anfo →
0.98-7+b3 →
armhf → 2020-07-18 05:16:10
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| anfo 0.98-7+b3 (armhf) Sat, 18 Jul 2020 05:07:01 +0000 |
+==============================================================================+
Package: anfo
Version: 0.98-7+b3
Source Version: 0.98-7
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-792287f8-d237-4299-88b3-e865328a5eab' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.8 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.6 MB in 9s (2818 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'anfo' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/anfo.git
Please use:
git clone https://salsa.debian.org/med-team/anfo.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 472 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main anfo 0.98-7 (dsc) [2139 B]
Get:2 http://172.17.0.1/private bullseye-staging/main anfo 0.98-7 (tar) [462 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main anfo 0.98-7 (diff) [7556 B]
Fetched 472 kB in 0s (2309 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/anfo-OIcV4W/anfo-0.98' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/anfo-OIcV4W' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-Ot4T3Y/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-Ot4T3Y/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-Ot4T3Y/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-Ot4T3Y/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Ot4T3Y/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Ot4T3Y/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Ot4T3Y/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Ot4T3Y/apt_archive ./ Packages [430 B]
Fetched 2106 B in 0s (9658 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
bsdextrautils libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 4 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Ot4T3Y/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (62.0 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12307 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), libpopt-dev, libprotobuf-dev, libelk0-dev, libelk0, zlib1g-dev, libbz2-dev, pkg-config, protobuf-compiler, d-shlibs (>= 0.77)
Filtered Build-Depends: debhelper (>= 11~), libpopt-dev, libprotobuf-dev, libelk0-dev, libelk0, zlib1g-dev, libbz2-dev, pkg-config, protobuf-compiler, d-shlibs (>= 0.77)
dpkg-deb: building package 'sbuild-build-depends-anfo-dummy' in '/<<BUILDDIR>>/resolver-Ot4T3Y/apt_archive/sbuild-build-depends-anfo-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-anfo-dummy sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-Ot4T3Y/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Ot4T3Y/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Ot4T3Y/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Ot4T3Y/apt_archive ./ Sources [550 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Ot4T3Y/apt_archive ./ Packages [632 B]
Fetched 2515 B in 0s (11.3 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install anfo build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev d-shlibs debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3
libdebhelper-perl libelf-dev libelf1 libelk0 libelk0-dev
libfile-stripnondeterminism-perl libglib2.0-0 libice-dev libice6 libicu67
libmagic-mgc libmagic1 libpipeline1 libpopt-dev libpopt0 libprotobuf-dev
libprotobuf-lite23 libprotobuf23 libprotoc23 libpthread-stubs0-dev
libsigsegv2 libsm-dev libsm6 libsub-override-perl libtool libuchardet0
libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev
libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxml2 libxmu-dev
libxmu-headers libxmu6 libxt-dev libxt6 m4 man-db pkg-config po-debconf
protobuf-compiler sensible-utils x11-common x11proto-core-dev x11proto-dev
x11proto-xext-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libice-doc libsm-doc libtool-doc
gfortran | fortran95-compiler gcj-jdk libx11-doc libxcb-doc libxext-doc
libxt-doc m4-doc apparmor less www-browser libmail-box-perl protobuf-mode-el
Recommended packages:
curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev d-shlibs debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libbz2-dev libcroco3
libdebhelper-perl libelf-dev libelf1 libelk0 libelk0-dev
libfile-stripnondeterminism-perl libglib2.0-0 libice-dev libice6 libicu67
libmagic-mgc libmagic1 libpipeline1 libpopt-dev libpopt0 libprotobuf-dev
libprotobuf-lite23 libprotobuf23 libprotoc23 libpthread-stubs0-dev
libsigsegv2 libsm-dev libsm6 libsub-override-perl libtool libuchardet0
libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev
libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxml2 libxmu-dev
libxmu-headers libxmu6 libxt-dev libxt6 m4 man-db pkg-config po-debconf
protobuf-compiler sbuild-build-depends-anfo-dummy sensible-utils x11-common
x11proto-core-dev x11proto-dev x11proto-xext-dev xorg-sgml-doctools
xtrans-dev zlib1g-dev
0 upgraded, 75 newly installed, 0 to remove and 4 not upgraded.
Need to get 26.4 MB of archives.
After this operation, 98.9 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Ot4T3Y/apt_archive ./ sbuild-build-depends-anfo-dummy 0.invalid.0 [920 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-3 [801 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf d-shlibs all 0.93 [17.7 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2 [187 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.3-2 [1158 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-2 [8286 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5+b1 [593 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2 [1007 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-3 [28.0 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libelf-dev armhf 0.176-1.1 [69.6 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf x11-common all 1:7.7+20 [252 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libice6 armhf 2:1.0.9-2 [51.6 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.14-2 [135 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.9-2 [298 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.9-2 [692 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libxt6 armhf 1:1.1.5-1+b3 [156 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libxmu6 armhf 2:1.1.2-2+b3 [52.1 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libelk0 armhf 3.99.8-4.2+b1 [155 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf x11proto-dev all 2020.1-1 [594 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf x11proto-core-dev all 2020.1-1 [3404 B]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libxau-dev armhf 1:1.0.8-1+b2 [22.4 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf xtrans-dev all 1.4.0-1 [98.7 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libxcb1-dev armhf 1.14-2 [173 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libx11-dev armhf 2:1.6.9-2 [766 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf x11proto-xext-dev all 2020.1-1 [3404 B]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libxext-dev armhf 2:1.3.3-1+b2 [102 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libice-dev armhf 2:1.0.9-2 [58.8 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libsm-dev armhf 2:1.2.3-1 [35.4 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libxt-dev armhf 1:1.1.5-1+b3 [390 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libxmu-headers all 2:1.1.2-2 [51.9 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libxmu-dev armhf 2:1.1.2-2+b3 [56.5 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libelk0-dev armhf 3.99.8-4.2+b1 [177 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libpopt0 armhf 1.18-1 [46.8 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libpopt-dev armhf 1.18-1 [51.4 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libprotobuf23 armhf 3.12.3-2 [762 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libprotobuf-lite23 armhf 3.12.3-2 [211 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libprotobuf-dev armhf 3.12.3-2 [1135 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libprotoc23 armhf 3.12.3-2 [677 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf protobuf-compiler armhf 3.12.3-2 [75.0 kB]
