DC-Build-Header: snap-aligner 1.0~beta.18+dfsg-2 / 2019-01-09 22:08:22 +0000
DC-Task: type:rebuild-binarch-only source:snap-aligner version:1.0~beta.18+dfsg-2 chroot:unstable esttime:109 logfile:/tmp/snap-aligner_1.0~beta.18+dfsg-2_unstable_clang7.log modes:clang7:binarch-only
DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v  --chroot-setup-commands=/tmp/clang7 snap-aligner_1.0~beta.18+dfsg-2'
sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-6-71.eu-central-1.compute.internal

+==============================================================================+
| snap-aligner 1.0~beta.18+dfsg-2 (amd64)      Wed, 09 Jan 2019 22:08:22 +0000 |
+==============================================================================+

Package: snap-aligner
Version: 1.0~beta.18+dfsg-2
Source Version: 1.0~beta.18+dfsg-2
Distribution: unstable
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-00ef5a51-b066-4a33-abe6-a5c787eed164' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Chroot Setup Commands                                                        |
+------------------------------------------------------------------------------+


/tmp/clang7
-----------

+ echo 'Entering customization script...'
Entering customization script...
+ CLANG_VERSION=7
+ echo 'Install of clang-7'
Install of clang-7
+ apt-get update
Get:1 http://127.0.0.1:9999/debian sid InRelease [238 kB]
Get:2 http://127.0.0.1:9999/debian sid/main Sources.diff/Index [27.9 kB]
Get:3 http://127.0.0.1:9999/debian sid/main amd64 Packages.diff/Index [27.9 kB]
Get:4 http://127.0.0.1:9999/debian sid/main Sources 2019-01-09-1430.36.pdiff [24.1 kB]
Get:5 http://127.0.0.1:9999/debian sid/main Sources 2019-01-09-2026.40.pdiff [16.8 kB]
Get:6 http://127.0.0.1:9999/debian sid/main amd64 Packages 2019-01-09-1430.36.pdiff [40.9 kB]
Get:7 http://127.0.0.1:9999/debian sid/main amd64 Packages 2019-01-09-2026.40.pdiff [32.0 kB]
Get:5 http://127.0.0.1:9999/debian sid/main Sources 2019-01-09-2026.40.pdiff [16.8 kB]
Get:7 http://127.0.0.1:9999/debian sid/main amd64 Packages 2019-01-09-2026.40.pdiff [32.0 kB]
Get:8 http://127.0.0.1:9999/debian sid/main Translation-en [6274 kB]
Fetched 6681 kB in 2s (3035 kB/s)
Reading package lists...
+ apt-get install --yes --no-install-recommends --force-yes clang-7 libomp-7-dev libobjc-8-dev
Reading package lists...
Building dependency tree...
The following additional packages will be installed:
  lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-7-dev libclang1-7
  libedit2 libgc1c2 libllvm7 libobjc4 libomp5-7
Suggested packages:
  clang-7-doc libomp-7-doc
Recommended packages:
  llvm-7-dev python
The following NEW packages will be installed:
  clang-7 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-7-dev
  libclang1-7 libedit2 libgc1c2 libllvm7 libobjc-8-dev libobjc4 libomp-7-dev
  libomp5-7
0 upgraded, 14 newly installed, 0 to remove and 5 not upgraded.
Need to get 34.5 MB of archives.
After this operation, 185 MB of additional disk space will be used.
Get:1 http://127.0.0.1:9999/debian sid/main amd64 libbsd0 amd64 0.9.1-1 [99.3 kB]
Get:2 http://127.0.0.1:9999/debian sid/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB]
Get:3 http://127.0.0.1:9999/debian sid/main amd64 libllvm7 amd64 1:7.0.1-4 [13.0 MB]
Get:4 http://127.0.0.1:9999/debian sid/main amd64 libgc1c2 amd64 1:7.6.4-0.4 [224 kB]
Get:5 http://127.0.0.1:9999/debian sid/main amd64 libobjc4 amd64 8.2.0-14 [50.4 kB]
Get:6 http://127.0.0.1:9999/debian sid/main amd64 libobjc-8-dev amd64 8.2.0-14 [225 kB]
Get:7 http://127.0.0.1:9999/debian sid/main amd64 libc6-i386 amd64 2.28-4 [2873 kB]
Get:8 http://127.0.0.1:9999/debian sid/main amd64 lib32gcc1 amd64 1:8.2.0-14 [47.9 kB]
Get:9 http://127.0.0.1:9999/debian sid/main amd64 lib32stdc++6 amd64 8.2.0-14 [406 kB]
Get:10 http://127.0.0.1:9999/debian sid/main amd64 libclang-common-7-dev amd64 1:7.0.1-4 [3155 kB]
Get:11 http://127.0.0.1:9999/debian sid/main amd64 libclang1-7 amd64 1:7.0.1-4 [5991 kB]
Get:12 http://127.0.0.1:9999/debian sid/main amd64 clang-7 amd64 1:7.0.1-4 [7887 kB]
Get:13 http://127.0.0.1:9999/debian sid/main amd64 libomp5-7 amd64 1:7.0.1-4 [318 kB]
Get:14 http://127.0.0.1:9999/debian sid/main amd64 libomp-7-dev amd64 1:7.0.1-4 [57.1 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 34.5 MB in 0s (115 MB/s)
Selecting previously unselected package libbsd0:amd64.
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(Reading database ... 11802 files and directories currently installed.)
Preparing to unpack .../00-libbsd0_0.9.1-1_amd64.deb ...
Unpacking libbsd0:amd64 (0.9.1-1) ...
Selecting previously unselected package libedit2:amd64.
Preparing to unpack .../01-libedit2_3.1-20181209-1_amd64.deb ...
Unpacking libedit2:amd64 (3.1-20181209-1) ...
Selecting previously unselected package libllvm7:amd64.
Preparing to unpack .../02-libllvm7_1%3a7.0.1-4_amd64.deb ...
Unpacking libllvm7:amd64 (1:7.0.1-4) ...
Selecting previously unselected package libgc1c2:amd64.
Preparing to unpack .../03-libgc1c2_1%3a7.6.4-0.4_amd64.deb ...
Unpacking libgc1c2:amd64 (1:7.6.4-0.4) ...
Selecting previously unselected package libobjc4:amd64.
Preparing to unpack .../04-libobjc4_8.2.0-14_amd64.deb ...
Unpacking libobjc4:amd64 (8.2.0-14) ...
Selecting previously unselected package libobjc-8-dev:amd64.
Preparing to unpack .../05-libobjc-8-dev_8.2.0-14_amd64.deb ...
Unpacking libobjc-8-dev:amd64 (8.2.0-14) ...
Selecting previously unselected package libc6-i386.
Preparing to unpack .../06-libc6-i386_2.28-4_amd64.deb ...
Unpacking libc6-i386 (2.28-4) ...
Selecting previously unselected package lib32gcc1.
Preparing to unpack .../07-lib32gcc1_1%3a8.2.0-14_amd64.deb ...
Unpacking lib32gcc1 (1:8.2.0-14) ...
Selecting previously unselected package lib32stdc++6.
Preparing to unpack .../08-lib32stdc++6_8.2.0-14_amd64.deb ...
Unpacking lib32stdc++6 (8.2.0-14) ...
Selecting previously unselected package libclang-common-7-dev.
Preparing to unpack .../09-libclang-common-7-dev_1%3a7.0.1-4_amd64.deb ...
Unpacking libclang-common-7-dev (1:7.0.1-4) ...
Selecting previously unselected package libclang1-7:amd64.
Preparing to unpack .../10-libclang1-7_1%3a7.0.1-4_amd64.deb ...
Unpacking libclang1-7:amd64 (1:7.0.1-4) ...
Selecting previously unselected package clang-7.
Preparing to unpack .../11-clang-7_1%3a7.0.1-4_amd64.deb ...
Unpacking clang-7 (1:7.0.1-4) ...
Selecting previously unselected package libomp5-7:amd64.
Preparing to unpack .../12-libomp5-7_1%3a7.0.1-4_amd64.deb ...
Unpacking libomp5-7:amd64 (1:7.0.1-4) ...
Selecting previously unselected package libomp-7-dev.
Preparing to unpack .../13-libomp-7-dev_1%3a7.0.1-4_amd64.deb ...
Unpacking libomp-7-dev (1:7.0.1-4) ...
Setting up libgc1c2:amd64 (1:7.6.4-0.4) ...
Setting up libc6-i386 (2.28-4) ...
Setting up libbsd0:amd64 (0.9.1-1) ...
Setting up libomp5-7:amd64 (1:7.0.1-4) ...
Processing triggers for libc-bin (2.28-4) ...
Setting up libomp-7-dev (1:7.0.1-4) ...
Setting up lib32gcc1 (1:8.2.0-14) ...
Setting up libedit2:amd64 (3.1-20181209-1) ...
Setting up libobjc4:amd64 (8.2.0-14) ...
Setting up libobjc-8-dev:amd64 (8.2.0-14) ...
Setting up libllvm7:amd64 (1:7.0.1-4) ...
Setting up libclang1-7:amd64 (1:7.0.1-4) ...
Setting up lib32stdc++6 (8.2.0-14) ...
Setting up libclang-common-7-dev (1:7.0.1-4) ...
Setting up clang-7 (1:7.0.1-4) ...
Processing triggers for libc-bin (2.28-4) ...
W: --force-yes is deprecated, use one of the options starting with --allow instead.
+ echo 'Replace gcc, g++ & cpp by clang'
Replace gcc, g++ & cpp by clang
+ VERSIONS='4.6 4.7 4.8 4.9 5 6 7 8'
+ cd /usr/bin
+ for VERSION in $VERSIONS
+ rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc
+ ln -s clang++-7 g++-4.6
+ ln -s clang-7 gcc-4.6
+ ln -s clang-7 cpp-4.6
+ ln -s clang-7 gcc
+ echo 'gcc-4.6 hold'
+ dpkg --set-selections
dpkg: warning: package not in status nor available database at line 1: gcc-4.6
dpkg: warning: found unknown packages; this might mean the available database
is outdated, and needs to be updated through a frontend method;
please see the FAQ <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ echo 'g++-4.6 hold'
+ dpkg --set-selections
dpkg: warning: package not in status nor available database at line 1: g++-4.6
dpkg: warning: found unknown packages; this might mean the available database
is outdated, and needs to be updated through a frontend method;
please see the FAQ <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ for VERSION in $VERSIONS
+ rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc
+ ln -s clang++-7 g++-4.7
+ ln -s clang-7 gcc-4.7
+ ln -s clang-7 cpp-4.7
+ ln -s clang-7 gcc
+ echo 'gcc-4.7 hold'
+ dpkg --set-selections
dpkg: warning: package not in status nor available database at line 1: gcc-4.7
dpkg: warning: found unknown packages; this might mean the available database
is outdated, and needs to be updated through a frontend method;
please see the FAQ <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ echo 'g++-4.7 hold'
+ dpkg --set-selections
dpkg: warning: package not in status nor available database at line 1: g++-4.7
dpkg: warning: found unknown packages; this might mean the available database
is outdated, and needs to be updated through a frontend method;
please see the FAQ <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ for VERSION in $VERSIONS
+ rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc
+ ln -s clang++-7 g++-4.8
+ ln -s clang-7 gcc-4.8
+ ln -s clang-7 cpp-4.8
+ ln -s clang-7 gcc
+ echo 'gcc-4.8 hold'
+ dpkg --set-selections
dpkg: warning: package not in status nor available database at line 1: gcc-4.8
dpkg: warning: found unknown packages; this might mean the available database
is outdated, and needs to be updated through a frontend method;
please see the FAQ <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ echo 'g++-4.8 hold'
+ dpkg --set-selections
dpkg: warning: package not in status nor available database at line 1: g++-4.8
dpkg: warning: found unknown packages; this might mean the available database
is outdated, and needs to be updated through a frontend method;
please see the FAQ <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ for VERSION in $VERSIONS
+ rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc
+ ln -s clang++-7 g++-4.9
+ ln -s clang-7 gcc-4.9
+ ln -s clang-7 cpp-4.9
+ ln -s clang-7 gcc
+ echo 'gcc-4.9 hold'
+ dpkg --set-selections
dpkg: warning: package not in status nor available database at line 1: gcc-4.9
dpkg: warning: found unknown packages; this might mean the available database
is outdated, and needs to be updated through a frontend method;
please see the FAQ <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ echo 'g++-4.9 hold'
+ dpkg --set-selections
dpkg: warning: package not in status nor available database at line 1: g++-4.9
dpkg: warning: found unknown packages; this might mean the available database
is outdated, and needs to be updated through a frontend method;
please see the FAQ <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ for VERSION in $VERSIONS
+ rm -f g++-5 gcc-5 cpp-5 gcc
+ ln -s clang++-7 g++-5
+ ln -s clang-7 gcc-5
+ ln -s clang-7 cpp-5
+ ln -s clang-7 gcc
+ echo 'gcc-5 hold'
+ dpkg --set-selections
dpkg: warning: package not in status nor available database at line 1: gcc-5
dpkg: warning: found unknown packages; this might mean the available database
is outdated, and needs to be updated through a frontend method;
please see the FAQ <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ echo 'g++-5 hold'
+ dpkg --set-selections
dpkg: warning: package not in status nor available database at line 1: g++-5
dpkg: warning: found unknown packages; this might mean the available database
is outdated, and needs to be updated through a frontend method;
please see the FAQ <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ for VERSION in $VERSIONS
+ rm -f g++-6 gcc-6 cpp-6 gcc
+ ln -s clang++-7 g++-6
+ ln -s clang-7 gcc-6
+ ln -s clang-7 cpp-6
+ ln -s clang-7 gcc
+ echo 'gcc-6 hold'
+ dpkg --set-selections
dpkg: warning: package not in status nor available database at line 1: gcc-6
dpkg: warning: found unknown packages; this might mean the available database
is outdated, and needs to be updated through a frontend method;
please see the FAQ <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ echo 'g++-6 hold'
+ dpkg --set-selections
dpkg: warning: package not in status nor available database at line 1: g++-6
dpkg: warning: found unknown packages; this might mean the available database
is outdated, and needs to be updated through a frontend method;
please see the FAQ <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ for VERSION in $VERSIONS
+ rm -f g++-7 gcc-7 cpp-7 gcc
+ ln -s clang++-7 g++-7
+ ln -s clang-7 gcc-7
+ ln -s clang-7 cpp-7
+ ln -s clang-7 gcc
+ echo 'gcc-7 hold'
+ dpkg --set-selections
dpkg: warning: package not in status nor available database at line 1: gcc-7
dpkg: warning: found unknown packages; this might mean the available database
is outdated, and needs to be updated through a frontend method;
please see the FAQ <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ echo 'g++-7 hold'
+ dpkg --set-selections
dpkg: warning: package not in status nor available database at line 1: g++-7
dpkg: warning: found unknown packages; this might mean the available database
is outdated, and needs to be updated through a frontend method;
please see the FAQ <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ for VERSION in $VERSIONS
+ rm -f g++-8 gcc-8 cpp-8 gcc
+ ln -s clang++-7 g++-8
+ ln -s clang-7 gcc-8
+ ln -s clang-7 cpp-8
+ ln -s clang-7 gcc
+ echo 'gcc-8 hold'
+ dpkg --set-selections
+ echo 'g++-8 hold'
+ dpkg --set-selections
+ cd -
/build/snap-aligner-5R5DHn
+ echo 'Check if gcc, g++ & cpp are actually clang'
Check if gcc, g++ & cpp are actually clang
+ gcc --version
+ grep clang
+ cpp --version
+ grep clang
+ g++ --version
+ grep clang

