anfo →
0.98-5 →
armhf → 2016-09-22 10:52:06
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on bm-wb-04
+==============================================================================+
| anfo 0.98-5 (armhf) 22 Sep 2016 10:19 |
+==============================================================================+
Package: anfo
Version: 0.98-5
Source Version: 0.98-5
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/anfo-e2SF45/anfo-0.98' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/anfo-e2SF45' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-e523f992-5dc0-4a63-a4d7-12dd4541bcce' 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 [9299 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.2 MB]
Fetched 20.5 MB in 23s (885 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'anfo' packaging is maintained in the '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 0.98-5 (dsc) [2166 B]
Get:2 http://172.17.0.1/private stretch-staging/main anfo 0.98-5 (tar) [462 kB]
Get:3 http://172.17.0.1/private stretch-staging/main anfo 0.98-5 (diff) [7552 B]
Fetched 472 kB in 0s (6037 kB/s)
Download complete and in download only mode
Check architectures
-------------------
Check dependencies
------------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-pbPoQZ/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-pbPoQZ/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-pbPoQZ/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-pbPoQZ/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-pbPoQZ/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-pbPoQZ/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-pbPoQZ/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-pbPoQZ/apt_archive ./ Sources [214 B]
Get:5 file:/<<BUILDDIR>>/resolver-pbPoQZ/apt_archive ./ Packages [528 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-pbPoQZ/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 36 not upgraded.
Need to get 0 B/764 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-pbPoQZ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [764 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 13715 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
Merged Build-Depends: debhelper (>= 9), libpopt-dev, libprotobuf-dev, libelk0-dev, libelk0, zlib1g-dev, libbz2-dev, pkg-config, protobuf-compiler, dh-autoreconf, d-shlibs (>= 0.77)
Filtered Build-Depends: debhelper (>= 9), libpopt-dev, libprotobuf-dev, libelk0-dev, libelk0, zlib1g-dev, libbz2-dev, pkg-config, protobuf-compiler, dh-autoreconf, d-shlibs (>= 0.77)
dpkg-deb: building package 'sbuild-build-depends-anfo-dummy' in '/<<BUILDDIR>>/resolver-tF4jhk/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-tF4jhk/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-tF4jhk/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-tF4jhk/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-tF4jhk/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-tF4jhk/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-tF4jhk/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-tF4jhk/apt_archive ./ Sources [280 B]
Get:5 file:/<<BUILDDIR>>/resolver-tF4jhk/apt_archive ./ Packages [598 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-tF4jhk/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 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 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, 74 newly installed, 0 to remove and 36 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-tF4jhk/apt_archive ./ sbuild-build-depends-anfo-dummy 0.invalid.0 [834 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf libpopt0 armhf 1.16-10 [46.2 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libelfg0 armhf 0.8.13-5 [55.7 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libxdmcp6 armhf 1:1.1.2-1.1 [24.9 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libxcb1 armhf 1.11.1-1.1 [41.3 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libx11-data all 2:1.6.3-1 [128 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.28-4 [210 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-4 [104 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-4 [62.7 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-4 [7407 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2 [805 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf d-shlibs all 0.77 [18.8 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.49.6-1 [2518 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10 [823 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 3.0.0-7 [585 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libprotobuf-lite10 armhf 3.0.0-7 [114 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libprotobuf-dev armhf 3.0.0-7 [894 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libprotoc10 armhf 3.0.0-7 [517 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf protobuf-compiler armhf 3.0.0-7 [52.2 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 26.6 MB in 3s (7743 kB/s)
Selecting previously unselected package libpopt0:armhf.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 13715 files and directories currently installed.)
Preparing to unpack .../libpopt0_1.16-10_armhf.deb ...
Unpacking libpopt0:armhf (1.16-10) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../groff-base_1.22.3-8_armhf.deb ...
Unpacking groff-base (1.22.3-8) ...
Selecting previously unselected package libbsd0:armhf.
Preparing to unpack .../libbsd0_0.8.3-1_armhf.deb ...
Unpacking libbsd0:armhf (0.8.3-1) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../bsdmainutils_9.0.10_armhf.deb ...
Unpacking bsdmainutils (9.0.10) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../libpipeline1_1.4.1-2_armhf.deb ...
Unpacking libpipeline1:armhf (1.4.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../man-db_2.7.5-1_armhf.deb ...
Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package libelfg0:armhf.
Preparing to unpack .../libelfg0_0.8.13-5_armhf.deb ...
Unpacking libelfg0:armhf (0.8.13-5) ...
Selecting previously unselected package libxau6:armhf.
Preparing to unpack .../libxau6_1%3a1.0.8-1_armhf.deb ...
Unpacking libxau6:armhf (1:1.0.8-1) ...
Selecting previously unselected package libxdmcp6:armhf.
Preparing to unpack .../libxdmcp6_1%3a1.1.2-1.1_armhf.deb ...
Unpacking libxdmcp6:armhf (1:1.1.2-1.1) ...
Selecting previously unselected package libxcb1:armhf.
Preparing to unpack .../libxcb1_1.11.1-1.1_armhf.deb ...
Unpacking libxcb1:armhf (1.11.1-1.1) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../libx11-data_2%3a1.6.3-1_all.deb ...
Unpacking libx11-data (2:1.6.3-1) ...
Selecting previously unselected package libx11-6:armhf.
Preparing to unpack .../libx11-6_2%3a1.6.3-1_armhf.deb ...
Unpacking libx11-6:armhf (2:1.6.3-1) ...
