DC-Build-Header: salmon 1.2.1+ds1-1 / 2020-05-03 02:12:52 +0000
DC-Task: type:rebuild-binarch-only source:salmon version:1.2.1+ds1-1 chroot:unstable esttime: logfile:/tmp/salmon_1.2.1+ds1-1_unstable_clang10.log modes:clang10:binarch-only
DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --no-run-lintian --chroot-setup-commands=/tmp/clang10 salmon_1.2.1+ds1-1'
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-1-184.eu-central-1.compute.internal

+==============================================================================+
| salmon 1.2.1+ds1-1 (amd64)                   Sun, 03 May 2020 02:12:52 +0000 |
+==============================================================================+

Package: salmon
Version: 1.2.1+ds1-1
Source Version: 1.2.1+ds1-1
Distribution: unstable
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
Build Type: binary

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-71766ce7-a336-4c91-a413-5bd5febeba3b' with '<<CHROOT>>'

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


/tmp/clang10
------------

+ echo 'Entering customization script...'
Entering customization script...
+ CLANG_VERSION=10
+ echo 'Install of clang-10'
Install of clang-10
+ apt-get update
Get:1 http://127.0.0.1:12990/debian sid InRelease [146 kB]
Get:2 http://127.0.0.1:12990/debian sid/main Sources.diff/Index [27.9 kB]
Get:3 http://127.0.0.1:12990/debian sid/main amd64 Packages.diff/Index [27.9 kB]
Get:4 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-0208.16.pdiff [3982 B]
Get:5 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-0807.49.pdiff [10.9 kB]
Get:6 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-1412.30.pdiff [12.9 kB]
Get:7 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-2007.10.pdiff [13.4 kB]
Get:7 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-2007.10.pdiff [13.4 kB]
Get:8 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-0208.16.pdiff [2772 B]
Get:9 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-0807.49.pdiff [3238 B]
Get:10 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-1412.30.pdiff [7641 B]
Get:11 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-2007.10.pdiff [10.5 kB]
Get:11 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-2007.10.pdiff [10.5 kB]
Get:12 http://127.0.0.1:12990/debian sid/main Translation-en [6192 kB]
Fetched 6459 kB in 2s (3872 kB/s)
Reading package lists...
+ apt-get install --yes --no-install-recommends --force-yes clang-10 libomp-10-dev libobjc-9-dev
Reading package lists...
Building dependency tree...
The following additional packages will be installed:
  lib32gcc-s1 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-10-dev
  libclang-cpp10 libclang1-10 libedit2 libgc1c2 libllvm10 libobjc4 libomp5-10
  libz3-4
Suggested packages:
  clang-10-doc libomp-10-doc
Recommended packages:
  llvm-10-dev python3
The following NEW packages will be installed:
  clang-10 lib32gcc-s1 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386
  libclang-common-10-dev libclang-cpp10 libclang1-10 libedit2 libgc1c2
  libllvm10 libobjc-9-dev libobjc4 libomp-10-dev libomp5-10 libz3-4
0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded.
Need to get 49.8 MB of archives.
After this operation, 259 MB of additional disk space will be used.
Get:1 http://127.0.0.1:12990/debian sid/main amd64 libbsd0 amd64 0.10.0-1 [107 kB]
Get:2 http://127.0.0.1:12990/debian sid/main amd64 libedit2 amd64 3.1-20191231-1 [95.4 kB]
Get:3 http://127.0.0.1:12990/debian sid/main amd64 libz3-4 amd64 4.8.7-4 [6790 kB]
Get:4 http://127.0.0.1:12990/debian sid/main amd64 libllvm10 amd64 1:10.0.0-4 [15.5 MB]
Get:5 http://127.0.0.1:12990/debian sid/main amd64 libclang-cpp10 amd64 1:10.0.0-4 [10.1 MB]