I: Finished running '/tmp/clang7'.

Finished processing commands.
--------------------------------------------------------------------------------

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Hit:1 http://127.0.0.1:9999/debian sid InRelease
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages will be upgraded:
  libmpfr6 libpam-modules libpam-modules-bin libpam-runtime libpam0g
5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 1519 kB of archives.
After this operation, 7168 B of additional disk space will be used.
Get:1 http://127.0.0.1:9999/debian sid/main amd64 libpam0g amd64 1.1.8-4 [124 kB]
Get:2 http://127.0.0.1:9999/debian sid/main amd64 libpam-modules-bin amd64 1.1.8-4 [106 kB]
Get:3 http://127.0.0.1:9999/debian sid/main amd64 libpam-modules amd64 1.1.8-4 [305 kB]
Get:4 http://127.0.0.1:9999/debian sid/main amd64 libpam-runtime all 1.1.8-4 [211 kB]
Get:5 http://127.0.0.1:9999/debian sid/main amd64 libmpfr6 amd64 4.0.2~rc1-1 [773 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Preparing to unpack .../libpam0g_1.1.8-4_amd64.deb ...
Unpacking libpam0g:amd64 (1.1.8-4) over (1.1.8-3.8) ...
Setting up libpam0g:amd64 (1.1.8-4) ...
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Preparing to unpack .../libpam-modules-bin_1.1.8-4_amd64.deb ...
Unpacking libpam-modules-bin (1.1.8-4) over (1.1.8-3.8) ...
Setting up libpam-modules-bin (1.1.8-4) ...
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Preparing to unpack .../libpam-modules_1.1.8-4_amd64.deb ...
Unpacking libpam-modules:amd64 (1.1.8-4) over (1.1.8-3.8) ...
Setting up libpam-modules:amd64 (1.1.8-4) ...
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Preparing to unpack .../libpam-runtime_1.1.8-4_all.deb ...
Unpacking libpam-runtime (1.1.8-4) over (1.1.8-3.8) ...
Setting up libpam-runtime (1.1.8-4) ...
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Preparing to unpack .../libmpfr6_4.0.2~rc1-1_amd64.deb ...
Unpacking libmpfr6:amd64 (4.0.2~rc1-1) over (4.0.1-2) ...
Setting up libmpfr6:amd64 (4.0.2~rc1-1) ...
Processing triggers for libc-bin (2.28-4) ...