Selecting previously unselected package libxext6:armhf.
Preparing to unpack .../libxext6_2%3a1.3.3-1_armhf.deb ...
Unpacking libxext6:armhf (2:1.3.3-1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../libmagic-mgc_1%3a5.28-4_armhf.deb ...
Unpacking libmagic-mgc (1:5.28-4) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../libmagic1_1%3a5.28-4_armhf.deb ...
Unpacking libmagic1:armhf (1:5.28-4) ...
Selecting previously unselected package file.
Preparing to unpack .../file_1%3a5.28-4_armhf.deb ...
Unpacking file (1:5.28-4) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.8.1-1_armhf.deb ...
Unpacking gettext-base (0.19.8.1-1) ...
Selecting previously unselected package libicu57:armhf.
Preparing to unpack .../libicu57_57.1-4_armhf.deb ...
Unpacking libicu57:armhf (57.1-4) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../libxml2_2.9.4+dfsg1-2_armhf.deb ...
Unpacking libxml2:armhf (2.9.4+dfsg1-2) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../libsigsegv2_2.10-5_armhf.deb ...
Unpacking libsigsegv2:armhf (2.10-5) ...
Selecting previously unselected package m4.
Preparing to unpack .../archives/m4_1.4.17-5_armhf.deb ...
Unpacking m4 (1.4.17-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../autoconf_2.69-10_all.deb ...
Unpacking autoconf (2.69-10) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../autotools-dev_20160430.1_all.deb ...
Unpacking autotools-dev (20160430.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../automake_1%3a1.15-4_all.deb ...
Unpacking automake (1:1.15-4) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../autopoint_0.19.8.1-1_all.deb ...
Unpacking autopoint (0.19.8.1-1) ...
Selecting previously unselected package d-shlibs.
Preparing to unpack .../archives/d-shlibs_0.77_all.deb ...
Unpacking d-shlibs (0.77) ...
Selecting previously unselected package libtool.
Preparing to unpack .../libtool_2.4.6-2_all.deb ...
Unpacking libtool (2.4.6-2) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../dh-autoreconf_12_all.deb ...
Unpacking dh-autoreconf (12) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../libarchive-zip-perl_1.59-1_all.deb ...
Unpacking libarchive-zip-perl (1.59-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../libfile-stripnondeterminism-perl_0.028-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (0.028-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../dh-strip-nondeterminism_0.028-1_all.deb ...
Unpacking dh-strip-nondeterminism (0.028-1) ...
Selecting previously unselected package libffi6:armhf.
Preparing to unpack .../libffi6_3.2.1-4_armhf.deb ...
Unpacking libffi6:armhf (3.2.1-4) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../libglib2.0-0_2.49.6-1_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.49.6-1) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../libcroco3_0.6.11-1_armhf.deb ...
Unpacking libcroco3:armhf (0.6.11-1) ...
Selecting previously unselected package libunistring0:armhf.
Preparing to unpack .../libunistring0_0.9.6+really0.9.3-0.1_armhf.deb ...
Unpacking libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../gettext_0.19.8.1-1_armhf.deb ...
Unpacking gettext (0.19.8.1-1) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.4) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../po-debconf_1.0.19_all.deb ...
Unpacking po-debconf (1.0.19) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../archives/debhelper_10_all.deb ...
Unpacking debhelper (10) ...
Selecting previously unselected package libbz2-dev:armhf.
Preparing to unpack .../libbz2-dev_1.0.6-8_armhf.deb ...
Unpacking libbz2-dev:armhf (1.0.6-8) ...
Selecting previously unselected package libelfg0-dev.
Preparing to unpack .../libelfg0-dev_0.8.13-5_armhf.deb ...
Unpacking libelfg0-dev (0.8.13-5) ...
Selecting previously unselected package x11-common.
Preparing to unpack .../x11-common_1%3a7.7+16_all.deb ...
Unpacking x11-common (1:7.7+16) ...
Selecting previously unselected package libice6:armhf.
Preparing to unpack .../libice6_2%3a1.0.9-1+b1_armhf.deb ...
Unpacking libice6:armhf (2:1.0.9-1+b1) ...
Selecting previously unselected package libsm6:armhf.
Preparing to unpack .../libsm6_2%3a1.2.2-1+b1_armhf.deb ...
Unpacking libsm6:armhf (2:1.2.2-1+b1) ...
Selecting previously unselected package libxt6:armhf.
Preparing to unpack .../libxt6_1%3a1.1.5-1_armhf.deb ...
Unpacking libxt6:armhf (1:1.1.5-1) ...
Selecting previously unselected package libxmu6:armhf.
Preparing to unpack .../libxmu6_2%3a1.1.2-2_armhf.deb ...
Unpacking libxmu6:armhf (2:1.1.2-2) ...
Selecting previously unselected package libelk0.
Preparing to unpack .../libelk0_3.99.8-2.1_armhf.deb ...
Unpacking libelk0 (3.99.8-2.1) ...
Selecting previously unselected package xorg-sgml-doctools.
Preparing to unpack .../xorg-sgml-doctools_1%3a1.11-1_all.deb ...
Unpacking xorg-sgml-doctools (1:1.11-1) ...
Selecting previously unselected package x11proto-core-dev.
Preparing to unpack .../x11proto-core-dev_7.0.29-1_all.deb ...
Unpacking x11proto-core-dev (7.0.29-1) ...
Selecting previously unselected package libxau-dev:armhf.