debconf: delaying package configuration, since apt-utils is not installed
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W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.34-8+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-14+rpi1 gcc-9_9.3.0-14+rpi1 libc6-dev_2.30-8+rpi1 libstdc++-9-dev_9.3.0-14+rpi1 libstdc++6_10.1.0-4+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.1.6 autoconf_2.69-11.1 automake_1:1.16.2-3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-8+rpi1 binutils-arm-linux-gnueabihf_2.34-8+rpi1 binutils-common_2.34-8+rpi1 bsdextrautils_2.35.2-6 bsdutils_1:2.35.2-6 build-essential_12.8 bzip2_1.0.8-3 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-14+rpi1 d-shlibs_0.93 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dmsetup_2:1.02.167-1+b2 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.2-6 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-14+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-4+rpi1 gcc-9_9.3.0-14+rpi1 gcc-9-base_9.3.0-14+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 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libelf-dev_0.176-1.1 libelf1_0.176-1.1 libelk0_3.99.8-4.2+b1 libelk0-dev_3.99.8-4.2+b1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.35.2-6 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-9-dev_9.3.0-14+rpi1 libgcc-s1_10.1.0-4+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.3-2 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2 libgomp1_10.1.0-4+rpi1 libgpg-error0_1.38-2 libhogweed5_3.5.1+really3.5.1-2 libice-dev_2:1.0.9-2 libice6_2:1.0.9-2 libicu67_67.1-2 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libjson-c4_0.13.1+dfsg-9 libksba8_1.4.0-2 libldap-2.4-2_2.4.50+dfsg-1 libldap-common_2.4.50+dfsg-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.2-6 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-2 libp11-kit0_0.23.20-1 libpam-cap_1:2.36-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2 libpopt-dev_1.18-1 libpopt0_1.18-1 libprotobuf-dev_3.12.3-2 libprotobuf-lite23_3.12.3-2 libprotobuf23_3.12.3-2 libprotoc23_3.12.3-2 libpthread-stubs0-dev_0.4-1 libreadline7_7.0-5 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsm-dev_2:1.2.3-1 libsm6_2:1.2.3-1 libsmartcols1_2.35.2-6 libsqlite3-0_3.32.3-1 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-14+rpi1 libstdc++6_10.1.0-4+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.6-2+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_245.6-2+rpi1 libunistring2_0.9.10-4 libuuid1_2.35.2-6 libx11-6_2:1.6.9-2 libx11-data_2:1.6.9-2 libx11-dev_2:1.6.9-2 libxau-dev_1:1.0.8-1+b2 libxau6_1:1.0.8-1+b2 libxcb1_1.14-2 libxcb1-dev_1.14-2 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext-dev_2:1.3.3-1+b2 libxext6_2:1.3.3-1+b2 libxml2_2.9.10+dfsg-5+b1 libxmu-dev_2:1.1.2-2+b3 libxmu-headers_2:1.1.2-2 libxmu6_2:1.1.2-2+b3 libxt-dev_1:1.1.5-1+b3 libxt6_1:1.1.5-1+b3 libzstd1_1.4.5+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.35.2-6 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21 protobuf-compiler_3.12.3-2 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-anfo-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.35.2-6 x11-common_1:7.7+20 x11proto-core-dev_2020.1-1 x11proto-dev_2020.1-1 x11proto-xext-dev_2020.1-1 xorg-sgml-doctools_1:1.11-1 xtrans-dev_1.4.0-1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Oct 15 14:55:48 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./anfo_0.98-7.dsc
dpkg-source: info: extracting anfo in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking anfo_0.98.orig.tar.gz
dpkg-source: info: unpacking anfo_0.98-7.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 01-silence-narrowing-conversion.patch
dpkg-source: info: applying 02-correct-minscore-self-initialization.patch
dpkg-source: info: applying 03-include-unistd-forF_OK.patch
dpkg-source: info: applying 04-reorder-template-for-new-scope-rules.patch
dpkg-source: info: applying 05-autoreconf.patch
Check disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 0.98-7+b3
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-792287f8-d237-4299-88b3-e865328a5eab
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package anfo
dpkg-buildpackage: info: source version 0.98-7+b3
dpkg-buildpackage: info: source distribution bullseye-staging
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
configure.ac:77: warning: LT_INIT was called before AM_PROG_AR
/usr/share/aclocal-1.16/ar-lib.m4:13: AM_PROG_AR is expanded from...
configure.ac:77: the top level
configure.ac:77: warning: LT_INIT was called before AM_PROG_AR
/usr/share/aclocal-1.16/ar-lib.m4:13: AM_PROG_AR is expanded from...
configure.ac:77: the top level
aclocal: overwriting 'm4/libtool.m4' with '/usr/share/aclocal/libtool.m4'
aclocal: overwriting 'm4/ltoptions.m4' with '/usr/share/aclocal/ltoptions.m4'
aclocal: overwriting 'm4/ltversion.m4' with '/usr/share/aclocal/ltversion.m4'
aclocal: overwriting 'm4/lt~obsolete.m4' with '/usr/share/aclocal/lt~obsolete.m4'
aclocal: overwriting 'm4/pkg.m4' with '/usr/share/aclocal/pkg.m4'
configure.ac:77: warning: LT_INIT was called before AM_PROG_AR
/usr/share/aclocal-1.16/ar-lib.m4:13: AM_PROG_AR is expanded from...
configure.ac:77: the top level
configure.ac:77: warning: LT_INIT was called before AM_PROG_AR
aclocal.m4:70: AM_PROG_AR is expanded from...
configure.ac:77: the top level
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:77: warning: LT_INIT was called before AM_PROG_AR
/usr/share/aclocal-1.16/ar-lib.m4:13: AM_PROG_AR is expanded from...
configure.ac:77: the top level
configure.ac:77: warning: LT_INIT was called before AM_PROG_AR
/usr/share/aclocal-1.16/ar-lib.m4:13: AM_PROG_AR is expanded from...
configure.ac:77: the top level
configure.ac:77: warning: LT_INIT was called before AM_PROG_AR
aclocal.m4:70: AM_PROG_AR is expanded from...
configure.ac:77: the top level
configure.ac:77: warning: LT_INIT was called before AM_PROG_AR
aclocal.m4:70: AM_PROG_AR is expanded from...
configure.ac:77: the top level
configure.ac:77: warning: LT_INIT was called before AM_PROG_AR
aclocal.m4:70: AM_PROG_AR is expanded from...
configure.ac:77: the top level
configure.ac:77: installing './ar-lib'
configure.ac:12: installing './compile'
configure.ac:6: installing './missing'
src/Makefile.am: installing './depcomp'
dh_auto_configure -a
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking how to print strings... printf
checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : 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 >= 2.1.0... 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
checking the archiver (ar) interface... ar
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make all-recursive
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
protoc -I. -I/usr/include --cpp_out=. config.proto
protoc -I. -I/usr/include --cpp_out=. output.proto
[libprotobuf WARNING google/protobuf/compiler/parser.cc:648] No syntax specified for the proto file: output.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.)
[libprotobuf WARNING google/protobuf/compiler/parser.cc:648] No syntax specified for the proto file: config.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.)
[libprotobuf WARNING google/protobuf/compiler/parser.cc:648] No syntax specified for the proto file: config.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.)