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'snap-aligner' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/snap-aligner.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/snap-aligner.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1985 kB of source archives.
Get:1 http://127.0.0.1:9999/debian sid/main snap-aligner 1.0~beta.18+dfsg-2 (dsc) [2223 B]
Get:2 http://127.0.0.1:9999/debian sid/main snap-aligner 1.0~beta.18+dfsg-2 (tar) [1976 kB]
Get:3 http://127.0.0.1:9999/debian sid/main snap-aligner 1.0~beta.18+dfsg-2 (diff) [7276 B]
Fetched 1985 kB in 1s (2544 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/snap-aligner-5R5DHn/snap-aligner-1.0~beta.18+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/snap-aligner-5R5DHn' 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-G2GU1Z/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.
Ign:1 copy:/<<BUILDDIR>>/resolver-G2GU1Z/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-G2GU1Z/apt_archive ./ Release [957 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-G2GU1Z/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-G2GU1Z/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-G2GU1Z/apt_archive ./ Packages [432 B]
Fetched 1738 B in 0s (0 B/s)
Reading package lists...
Reading package lists...

Install core build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 856 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-G2GU1Z/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 856 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12592 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (amd64 included in amd64 arm64 mips64el ppc64el alpha kfreebsd-amd64 ppc64 sparc64)

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper (>= 10), help2man, zlib1g-dev
Filtered Build-Depends: debhelper (>= 10), help2man, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-snap-aligner-dummy' in '/<<BUILDDIR>>/resolver-G2GU1Z/apt_archive/sbuild-build-depends-snap-aligner-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-snap-aligner-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
Ign:1 copy:/<<BUILDDIR>>/resolver-G2GU1Z/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-G2GU1Z/apt_archive ./ Release [963 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-G2GU1Z/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-G2GU1Z/apt_archive ./ Sources [506 B]
Get:5 copy:/<<BUILDDIR>>/resolver-G2GU1Z/apt_archive ./ Packages [585 B]
Fetched 2054 B in 0s (0 B/s)
Reading package lists...
Reading package lists...

Install snap-aligner build dependencies (apt-based resolver)
------------------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils debhelper
  dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
  groff-base help2man intltool-debian libarchive-zip-perl libcroco3 libelf1
  libfile-stripnondeterminism-perl libglib2.0-0 libicu63
  liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libpipeline1
  libsigsegv2 libtool libuchardet0 libxml2 m4 man-db po-debconf sensible-utils
  zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
  libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
  www-browser libmail-box-perl
Recommended packages:
  curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
  xdg-user-dirs libgpm2 libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils debhelper
  dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
  groff-base help2man intltool-debian libarchive-zip-perl libcroco3 libelf1
  libfile-stripnondeterminism-perl libglib2.0-0 libicu63
  liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libpipeline1
  libsigsegv2 libtool libuchardet0 libxml2 m4 man-db po-debconf
  sbuild-build-depends-snap-aligner-dummy sensible-utils zlib1g-dev
0 upgraded, 36 newly installed, 0 to remove and 0 not upgraded.
Need to get 19.3 MB of archives.
After this operation, 70.3 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-G2GU1Z/apt_archive ./ sbuild-build-depends-snap-aligner-dummy 0.invalid.0 [880 B]
Get:2 http://127.0.0.1:9999/debian sid/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB]
Get:3 http://127.0.0.1:9999/debian sid/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB]
Get:4 http://127.0.0.1:9999/debian sid/main amd64 groff-base amd64 1.22.4-2 [917 kB]
Get:5 http://127.0.0.1:9999/debian sid/main amd64 libpipeline1 amd64 1.5.0-2 [29.5 kB]
Get:6 http://127.0.0.1:9999/debian sid/main amd64 man-db amd64 2.8.5-1 [1274 kB]
Get:7 http://127.0.0.1:9999/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB]
Get:8 http://127.0.0.1:9999/debian sid/main amd64 sensible-utils all 0.0.12 [15.8 kB]
Get:9 http://127.0.0.1:9999/debian sid/main amd64 libmagic-mgc amd64 1:5.34-2 [239 kB]
Get:10 http://127.0.0.1:9999/debian sid/main amd64 libmagic1 amd64 1:5.34-2 [116 kB]
Get:11 http://127.0.0.1:9999/debian sid/main amd64 file amd64 1:5.34-2 [65.8 kB]
Get:12 http://127.0.0.1:9999/debian sid/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB]
Get:13 http://127.0.0.1:9999/debian sid/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB]
Get:14 http://127.0.0.1:9999/debian sid/main amd64 m4 amd64 1.4.18-2 [203 kB]
Get:15 http://127.0.0.1:9999/debian sid/main amd64 autoconf all 2.69-11 [341 kB]
Get:16 http://127.0.0.1:9999/debian sid/main amd64 autotools-dev all 20180224.1 [77.0 kB]
Get:17 http://127.0.0.1:9999/debian sid/main amd64 automake all 1:1.16.1-4 [771 kB]
Get:18 http://127.0.0.1:9999/debian sid/main amd64 autopoint all 0.19.8.1-9 [434 kB]
Get:19 http://127.0.0.1:9999/debian sid/main amd64 libtool all 2.4.6-6 [547 kB]
Get:20 http://127.0.0.1:9999/debian sid/main amd64 dh-autoreconf all 19 [16.9 kB]
Get:21 http://127.0.0.1:9999/debian sid/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:22 http://127.0.0.1:9999/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.0.0-1 [19.5 kB]
Get:23 http://127.0.0.1:9999/debian sid/main amd64 dh-strip-nondeterminism all 1.0.0-1 [12.5 kB]
Get:24 http://127.0.0.1:9999/debian sid/main amd64 libelf1 amd64 0.175-2 [160 kB]
Get:25 http://127.0.0.1:9999/debian sid/main amd64 dwz amd64 0.12-3 [78.0 kB]
Get:26 http://127.0.0.1:9999/debian sid/main amd64 libglib2.0-0 amd64 2.58.2-3 [1257 kB]
Get:27 http://127.0.0.1:9999/debian sid/main amd64 libicu63 amd64 63.1-5 [8293 kB]
Get:28 http://127.0.0.1:9999/debian sid/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB]
Get:29 http://127.0.0.1:9999/debian sid/main amd64 libcroco3 amd64 0.6.12-3 [145 kB]
Get:30 http://127.0.0.1:9999/debian sid/main amd64 libncurses6 amd64 6.1+20181013-1 [102 kB]
Get:31 http://127.0.0.1:9999/debian sid/main amd64 gettext amd64 0.19.8.1-9 [1303 kB]
Get:32 http://127.0.0.1:9999/debian sid/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:33 http://127.0.0.1:9999/debian sid/main amd64 po-debconf all 1.0.21 [248 kB]
Get:34 http://127.0.0.1:9999/debian sid/main amd64 debhelper all 12 [1002 kB]
Get:35 http://127.0.0.1:9999/debian sid/main amd64 help2man amd64 1.47.8 [177 kB]
Get:36 http://127.0.0.1:9999/debian sid/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 19.3 MB in 0s (88.2 MB/s)
Selecting previously unselected package bsdmainutils.
(Reading database ... 12592 files and directories currently installed.)
Preparing to unpack .../00-bsdmainutils_11.1.2+b1_amd64.deb ...
Unpacking bsdmainutils (11.1.2+b1) ...
Selecting previously unselected package libuchardet0:amd64.
Preparing to unpack .../01-libuchardet0_0.0.6-3_amd64.deb ...
Unpacking libuchardet0:amd64 (0.0.6-3) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../02-groff-base_1.22.4-2_amd64.deb ...
Unpacking groff-base (1.22.4-2) ...
Selecting previously unselected package libpipeline1:amd64.
Preparing to unpack .../03-libpipeline1_1.5.0-2_amd64.deb ...
Unpacking libpipeline1:amd64 (1.5.0-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../04-man-db_2.8.5-1_amd64.deb ...
Unpacking man-db (2.8.5-1) ...
Selecting previously unselected package liblocale-gettext-perl.
Preparing to unpack .../05-liblocale-gettext-perl_1.07-3+b4_amd64.deb ...
Unpacking liblocale-gettext-perl (1.07-3+b4) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ...
Unpacking sensible-utils (0.0.12) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../07-libmagic-mgc_1%3a5.34-2_amd64.deb ...
Unpacking libmagic-mgc (1:5.34-2) ...
Selecting previously unselected package libmagic1:amd64.
Preparing to unpack .../08-libmagic1_1%3a5.34-2_amd64.deb ...
Unpacking libmagic1:amd64 (1:5.34-2) ...
Selecting previously unselected package file.
Preparing to unpack .../09-file_1%3a5.34-2_amd64.deb ...
Unpacking file (1:5.34-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../10-gettext-base_0.19.8.1-9_amd64.deb ...
Unpacking gettext-base (0.19.8.1-9) ...
Selecting previously unselected package libsigsegv2:amd64.
Preparing to unpack .../11-libsigsegv2_2.12-2_amd64.deb ...
Unpacking libsigsegv2:amd64 (2.12-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../12-m4_1.4.18-2_amd64.deb ...
Unpacking m4 (1.4.18-2) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../13-autoconf_2.69-11_all.deb ...
Unpacking autoconf (2.69-11) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ...
Unpacking autotools-dev (20180224.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ...
Unpacking automake (1:1.16.1-4) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ...
Unpacking autopoint (0.19.8.1-9) ...
Selecting previously unselected package libtool.
Preparing to unpack .../17-libtool_2.4.6-6_all.deb ...
Unpacking libtool (2.4.6-6) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../18-dh-autoreconf_19_all.deb ...
Unpacking dh-autoreconf (19) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../19-libarchive-zip-perl_1.64-1_all.deb ...
Unpacking libarchive-zip-perl (1.64-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.0.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.0.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
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Unpacking dh-strip-nondeterminism (1.0.0-1) ...
Selecting previously unselected package libelf1:amd64.
Preparing to unpack .../22-libelf1_0.175-2_amd64.deb ...
Unpacking libelf1:amd64 (0.175-2) ...
Selecting previously unselected package dwz.
Preparing to unpack .../23-dwz_0.12-3_amd64.deb ...
Unpacking dwz (0.12-3) ...
Selecting previously unselected package libglib2.0-0:amd64.
Preparing to unpack .../24-libglib2.0-0_2.58.2-3_amd64.deb ...
Unpacking libglib2.0-0:amd64 (2.58.2-3) ...
Selecting previously unselected package libicu63:amd64.
Preparing to unpack .../25-libicu63_63.1-5_amd64.deb ...
Unpacking libicu63:amd64 (63.1-5) ...
Selecting previously unselected package libxml2:amd64.
Preparing to unpack .../26-libxml2_2.9.4+dfsg1-7+b3_amd64.deb ...
Unpacking libxml2:amd64 (2.9.4+dfsg1-7+b3) ...
Selecting previously unselected package libcroco3:amd64.
Preparing to unpack .../27-libcroco3_0.6.12-3_amd64.deb ...
Unpacking libcroco3:amd64 (0.6.12-3) ...
Selecting previously unselected package libncurses6:amd64.
Preparing to unpack .../28-libncurses6_6.1+20181013-1_amd64.deb ...
Unpacking libncurses6:amd64 (6.1+20181013-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../29-gettext_0.19.8.1-9_amd64.deb ...
Unpacking gettext (0.19.8.1-9) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../30-intltool-debian_0.35.0+20060710.4_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.4) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../31-po-debconf_1.0.21_all.deb ...
Unpacking po-debconf (1.0.21) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../32-debhelper_12_all.deb ...
Unpacking debhelper (12) ...
Selecting previously unselected package help2man.
Preparing to unpack .../33-help2man_1.47.8_amd64.deb ...
Unpacking help2man (1.47.8) ...
Selecting previously unselected package zlib1g-dev:amd64.
Preparing to unpack .../34-zlib1g-dev_1%3a1.2.11.dfsg-1_amd64.deb ...
Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ...
Selecting previously unselected package sbuild-build-depends-snap-aligner-dummy.
Preparing to unpack .../35-sbuild-build-depends-snap-aligner-dummy_0.invalid.0_amd64.deb ...
Unpacking sbuild-build-depends-snap-aligner-dummy (0.invalid.0) ...
Setting up libarchive-zip-perl (1.64-1) ...
Setting up libicu63:amd64 (63.1-5) ...
Setting up libsigsegv2:amd64 (2.12-2) ...
Setting up libelf1:amd64 (0.175-2) ...
Setting up libglib2.0-0:amd64 (2.58.2-3) ...
No schema files found: doing nothing.
Setting up gettext-base (0.19.8.1-9) ...
Setting up libpipeline1:amd64 (1.5.0-2) ...
Setting up m4 (1.4.18-2) ...
Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ...
Setting up libuchardet0:amd64 (0.0.6-3) ...
Setting up libmagic-mgc (1:5.34-2) ...
Setting up libmagic1:amd64 (1:5.34-2) ...
Setting up libcroco3:amd64 (0.6.12-3) ...
Setting up sensible-utils (0.0.12) ...
Processing triggers for libc-bin (2.28-4) ...
Setting up dwz (0.12-3) ...
Setting up autotools-dev (20180224.1) ...
Setting up liblocale-gettext-perl (1.07-3+b4) ...
Setting up bsdmainutils (11.1.2+b1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libncurses6:amd64 (6.1+20181013-1) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (1.0.0-1) ...
Setting up gettext (0.19.8.1-9) ...
Setting up groff-base (1.22.4-2) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.34-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up help2man (1.47.8) ...
Setting up man-db (2.8.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-6) ...
Setting up po-debconf (1.0.21) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.0.0-1) ...
Setting up debhelper (12) ...
Setting up sbuild-build-depends-snap-aligner-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-4) ...