Preparing to unpack .../libxau-dev_1%3a1.0.8-1_armhf.deb ...
Unpacking libxau-dev:armhf (1:1.0.8-1) ...
Selecting previously unselected package libxdmcp-dev:armhf.
Preparing to unpack .../libxdmcp-dev_1%3a1.1.2-1.1_armhf.deb ...
Unpacking libxdmcp-dev:armhf (1:1.1.2-1.1) ...
Selecting previously unselected package x11proto-input-dev.
Preparing to unpack .../x11proto-input-dev_2.3.2-1_all.deb ...
Unpacking x11proto-input-dev (2.3.2-1) ...
Selecting previously unselected package x11proto-kb-dev.
Preparing to unpack .../x11proto-kb-dev_1.0.7-1_all.deb ...
Unpacking x11proto-kb-dev (1.0.7-1) ...
Selecting previously unselected package xtrans-dev.
Preparing to unpack .../xtrans-dev_1.3.5-1_all.deb ...
Unpacking xtrans-dev (1.3.5-1) ...
Selecting previously unselected package libpthread-stubs0-dev:armhf.
Preparing to unpack .../libpthread-stubs0-dev_0.3-4_armhf.deb ...
Unpacking libpthread-stubs0-dev:armhf (0.3-4) ...
Selecting previously unselected package libxcb1-dev:armhf.
Preparing to unpack .../libxcb1-dev_1.11.1-1.1_armhf.deb ...
Unpacking libxcb1-dev:armhf (1.11.1-1.1) ...
Selecting previously unselected package libx11-dev:armhf.
Preparing to unpack .../libx11-dev_2%3a1.6.3-1_armhf.deb ...
Unpacking libx11-dev:armhf (2:1.6.3-1) ...
Selecting previously unselected package x11proto-xext-dev.
Preparing to unpack .../x11proto-xext-dev_7.3.0-1_all.deb ...
Unpacking x11proto-xext-dev (7.3.0-1) ...
Selecting previously unselected package libxext-dev:armhf.
Preparing to unpack .../libxext-dev_2%3a1.3.3-1_armhf.deb ...
Unpacking libxext-dev:armhf (2:1.3.3-1) ...
Selecting previously unselected package libice-dev:armhf.
Preparing to unpack .../libice-dev_2%3a1.0.9-1+b1_armhf.deb ...
Unpacking libice-dev:armhf (2:1.0.9-1+b1) ...
Selecting previously unselected package libsm-dev:armhf.
Preparing to unpack .../libsm-dev_2%3a1.2.2-1+b1_armhf.deb ...
Unpacking libsm-dev:armhf (2:1.2.2-1+b1) ...
Selecting previously unselected package libxt-dev:armhf.
Preparing to unpack .../libxt-dev_1%3a1.1.5-1_armhf.deb ...
Unpacking libxt-dev:armhf (1:1.1.5-1) ...
Selecting previously unselected package libxmu-headers.
Preparing to unpack .../libxmu-headers_2%3a1.1.2-2_all.deb ...
Unpacking libxmu-headers (2:1.1.2-2) ...
Selecting previously unselected package libxmu-dev:armhf.
Preparing to unpack .../libxmu-dev_2%3a1.1.2-2_armhf.deb ...
Unpacking libxmu-dev:armhf (2:1.1.2-2) ...
Selecting previously unselected package libelk0-dev.
Preparing to unpack .../libelk0-dev_3.99.8-2.1_armhf.deb ...
Unpacking libelk0-dev (3.99.8-2.1) ...
Selecting previously unselected package libpopt-dev:armhf.
Preparing to unpack .../libpopt-dev_1.16-10_armhf.deb ...
Unpacking libpopt-dev:armhf (1.16-10) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Selecting previously unselected package libprotobuf10:armhf.
Preparing to unpack .../libprotobuf10_3.0.0-7_armhf.deb ...
Unpacking libprotobuf10:armhf (3.0.0-7) ...
Selecting previously unselected package libprotobuf-lite10:armhf.
Preparing to unpack .../libprotobuf-lite10_3.0.0-7_armhf.deb ...
Unpacking libprotobuf-lite10:armhf (3.0.0-7) ...
Selecting previously unselected package libprotobuf-dev:armhf.
Preparing to unpack .../libprotobuf-dev_3.0.0-7_armhf.deb ...
Unpacking libprotobuf-dev:armhf (3.0.0-7) ...
Selecting previously unselected package libprotoc10:armhf.
Preparing to unpack .../libprotoc10_3.0.0-7_armhf.deb ...
Unpacking libprotoc10:armhf (3.0.0-7) ...
Selecting previously unselected package pkg-config.
Preparing to unpack .../pkg-config_0.29-4_armhf.deb ...
Unpacking pkg-config (0.29-4) ...
Selecting previously unselected package protobuf-compiler.
Preparing to unpack .../protobuf-compiler_3.0.0-7_armhf.deb ...
Unpacking protobuf-compiler (3.0.0-7) ...
Selecting previously unselected package sbuild-build-depends-anfo-dummy.
Preparing to unpack .../sbuild-build-depends-anfo-dummy.deb ...
Unpacking sbuild-build-depends-anfo-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.23-4) ...
Processing triggers for systemd (230-7+b1) ...
Setting up libpopt0:armhf (1.16-10) ...
Setting up libbz2-dev:armhf (1.0.6-8) ...
Setting up libpopt-dev:armhf (1.16-10) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up libpthread-stubs0-dev:armhf (0.3-4) ...