make all-am
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fa2dna.o fa2dna.cc
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o align.lo align.cc
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo_common.lo anfo_common.cc
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o concurrent_stream.lo concurrent_stream.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c align.cc -fPIC -DPIC -o .libs/align.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c concurrent_stream.cc -fPIC -DPIC -o .libs/concurrent_stream.o
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,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
compress_stream.h: In function 'google::protobuf::io::FileOutputStream* make_output_stream(const char*)':
compress_stream.h:395:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from concurrent_stream.h:23,
from concurrent_stream.cc:1:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~
compress_stream.h:198:36: note: in C++11 destructors default to noexcept
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate]
379 | 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]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
concurrent_stream.cc: In member function 'virtual output::Result streams::ConcurrentStream::fetch_result()':
concurrent_stream.cc:178:2: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
178 | auto_ptr< Result > r( outgoing_[ next_out_++ ] ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
concurrent_stream.cc: In member function 'void streams::ConcurrentStream::dequeue(streams::Stream*)':
concurrent_stream.cc:212:2: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
212 | auto_ptr< Result > r( incoming_[ next_in_ ] ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from concurrent_stream.h:23,
from concurrent_stream.cc:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from align.cc:21:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from align.cc:21:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from align.cc:21:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~
compress_stream.h:198:36: note: in C++11 destructors default to noexcept
In file included from stream.h:20,
from align.h:22,
from align.cc:21:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from align.cc:21:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from align.cc:21:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate]
379 | 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]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo_common.cc:21:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from align.cc:21:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from align.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c align.cc -o align.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c concurrent_stream.cc -o concurrent_stream.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ducttape.lo ducttape.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c ducttape.cc -fPIC -DPIC -o .libs/ducttape.o
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from /usr/include/google/protobuf/stubs/common.h:38,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Distance = int; _Tp = Matches; _Compare = __gnu_cxx::__ops::_Iter_comp_val<compare_matches_for_heap>]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Distance = int; _Tp = Matches; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_matches_for_heap>]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /usr/include/google/protobuf/stubs/common.h:38,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<compare_match_lists>]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_match_lists>]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from /usr/include/google/protobuf/stubs/common.h:38,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Distance = int; _Tp = Matches; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_match_lists>]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /usr/include/google/protobuf/stubs/common.h:38,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo_common.cc:21:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_match_lists>]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'int combine_seeds(PreSeeds&, uint32_t, output::Seeds*)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from stream.h:20,
from ducttape.h:21,
from ducttape.cc:21:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from ducttape.h:21,
from ducttape.cc:21:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from ducttape.h:21,
from ducttape.cc:21:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~
compress_stream.h:198:36: note: in C++11 destructors default to noexcept
In file included from stream.h:20,
from ducttape.h:21,
from ducttape.cc:21:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from ducttape.h:21,
from ducttape.cc:21:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from ducttape.h:21,
from ducttape.cc:21:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate]
379 | 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]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from ducttape.cc:21:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.cc:21:
ducttape.h:139:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
139 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o 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
In file included from /usr/include/c++/9/vector:72,
from sequence.h:25,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {streams::DuctTaper::Acc}; _Tp = streams::DuctTaper::Acc; _Alloc = std::allocator<streams::DuctTaper::Acc>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<streams::DuctTaper::Acc>::iterator' {aka '__gnu_cxx::__normal_iterator<streams::DuctTaper::Acc*, std::vector<streams::DuctTaper::Acc> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_insert_rval(std::vector<_Tp, _Alloc>::const_iterator, std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = streams::DuctTaper::Acc; _Alloc = std::allocator<streams::DuctTaper::Acc>]':
/usr/include/c++/9/bits/vector.tcc:340:5: note: parameter passing for argument of type 'std::vector<streams::DuctTaper::Acc>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const streams::DuctTaper::Acc*, std::vector<streams::DuctTaper::Acc> >'} changed in GCC 7.1
340 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:356:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<streams::DuctTaper::Acc*, std::vector<streams::DuctTaper::Acc> >' changed in GCC 7.1
356 | _M_realloc_insert(begin() + __n, std::move(__v));
| ^~~~~~~~~~~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o misc_streams.lo misc_streams.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c misc_streams.cc -fPIC -DPIC -o .libs/misc_streams.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo_common.cc -o anfo_common.o >/dev/null 2>&1
In file included from /usr/include/c++/9/vector:67,
from sequence.h:25,
from align_fwd.h:5,
from ducttape.h:20,
from ducttape.cc:21:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void streams::DuctTaper::put_result_ancient(const output::Result&)':
/usr/include/c++/9/bits/stl_vector.h:1291:57: note: parameter passing for argument of type 'std::vector<streams::DuctTaper::Acc>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const streams::DuctTaper::Acc*, std::vector<streams::DuctTaper::Acc> >'} changed in GCC 7.1
1291 | { return _M_insert_rval(__position, std::move(__x)); }
| ^
/usr/include/c++/9/bits/stl_vector.h:1291:57: note: parameter passing for argument of type 'std::vector<streams::DuctTaper::Acc>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const streams::DuctTaper::Acc*, std::vector<streams::DuctTaper::Acc> >'} changed in GCC 7.1
1291 | { return _M_insert_rval(__position, std::move(__x)); }
| ^
In file included from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~
compress_stream.h:198:36: note: in C++11 destructors default to noexcept
In file included from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate]
379 | 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]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void streams::DuctTaper::put_result_recent(const output::Result&)':
/usr/include/c++/9/bits/stl_vector.h:1291:57: note: parameter passing for argument of type 'std::vector<streams::DuctTaper::Acc>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const streams::DuctTaper::Acc*, std::vector<streams::DuctTaper::Acc> >'} changed in GCC 7.1
1291 | { return _M_insert_rval(__position, std::move(__x)); }
| ^
/usr/include/c++/9/bits/stl_vector.h:1291:57: note: parameter passing for argument of type 'std::vector<streams::DuctTaper::Acc>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const streams::DuctTaper::Acc*, std::vector<streams::DuctTaper::Acc> >'} changed in GCC 7.1
1291 | { return _M_insert_rval(__position, std::move(__x)); }
| ^
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from misc_streams.cc:5:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c ducttape.cc -o ducttape.o >/dev/null 2>&1
misc_streams.cc: In constructor 'streams::RegionFilter::RegionFilter(const std::pair<std::basic_istream<char>*, std::__cxx11::basic_string<char> >&)':
misc_streams.cc:489:2: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
489 | auto_ptr< istream > deffile( p.first ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.h:20,
from misc_streams.h:4,
from misc_streams.cc:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /usr/include/google/protobuf/stubs/common.h:44,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from index.cc:21:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Matches}; _Tp = Matches; _Alloc = std::allocator<Matches>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Matches>::iterator' {aka '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'unsigned int FixedIndex::lookup1(Oligo, PreSeeds&, const FixedIndex::LookupParams&, int32_t, int*) const':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c index.cc -o index.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c misc_streams.cc -o misc_streams.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o output_streams.lo output_streams.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c output_streams.cc -fPIC -DPIC -o .libs/output_streams.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence.lo sequence.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c sequence.cc -fPIC -DPIC -o .libs/sequence.o
In file included from stream.h:20,
from output_streams.h:21,
from output_streams.cc:21:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from output_streams.h:21,
from output_streams.cc:21:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from output_streams.h:21,
from output_streams.cc:21:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~
compress_stream.h:198:36: note: in C++11 destructors default to noexcept
In file included from stream.h:20,
from output_streams.h:21,
from output_streams.cc:21:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from output_streams.h:21,
from output_streams.cc:21:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from output_streams.h:21,
from output_streams.cc:21:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate]