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.9.0-8-amd64 amd64 (x86_64)
Toolchain package versions: binutils_2.31.1-11 dpkg-dev_1.19.2 g++-8_8.2.0-14 gcc-8_8.2.0-14 libc6-dev_2.28-4 libstdc++-8-dev_8.2.0-14 libstdc++6_8.2.0-14 linux-libc-dev_4.19.13-1
Package versions: adduser_3.118 apt_1.8.0~alpha3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-11 binutils-common_2.31.1-11 binutils-x86-64-linux-gnu_2.31.1-11 bsdmainutils_11.1.2+b1 bsdutils_1:2.33-0.2 build-essential_12.5 bzip2_1.0.6-9 clang-7_1:7.0.1-4 coreutils_8.30-1 cpp_4:8.2.0-2 cpp-8_8.2.0-14 dash_0.5.10.2-4 debconf_1.5.69 debhelper_12 debian-archive-keyring_2018.1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_1.0.0-1 diffutils_1:3.6-1 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33-0.2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 g++_4:8.2.0-2 g++-8_8.2.0-14 gcc_4:8.2.0-2 gcc-8_8.2.0-14 gcc-8-base_8.2.0-14 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.12-1 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 help2man_1.47.8 hostname_3.21 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.4 lib32gcc1_1:8.2.0-14 lib32stdc++6_8.2.0-14 libacl1_2.2.52-3+b1 libapt-pkg5.0_1.8.0~alpha3 libarchive-zip-perl_1.64-1 libasan5_8.2.0-14 libatomic1_8.2.0-14 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libbinutils_2.31.1-11 libblkid1_2.33-0.2 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-4 libc-dev-bin_2.28-4 libc6_2.28-4 libc6-dev_2.28-4 libc6-i386_2.28-4 libcap-ng0_0.7.9-1+b1 libcc1-0_8.2.0-14 libclang-common-7-dev_1:7.0.1-4 libclang1-7_1:7.0.1-4 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libdb5.3_5.3.28+dfsg1-0.2 libdebconfclient0_0.246 libdpkg-perl_1.19.2 libedit2_3.1-20181209-1 libelf1_0.175-2 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33-0.2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.0.0-1 libgc1c2_1:7.6.4-0.4 libgcc-8-dev_8.2.0-14 libgcc1_1:8.2.0-14 libgcrypt20_1.8.4-4 libgdbm-compat4_1.18.1-2 libgdbm6_1.18.1-2 libglib2.0-0_2.58.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.5-2 libgomp1_8.2.0-14 libgpg-error0_1.33-3 libhogweed4_3.4.1~rc1-1 libicu63_63.1-5 libidn2-0_2.0.5-1 libisl19_0.20-2 libitm1_8.2.0-14 libllvm7_1:7.0.1-4 liblocale-gettext-perl_1.07-3+b4 liblsan0_8.2.0-14 liblz4-1_1.8.3-1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.33-0.2 libmpc3_1.1.0-1 libmpfr6_4.0.2~rc1-1 libmpx2_8.2.0-14 libncurses6_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4.1~rc1-1 libobjc-8-dev_8.2.0-14 libobjc4_8.2.0-14 libomp-7-dev_1:7.0.1-4 libomp5-7_1:7.0.1-4 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-4 libpam-modules-bin_1.1.8-4 libpam-runtime_1.1.8-4 libpam0g_1.1.8-4 libpcre3_2:8.39-11 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libquadmath0_8.2.0-14 libseccomp2_2.3.3-3 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33-0.2 libss2_1.44.5-1 libstdc++-8-dev_8.2.0-14 libstdc++6_8.2.0-14 libsystemd0_240-2 libtasn1-6_4.13-3 libtinfo6_6.1+20181013-1 libtool_2.4.6-6 libtsan0_8.2.0-14 libubsan1_8.2.0-14 libuchardet0_0.0.6-3 libudev1_240-2 libunistring2_0.9.10-1 libuuid1_2.33-0.2 libxml2_2.9.4+dfsg1-7+b3 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.13-1 login_1:4.5-1.1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-1 mawk_1.3.3-17+b3 mount_2.33-0.2 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.28_5.28.1-3 po-debconf_1.0.21 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-snap-aligner-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-3 tar_1.30+dfsg-4 tzdata_2018i-1 util-linux_2.33-0.2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Dec 21 08:52:43 2017 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 ./snap-aligner_1.0~beta.18+dfsg-2.dsc
dpkg-source: info: extracting snap-aligner in /<<BUILDDIR>>/snap-aligner-1.0~beta.18+dfsg
dpkg-source: info: unpacking snap-aligner_1.0~beta.18+dfsg.orig.tar.xz
dpkg-source: info: unpacking snap-aligner_1.0~beta.18+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying non-x86-and-kfreebsd
dpkg-source: info: applying drop-msse
dpkg-source: info: applying spelling
dpkg-source: info: applying finish-rename

Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=POSIX
LOGNAME=user42
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=unstable
SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1001
SCHROOT_GROUP=user42
SCHROOT_SESSION_ID=sid-amd64-sbuild-00ef5a51-b066-4a33-abe6-a5c787eed164
SCHROOT_UID=1001
SCHROOT_USER=user42
SHELL=/bin/sh
USER=user42

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package snap-aligner
dpkg-buildpackage: info: source version 1.0~beta.18+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 fakeroot debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/snap-aligner-1.0~beta.18+dfsg'
dh_auto_clean
	make -j4 clean
make[2]: Entering directory '/<<BUILDDIR>>/snap-aligner-1.0~beta.18+dfsg'
rm -f  SNAPLib/FASTA.o  SNAPLib/BigAlloc.o  SNAPLib/HashTable.o  SNAPLib/GenericFile_stdio.o  SNAPLib/ReadSupplierQueue.o  SNAPLib/SeedSequencer.o  SNAPLib/GenericFile.o  SNAPLib/CommandProcessor.o  SNAPLib/ChimericPairedEndAligner.o  SNAPLib/Histogram.o  SNAPLib/mapq.o  SNAPLib/SAM.o  SNAPLib/BufferedAsync.o  SNAPLib/Util.o  SNAPLib/MultiInputReadSupplier.o  SNAPLib/ParallelTask.o  SNAPLib/Read.o  SNAPLib/Error.o  SNAPLib/DataReader.o  SNAPLib/ProbabilityDistance.o  SNAPLib/AlignerOptions.o  SNAPLib/exit.o  SNAPLib/AlignerStats.o  SNAPLib/BaseAligner.o  SNAPLib/Bam.o  SNAPLib/DataWriter.o  SNAPLib/ReadWriter.o  SNAPLib/stdafx.o  SNAPLib/GenericFile_map.o  SNAPLib/GenericFile_Blob.o  SNAPLib/PairedAligner.o  SNAPLib/SortedDataWriter.o  SNAPLib/ReadReader.o  SNAPLib/SingleAligner.o  SNAPLib/FASTQ.o  SNAPLib/GenericFile_HDFS.o  SNAPLib/GzipDataWriter.o  SNAPLib/LandauVishkin.o  SNAPLib/IntersectingPairedEndAligner.o  SNAPLib/RangeSplitter.o  SNAPLib/AlignerContext.o  SNAPLib/GenomeIndex.o  SNAPLib/Genome.o  SNAPLib/BiasTables.o  SNAPLib/Compat.o  SNAPLib/PairedReadMatcher.o  SNAPLib/AlignmentResult.o  SNAPLib/ApproximateCounter.o  SNAPLib/Tables.o  SNAPLib/Seed.o  apps/snap/Main.o  apps/snap/stdafx.o  tests/ProbabilityDistanceTest.o  tests/LandauVishkinTest.o  tests/TestLib.o  tests/EventTest.o  tests/main.o  apps/SNAPCommand/SNAPCommand.o  apps/SNAPCommand/stdafx.o  snap-aligner unit_tests SNAPCommand snap SNAP
make[2]: Leaving directory '/<<BUILDDIR>>/snap-aligner-1.0~beta.18+dfsg'
rm -f debian/*.1
rm -f */*.d */*/*.d
make[1]: Leaving directory '/<<BUILDDIR>>/snap-aligner-1.0~beta.18+dfsg'
   dh_clean
 debian/rules build-arch
dh build-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   dh_auto_configure -a
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/snap-aligner-1.0~beta.18+dfsg'
dh_auto_build
	make -j4
make[2]: Entering directory '/<<BUILDDIR>>/snap-aligner-1.0~beta.18+dfsg'
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/FASTA.o SNAPLib/FASTA.cpp
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/BigAlloc.o SNAPLib/BigAlloc.cpp
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/HashTable.o SNAPLib/HashTable.cpp
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/GenericFile_stdio.o SNAPLib/GenericFile_stdio.cpp
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadSupplierQueue.cpp
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/SeedSequencer.o SNAPLib/SeedSequencer.cpp
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/GenericFile.o SNAPLib/GenericFile.cpp
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/CommandProcessor.o SNAPLib/CommandProcessor.cpp
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/ChimericPairedEndAligner.o SNAPLib/ChimericPairedEndAligner.cpp
In file included from SNAPLib/ReadSupplierQueue.cpp:25:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
In file included from SNAPLib/SeedSequencer.cpp:25:
In file included from SNAPLib/SeedSequencer.h:27:
In file included from SNAPLib/Seed.h:29:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
        return a <= b && a+distance >= b || a >= b && a <= b + distance;                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~

                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
SNAPLib/Util.h:506:        return a <= b && a+distance >= b || a >= b && a <= b + distance;45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;