Setting up groff-base (1.22.3-8) ...
Setting up xorg-sgml-doctools (1:1.11-1) ...
Setting up d-shlibs (0.77) ...
Setting up gettext-base (0.19.8.1-1) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up x11proto-kb-dev (1.0.7-1) ...
Setting up m4 (1.4.17-5) ...
Setting up libicu57:armhf (57.1-4) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2) ...
Setting up libmagic-mgc (1:5.28-4) ...
Setting up libmagic1:armhf (1:5.28-4) ...
Setting up libprotobuf10:armhf (3.0.0-7) ...
Setting up xtrans-dev (1.3.5-1) ...
Setting up autotools-dev (20160430.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up libffi6:armhf (3.2.1-4) ...
Setting up libxdmcp6:armhf (1:1.1.2-1.1) ...
Setting up bsdmainutils (9.0.10) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up x11-common (1:7.7+16) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
Running in chroot, ignoring request.
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libprotobuf-lite10:armhf (3.0.0-7) ...
Setting up libprotoc10:armhf (3.0.0-7) ...
Setting up libx11-data (2:1.6.3-1) ...
Setting up libxau6:armhf (1:1.0.8-1) ...
Setting up autopoint (0.19.8.1-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up libelfg0:armhf (0.8.13-5) ...
Setting up libfile-stripnondeterminism-perl (0.028-1) ...
Setting up x11proto-core-dev (7.0.29-1) ...
Setting up protobuf-compiler (3.0.0-7) ...
Setting up libglib2.0-0:armhf (2.49.6-1) ...
No schema files found: doing nothing.
Setting up libprotobuf-dev:armhf (3.0.0-7) ...
Setting up libxau-dev:armhf (1:1.0.8-1) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.28-4) ...
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up libelfg0-dev (0.8.13-5) ...
Setting up pkg-config (0.29-4) ...
Setting up libxdmcp-dev:armhf (1:1.1.2-1.1) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up libice6:armhf (2:1.0.9-1+b1) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxcb1:armhf (1.11.1-1.1) ...
Setting up x11proto-input-dev (2.3.2-1) ...
Setting up libtool (2.4.6-2) ...
Setting up libsm6:armhf (2:1.2.2-1+b1) ...
Setting up gettext (0.19.8.1-1) ...
Setting up libx11-6:armhf (2:1.6.3-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up x11proto-xext-dev (7.3.0-1) ...
Setting up libice-dev:armhf (2:1.0.9-1+b1) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up libxcb1-dev:armhf (1.11.1-1.1) ...
Setting up libx11-dev:armhf (2:1.6.3-1) ...
Setting up libsm-dev:armhf (2:1.2.2-1+b1) ...
Setting up libxext6:armhf (2:1.3.3-1) ...
Setting up po-debconf (1.0.19) ...
Setting up libxmu-headers (2:1.1.2-2) ...
Setting up libxmu6:armhf (2:1.1.2-2) ...
Setting up libelk0 (3.99.8-2.1) ...
Setting up libxext-dev:armhf (2:1.3.3-1) ...
Setting up libxt-dev:armhf (1:1.1.5-1) ...
Setting up libxmu-dev:armhf (2:1.1.2-2) ...
Setting up libelk0-dev (3.99.8-2.1) ...
Setting up dh-strip-nondeterminism (0.028-1) ...
Setting up debhelper (10) ...
Setting up dh-autoreconf (12) ...
Setting up sbuild-build-depends-anfo-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.23-4) ...
Processing triggers for systemd (230-7+b1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-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++-4.9-dev_4.9.3-14 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: acl_2.2.52-3 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 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.1.1-11+rpi1 d-shlibs_0.77 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 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 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 hostname_3.18 init_1.42 init-system-helpers_1.42 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10.95-4 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.3~pre3 libarchive-zip-perl_1.59-1 libasan1_4.9.3-14 libasan3_6.1.1-11+rpi1 libatomic1_6.1.1-11+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.5-1 libaudit1_1:2.6.5-1 libblkid1_2.28-6 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libbz2-dev_1.0.6-8 libc-bin_2.23-4 libc-dev-bin_2.23-4 libc6_2.23-4 libc6-dev_2.23-4 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-11+rpi1 libcomerr2_1.43.1-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-12 libdbus-1-3_1.10.8-1 libdebconfclient0_0.215 libdevmapper1.02.1_2:1.02.130-1 libdpkg-perl_1.18.10 libdrm2_2.4.70-1 libelfg0_0.8.13-5 libelfg0-dev_0.8.13-5 libelk0_3.99.8-2.1 libelk0-dev_3.99.8-2.1 libfakeroot_1.21-1 libfdisk1_2.28-6 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.028-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-4.9-dev_4.9.3-14 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_2.49.6-1 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_57.1-4 libidn11_1.33-1 libisl15_0.17.1-1 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 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 libpng12-0_1.2.54-6 libpopt-dev_1.16-10 libpopt0_1.16-10 libprocps3_2:3.3.9-9 libprocps6_2:3.3.12-2 libprotobuf-dev_3.0.0-7 libprotobuf-lite10_3.0.0-7 libprotobuf10_3.0.0-7 libprotoc10_3.0.0-7 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 libslang2_2.3.0-3 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++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 libsystemd0_230-7+b1 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+dfsg1-2 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 nano_2.6.2-1 ncurses-base_6.0+20160625-1 ncurses-bin_6.0+20160625-1 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_3.0.0-7 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 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 Mon Sep 5 07:38:54 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./anfo_0.98-5.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_0.98-5.debian.tar.xz
dpkg-source: info: applying 01-silence-narrowing-conversion.patch
dpkg-source: info: applying 02-correct-minscore-self-initialization.patch
dpkg-source: info: applying 03-include-unistd-forF_OK.patch
dpkg-source: info: applying 04-reorder-template-for-new-scope-rules.patch
dpkg-source: info: applying 05-autoreconf.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
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-e523f992-5dc0-4a63-a4d7-12dd4541bcce
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package anfo
dpkg-buildpackage: info: source version 0.98-5
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build anfo-0.98