Get:6 http://127.0.0.1:12990/debian sid/main amd64 libgc1c2 amd64 1:7.6.4-0.4 [224 kB]
Get:7 http://127.0.0.1:12990/debian sid/main amd64 libobjc4 amd64 10-20200418-1 [41.7 kB]
Get:8 http://127.0.0.1:12990/debian sid/main amd64 libobjc-9-dev amd64 9.3.0-11 [218 kB]
Get:9 http://127.0.0.1:12990/debian sid/main amd64 libc6-i386 amd64 2.30-4 [2926 kB]
Get:10 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc-s1 amd64 10-20200418-1 [49.4 kB]
Get:11 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc1 amd64 1:10-20200418-1 [1100 B]
Get:12 http://127.0.0.1:12990/debian sid/main amd64 lib32stdc++6 amd64 10-20200418-1 [510 kB]
Get:13 http://127.0.0.1:12990/debian sid/main amd64 libclang-common-10-dev amd64 1:10.0.0-4 [5062 kB]
Get:14 http://127.0.0.1:12990/debian sid/main amd64 libclang1-10 amd64 1:10.0.0-4 [7609 kB]
Get:15 http://127.0.0.1:12990/debian sid/main amd64 clang-10 amd64 1:10.0.0-4 [105 kB]
Get:16 http://127.0.0.1:12990/debian sid/main amd64 libomp5-10 amd64 1:10.0.0-4 [338 kB]
Get:17 http://127.0.0.1:12990/debian sid/main amd64 libomp-10-dev amd64 1:10.0.0-4 [85.0 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 49.8 MB in 0s (138 MB/s)
Selecting previously unselected package libbsd0:amd64.
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(Reading database ... 12123 files and directories currently installed.)
Preparing to unpack .../00-libbsd0_0.10.0-1_amd64.deb ...
Unpacking libbsd0:amd64 (0.10.0-1) ...
Selecting previously unselected package libedit2:amd64.
Preparing to unpack .../01-libedit2_3.1-20191231-1_amd64.deb ...
Unpacking libedit2:amd64 (3.1-20191231-1) ...
Selecting previously unselected package libz3-4:amd64.
Preparing to unpack .../02-libz3-4_4.8.7-4_amd64.deb ...
Unpacking libz3-4:amd64 (4.8.7-4) ...
Selecting previously unselected package libllvm10:amd64.
Preparing to unpack .../03-libllvm10_1%3a10.0.0-4_amd64.deb ...
Unpacking libllvm10:amd64 (1:10.0.0-4) ...
Selecting previously unselected package libclang-cpp10.
Preparing to unpack .../04-libclang-cpp10_1%3a10.0.0-4_amd64.deb ...
Unpacking libclang-cpp10 (1:10.0.0-4) ...
Selecting previously unselected package libgc1c2:amd64.
Preparing to unpack .../05-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 .../06-libobjc4_10-20200418-1_amd64.deb ...
Unpacking libobjc4:amd64 (10-20200418-1) ...
Selecting previously unselected package libobjc-9-dev:amd64.
Preparing to unpack .../07-libobjc-9-dev_9.3.0-11_amd64.deb ...
Unpacking libobjc-9-dev:amd64 (9.3.0-11) ...
Selecting previously unselected package libc6-i386.
Preparing to unpack .../08-libc6-i386_2.30-4_amd64.deb ...
Unpacking libc6-i386 (2.30-4) ...
Selecting previously unselected package lib32gcc-s1.
Preparing to unpack .../09-lib32gcc-s1_10-20200418-1_amd64.deb ...
Unpacking lib32gcc-s1 (10-20200418-1) ...
Selecting previously unselected package lib32gcc1.
Preparing to unpack .../10-lib32gcc1_1%3a10-20200418-1_amd64.deb ...
Unpacking lib32gcc1 (1:10-20200418-1) ...
Selecting previously unselected package lib32stdc++6.
Preparing to unpack .../11-lib32stdc++6_10-20200418-1_amd64.deb ...
Unpacking lib32stdc++6 (10-20200418-1) ...
Selecting previously unselected package libclang-common-10-dev.
Preparing to unpack .../12-libclang-common-10-dev_1%3a10.0.0-4_amd64.deb ...
Unpacking libclang-common-10-dev (1:10.0.0-4) ...
Selecting previously unselected package libclang1-10.
Preparing to unpack .../13-libclang1-10_1%3a10.0.0-4_amd64.deb ...
Unpacking libclang1-10 (1:10.0.0-4) ...
Selecting previously unselected package clang-10.
Preparing to unpack .../14-clang-10_1%3a10.0.0-4_amd64.deb ...
Unpacking clang-10 (1:10.0.0-4) ...
Selecting previously unselected package libomp5-10:amd64.