379 | 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]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.h:21,
from output_streams.cc:21:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.cc:21:
output_streams.h:45:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
45 | auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.cc:21:
output_streams.h:72:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
72 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.cc:21:
output_streams.h:123:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
123 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.cc:21:
output_streams.h:138:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
138 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.cc:21:
output_streams.h:149:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
149 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from output_streams.cc:21:
output_streams.h:176:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
176 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/coded_stream.h:141,
from config.pb.h:23,
from index.h:20,
from output_streams.h:20,
from output_streams.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from sequence.cc:23:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from sequence.cc:23:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from sequence.cc:23:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~
compress_stream.h:198:36: note: in C++11 destructors default to noexcept
In file included from stream.h:20,
from sequence.cc:23:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from sequence.cc:23:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from sequence.cc:23:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate]
379 | 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]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence.cc:23:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from sequence.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stream.lo stream.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c stream.cc -fPIC -DPIC -o .libs/stream.o
In file included from stream.cc:21:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.cc:21:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.cc:21:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~
compress_stream.h:198:36: note: in C++11 destructors default to noexcept
In file included from stream.cc:21:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.cc:21:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.cc:21:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate]
379 | 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]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc:81:30: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
81 | AnfoReader::AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc: In member function 'virtual void streams::ChunkedWriter::put_result(const output::Result&)':
stream.cc:344:27: warning: 'int google::protobuf::MessageLite::ByteSize() const' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations]
344 | flush_buffer( r.ByteSize() ) ;
| ^
In file included from /usr/include/google/protobuf/generated_enum_util.h:36,
from /usr/include/google/protobuf/map.h:55,
from /usr/include/google/protobuf/generated_message_table_driven.h:34,
from output.pb.h:26,
from stream.h:22,
from misc_streams.h:4,
from stream.cc:22:
/usr/include/google/protobuf/message_lite.h:420:7: note: declared here
420 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); }
| ^~~~~~~~
stream.cc: At global scope:
stream.cc:421:36: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
421 | ChunkedReader::ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) : is_( is ), name_( name )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc:1093:9: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
1093 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc:1114:29: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
1114 | StreamWithProgress( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, int64_t total )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c output_streams.cc -o output_streams.o >/dev/null 2>&1
stream.cc:1149:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
1149 | StreamHolder make_input_stream_( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, bool solexa_scores, char origin, const string& genome )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc: In function 'streams::StreamHolder streams::{anonymous}::make_input_stream_(std::auto_ptr<google::protobuf::io::ZeroCopyInputStream>, const string&, bool, char, const string&)':
stream.cc:1179:9: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
1179 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > bs( new BunzipStream( is ) ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc:1189:9: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
1189 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > zs( new InflateStream( is ) ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc: In member function 'virtual output::Header streams::UniversalReader::fetch_header()':
stream.cc:1233:9: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
1233 | std::auto_ptr< google::protobuf::io::FileInputStream > s( new google::protobuf::io::FileInputStream( fd ) ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc:1238:12: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
1238 | std::auto_ptr<google::protobuf::io::ZeroCopyInputStream>(s), name_, st.st_size ) ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
stream.cc: At global scope:
stream.cc:1378:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
1378 | BamReader::BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from stream.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c sequence.cc -o sequence.o >/dev/null 2>&1
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h: In instantiation of 'void streams::write_delimited_message(google::protobuf::io::CodedOutputStream&, int, const Msg&) [with Msg = output::Header]':
stream.h:102:25: required from 'void streams::write_delimited_message(google::protobuf::io::ZeroCopyOutputStream*, int, const Msg&) [with Msg = output::Header]'
stream.cc:322:44: required from here
stream.h:88:2: warning: 'int google::protobuf::MessageLite::ByteSize() const' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations]
88 | os.WriteVarint32( m.ByteSize() ) ;
| ^~
In file included from /usr/include/google/protobuf/generated_enum_util.h:36,
from /usr/include/google/protobuf/map.h:55,
from /usr/include/google/protobuf/generated_message_table_driven.h:34,
from output.pb.h:26,
from stream.h:22,
from misc_streams.h:4,
from stream.cc:22:
/usr/include/google/protobuf/message_lite.h:420:7: note: declared here
420 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); }
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h: In instantiation of 'void streams::write_delimited_message(google::protobuf::io::CodedOutputStream&, int, const Msg&) [with Msg = output::Footer]':
stream.h:102:25: required from 'void streams::write_delimited_message(google::protobuf::io::ZeroCopyOutputStream*, int, const Msg&) [with Msg = output::Footer]'
stream.cc:331:44: required from here
stream.h:88:2: warning: 'int google::protobuf::MessageLite::ByteSize() const' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations]
88 | os.WriteVarint32( m.ByteSize() ) ;
| ^~
In file included from /usr/include/google/protobuf/generated_enum_util.h:36,
from /usr/include/google/protobuf/map.h:55,
from /usr/include/google/protobuf/generated_message_table_driven.h:34,
from output.pb.h:26,
from stream.h:22,
from misc_streams.h:4,
from stream.cc:22:
/usr/include/google/protobuf/message_lite.h:420:7: note: declared here
420 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); }
| ^~~~~~~~
In file included from misc_streams.h:4,
from stream.cc:22:
stream.h: In instantiation of 'void streams::write_delimited_message(google::protobuf::io::CodedOutputStream&, int, const Msg&) [with Msg = output::Result]':
stream.h:102:25: required from 'void streams::write_delimited_message(google::protobuf::io::ZeroCopyOutputStream*, int, const Msg&) [with Msg = output::Result]'
stream.cc:345:44: required from here
stream.h:88:2: warning: 'int google::protobuf::MessageLite::ByteSize() const' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations]
88 | os.WriteVarint32( m.ByteSize() ) ;
| ^~
In file included from /usr/include/google/protobuf/generated_enum_util.h:36,
from /usr/include/google/protobuf/map.h:55,
from /usr/include/google/protobuf/generated_message_table_driven.h:34,
from output.pb.h:26,
from stream.h:22,
from misc_streams.h:4,
from stream.cc:22:
/usr/include/google/protobuf/message_lite.h:420:7: note: declared here
420 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); }
| ^~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo util.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c util.cc -fPIC -DPIC -o .libs/util.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c util.cc -o util.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo-elk.lo anfo-elk.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo-elk.cc -fPIC -DPIC -o .libs/anfo-elk.o
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fastlz.lo fastlz.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c fastlz.c -fPIC -DPIC -o .libs/fastlz.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c fastlz.c -o fastlz.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o config.pb.lo config.pb.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c config.pb.cc -fPIC -DPIC -o .libs/config.pb.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o output.pb.lo output.pb.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c output.pb.cc -fPIC -DPIC -o .libs/output.pb.o
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~
compress_stream.h:198:36: note: in C++11 destructors default to noexcept
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate]
379 | 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]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo-elk.cc:27:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-elk.cc:28:
ducttape.h:139:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
139 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-elk.cc:31:
output_streams.h:45:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
45 | auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-elk.cc:31:
output_streams.h:72:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
72 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-elk.cc:31:
output_streams.h:123:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
123 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-elk.cc:31:
output_streams.h:138:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
138 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-elk.cc:31:
output_streams.h:149:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
149 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-elk.cc:31:
output_streams.h:176:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
176 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-elk.cc:30:
misc_streams.h: In instantiation of 'void streams::SortingStream<Comp>::put_result(const output::Result&) [with Comp = streams::by_seqid]':