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --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>>=. -fPIE -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 -fPIE -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>>=. -fPIE -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 -fPIE -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>>=. -fPIE -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 -fPIE -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>>=. -fPIE -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 -fPIE -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>>=. -fPIE -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 -fPIE -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>>=. -fPIE -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 -fPIE -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>>=. -fPIE -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 -fPIE -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>>=. -fPIE -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 -fPIE -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>>=. -fPIE -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 -fPIE -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>>=. -fPIE -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 -fPIE -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>>=. -fPIE -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 -fPIE -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>>=. -fPIE -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 -fPIE -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>>=. -fPIE -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 -fPIE -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>>=. -fPIE -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 -fPIE -o output.pb.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -fPIE -pie -Wl,-z,relro -Wl,-z,now -o libanfo.la -rpath /usr/lib/arm-linux-gnueabihf align.lo anfo_common.lo concurrent_stream.lo ducttape.lo index.lo misc_streams.lo output_streams.lo sequence.lo stream.lo util.lo anfo-elk.lo fastlz.lo config.pb.lo output.pb.lo -lprotobuf -pthread -lpthread -lpthread -lelk -lbz2 -lz -lpopt
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/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 -Wl,-z -Wl,now -pthread -pthread -Wl,-soname -Wl,libanfo.so.0 -o .libs/libanfo.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libanfo.so.0" && ln -s "libanfo.so.0.0.0" "libanfo.so.0")
libtool: link: (cd ".libs" && rm -f "libanfo.so" && ln -s "libanfo.so.0.0.0" "libanfo.so")
libtool: link: ar cru .libs/libanfo.a align.o anfo_common.o concurrent_stream.o ducttape.o index.o misc_streams.o output_streams.o sequence.o stream.o util.o anfo-elk.o fastlz.o config.pb.o output.pb.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libanfo.a
libtool: link: ( cd ".libs" && rm -f "libanfo.la" && ln -s "../libanfo.la" "libanfo.la" )
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -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>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z,relro -Wl,-z,now -o fa2dna fa2dna.o libanfo.la -lprotobuf -pthread -lpthread -lelk -lbz2 -lz -lpopt
libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -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>>=. -fPIE -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>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z,relro -Wl,-z,now -o dnaindex dnaindex.o libanfo.la -lprotobuf -pthread -lpthread -lelk -lbz2 -lz -lpopt
libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -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>>=. -fPIE -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>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z,relro -Wl,-z,now -o anfo-tool anfo-tool.o libanfo.la -lprotobuf -pthread -lpthread -lelk -lbz2 -lz -lpopt
libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -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>>=. -fPIE -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>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z,relro -Wl,-z,now -o anfo anfo.o libanfo.la -lprotobuf -pthread -lpthread -lelk -lbz2 -lz -lpopt
libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -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>>=. -fPIE -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>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z,relro -Wl,-z,now -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>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -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>>=. -fPIE -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>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z,relro -Wl,-z,now -o file-info file-info.o libanfo.la -lprotobuf -pthread -lpthread -lelk -lbz2 -lz -lpopt
libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z -Wl,relro -Wl,-z -Wl,now -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 \
--movedev debian/tmp/usr/include/* usr/include \
debian/tmp/usr/lib/*/libanfo.so
Library package automatic movement utility
--> libbz2-dev package exists.
--> libelk0-dev package exists.
--> libpopt-dev package exists.
--> libprotobuf-dev package exists.
--> zlib1g-dev package exists.
set -e
install -d -m 755 debian/libanfo0-dev/usr/lib/arm-linux-gnueabihf
install -d -m 755 debian/libanfo0/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.a debian/libanfo0-dev/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.la debian/libanfo0-dev/usr/lib/arm-linux-gnueabihf || true
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.so debian/libanfo0-dev/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.so.0 debian/libanfo0/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0 debian/libanfo0/usr/lib/arm-linux-gnueabihf
PKGDEV=libanfo0-dev
PKGSHL=libanfo0
install -d -m 755 debian/libanfo0-dev/usr/include
mv debian/tmp/usr/include/anfo debian/libanfo0-dev/usr/include
mv: cannot stat 'debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.la': No such file or directory
dh_install
mv debian/anfo/usr/lib/* debian/anfo/usr/lib/anfo
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installman
# delete unused manpage
find debian/anfo -name anfo-sge.1 -delete
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_fixperms
find debian/anfo -perm -5 -type f \( -name '*.scm' \) -print0 2>/dev/null | xargs -0r chmod 644
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/anfo/usr/lib/anfo/index-test debian/anfo/usr/bin/anfo-tool debian/anfo/usr/bin/fa2dna debian/anfo/usr/bin/dnaindex debian/anfo/usr/bin/anfo debian/anfo/usr/lib/anfo/file-info were not linked against libbz2.so.1.0 (they use none of the library's symbols)
dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libanfo0/usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0 found in none of the libraries
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libanfo0/usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0 was not linked against libpopt.so.0 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'anfo-dbgsym' in '../anfo-dbgsym_0.98-5_armhf.deb'.