Preparing to unpack .../15-libomp5-10_1%3a10.0.0-4_amd64.deb ...
Unpacking libomp5-10:amd64 (1:10.0.0-4) ...
Selecting previously unselected package libomp-10-dev.
Preparing to unpack .../16-libomp-10-dev_1%3a10.0.0-4_amd64.deb ...
Unpacking libomp-10-dev (1:10.0.0-4) ...
Setting up libgc1c2:amd64 (1:7.6.4-0.4) ...
Setting up libobjc4:amd64 (10-20200418-1) ...
Setting up libz3-4:amd64 (4.8.7-4) ...
Setting up libobjc-9-dev:amd64 (9.3.0-11) ...
Setting up libomp5-10:amd64 (1:10.0.0-4) ...
Setting up libc6-i386 (2.30-4) ...
Setting up libbsd0:amd64 (0.10.0-1) ...
Setting up libomp-10-dev (1:10.0.0-4) ...
Setting up libedit2:amd64 (3.1-20191231-1) ...
Setting up libllvm10:amd64 (1:10.0.0-4) ...
Setting up lib32gcc-s1 (10-20200418-1) ...
Setting up libclang1-10 (1:10.0.0-4) ...
Setting up lib32gcc1 (1:10-20200418-1) ...
Setting up libclang-cpp10 (1:10.0.0-4) ...
Setting up lib32stdc++6 (10-20200418-1) ...
Setting up libclang-common-10-dev (1:10.0.0-4) ...
Setting up clang-10 (1:10.0.0-4) ...
Processing triggers for libc-bin (2.30-4) ...
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 9 10'
+ cd /usr/bin
+ for VERSION in $VERSIONS
+ rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc
+ ln -s clang++-10 g++-4.6
+ ln -s clang-10 gcc-4.6
+ ln -s clang-10 cpp-4.6
+ ln -s clang-10 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++-10 g++-4.7
+ ln -s clang-10 gcc-4.7
+ ln -s clang-10 cpp-4.7
+ ln -s clang-10 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++-10 g++-4.8
+ ln -s clang-10 gcc-4.8
+ ln -s clang-10 cpp-4.8
+ ln -s clang-10 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++-10 g++-4.9
+ ln -s clang-10 gcc-4.9
+ ln -s clang-10 cpp-4.9
+ ln -s clang-10 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++-10 g++-5
+ ln -s clang-10 gcc-5
+ ln -s clang-10 cpp-5
+ ln -s clang-10 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++-10 g++-6
+ ln -s clang-10 gcc-6
+ ln -s clang-10 cpp-6
+ ln -s clang-10 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++-10 g++-7
+ ln -s clang-10 gcc-7
+ ln -s clang-10 cpp-7
+ ln -s clang-10 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++-10 g++-8
+ ln -s clang-10 gcc-8
+ ln -s clang-10 cpp-8
+ ln -s clang-10 gcc
+ echo 'gcc-8 hold'
+ dpkg --set-selections
dpkg: warning: package not in status nor available database at line 1: gcc-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++-8 hold'
+ dpkg --set-selections
dpkg: warning: package not in status nor available database at line 1: g++-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++-9 gcc-9 cpp-9 gcc
+ ln -s clang++-10 g++-9
+ ln -s clang-10 gcc-9
+ ln -s clang-10 cpp-9
+ ln -s clang-10 gcc
+ echo 'gcc-9 hold'
+ dpkg --set-selections
+ echo 'g++-9 hold'
+ dpkg --set-selections
+ for VERSION in $VERSIONS
+ rm -f g++-10 gcc-10 cpp-10 gcc
+ ln -s clang++-10 g++-10
+ ln -s clang-10 gcc-10
+ ln -s clang-10 cpp-10
+ ln -s clang-10 gcc
+ echo 'gcc-10 hold'
+ dpkg --set-selections
dpkg: warning: package not in status nor available database at line 1: gcc-10
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++-10 hold'
+ dpkg --set-selections
dpkg: warning: package not in status nor available database at line 1: g++-10
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>
+ cd -
/build/salmon-Hqv1E1
+ 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
+ cd /usr/bin/
+ rm -f clang++ clang
+ ln -s clang-10 clang++
+ ln -s clang-10 clang
+ clang++ --version
clang version 10.0.0-4 
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin
+ clang --version
clang version 10.0.0-4 
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin
+ cd -
/build/salmon-Hqv1E1
+ apt install --yes --no-install-recommends --force-yes qt5-qmake

