream.h:23:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from concurrent_stream.h:23:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from concurrent_stream.h:23:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from concurrent_stream.h:23:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from concurrent_stream.h:23:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from concurrent_stream.h:23:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from concurrent_stream.h:23:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from concurrent_stream.h:23:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from concurrent_stream.h:23:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from concurrent_stream.h:23:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from concurrent_stream.h:23:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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 concurrent_stream.cc -o concurrent_stream.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -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
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.cc:21:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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
/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
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
/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
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
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
misc_streams.cc: In constructor 'streams::RegionFilter::RegionFilter(const std::pair<std::basic_istream<char>*, std::__cxx11::basic_string<char> >&)':
misc_streams.cc:489:2: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
auto_ptr< istream > deffile( p.first ) ;
^~~~~~~~
In file included from /usr/include/c++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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 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
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.cc:21:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.cc:21:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.cc:21:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.cc:21:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.cc:21:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from output_streams.cc:21:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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 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:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from sequence.cc:23:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from sequence.cc:23:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from sequence.cc:23:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from sequence.cc:23:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from sequence.cc:23:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from sequence.cc:23:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from sequence.cc:23:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from sequence.cc:23:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from sequence.cc:23:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from sequence.cc:23:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from sequence.cc:23:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from sequence.cc:23:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from sequence.cc:23:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from sequence.cc:23:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from sequence.cc:23:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from sequence.cc:23:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from sequence.cc:23:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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 sequence.cc -o sequence.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 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.cc:21:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.cc:21:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.cc:21:0:
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:21:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.cc:21:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.cc:21:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from misc_streams.h:4:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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
/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 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
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-elk.cc:28:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-elk.cc:31:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-elk.cc:31:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-elk.cc:31:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-elk.cc:31:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-elk.cc:31:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-elk.cc:31:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: 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-elk.cc -o anfo-elk.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -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
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 config.pb.cc -o config.pb.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.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 output.pb.cc -fPIC -DPIC -o .libs/output.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 -o output.pb.o >/dev/null 2>&1
/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 -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/6/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/6/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 /usr/lib/arm-linux-gnueabihf/libpopt.so -L/usr/lib/gcc/arm-linux-gnueabihf/6 -L/usr/lib/gcc/arm-linux-gnueabihf/6/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/6/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/6/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/6/../../../arm-linux-gnueabihf/crtn.o -pthread -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -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" )
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=link g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o fa2dna fa2dna.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 -o .libs/fa2dna fa2dna.o -pthread ./.libs/libanfo.so -lprotobuf -lpthread -lelk -lbz2 -lz /usr/lib/arm-linux-gnueabihf/libpopt.so -pthread
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
/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 -o dnaindex dnaindex.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 -o .libs/dnaindex dnaindex.o -pthread ./.libs/libanfo.so -lprotobuf -lpthread -lelk -lbz2 -lz /usr/lib/arm-linux-gnueabihf/libpopt.so -pthread
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:21:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-tool.cc:21:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-tool.cc:21:0:
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:21:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-tool.cc:21:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-tool.cc:21:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ducttape.h:21:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-tool.cc:22:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-tool.cc:24:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-tool.cc:24:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-tool.cc:24:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-tool.cc:24:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-tool.cc:24:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from anfo-tool.cc:24:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
/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 -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 -o .libs/anfo-tool anfo-tool.o -pthread ./.libs/libanfo.so -lprotobuf -lpthread -lelk -lbz2 -lz /usr/lib/arm-linux-gnueabihf/libpopt.so -pthread
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 stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from align.h:22:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
/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 -o anfo anfo.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 -o .libs/anfo anfo.o -pthread ./.libs/libanfo.so -lprotobuf -lpthread -lelk -lbz2 -lz /usr/lib/arm-linux-gnueabihf/libpopt.so -pthread
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:27:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:27:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:27:0:
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:27:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:27:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:27:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:30:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:30:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:30:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:30:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:30:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:30:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:30:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:30:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:30:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:30:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:30:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:30:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:30:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:30:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:30:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:30:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from index-test.cc:30:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
/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 -o index-test index-test.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 -o .libs/index-test index-test.o -pthread ./.libs/libanfo.so -lprotobuf -lpthread -lelk -lbz2 -lz /usr/lib/arm-linux-gnueabihf/libpopt.so -pthread
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 stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from stream.h:20:0,
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from file-info.cc:25:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from file-info.cc:25:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from file-info.cc:25:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from file-info.cc:25:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from file-info.cc:25:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from file-info.cc:25:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from file-info.cc:25:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from file-info.cc:25:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from file-info.cc:25:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from file-info.cc:25:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from file-info.cc:25:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from file-info.cc:25:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from file-info.cc:25:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from file-info.cc:25:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from file-info.cc:25:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from file-info.cc:25:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from file-info.cc:25:0:
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++/6/memory:81:0,
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++/6/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
/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 -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 -o .libs/file-info file-info.o -pthread ./.libs/libanfo.so -lprotobuf -lpthread -lelk -lbz2 -lz /usr/lib/arm-linux-gnueabihf/libpopt.so -pthread
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
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 -j1 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>>'
fakeroot debian/rules binary-arch
dh binary-arch --with autoreconf
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 \
--override s/libpopt0-dev/libpopt-dev/ \
--override s/libprotobuf7-dev/libprotobuf-dev/ \
--override s/libprotobuf8-dev/libprotobuf-dev/ \
--override s/libbz2-1.0-dev/libbz2-dev/ \
--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.
devlibs error: There is no package matching [libprotobuf10-dev] and noone provides it, please report bug to d-shlibs maintainer
--> zlib1g-dev package exists.
debian/rules:11: recipe for target 'override_dh_install' failed
make[1]: *** [override_dh_install] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules:8: recipe for target 'binary-arch' failed
make: *** [binary-arch] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-arch gave error exit status 2
--------------------------------------------------------------------------------
Build finished at 20160901-1649
Finished
--------
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 91236
Build-Time: 1342
Distribution: stretch-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 297
Job: anfo_0.98-4
Machine Architecture: armhf
Package: anfo
Package-Time: 1693
Source-Version: 0.98-4
Space: 91236
Status: attempted
Version: 0.98-4+b3
--------------------------------------------------------------------------------
Finished at 20160901-1649
Build needed 00:28:13, 91236k disc space