misc_streams.h:282:16: required from here
misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations]
284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from output.pb.h:31,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/google/protobuf/message.h:299:7: note: declared here
299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); }
| ^~~~~~~~~
In file included from anfo-elk.cc:30:
misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations]
284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from output.pb.h:31,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/google/protobuf/message.h:299:7: note: declared here
299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); }
| ^~~~~~~~~
In file included from anfo-elk.cc:30:
misc_streams.h: In instantiation of 'void streams::SortingStream<Comp>::put_result(const output::Result&) [with Comp = streams::by_genome_coordinate]':
misc_streams.h:282:16: required from here
misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations]
284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from output.pb.h:31,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/google/protobuf/message.h:299:7: note: declared here
299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); }
| ^~~~~~~~~
In file included from anfo-elk.cc:30:
misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations]
284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from output.pb.h:31,
from sequence.h:32,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo-elk.cc:27:
/usr/include/google/protobuf/message.h:299:7: note: declared here
299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); }
| ^~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c stream.cc -o stream.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c config.pb.cc -o config.pb.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c output.pb.cc -o output.pb.o >/dev/null 2>&1
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o dnaindex.o dnaindex.cc
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo-tool.o anfo-tool.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c anfo-elk.cc -o anfo-elk.o >/dev/null 2>&1
In file included from anfo-tool.cc:21:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:21:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:21:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~
compress_stream.h:198:36: note: in C++11 destructors default to noexcept
In file included from anfo-tool.cc:21:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:21:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:21:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate]
379 | 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]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ducttape.h:21,
from anfo-tool.cc:22:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:22:
ducttape.h:139:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
139 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:24:
output_streams.h:45:3: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
45 | auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:24:
output_streams.h:72:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
72 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:24:
output_streams.h:123:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
123 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:24:
output_streams.h:138:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
138 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:24:
output_streams.h:149:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
149 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:24:
output_streams.h:176:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
176 | std::auto_ptr< std::ostream > out_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from anfo-tool.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from anfo-tool.cc:23:
misc_streams.h: In instantiation of 'void streams::SortingStream<Comp>::put_result(const output::Result&) [with Comp = streams::by_seqid]':
misc_streams.h:282:16: required from here
misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations]
284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from output.pb.h:31,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from anfo-tool.cc:22:
/usr/include/google/protobuf/message.h:299:7: note: declared here
299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); }
| ^~~~~~~~~
In file included from anfo-tool.cc:23:
misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations]
284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from output.pb.h:31,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from anfo-tool.cc:22:
/usr/include/google/protobuf/message.h:299:7: note: declared here
299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); }
| ^~~~~~~~~
In file included from anfo-tool.cc:23:
misc_streams.h: In instantiation of 'void streams::SortingStream<Comp>::put_result(const output::Result&) [with Comp = streams::by_genome_coordinate]':
misc_streams.h:282:16: required from here
misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations]
284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from output.pb.h:31,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from anfo-tool.cc:22:
/usr/include/google/protobuf/message.h:299:7: note: declared here
299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); }
| ^~~~~~~~~
In file included from anfo-tool.cc:23:
misc_streams.h:284:59: warning: 'int google::protobuf::Message::SpaceUsed() const' is deprecated: Please use SpaceUsedLong() instead [-Wdeprecated-declarations]
284 | total_scratch_size_ += scratch_space_.back()->SpaceUsed() ;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from output.pb.h:31,
from sequence.h:32,
from align_fwd.h:5,
from ducttape.h:20,
from anfo-tool.cc:22:
/usr/include/google/protobuf/message.h:299:7: note: declared here
299 | int SpaceUsed() const { return internal::ToIntSize(SpaceUsedLong()); }
| ^~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o anfo.o anfo.cc
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~
compress_stream.h:198:36: note: in C++11 destructors default to noexcept
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate]
379 | 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]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from align.h:22,
from anfo_common.h:22,
from anfo.cc:21:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from align.h:20,
from anfo_common.h:22,
from anfo.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o index-test.o index-test.cc
In file included from index-test.cc:27:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:27:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:27:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~
compress_stream.h:198:36: note: in C++11 destructors default to noexcept
In file included from index-test.cc:27:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:27:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:27:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate]
379 | 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]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from index-test.cc:30:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from /usr/include/google/protobuf/stubs/common.h:38,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Distance = int; _Tp = Matches; _Compare = __gnu_cxx::__ops::_Iter_comp_val<compare_matches_for_heap>]':
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Distance = int; _Tp = Matches; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_matches_for_heap>]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o file-info.o file-info.cc
In file included from /usr/include/c++/9/algorithm:62,
from /usr/include/google/protobuf/stubs/common.h:38,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<compare_match_lists>]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_match_lists>]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from /usr/include/google/protobuf/stubs/common.h:38,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Distance = int; _Tp = Matches; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_match_lists>]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /usr/include/google/protobuf/stubs/common.h:38,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from compress_stream.h:22,
from index-test.cc:27:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<compare_match_lists>]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'int combine_seeds(PreSeeds&, uint32_t, output::Seeds*)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Matches*, std::vector<Matches> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
echo "; DO NOT EDIT THIS FILE! EDIT anfo.scm.in AND RUN MAKE INSTEAD!" > anfo.scm
sed -e "s#__LIBDIR__#/usr/lib/arm-linux-gnueabihf#g" < ./anfo.scm.in >> anfo.scm
In file included from stream.h:20,
from file-info.cc:25:
compress_stream.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
34 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from file-info.cc:25:
compress_stream.h:97:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
97 | InflateStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is ), total_( 0 )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from file-info.cc:25:
compress_stream.h: In destructor 'virtual DeflateStream::~DeflateStream()':
compress_stream.h:198:36: warning: throw will always call terminate() [-Wterminate]
198 | else if( r != Z_OK ) throw zs_.msg ;
| ^~~
compress_stream.h:198:36: note: in C++11 destructors default to noexcept
In file included from stream.h:20,
from file-info.cc:25:
compress_stream.h: At global scope:
compress_stream.h:225:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
225 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from file-info.cc:25:
compress_stream.h:278:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
278 | BunzipStream( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is ) : is_( is )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from stream.h:20,
from file-info.cc:25:
compress_stream.h: In destructor 'virtual BzipStream::~BzipStream()':
compress_stream.h:379:45: warning: throw will always call terminate() [-Wterminate]
379 | 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]
395 | std::auto_ptr< google::protobuf::io::FileOutputStream > fos(
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h: At global scope:
stream.h:319:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
319 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:323:20: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
323 | AnfoReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:345:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
345 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:385:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
385 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > zos_ ; // final output
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:387:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
387 | std::auto_ptr< google::protobuf::io::ArrayOutputStream > aos_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:414:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