                                                   ^
                                            (                          )
                                                   ^
                                            (                          )
In file included from SNAPLib/CommandProcessor.cpp:28:
In file included from SNAPLib/GenomeIndex.h:28:
In file included from SNAPLib/Seed.h:29:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/CommandProcessor.cpp:28:
SNAPLib/GenomeIndex.h:193:12: warning: class member cannot be redeclared [-Wredeclared-class-member]
    struct OverflowBackpointer;
           ^
SNAPLib/GenomeIndex.h:119:12: note: previous declaration is here
    struct OverflowBackpointer {
           ^
2 warnings generated.
In file included from SNAPLib/ReadSupplierQueue.cpp:25:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/Histogram.o SNAPLib/Histogram.cpp
In file included from SNAPLib/CommandProcessor.cpp:29:
In file included from SNAPLib/SingleAligner.h:27:
In file included from SNAPLib/AlignerContext.h:28:
In file included from SNAPLib/RangeSplitter.h:30:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
SNAPLib/ReadSupplierQueue.cpp:247:20: warning: implicit conversion of NULL constant to 'bool' [-Wnull-conversion]
            return NULL;
            ~~~~~~ ^~~~
                   false
4 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/mapq.o SNAPLib/mapq.cpp
4 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/SAM.o SNAPLib/SAM.cpp
In file included from SNAPLib/ChimericPairedEndAligner.cpp:27:
In file included from SNAPLib/ChimericPairedEndAligner.h:27:
In file included from SNAPLib/PairedEndAligner.h:28:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/BufferedAsync.o SNAPLib/BufferedAsync.cpp
In file included from SNAPLib/ChimericPairedEndAligner.cpp:27:
In file included from SNAPLib/ChimericPairedEndAligner.h:27:
In file included from SNAPLib/PairedEndAligner.h:28:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
In file included from SNAPLib/ChimericPairedEndAligner.cpp:27:
In file included from SNAPLib/ChimericPairedEndAligner.h:28:
In file included from SNAPLib/BaseAligner.h:36:
SNAPLib/GenomeIndex.h:193:12: warning: class member cannot be redeclared [-Wredeclared-class-member]
    struct OverflowBackpointer;
           ^
SNAPLib/GenomeIndex.h:119:12: note: previous declaration is here
    struct OverflowBackpointer {
           ^
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/Util.o SNAPLib/Util.cpp
4 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/MultiInputReadSupplier.o SNAPLib/MultiInputReadSupplier.cpp
In file included from SNAPLib/SAM.cpp:22:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/SAM.cpp:22:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
SNAPLib/SAM.cpp:222:85: warning: '&&' within '||' [-Wlogical-op-parentheses]
            if (nextLineToProcess + 3 >= endOfBuffer || ' ' != nextLineToProcess[3] && '\t' != nextLineToProcess[3]) {
                                                     ~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SNAPLib/SAM.cpp:222:85: note: place parentheses around the '&&' expression to silence this warning
            if (nextLineToProcess + 3 >= endOfBuffer || ' ' != nextLineToProcess[3] && '\t' != nextLineToProcess[3]) {
                                                                                    ^
                                                        (                                                          )
SNAPLib/SAM.cpp:922:137: warning: format specifies type 'unsigned int' but the argument has type 'long' [-Wformat]
            bytesConsumed += snprintf(header + bytesConsumed, headerBufferSize - bytesConsumed, "@SQ\tSN:%s\tLN:%u\n", contigs[i].name, end - start);
                                                                                                                ~~                      ^~~~~~~~~~~
                                                                                                                %ld
SNAPLib/SAM.cpp:1252:58: warning: field precision should have type 'int', but argument has type 'size_t' (aka 'unsigned long') [-Wformat]
    int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%u\t%d\t%s\t%s\t%u\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s\n",
                                                       ~~^~
SNAPLib/SAM.cpp:1459:63: warning: format specifies type 'unsigned long long' but the argument has type 'long' [-Wformat]
            snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore);
                                                      ~~~~    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                      %ld
SNAPLib/SAM.cpp:1462:61: warning: format specifies type 'unsigned long long' but the argument has type 'long' [-Wformat]
            snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter);
                                                    ~~~~    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                    %ld
8 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/ParallelTask.o SNAPLib/ParallelTask.cpp
SNAPLib/BufferedAsync.cpp:132:5: warning: delete called on 'AsyncFile::Reader' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
    delete reader[0];
    ^
SNAPLib/BufferedAsync.cpp:133:5: warning: delete called on 'AsyncFile::Reader' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
    delete reader[1];
    ^
SNAPLib/BufferedAsync.cpp:217:5: warning: delete called on 'AsyncFile::Writer' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
    delete writer[0];
    ^
SNAPLib/BufferedAsync.cpp:218:5: warning: delete called on 'AsyncFile::Writer' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
    delete writer[1];
    ^
4 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/Read.o SNAPLib/Read.cpp
In file included from SNAPLib/Util.cpp:26:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
SNAPLib/Util.cpp:164:32: warning: format specifies type 'long long' but the argument has type 'unsigned long' [-Wformat]
                        sprintf(tempBuf, ",%03lld", x % 1000);
                                           ~~~~~~   ^~~~~~~~
                                           %03lu
SNAPLib/Util.cpp:167:27: warning: format specifies type 'int' but the argument has type '_uint64' (aka 'unsigned long') [-Wformat]
                        sprintf(tempBuf, "%d", x);
                                          ~~   ^
                                          %lu
4 warnings generated.
In file included from SNAPLib/MultiInputReadSupplier.cpp:25:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/Error.o SNAPLib/Error.cpp
In file included from SNAPLib/MultiInputReadSupplier.cpp:25:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
SNAPLib/MultiInputReadSupplier.cpp:144:16: warning: implicit conversion of NULL constant to 'bool' [-Wnull-conversion]
        return NULL;
        ~~~~~~ ^~~~
               false
4 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/DataReader.o SNAPLib/DataReader.cpp
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/ProbabilityDistance.o SNAPLib/ProbabilityDistance.cpp
In file included from SNAPLib/Read.cpp:25:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/Read.cpp:25:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
3 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/AlignerOptions.o SNAPLib/AlignerOptions.cpp
In file included from SNAPLib/Error.cpp:27:
In file included from SNAPLib/AlignerOptions.h:30:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/Error.cpp:27:
In file included from SNAPLib/AlignerOptions.h:30:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
SNAPLib/Error.cpp:87:68: warning: format specifies type 'long long' but the argument has type '_int64' (aka 'long') [-Wformat]
    fprintf(stderr,"reporter:counter:SNAP,%s,%lld\n", counterName, increment);
                                             ~~~~                  ^~~~~~~~~
                                             %ld
4 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/exit.o SNAPLib/exit.cpp
In file included from SNAPLib/DataReader.cpp:23:
In file included from SNAPLib/RangeSplitter.h:30:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/DataReader.cpp:23:
In file included from SNAPLib/RangeSplitter.h:30:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
SNAPLib/DataReader.cpp:1685:57: warning: format specifies type 'long long' but the argument has type 'long' [-Wformat]
            sprintf(result, "compressed #%d @ %lld", i, (char*)p - e->compressed);
                                              ~~~~      ^~~~~~~~~~~~~~~~~~~~~~~~
                                              %ld
SNAPLib/DataReader.cpp:1689:57: warning: format specifies type 'long long' but the argument has type 'long' [-Wformat]
            sprintf(result, "decompressed #%d %lld", i, (char*) p - e->decompressed);
                                              ~~~~      ^~~~~~~~~~~~~~~~~~~~~~~~~~~
                                              %ld
SNAPLib/DataReader.cpp:1693:50: warning: format specifies type 'long long' but the argument has type 'long' [-Wformat]
            sprintf(result, "extra #%d %lld", i, (char*) p - e->decompressed - extraBytes);
                                       ~~~~      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                       %ld
SNAPLib/DataReader.cpp:1813:80: warning: format specifies type 'long long' but the argument has type '_int64' (aka 'long') [-Wformat]
                    fprintf(stderr, "error reading BAM file at offset %lld\n", reader->getFileOffset());
                                                                      ~~~~     ^~~~~~~~~~~~~~~~~~~~~~~
                                                                      %ld
SNAPLib/DataReader.cpp:1812:68: warning: result of comparison of constant 65536 with expression of type '_uint16' (aka 'unsigned short') is always false [-Wtautological-constant-out-of-range-compare]
                if (input > entry->compressedValid || zip->BSIZE() >= BAM_BLOCK || zip->ISIZE() > BAM_BLOCK) {
                                                      ~~~~~~~~~~~~ ^  ~~~~~~~~~
In file included from SNAPLib/ProbabilityDistance.cpp:2:
In file included from SNAPLib/ProbabilityDistance.h:3:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/ProbabilityDistance.cpp:2:
In file included from SNAPLib/ProbabilityDistance.h:3:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
3 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/AlignerStats.o SNAPLib/AlignerStats.cpp