dpkg-deb: building package 'libanfo0-dbgsym' in '../libanfo0-dbgsym_0.98-5_armhf.deb'.
dpkg-deb: building package 'libanfo0-dev' in '../libanfo0-dev_0.98-5_armhf.deb'.
dpkg-deb: building package 'anfo' in '../anfo_0.98-5_armhf.deb'.
dpkg-deb: building package 'libanfo0' in '../libanfo0_0.98-5_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../anfo_0.98-5_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build anfo-0.98
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160922-1047
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
anfo_0.98-5_armhf.changes:
--------------------------
Format: 1.8
Date: Mon, 05 Sep 2016 09:35:51 +0200
Source: anfo
Binary: anfo libanfo0 libanfo0-dev
Architecture: armhf
Version: 0.98-5
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
anfo - Short Read Aligner/Mapper from MPG
libanfo0 - Library for Short Read Aligner/Mapper from MPG
libanfo0-dev - Development files for Short Read Aligner/Mapper from MPG
Changes:
anfo (0.98-5) unstable; urgency=medium
.
* Moved debian/upstream to debian/upstream/metadata
* cme fix dpkg-control
* versioned Build-Depends: d-shlibs (>= 0.77)
* DEP5 fixes
Checksums-Sha1:
86edb6b4cb7f1848c114f01c20af3feef8c5751b 1016332 anfo-dbgsym_0.98-5_armhf.deb
fab02943ef0b47d1374822a3a6c296cb25a3d738 105590 anfo_0.98-5_armhf.deb
994c7db96e97a935b218009259116e91fdfdec7c 2402398 libanfo0-dbgsym_0.98-5_armhf.deb
4e2658b1753040d740d6830021ca20659f1ee710 327440 libanfo0-dev_0.98-5_armhf.deb
8ade22dae88bfeba4ac6731ae7a3dbc0c7a03388 234924 libanfo0_0.98-5_armhf.deb
Checksums-Sha256:
854c10592a2e7878205b8de569bf17dab80e1538589450f302b069b003214893 1016332 anfo-dbgsym_0.98-5_armhf.deb
caa31388f5992f9cb865482db175d802adf78e2d76a8d89f37e50ec3c13e79ef 105590 anfo_0.98-5_armhf.deb
f06146076e85161546237fe94dfc545af17c9518054fc268c4a890189159e541 2402398 libanfo0-dbgsym_0.98-5_armhf.deb
9fa3be5ebde0c383068aa4be420e6c70c69a59a0d7b613179b4435f9bc86115c 327440 libanfo0-dev_0.98-5_armhf.deb
b03bd220168a9b77935477dc4faae39089c589edb91e1c14d20bd63cf61c7594 234924 libanfo0_0.98-5_armhf.deb
Files:
023fc840b848abe44a00888f7190f8db 1016332 debug extra anfo-dbgsym_0.98-5_armhf.deb
5b47478c17461e847612601775d868a5 105590 science optional anfo_0.98-5_armhf.deb
c437ce106fd66dcbaac7e7496b210624 2402398 debug extra libanfo0-dbgsym_0.98-5_armhf.deb
6aa945315bb6fa85bace1e2f029ba784 327440 libdevel optional libanfo0-dev_0.98-5_armhf.deb
602de9460588e5df016f8fa9a1cc2fa6 234924 libs optional libanfo0_0.98-5_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
anfo-dbgsym_0.98-5_armhf.deb
----------------------------
new debian package, version 2.0.
size 1016332 bytes: control archive=760 bytes.
600 bytes, 13 lines control
636 bytes, 6 lines md5sums
Package: anfo-dbgsym
Source: anfo
Version: 0.98-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1096
Depends: anfo (= 0.98-5)
Section: debug
Priority: extra
Homepage: http://bioinf.eva.mpg.de/anfo/
Description: Debug symbols for anfo
Auto-Built-Package: debug-symbols
Build-Ids: 4dfd5723e5c8f460b6d8950670122206213d66f6 62578aa2dfea8dba0a2070ba030db4a6f7277b76 995127aebcd7c4a3187f995eb1e88504af95b261 9dd78acd7a5262ff411417847435609ebf2945f1 b823795319f3c62503370a593aa2a56544859559 c3c7766e1885cd7e355d01570fb293a9151cfa8e
drwxr-xr-x root/root 0 2016-09-05 07:35 ./
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/debug/.build-id/4d/
-rw-r--r-- root/root 143488 2016-09-05 07:35 ./usr/lib/debug/.build-id/4d/fd5723e5c8f460b6d8950670122206213d66f6.debug
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/debug/.build-id/62/
-rw-r--r-- root/root 127792 2016-09-05 07:35 ./usr/lib/debug/.build-id/62/578aa2dfea8dba0a2070ba030db4a6f7277b76.debug
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/debug/.build-id/99/
-rw-r--r-- root/root 400580 2016-09-05 07:35 ./usr/lib/debug/.build-id/99/5127aebcd7c4a3187f995eb1e88504af95b261.debug
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/debug/.build-id/9d/
-rw-r--r-- root/root 212500 2016-09-05 07:35 ./usr/lib/debug/.build-id/9d/d78acd7a5262ff411417847435609ebf2945f1.debug
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/debug/.build-id/b8/
-rw-r--r-- root/root 130096 2016-09-05 07:35 ./usr/lib/debug/.build-id/b8/23795319f3c62503370a593aa2a56544859559.debug
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/debug/.build-id/c3/
-rw-r--r-- root/root 89020 2016-09-05 07:35 ./usr/lib/debug/.build-id/c3/c7766e1885cd7e355d01570fb293a9151cfa8e.debug
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/share/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-09-05 07:35 ./usr/share/doc/anfo-dbgsym -> anfo
anfo_0.98-5_armhf.deb
---------------------
new debian package, version 2.0.
size 105590 bytes: control archive=1437 bytes.