414 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:416:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
416 | std::auto_ptr< google::protobuf::io::ArrayInputStream > ais_ ; // output to buffer
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:422:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
422 | ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:747:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
747 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:762:21: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
762 | FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:772:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
772 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:795:19: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
795 | SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:806:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
806 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:821:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
821 | SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:832:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
832 | std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:846:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
846 | BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from file-info.cc:25:
stream.h:880:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
880 | std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /usr/include/google/protobuf/stubs/common.h:41,
from /usr/include/google/protobuf/io/zero_copy_stream.h:113,
from sequence.h:30,
from align_fwd.h:5,
from file-info.cc:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libanfo.la -rpath /usr/lib/arm-linux-gnueabihf align.lo anfo_common.lo concurrent_stream.lo ducttape.lo index.lo misc_streams.lo output_streams.lo sequence.lo stream.lo util.lo anfo-elk.lo fastlz.lo config.pb.lo output.pb.lo -lprotobuf -lpthread -lelk -lbz2 -lz -lpopt
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/9/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/9/crtbeginS.o .libs/align.o .libs/anfo_common.o .libs/concurrent_stream.o .libs/ducttape.o .libs/index.o .libs/misc_streams.o .libs/output_streams.o .libs/sequence.o .libs/stream.o .libs/util.o .libs/anfo-elk.o .libs/fastlz.o .libs/config.pb.o .libs/output.pb.o -lprotobuf -lpthread -lelk -lbz2 -lz -lpopt -L/usr/lib/gcc/arm-linux-gnueabihf/9 -L/usr/lib/gcc/arm-linux-gnueabihf/9/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/9/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/9/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/9/../../../arm-linux-gnueabihf/crtn.o -pthread -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -Wl,-soname -Wl,libanfo.so.0 -o .libs/libanfo.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libanfo.so.0" && ln -s "libanfo.so.0.0.0" "libanfo.so.0")
libtool: link: (cd ".libs" && rm -f "libanfo.so" && ln -s "libanfo.so.0.0.0" "libanfo.so")
libtool: link: ar cr .libs/libanfo.a align.o anfo_common.o concurrent_stream.o ducttape.o index.o misc_streams.o output_streams.o sequence.o stream.o util.o anfo-elk.o fastlz.o config.pb.o output.pb.o
libtool: link: ranlib .libs/libanfo.a
libtool: link: ( cd ".libs" && rm -f "libanfo.la" && ln -s "../libanfo.la" "libanfo.la" )
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fa2dna fa2dna.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o dnaindex dnaindex.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o anfo-tool anfo-tool.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o anfo anfo.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt
libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/fa2dna fa2dna.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread
libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/anfo-tool anfo-tool.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread
libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/dnaindex dnaindex.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread
libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/anfo anfo.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o index-test index-test.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt
/bin/bash ../libtool --tag=CXX --mode=link g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o file-info file-info.o libanfo.la -lprotobuf -lelk -lbz2 -lz -lpopt
libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/index-test index-test.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread
libtool: link: g++ -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/file-info file-info.o ./.libs/libanfo.so -lprotobuf -lelk -lbz2 -lz -lpopt -pthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making all in man
make[3]: Entering directory '/<<PKGBUILDDIR>>/man'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/man'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 check VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making check in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make check-am
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Nothing to be done for 'check-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making check in man
make[2]: Entering directory '/<<PKGBUILDDIR>>/man'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/man'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
make -j1 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making install in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make install-am
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
/bin/bash ../libtool --mode=install /usr/bin/install -c libanfo.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/libanfo.so.0.0.0 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libanfo.so.0.0.0 libanfo.so.0 || { rm -f libanfo.so.0 && ln -s libanfo.so.0.0.0 libanfo.so.0; }; })
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libanfo.so.0.0.0 libanfo.so || { rm -f libanfo.so && ln -s libanfo.so.0.0.0 libanfo.so; }; })
libtool: install: /usr/bin/install -c .libs/libanfo.lai /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.la
libtool: install: /usr/bin/install -c .libs/libanfo.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.a
libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/bin/bash ../libtool --mode=install /usr/bin/install -c fa2dna dnaindex anfo-tool anfo '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/fa2dna /<<PKGBUILDDIR>>/debian/tmp/usr/bin/fa2dna
libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/dnaindex /<<PKGBUILDDIR>>/debian/tmp/usr/bin/dnaindex
libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/anfo-tool /<<PKGBUILDDIR>>/debian/tmp/usr/bin/anfo-tool
libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/anfo /<<PKGBUILDDIR>>/debian/tmp/usr/bin/anfo
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
/bin/bash ../libtool --mode=install /usr/bin/install -c index-test file-info '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/index-test /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/index-test
libtool: warning: 'libanfo.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/file-info /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/file-info
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/anfo'
/usr/bin/install -c -m 644 config.proto output.proto '/<<PKGBUILDDIR>>/debian/tmp/usr/share/anfo'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/elk'
/usr/bin/install -c srfi-88.scm srfi-89.scm '/<<PKGBUILDDIR>>/debian/tmp/usr/share/elk'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/include/anfo'
/usr/bin/install -c -m 644 align.h align_fwd.h anfo_common.h compress_stream.h concurrent_stream.h conffile.h ducttape.h index.h logdom.h misc_streams.h output_streams.h sequence.h stream.h trim.h util.h '/<<PKGBUILDDIR>>/debian/tmp/usr/include/anfo'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/elk'
/usr/bin/install -c anfo.scm '/<<PKGBUILDDIR>>/debian/tmp/usr/share/elk'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making install in man
make[2]: Entering directory '/<<PKGBUILDDIR>>/man'
make[3]: Entering directory '/<<PKGBUILDDIR>>/man'
make[3]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1'
/usr/bin/install -c -m 644 fa2dna.1 dnaindex.1 anfo-sge.1 anfo-tool.1 file-info.1 '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/man'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/man'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/anfo'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/anfo/example'
/usr/bin/install -c -m 644 example/ancient.cfg example/default.cfg example/split-anfo.scm example/threebam.scm '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/anfo/example'
/usr/bin/install -c -m 644 README '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/anfo/.'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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.
--> libprotobuf-dev package exists.
--> zlib1g-dev package exists.
set -e
install -d -m 755 debian/libanfo0-dev/usr/lib/arm-linux-gnueabihf
install -d -m 755 debian/libanfo0/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.a debian/libanfo0-dev/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.la debian/libanfo0-dev/usr/lib/arm-linux-gnueabihf || true
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.so debian/libanfo0-dev/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.so.0 debian/libanfo0/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0 debian/libanfo0/usr/lib/arm-linux-gnueabihf
PKGDEV=libanfo0-dev
PKGSHL=libanfo0
install -d -m 755 debian/libanfo0-dev/usr/include
mv debian/tmp/usr/include/anfo debian/libanfo0-dev/usr/include
mv: cannot stat 'debian/tmp/usr/lib/arm-linux-gnueabihf/libanfo.la': No such file or directory
dh_install
mv debian/anfo/usr/lib/* debian/anfo/usr/lib/anfo
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installman
# delete unused manpage
find debian/anfo -name anfo-sge.1 -delete
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_fixperms
find debian/anfo -perm -5 -type f \( -name '*.scm' \) -print0 2>/dev/null | xargs -0r chmod 644
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/anfo/usr/lib/anfo/file-info contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/anfo/usr/bin/anfo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libanfo0/usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0 found in none of the libraries
dpkg-shlibdeps: warning: debian/anfo/usr/bin/anfo-tool contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/anfo/usr/lib/anfo/index-test contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/anfo/usr/bin/fa2dna contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/anfo/usr/bin/dnaindex contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/anfo/usr/lib/anfo/file-info debian/anfo/usr/bin/anfo debian/anfo/usr/bin/anfo-tool debian/anfo/usr/lib/anfo/index-test debian/anfo/usr/bin/fa2dna debian/anfo/usr/bin/dnaindex were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'anfo' in '../anfo_0.98-7+b3_armhf.deb'.
dpkg-deb: building package 'libanfo0' in '../libanfo0_0.98-7+b3_armhf.deb'.
dpkg-deb: building package 'libanfo0-dev' in '../libanfo0-dev_0.98-7+b3_armhf.deb'.
dpkg-deb: building package 'anfo-dbgsym' in '../anfo-dbgsym_0.98-7+b3_armhf.deb'.