8 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/BaseAligner.o SNAPLib/BaseAligner.cpp
In file included from SNAPLib/AlignerOptions.cpp:27:
In file included from SNAPLib/AlignerOptions.h:30:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/AlignerOptions.cpp:27:
In file included from SNAPLib/AlignerOptions.h:30:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/Bam.o SNAPLib/Bam.cpp
In file included from SNAPLib/AlignerOptions.cpp:33:
In file included from SNAPLib/BaseAligner.h:36:
SNAPLib/GenomeIndex.h:193:12: warning: class member cannot be redeclared [-Wredeclared-class-member]
    struct OverflowBackpointer;
           ^
SNAPLib/GenomeIndex.h:119:12: note: previous declaration is here
    struct OverflowBackpointer {
           ^
SNAPLib/AlignerOptions.cpp:706:55: warning: '&&' within '||' [-Wlogical-op-parentheses]
        if (strlen(argv[n]) != 4 || '-' != argv[n][2] && '+' != argv[n][2] ||
                                 ~~ ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/AlignerOptions.cpp:706:55: note: place parentheses around the '&&' expression to silence this warning
        if (strlen(argv[n]) != 4 || '-' != argv[n][2] && '+' != argv[n][2] ||
                                                      ^
                                    (                                     )
SNAPLib/AlignerOptions.cpp:707:31: warning: '&&' within '||' [-Wlogical-op-parentheses]
            '-' != argv[n][3] && '+' != argv[n][3]) {
            ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/AlignerOptions.cpp:707:31: note: place parentheses around the '&&' expression to silence this warning
            '-' != argv[n][3] && '+' != argv[n][3]) {
                              ^
            (                                     )
6 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/DataWriter.o SNAPLib/DataWriter.cpp
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/ReadWriter.o SNAPLib/ReadWriter.cpp
In file included from SNAPLib/BaseAligner.cpp:29:
In file included from SNAPLib/BaseAligner.h:33:
In file included from SNAPLib/ProbabilityDistance.h:3:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/BaseAligner.cpp:29:
In file included from SNAPLib/BaseAligner.h:33:
In file included from SNAPLib/ProbabilityDistance.h:3:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
In file included from SNAPLib/BaseAligner.cpp:29:
In file included from SNAPLib/BaseAligner.h:36:
SNAPLib/GenomeIndex.h:193:12: warning: class member cannot be redeclared [-Wredeclared-class-member]
    struct OverflowBackpointer;
           ^
SNAPLib/GenomeIndex.h:119:12: note: previous declaration is here
    struct OverflowBackpointer {
           ^
SNAPLib/BaseAligner.cpp:943:97: warning: '&&' within '||' [-Wlogical-op-parentheses]
                    if (elementToScore->bestScore < score || elementToScore->bestScore == score && matchProbability <= elementToScore->matchProbabilityForBestScore) {
                                                          ~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SNAPLib/BaseAligner.cpp:943:97: note: place parentheses around the '&&' expression to silence this warning
                    if (elementToScore->bestScore < score || elementToScore->bestScore == score && matchProbability <= elementToScore->matchProbabilityForBestScore) {
                                                                                                ^
                                                             (                                                                                                     )
SNAPLib/BaseAligner.cpp:990:99: warning: '&&' within '||' [-Wlogical-op-parentheses]
                        if (nearbyElement->bestScore < score || nearbyElement->bestScore == score && nearbyElement->matchProbabilityForBestScore >= matchProbability) {
                                                             ~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SNAPLib/BaseAligner.cpp:990:99: note: place parentheses around the '&&' expression to silence this warning
                        if (nearbyElement->bestScore < score || nearbyElement->bestScore == score && nearbyElement->matchProbabilityForBestScore >= matchProbability) {
                                                                                                  ^
                                                                (                                                                                                   )
In file included from SNAPLib/Bam.cpp:20:
In file included from SNAPLib/SAM.h:24:
In file included from SNAPLib/PairedEndAligner.h:28:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/Bam.cpp:20:
In file included from SNAPLib/SAM.h:24:
In file included from SNAPLib/PairedEndAligner.h:28:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
6 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/stdafx.o SNAPLib/stdafx.cpp
In file included from SNAPLib/Bam.cpp:34:
In file included from SNAPLib/PairedAligner.h:27:
In file included from SNAPLib/AlignerContext.h:32:
SNAPLib/GenomeIndex.h:193:12: warning: class member cannot be redeclared [-Wredeclared-class-member]
    struct OverflowBackpointer;
           ^
SNAPLib/GenomeIndex.h:119:12: note: previous declaration is here
    struct OverflowBackpointer {
           ^
In file included from SNAPLib/DataWriter.cpp:22:
In file included from SNAPLib/DataWriter.h:26:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/DataWriter.cpp:22:
In file included from SNAPLib/DataWriter.h:26:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
SNAPLib/DataWriter.cpp:68:13: warning: delete called on 'AsyncFile::Writer' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
            delete batches[i].file;
            ^
4 warnings generated.
In file included from SNAPLib/ReadWriter.cpp:22:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_map.cpp
In file included from SNAPLib/ReadWriter.cpp:22:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
3 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_Blob.cpp
4 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.cpp
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/SortedDataWriter.o SNAPLib/SortedDataWriter.cpp
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/ReadReader.o SNAPLib/ReadReader.cpp
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/SingleAligner.o SNAPLib/SingleAligner.cpp
In file included from SNAPLib/PairedAligner.cpp:35:
In file included from SNAPLib/RangeSplitter.h:30:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/PairedAligner.cpp:35:
In file included from SNAPLib/RangeSplitter.h:30:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
In file included from SNAPLib/PairedAligner.cpp:36:
SNAPLib/GenomeIndex.h:193:12: warning: class member cannot be redeclared [-Wredeclared-class-member]
    struct OverflowBackpointer;
           ^
SNAPLib/GenomeIndex.h:119:12: note: previous declaration is here
    struct OverflowBackpointer {
           ^
In file included from SNAPLib/SortedDataWriter.cpp:22:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/SortedDataWriter.cpp:23:
In file included from SNAPLib/DataWriter.h:26:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
4 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/FASTQ.o SNAPLib/FASTQ.cpp
3 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_HDFS.cpp
In file included from SNAPLib/ReadReader.cpp:20:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/ReadReader.cpp:20:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
SNAPLib/ReadReader.cpp:44:5: warning: control reaches end of non-void function [-Wreturn-type]
    }
    ^
4 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/GzipDataWriter.o SNAPLib/GzipDataWriter.cpp
In file included from SNAPLib/SingleAligner.cpp:27:
In file included from SNAPLib/BaseAligner.h:33:
In file included from SNAPLib/ProbabilityDistance.h:3:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/SingleAligner.cpp:27:
In file included from SNAPLib/BaseAligner.h:33:
In file included from SNAPLib/ProbabilityDistance.h:3:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
In file included from SNAPLib/SingleAligner.cpp:27:
In file included from SNAPLib/BaseAligner.h:36:
SNAPLib/GenomeIndex.h:193:12: warning: class member cannot be redeclared [-Wredeclared-class-member]
    struct OverflowBackpointer;
           ^
SNAPLib/GenomeIndex.h:119:12: note: previous declaration is here
    struct OverflowBackpointer {
           ^
4 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/LandauVishkin.o SNAPLib/LandauVishkin.cpp
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/IntersectingPairedEndAligner.cpp
In file included from SNAPLib/FASTQ.cpp:29:
In file included from SNAPLib/FASTQ.h:31:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/FASTQ.cpp:29:
In file included from SNAPLib/FASTQ.h:31:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
3 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/RangeSplitter.o SNAPLib/RangeSplitter.cpp
In file included from SNAPLib/GzipDataWriter.cpp:20:
In file included from SNAPLib/GzipDataWriter.h:26:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/GzipDataWriter.cpp:20:
In file included from SNAPLib/GzipDataWriter.h:26:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
3 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/AlignerContext.o SNAPLib/AlignerContext.cpp
In file included from SNAPLib/LandauVishkin.cpp:5:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/LandauVishkin.cpp:5:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
In file included from SNAPLib/LandauVishkin.cpp:6:
In file included from SNAPLib/BaseAligner.h:36:
SNAPLib/GenomeIndex.h:193:12: warning: class member cannot be redeclared [-Wredeclared-class-member]
    struct OverflowBackpointer;
           ^
SNAPLib/GenomeIndex.h:119:12: note: previous declaration is here
    struct OverflowBackpointer {
           ^
SNAPLib/LandauVishkin.cpp:54:22: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            *o_buf = '\0';
                     ^~~~
In file included from SNAPLib/IntersectingPairedEndAligner.cpp:24:
In file included from SNAPLib/IntersectingPairedEndAligner.h:25:
In file included from SNAPLib/PairedEndAligner.h:28:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16:SNAPLib/LandauVishkin.cpp:259:57: warning: '&&' within '||' [-Wlogical-op-parentheses]
                if (best > bestbest || best == bestbest && bestIndels < bestBestIndels) { warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~