867 bytes, 16 lines control
1508 bytes, 24 lines md5sums
Package: anfo
Version: 0.98-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 352
Depends: libanfo0, libbz2-1.0, libc6 (>= 2.4), libelk0, libgcc1 (>= 1:3.5), libpopt0 (>= 1.14), libprotobuf10, libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4)
Section: science
Priority: optional
Homepage: http://bioinf.eva.mpg.de/anfo/
Description: Short Read Aligner/Mapper from MPG
Anfo is a mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes
more after BLAST/BLAT. It's most useful for the alignment of sequencing reads
where the DNA sequence is somehow modified (think ancient DNA or bisulphite
treatment) and/or there is more divergence between sample and reference than
what fast mappers will handle gracefully (say the reference genome is missing
and a related species is used instead).
drwxr-xr-x root/root 0 2016-09-05 07:35 ./
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/bin/
-rwxr-xr-x root/root 34364 2016-09-05 07:35 ./usr/bin/anfo
-rwxr-xr-x root/root 112716 2016-09-05 07:35 ./usr/bin/anfo-tool
-rwxr-xr-x root/root 42556 2016-09-05 07:35 ./usr/bin/dnaindex
-rwxr-xr-x root/root 30216 2016-09-05 07:35 ./usr/bin/fa2dna
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/anfo/
-rwxr-xr-x root/root 17980 2016-09-05 07:35 ./usr/lib/anfo/file-info
-rwxr-xr-x root/root 30216 2016-09-05 07:35 ./usr/lib/anfo/index-test
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/share/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/share/anfo/
-rw-r--r-- root/root 6784 2016-09-05 07:35 ./usr/share/anfo/config.proto
-rw-r--r-- root/root 14546 2016-09-05 07:35 ./usr/share/anfo/output.proto
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/share/doc/anfo/
-rw-r--r-- root/root 909 2016-09-05 06:45 ./usr/share/doc/anfo/README.Debian
-rw-r--r-- root/root 2441 2016-09-05 07:35 ./usr/share/doc/anfo/README.gz
-rw-r--r-- root/root 885 2016-09-05 07:35 ./usr/share/doc/anfo/changelog.Debian.gz
-rw-r--r-- root/root 2544 2016-09-05 06:44 ./usr/share/doc/anfo/copyright
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/share/doc/anfo/example/
-rw-r--r-- root/root 1807 2016-09-05 07:35 ./usr/share/doc/anfo/example/ancient.cfg
-rw-r--r-- root/root 2056 2016-09-05 07:35 ./usr/share/doc/anfo/example/default.cfg
-rw-r--r-- root/root 521 2016-09-05 07:35 ./usr/share/doc/anfo/example/split-anfo.scm
-rw-r--r-- root/root 567 2016-09-05 07:35 ./usr/share/doc/anfo/example/threebam.scm
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/share/elk/
-rw-r--r-- root/root 9717 2016-09-05 07:35 ./usr/share/elk/anfo.scm
-rw-r--r-- root/root 2593 2016-09-05 07:35 ./usr/share/elk/srfi-88.scm
-rw-r--r-- root/root 12138 2016-09-05 07:35 ./usr/share/elk/srfi-89.scm
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/share/man/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/share/man/man1/
-rw-r--r-- root/root 4029 2016-09-05 07:35 ./usr/share/man/man1/anfo-tool.1.gz
-rw-r--r-- root/root 1616 2016-09-05 07:35 ./usr/share/man/man1/anfo.1.gz
-rw-r--r-- root/root 1684 2016-09-05 07:35 ./usr/share/man/man1/dnaindex.1.gz
-rw-r--r-- root/root 1202 2016-09-05 07:35 ./usr/share/man/man1/fa2dna.1.gz
-rw-r--r-- root/root 634 2016-09-05 07:35 ./usr/share/man/man1/file-info.1.gz
libanfo0-dbgsym_0.98-5_armhf.deb
--------------------------------
new debian package, version 2.0.
size 2402398 bytes: control archive=485 bytes.
407 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libanfo0-dbgsym
Source: anfo
Version: 0.98-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2524
Depends: libanfo0 (= 0.98-5)
Section: debug
Priority: extra
Homepage: http://bioinf.eva.mpg.de/anfo/
Description: Debug symbols for libanfo0
Auto-Built-Package: debug-symbols
Build-Ids: fb7886c751cfccc59fc3bac9ea3ca709e4ace01d
drwxr-xr-x root/root 0 2016-09-05 07:35 ./
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/debug/.build-id/fb/
-rw-r--r-- root/root 2574192 2016-09-05 07:35 ./usr/lib/debug/.build-id/fb/7886c751cfccc59fc3bac9ea3ca709e4ace01d.debug
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/share/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-09-05 07:35 ./usr/share/doc/libanfo0-dbgsym -> libanfo0
libanfo0-dev_0.98-5_armhf.deb
-----------------------------
new debian package, version 2.0.
size 327440 bytes: control archive=1344 bytes.