dpkg-deb: building package 'libanfo0-dbgsym' in '../libanfo0-dbgsym_0.98-7+b3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../anfo_0.98-7+b3_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-07-18T05:16:06Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
anfo_0.98-7+b3_armhf.changes:
-----------------------------
Format: 1.8
Date: Mon, 15 Oct 2018 15:41:57 +0200
Source: anfo (0.98-7)
Binary: anfo anfo-dbgsym libanfo0 libanfo0-dbgsym libanfo0-dev
Binary-Only: yes
Architecture: armhf
Version: 0.98-7+b3
Distribution: bullseye-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
anfo - Short Read Aligner/Mapper from MPG
libanfo0 - Library for Short Read Aligner/Mapper from MPG
libanfo0-dev - Development files for Short Read Aligner/Mapper from MPG
Changes:
anfo (0.98-7+b3) bullseye-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
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Files:
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ca0649dfaa4620bef7a2feae16aacc6c 7958 science optional anfo_0.98-7+b3_armhf.buildinfo
a3a08ab46426609d69eb12414ffcb1c6 103468 science optional anfo_0.98-7+b3_armhf.deb
8415998b29a4aff11d42a1b7623fb76a 4018300 debug optional libanfo0-dbgsym_0.98-7+b3_armhf.deb
36d50376d2f6078df61b8fc65ad1c785 315840 libdevel optional libanfo0-dev_0.98-7+b3_armhf.deb
09dbf80cf4df2caaf7284d00f983fbf9 236896 libs optional libanfo0_0.98-7+b3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
anfo-dbgsym_0.98-7+b3_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 1836692 bytes: control archive=808 bytes.
577 bytes, 12 lines control
636 bytes, 6 lines md5sums
Package: anfo-dbgsym
Source: anfo (0.98-7)
Version: 0.98-7+b3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1896
Depends: anfo (= 0.98-7+b3)
Section: debug
Priority: optional
Description: debug symbols for anfo
Build-Ids: 4531fafa9671dd712fc05fe0d1b7e3a571bd35cd 77537c070c0e0f126de6eb3f1892242f518eff91 8efd7dd822580920312cb78c2227ba7a1c56f619 a87732b212eeee342db7ff6dea1a76bf8b5d9503 f579a5d519bc3d439ceec0d1cf3fce0e94f9d8d3 f5cf546edbb3c8fa930fbe473034d17b16deda8e
drwxr-xr-x root/root 0 2018-10-15 13:41 ./
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/.build-id/45/
-rw-r--r-- root/root 343884 2018-10-15 13:41 ./usr/lib/debug/.build-id/45/31fafa9671dd712fc05fe0d1b7e3a571bd35cd.debug
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/.build-id/77/
-rw-r--r-- root/root 251684 2018-10-15 13:41 ./usr/lib/debug/.build-id/77/537c070c0e0f126de6eb3f1892242f518eff91.debug
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/.build-id/8e/
-rw-r--r-- root/root 204824 2018-10-15 13:41 ./usr/lib/debug/.build-id/8e/fd7dd822580920312cb78c2227ba7a1c56f619.debug
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/.build-id/a8/
-rw-r--r-- root/root 258432 2018-10-15 13:41 ./usr/lib/debug/.build-id/a8/7732b212eeee342db7ff6dea1a76bf8b5d9503.debug
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/.build-id/f5/
-rw-r--r-- root/root 205556 2018-10-15 13:41 ./usr/lib/debug/.build-id/f5/79a5d519bc3d439ceec0d1cf3fce0e94f9d8d3.debug
-rw-r--r-- root/root 659780 2018-10-15 13:41 ./usr/lib/debug/.build-id/f5/cf546edbb3c8fa930fbe473034d17b16deda8e.debug
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-10-15 13:41 ./usr/share/doc/anfo-dbgsym -> anfo
anfo_0.98-7+b3_armhf.deb
------------------------
new Debian package, version 2.0.
size 103468 bytes: control archive=1540 bytes.
891 bytes, 17 lines control
1587 bytes, 25 lines md5sums
Package: anfo
Source: anfo (0.98-7)
Version: 0.98-7+b3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 344
Depends: libanfo0, libc6 (>= 2.29), libelk0, libgcc-s1 (>= 3.5), libpopt0 (>= 1.14), libprotobuf23 (>= 3.12.3), libstdc++6 (>= 9), zlib1g (>= 1:1.1.4)
Section: science
Priority: optional
Homepage: http://bioinf.eva.mpg.de/anfo/
Description: Short Read Aligner/Mapper from MPG
Anfo is a mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes
more after BLAST/BLAT. It's most useful for the alignment of sequencing reads
where the DNA sequence is somehow modified (think ancient DNA or bisulphite
treatment) and/or there is more divergence between sample and reference than
what fast mappers will handle gracefully (say the reference genome is missing
and a related species is used instead).
drwxr-xr-x root/root 0 2018-10-15 13:41 ./
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/bin/
-rwxr-xr-x root/root 38408 2018-10-15 13:41 ./usr/bin/anfo
-rwxr-xr-x root/root 120328 2018-10-15 13:41 ./usr/bin/anfo-tool
-rwxr-xr-x root/root 30216 2018-10-15 13:41 ./usr/bin/dnaindex
-rwxr-xr-x root/root 26120 2018-10-15 13:41 ./usr/bin/fa2dna
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/anfo/
-rwxr-xr-x root/root 17928 2018-10-15 13:41 ./usr/lib/anfo/file-info
-rwxr-xr-x root/root 26120 2018-10-15 13:41 ./usr/lib/anfo/index-test
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/anfo/
-rw-r--r-- root/root 6784 2018-10-15 13:41 ./usr/share/anfo/config.proto
-rw-r--r-- root/root 14546 2018-10-15 13:41 ./usr/share/anfo/output.proto
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/anfo/
-rw-r--r-- root/root 909 2018-10-15 13:41 ./usr/share/doc/anfo/README.Debian
-rw-r--r-- root/root 2441 2018-10-15 13:41 ./usr/share/doc/anfo/README.gz
-rw-r--r-- root/root 219 2018-10-15 13:41 ./usr/share/doc/anfo/changelog.Debian.armhf.gz
-rw-r--r-- root/root 1006 2018-10-15 13:41 ./usr/share/doc/anfo/changelog.Debian.gz
-rw-r--r-- root/root 2550 2018-10-15 13:41 ./usr/share/doc/anfo/copyright
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/anfo/example/
-rw-r--r-- root/root 1807 2018-10-15 13:41 ./usr/share/doc/anfo/example/ancient.cfg
-rw-r--r-- root/root 2056 2018-10-15 13:41 ./usr/share/doc/anfo/example/default.cfg
-rw-r--r-- root/root 521 2018-10-15 13:41 ./usr/share/doc/anfo/example/split-anfo.scm
-rw-r--r-- root/root 567 2018-10-15 13:41 ./usr/share/doc/anfo/example/threebam.scm
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/elk/
-rw-r--r-- root/root 9717 2018-10-15 13:41 ./usr/share/elk/anfo.scm
-rw-r--r-- root/root 2593 2018-10-15 13:41 ./usr/share/elk/srfi-88.scm
-rw-r--r-- root/root 12138 2018-10-15 13:41 ./usr/share/elk/srfi-89.scm
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/man/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/man/man1/
-rw-r--r-- root/root 4029 2018-10-15 13:41 ./usr/share/man/man1/anfo-tool.1.gz
-rw-r--r-- root/root 1616 2018-10-15 13:41 ./usr/share/man/man1/anfo.1.gz
-rw-r--r-- root/root 1684 2018-10-15 13:41 ./usr/share/man/man1/dnaindex.1.gz
-rw-r--r-- root/root 1202 2018-10-15 13:41 ./usr/share/man/man1/fa2dna.1.gz
-rw-r--r-- root/root 634 2018-10-15 13:41 ./usr/share/man/man1/file-info.1.gz
libanfo0-dbgsym_0.98-7+b3_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 4018300 bytes: control archive=544 bytes.