                                    ~~ ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:16SNAPLib/LandauVishkin.cpp: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
:259SNAPLib/Util.h::57: note: place parentheses around the '&&' expression to silence this warning
506:45: warning                if (best > bestbest || best == bestbest && bestIndels < bestBestIndels) {
                                                        ^
                                       (                                              )
: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/IntersectingPairedEndAligner.cpp:24:
In file included from SNAPLib/IntersectingPairedEndAligner.h:25:
In file included from SNAPLib/PairedEndAligner.h:28:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
6 warnings generated.
In file included from SNAPLib/IntersectingPairedEndAligner.cpp:24:
In file included from SNAPLib/IntersectingPairedEndAligner.h:26:
In file included from SNAPLib/BaseAligner.h:36:
SNAPLib/GenomeIndex.h:193:12: warning: class member cannot be redeclared [-Wredeclared-class-member]
    struct OverflowBackpointer;
           ^
SNAPLib/GenomeIndex.h:119:12: note: previous declaration is here
    struct OverflowBackpointer {
           ^
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/GenomeIndex.o SNAPLib/GenomeIndex.cpp
SNAPLib/IntersectingPairedEndAligner.cpp:636:64: warning: '&&' within '||' [-Wlogical-op-parentheses]
                    if (mate->score == -2 || mate->score == -1 && mate->scoreLimit < scoreLimit - fewerEndScore) {
                                          ~~ ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SNAPLib/IntersectingPairedEndAligner.cpp:636:64: note: place parentheses around the '&&' expression to silence this warning
                    if (mate->score == -2 || mate->score == -1 && mate->scoreLimit < scoreLimit - fewerEndScore) {
                                                               ^
                                             (                                                                 )
SNAPLib/IntersectingPairedEndAligner.cpp:1392:67: warning: '&&' within '||' [-Wlogical-op-parentheses]
        if (newPairScore < pairScore || newPairScore == pairScore && newMatchProbability > matchProbability) {
                                     ~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SNAPLib/IntersectingPairedEndAligner.cpp:1392:67: note: place parentheses around the '&&' expression to silence this warning
        if (newPairScore < pairScore || newPairScore == pairScore && newMatchProbability > matchProbability) {
                                                                  ^
                                        (                                                                  )
In file included from SNAPLib/RangeSplitter.cpp:28:
In file included from SNAPLib/RangeSplitter.h:30:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/RangeSplitter.cpp:28:
In file included from SNAPLib/RangeSplitter.h:30:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
6 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/Genome.o SNAPLib/Genome.cpp
3 warnings generated.
g++ -std=gnu++98 -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2  -c -o SNAPLib/BiasTables.o SNAPLib/BiasTables.cpp
In file included from SNAPLib/AlignerContext.cpp:29:
In file included from SNAPLib/AlignerOptions.h:30:
In file included from SNAPLib/Read.h:30:
In file included from SNAPLib/DataReader.h:26:
In file included from SNAPLib/VariableSizeMap.h:5:
In file included from SNAPLib/VariableSizeVector.h:3:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/AlignerContext.cpp:29:
In file included from SNAPLib/AlignerOptions.h:30:
SNAPLib/Read.h:315:31: warning: comparison of array 'other.localBuffer' equal to a null pointer is always false [-Wtautological-pointer-compare]
            if (NULL == other.localBuffer || other.data < other.localBuffer || other.data >= other.localBuffer + other.localBufferAllocationOffset - dataLength) {
                ~~~~    ~~~~~~^~~~~~~~~~~
In file included from SNAPLib/AlignerContext.cpp:30:
In file included from SNAPLib/AlignerContext.h:32:
SNAPLib/GenomeIndex.h:193:12: warning: class member cannot be redeclared [-Wredeclared-class-member]
    struct OverflowBackpointer;
           ^
SNAPLib/GenomeIndex.h:119:12: note: previous declaration is here
    struct OverflowBackpointer {
           ^
SNAPLib/AlignerContext.cpp:275:9: warning: delete called on 'ReadWriterSupplier' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
        delete writerSupplier;
        ^
SNAPLib/AlignerContext.cpp:341:34: error: expected ')'
                FormatUIntWithCommas((unsigned _int64)(1000 * stats->totalReads / max(alignTime, (_int64)1)), readsPerSecond, strBufLen),       // Aligntime is in ms
                                               ^
SNAPLib/AlignerContext.cpp:341:24: note: to match this '('
                FormatUIntWithCommas((unsigned _int64)(1000 * stats->totalReads / max(alignTime, (_int64)1)), readsPerSecond, strBufLen),       // Aligntime is in ms
                                     ^
SNAPLib/AlignerContext.cpp:352:17: warning: format specifies type 'double' but the argument has type '_int64' (aka 'long') [-Wformat]
                stats->lvCalls,
                ^~~~~~~~~~~~~~
SNAPLib/AlignerContext.cpp:353:5: warning: format specifies type 'long long' but the argument has type 'double' [-Wformat]
                                100.0 * stats->alignedAsPairs / stats->totalReads,
                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SNAPLib/AlignerContext.cpp:354:17: warning: format specifies type 'long long' but the argument has type '_int64' (aka 'long') [-Wformat]
                stats->totalReads,
                ^~~~~~~~~~~~~~~~~
8 warnings and 1 error generated.
make[2]: *** [<builtin>: SNAPLib/AlignerContext.o] Error 1
make[2]: *** Waiting for unfinished jobs....
In file included from SNAPLib/GenomeIndex.cpp:35:
In file included from SNAPLib/GenomeIndex.h:28:
In file included from SNAPLib/Seed.h:29:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/GenomeIndex.cpp:35:
SNAPLib/GenomeIndex.h:193:12: warning: class member cannot be redeclared [-Wredeclared-class-member]
    struct OverflowBackpointer;
           ^
SNAPLib/GenomeIndex.h:119:12: note: previous declaration is here
    struct OverflowBackpointer {
           ^
SNAPLib/GenomeIndex.cpp:291:28: warning: format specifies type 'long long' but the argument has type 'long' [-Wformat]
        fprintf(stderr,"%llds\n", (timeInMillis() + 500 - start) / 1000);
                        ~~~~      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                        %ld
SNAPLib/GenomeIndex.cpp:679:103: warning: format specifies type 'int' but the argument has type '_uint64' (aka 'unsigned long') [-Wformat]
        fprintf(histogramFile, "%d larger than %d with %d total genome locations, largest seed %d\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed);
                                ~~                                                                    ^~~~~~~~~~~~~~~~~~~~~~~~~
                                %lu
SNAPLib/GenomeIndex.cpp:679:149: warning: format specifies type 'int' but the argument has type '_uint64' (aka 'unsigned long') [-Wformat]
        fprintf(histogramFile, "%d larger than %d with %d total genome locations, largest seed %d\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed);
                                                       ~~                                                                                           ^~~~~~~~~~~~~~~~~~~~~~~
                                                       %lu
SNAPLib/GenomeIndex.cpp:679:174: warning: format specifies type 'int' but the argument has type '_uint64' (aka 'unsigned long') [-Wformat]
        fprintf(histogramFile, "%d larger than %d with %d total genome locations, largest seed %d\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed);
                                                                                               ~~                                                                            ^~~~~~~~~~~
                                                                                               %lu
SNAPLib/GenomeIndex.cpp:732:9: warning: format specifies type 'long long' but the argument has type '_uint64' (aka 'unsigned long') [-Wformat]
        index->overflowTableSize, seedLen, chromosomePaddingSize, hashTableKeySize, totalBytesWritten, large ? 0 : 1, locationSize); 
        ^~~~~~~~~~~~~~~~~~~~~~~~
SNAPLib/GenomeIndex.cpp:732:85: warning: format specifies type 'long long' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
        index->overflowTableSize, seedLen, chromosomePaddingSize, hashTableKeySize, totalBytesWritten, large ? 0 : 1, locationSize); 
                                                                                    ^~~~~~~~~~~~~~~~~
SNAPLib/GenomeIndex.cpp:1625:125: warning: format specifies type 'long long *' but the argument has type '_int64 *' (aka 'long *') [-Wformat]
    if (10 != (nRead = sscanf(indexFileBuf,"%d %d %d %lld %d %d %d %lld %d %d", &majorVersion, &minorVersion, &nHashTables, &overflowTableSize, &seedLen, &chromosomePadding, 
                                                     ~~~~                                                                   ^~~~~~~~~~~~~~~~~~
                                                     %ld
SNAPLib/GenomeIndex.cpp:1626:31: warning: format specifies type 'long long *' but the argument has type 'size_t *' (aka 'unsigned long *') [-Wformat]
                                                                                        &hashTableKeySize, &hashTablesFileSize, &smallHashTable, &locationSize))) {
                                                                                                           ^~~~~~~~~~~~~~~~~~~
SNAPLib/Genome.cpp:143:34: warning: format specifies type 'long long' but the argument has type 'GenomeDistance' (aka 'long') [-Wformat]
    fprintf(saveFile,"%lld %d\n",nBases, nContigs);
                      ~~~~       ^~~~~~
                      %ld
SNAPLib/Genome.cpp:151:38: warning: format specifies type 'long long' but the argument has type 'GenomeLocation' (aka 'long') [-Wformat]
        fprintf(saveFile,"%lld %s\n",contigs[i].beginningLocation, contigs[i].name);
                          ~~~~       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
                          %ld
SNAPLib/Genome.cpp:239:47: warning: format specifies type 'long long *' but the argument has type '_int64 *' (aka 'long *') [-Wformat]
    if (1 != sscanf(contigNameBuffer, "%lld", &contigStart)) {
                                       ~~~~   ^~~~~~~~~~~~
                                       %ld
SNAPLib/Genome.cpp:323:60: warning: format specifies type 'long long *' but the argument has type 'GenomeDistance *' (aka 'long *') [-Wformat]
    if (NULL == retval || 2 != sscanf(linebuf,"%lld %d\n", nBases, nContigs)) {
                                               ~~~~        ^~~~~~
                                               %ld
4 warnings generated.
11 warnings generated.
In file included from SNAPLib/BiasTables.cpp:26:
In file included from SNAPLib/GenomeIndex.h:28:
In file included from SNAPLib/Seed.h:29:
SNAPLib/Util.h:506:16: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
               ~~~~~~~^~~~~~~~~~~~~~~~~~ ~~
SNAPLib/Util.h:506:16: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                      ^
               (                        )
SNAPLib/Util.h:506:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                         ~~ ~~~~~~~^~~~~~~~~~~~~~~~~~~~
SNAPLib/Util.h:506:45: note: place parentheses around the '&&' expression to silence this warning
        return a <= b && a+distance >= b || a >= b && a <= b + distance;
                                                   ^
                                            (                          )
In file included from SNAPLib/BiasTables.cpp:26:
SNAPLib/GenomeIndex.h:193:12: warning: class member cannot be redeclared [-Wredeclared-class-member]
    struct OverflowBackpointer;
           ^
SNAPLib/GenomeIndex.h:119:12: note: previous declaration is here
    struct OverflowBackpointer {
           ^
3 warnings generated.
make[2]: Leaving directory '/<<BUILDDIR>>/snap-aligner-1.0~beta.18+dfsg'
dh_auto_build: make -j4 returned exit code 2
make[1]: *** [debian/rules:19: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<BUILDDIR>>/snap-aligner-1.0~beta.18+dfsg'
make: *** [debian/rules:12: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2019-01-09T22:08:53Z

Finished
--------


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: amd64
Build Type: any
Build-Space: 16916
Build-Time: 9
Distribution: unstable
Fail-Stage: build
Host Architecture: amd64
Install-Time: 7
Job: snap-aligner_1.0~beta.18+dfsg-2
Machine Architecture: amd64
Package: snap-aligner
Package-Time: 31
Source-Version: 1.0~beta.18+dfsg-2
Space: 16916
Status: attempted
Version: 1.0~beta.18+dfsg-2
--------------------------------------------------------------------------------
Finished at 2019-01-09T22:08:53Z
Build needed 00:00:31, 16916k disk space
E: Build failure (dpkg-buildpackage died)
DC-Status: Failed 31.474074795s
DC-Time-Estimation: 31.474074795 versus expected 109 (r/m: 2.463167724864015 ; m: 31.474074795)