1007 bytes, 22 lines control
1166 bytes, 18 lines md5sums
Package: libanfo0-dev
Source: anfo
Version: 0.98-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1773
Depends: libanfo0 (= 0.98-5), libbz2-dev, libelk0-dev, libpopt-dev, libprotobuf-dev, zlib1g-dev
Conflicts: libanfo-dev
Provides: libanfo-dev
Section: libdevel
Priority: optional
Homepage: http://bioinf.eva.mpg.de/anfo/
Description: Development files for Short Read Aligner/Mapper from MPG
Anfo is a mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes
more after BLAST/BLAT. It's most useful for the alignment of sequencing reads
where the DNA sequence is somehow modified (think ancient DNA or bisulphite
treatment) and/or there is more divergence between sample and reference than
what fast mappers will handle gracefully (say the reference genome is missing
and a related species is used instead).
.
This package contains the development files that might be used in connection
with the anfo binaries.
drwxr-xr-x root/root 0 2016-09-05 07:35 ./
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/include/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/include/anfo/
-rw-r--r-- root/root 14361 2016-09-05 07:35 ./usr/include/anfo/align.h
-rw-r--r-- root/root 2595 2016-09-05 07:35 ./usr/include/anfo/align_fwd.h
-rw-r--r-- root/root 3399 2016-09-05 07:35 ./usr/include/anfo/anfo_common.h
-rw-r--r-- root/root 11973 2016-09-05 07:35 ./usr/include/anfo/compress_stream.h
-rw-r--r-- root/root 4906 2016-09-05 07:35 ./usr/include/anfo/concurrent_stream.h
-rw-r--r-- root/root 2979 2016-09-05 07:35 ./usr/include/anfo/conffile.h
-rw-r--r-- root/root 5051 2016-09-05 07:35 ./usr/include/anfo/ducttape.h
-rw-r--r-- root/root 17630 2016-09-05 07:35 ./usr/include/anfo/index.h
-rw-r--r-- root/root 5881 2016-09-05 07:35 ./usr/include/anfo/logdom.h
-rw-r--r-- root/root 22028 2016-09-05 07:35 ./usr/include/anfo/misc_streams.h
-rw-r--r-- root/root 5942 2016-09-05 07:35 ./usr/include/anfo/output_streams.h
-rw-r--r-- root/root 14774 2016-09-05 07:35 ./usr/include/anfo/sequence.h
-rw-r--r-- root/root 30889 2016-09-05 07:35 ./usr/include/anfo/stream.h
-rw-r--r-- root/root 5292 2016-09-05 07:35 ./usr/include/anfo/trim.h
-rw-r--r-- root/root 9473 2016-09-05 07:35 ./usr/include/anfo/util.h
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 1635256 2016-09-05 07:35 ./usr/lib/arm-linux-gnueabihf/libanfo.a
lrwxrwxrwx root/root 0 2016-09-05 07:35 ./usr/lib/arm-linux-gnueabihf/libanfo.so -> libanfo.so.0.0.0
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/share/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/share/doc/libanfo0-dev/
-rw-r--r-- root/root 885 2016-09-05 07:35 ./usr/share/doc/libanfo0-dev/changelog.Debian.gz
-rw-r--r-- root/root 2544 2016-09-05 06:44 ./usr/share/doc/libanfo0-dev/copyright
libanfo0_0.98-5_armhf.deb
-------------------------
new debian package, version 2.0.
size 234924 bytes: control archive=987 bytes.
952 bytes, 19 lines control
223 bytes, 3 lines md5sums
19 bytes, 1 lines shlibs
60 bytes, 2 lines triggers
Package: libanfo0
Source: anfo
Version: 0.98-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 781
Depends: libbz2-1.0, libc6 (>= 2.4), libelk0, libgcc1 (>= 1:3.5), libpopt0 (>= 1.14), libprotobuf10, libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.0)
Section: libs
Priority: optional
Homepage: http://bioinf.eva.mpg.de/anfo/
Description: Library for Short Read Aligner/Mapper from MPG
Anfo is a mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes
more after BLAST/BLAT. It's most useful for the alignment of sequencing reads
where the DNA sequence is somehow modified (think ancient DNA or bisulphite
treatment) and/or there is more divergence between sample and reference than
what fast mappers will handle gracefully (say the reference genome is missing
and a related species is used instead).
.
This package contains the dynamic library for the anfo binaries.
drwxr-xr-x root/root 0 2016-09-05 07:35 ./
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2016-09-05 07:35 ./usr/lib/arm-linux-gnueabihf/libanfo.so.0 -> libanfo.so.0.0.0
-rw-r--r-- root/root 783992 2016-09-05 07:35 ./usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/share/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-09-05 07:35 ./usr/share/doc/libanfo0/
-rw-r--r-- root/root 885 2016-09-05 07:35 ./usr/share/doc/libanfo0/changelog.Debian.gz
-rw-r--r-- root/root 2544 2016-09-05 06:44 ./usr/share/doc/libanfo0/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 79788
Build-Time: 1301
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 335
Job: anfo_0.98-5
Machine Architecture: armhf
Package: anfo
Package-Time: 1682
Source-Version: 0.98-5
Space: 79788
Status: successful
Version: 0.98-5
--------------------------------------------------------------------------------
Finished at 20160922-1047
Build needed 00:28:02, 79788k disc space