384 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: libanfo0-dbgsym
Source: anfo (0.98-7)
Version: 0.98-7+b3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4093
Depends: libanfo0 (= 0.98-7+b3)
Section: debug
Priority: optional
Description: debug symbols for libanfo0
Build-Ids: 4495a965a28e70fb8a259f45e11bf5c305d078fd
drwxr-xr-x root/root 0 2018-10-15 13:41 ./
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/debug/.build-id/44/
-rw-r--r-- root/root 4180112 2018-10-15 13:41 ./usr/lib/debug/.build-id/44/95a965a28e70fb8a259f45e11bf5c305d078fd.debug
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-10-15 13:41 ./usr/share/doc/libanfo0-dbgsym -> libanfo0
libanfo0-dev_0.98-7+b3_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 315840 bytes: control archive=1432 bytes.
1009 bytes, 22 lines control
1253 bytes, 19 lines md5sums
Package: libanfo0-dev
Source: anfo (0.98-7)
Version: 0.98-7+b3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1761
Depends: libanfo0 (= 0.98-7+b3), libbz2-dev, libelk0-dev, libprotobuf-dev, zlib1g-dev
Conflicts: libanfo-dev
Provides: libanfo-dev
Section: libdevel
Priority: optional
Homepage: http://bioinf.eva.mpg.de/anfo/
Description: Development files for Short Read Aligner/Mapper from MPG
Anfo is a mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes
more after BLAST/BLAT. It's most useful for the alignment of sequencing reads
where the DNA sequence is somehow modified (think ancient DNA or bisulphite
treatment) and/or there is more divergence between sample and reference than
what fast mappers will handle gracefully (say the reference genome is missing
and a related species is used instead).
.
This package contains the development files that might be used in connection
with the anfo binaries.
drwxr-xr-x root/root 0 2018-10-15 13:41 ./
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/include/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/include/anfo/
-rw-r--r-- root/root 14361 2018-10-15 13:41 ./usr/include/anfo/align.h
-rw-r--r-- root/root 2595 2018-10-15 13:41 ./usr/include/anfo/align_fwd.h
-rw-r--r-- root/root 3399 2018-10-15 13:41 ./usr/include/anfo/anfo_common.h
-rw-r--r-- root/root 11973 2018-10-15 13:41 ./usr/include/anfo/compress_stream.h
-rw-r--r-- root/root 4906 2018-10-15 13:41 ./usr/include/anfo/concurrent_stream.h
-rw-r--r-- root/root 2979 2018-10-15 13:41 ./usr/include/anfo/conffile.h
-rw-r--r-- root/root 5051 2018-10-15 13:41 ./usr/include/anfo/ducttape.h
-rw-r--r-- root/root 17630 2018-10-15 13:41 ./usr/include/anfo/index.h
-rw-r--r-- root/root 5881 2018-10-15 13:41 ./usr/include/anfo/logdom.h
-rw-r--r-- root/root 22028 2018-10-15 13:41 ./usr/include/anfo/misc_streams.h
-rw-r--r-- root/root 5942 2018-10-15 13:41 ./usr/include/anfo/output_streams.h
-rw-r--r-- root/root 14774 2018-10-15 13:41 ./usr/include/anfo/sequence.h
-rw-r--r-- root/root 30889 2018-10-15 13:41 ./usr/include/anfo/stream.h
-rw-r--r-- root/root 5292 2018-10-15 13:41 ./usr/include/anfo/trim.h
-rw-r--r-- root/root 9473 2018-10-15 13:41 ./usr/include/anfo/util.h
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 1621634 2018-10-15 13:41 ./usr/lib/arm-linux-gnueabihf/libanfo.a
lrwxrwxrwx root/root 0 2018-10-15 13:41 ./usr/lib/arm-linux-gnueabihf/libanfo.so -> libanfo.so.0.0.0
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/libanfo0-dev/
-rw-r--r-- root/root 219 2018-10-15 13:41 ./usr/share/doc/libanfo0-dev/changelog.Debian.armhf.gz
-rw-r--r-- root/root 1006 2018-10-15 13:41 ./usr/share/doc/libanfo0-dev/changelog.Debian.gz
-rw-r--r-- root/root 2550 2018-10-15 13:41 ./usr/share/doc/libanfo0-dev/copyright
libanfo0_0.98-7+b3_armhf.deb
----------------------------
new Debian package, version 2.0.
size 236896 bytes: control archive=1112 bytes.
955 bytes, 19 lines control
306 bytes, 4 lines md5sums
19 bytes, 1 lines shlibs
65 bytes, 2 lines triggers
Package: libanfo0
Source: anfo (0.98-7)
Version: 0.98-7+b3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 794
Depends: libbz2-1.0, libc6 (>= 2.29), libelk0, libgcc-s1 (>= 3.5), libprotobuf23 (>= 3.12.3), libstdc++6 (>= 9), zlib1g (>= 1:1.2.0)
Section: libs
Priority: optional
Homepage: http://bioinf.eva.mpg.de/anfo/
Description: Library for Short Read Aligner/Mapper from MPG
Anfo is a mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes
more after BLAST/BLAT. It's most useful for the alignment of sequencing reads
where the DNA sequence is somehow modified (think ancient DNA or bisulphite
treatment) and/or there is more divergence between sample and reference than
what fast mappers will handle gracefully (say the reference genome is missing
and a related species is used instead).
.
This package contains the dynamic library for the anfo binaries.
drwxr-xr-x root/root 0 2018-10-15 13:41 ./
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2018-10-15 13:41 ./usr/lib/arm-linux-gnueabihf/libanfo.so.0 -> libanfo.so.0.0.0
-rw-r--r-- root/root 796612 2018-10-15 13:41 ./usr/lib/arm-linux-gnueabihf/libanfo.so.0.0.0
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-10-15 13:41 ./usr/share/doc/libanfo0/
-rw-r--r-- root/root 219 2018-10-15 13:41 ./usr/share/doc/libanfo0/changelog.Debian.armhf.gz
-rw-r--r-- root/root 1006 2018-10-15 13:41 ./usr/share/doc/libanfo0/changelog.Debian.gz
-rw-r--r-- root/root 2550 2018-10-15 13:41 ./usr/share/doc/libanfo0/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 127916
Build-Time: 189
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 340
Job: anfo_0.98-7
Machine Architecture: armhf
Package: anfo
Package-Time: 545
Source-Version: 0.98-7
Space: 127916
Status: successful
Version: 0.98-7+b3
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Finished at 2020-07-18T05:16:06Z
Build needed 00:09:05, 127916k disk space