WARNING: apt does not have a stable CLI interface. Use with caution in scripts.

Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  qt5-qmake-bin qtchooser
The following NEW packages will be installed:
  qt5-qmake qt5-qmake-bin qtchooser
0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded.
Need to get 1270 kB of archives.
After this operation, 4788 kB of additional disk space will be used.
Get:1 http://127.0.0.1:12990/debian sid/main amd64 qt5-qmake-bin amd64 5.12.5+dfsg-10 [1015 kB]
Get:2 http://127.0.0.1:12990/debian sid/main amd64 qtchooser amd64 66-2 [26.3 kB]
Get:3 http://127.0.0.1:12990/debian sid/main amd64 qt5-qmake amd64 5.12.5+dfsg-10 [229 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 1270 kB in 0s (20.5 MB/s)
Selecting previously unselected package qt5-qmake-bin.
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(Reading database ... 12968 files and directories currently installed.)
Preparing to unpack .../qt5-qmake-bin_5.12.5+dfsg-10_amd64.deb ...
Unpacking qt5-qmake-bin (5.12.5+dfsg-10) ...
Selecting previously unselected package qtchooser.
Preparing to unpack .../qtchooser_66-2_amd64.deb ...
Unpacking qtchooser (66-2) ...
Selecting previously unselected package qt5-qmake:amd64.
Preparing to unpack .../qt5-qmake_5.12.5+dfsg-10_amd64.deb ...
Unpacking qt5-qmake:amd64 (5.12.5+dfsg-10) ...
Setting up qt5-qmake-bin (5.12.5+dfsg-10) ...
Setting up qtchooser (66-2) ...
Setting up qt5-qmake:amd64 (5.12.5+dfsg-10) ...
W: --force-yes is deprecated, use one of the options starting with --allow instead.
+ cp /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/qmake.conf /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/qplatformdefs.h /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/
+ ls -al /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/
total 16
drwxr-xr-x  2 root root 4096 May  3 02:13 .
drwxr-xr-x 75 root root 4096 May  3 02:13 ..
-rw-r--r--  1 root root  276 May  3 02:13 qmake.conf
-rw-r--r--  1 root root 3218 May  3 02:13 qplatformdefs.h
+ cat /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/qmake.conf
#
# qmake configuration for linux-clang
#

MAKEFILE_GENERATOR = UNIX
CONFIG += incremental

QMAKE_INCREMENTAL_STYLE = sublib

include(../common/linux.conf)
include(../common/gcc-base-unix.conf)
include(../common/clang.conf)

QMAKE_LFLAGS += -ccc-gcc-name g++

load(qt_config)
+ export QMAKESPEC=/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/
+ QMAKESPEC=/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/
+ sed -i -e 's|compare_problem(2,|compare_problem(0,|g' /usr/bin/dpkg-gensymbols
+ sed -i -e 's|compare_problem(1,|compare_problem(0,|g' /usr/bin/dpkg-gensymbols
+ grep 'compare_problem(' /usr/bin/dpkg-gensymbols
        compare_problem(4, g_('new libraries appeared in the symbols file: %s'), "@libs");
        compare_problem(3, g_('some libraries disappeared in the symbols file: %s'), "@libs");
        compare_problem(0, g_('some new symbols appeared in the symbols file: %s'),
        compare_problem(0, g_('some symbols or patterns disappeared in the symbols file: %s'),

I: Finished running '/tmp/clang10'.

Finished processing commands.
--------------------------------------------------------------------------------
I: NOTICE: Log filtering will replace 'build/salmon-Hqv1E1/resolver-Xz3K0W' with '<<RESOLVERDIR>>'

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

Hit:1 http://127.0.0.1:12990/debian sid InRelease
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

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


Check APT
---------

Checking available source versions...

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

Reading package lists...
NOTICE: 'salmon' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/salmon.git
Please use:
git clone https://salsa.debian.org/med-team/salmon.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 6460 kB of source archives.
Get:1 http://127.0.0.1:12990/debian sid/main salmon 1.2.1+ds1-1 (dsc) [2478 B]
Get:2 http://127.0.0.1:12990/debian sid/main salmon 1.2.1+ds1-1 (tar) [5502 kB]
Get:3 http://127.0.0.1:12990/debian sid/main salmon 1.2.1+ds1-1 (diff) [955 kB]
Fetched 6460 kB in 0s (41.1 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/salmon-Hqv1E1/salmon-1.2.1+ds1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/salmon-Hqv1E1' with '<<BUILDDIR>>'

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


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

Merged Build-Depends: debhelper-compat (= 12), cmake, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, libboost-thread-dev, libboost-program-options-dev, libboost-timer-dev, libjellyfish-2.0-dev (>> 2.2.3-2), libpthread-stubs0-dev, libsparsehash-dev, libdivsufsort-dev, libbwa-dev, pkg-config, libjemalloc-dev, libcereal-dev, libtbb-dev, libgff-dev, libstaden-read-dev, libspdlog-dev, libtclap-dev, help2man, sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, zlib1g-dev, libeigen3-dev, libbz2-dev, liblzma-dev, rapmap-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 12), cmake, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, libboost-thread-dev, libboost-program-options-dev, libboost-timer-dev, libjellyfish-2.0-dev (>> 2.2.3-2), libpthread-stubs0-dev, libsparsehash-dev, libdivsufsort-dev, libbwa-dev, pkg-config, libjemalloc-dev, libcereal-dev, libtbb-dev, libgff-dev, libstaden-read-dev, libspdlog-dev, libtclap-dev, help2man, sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, zlib1g-dev, libeigen3-dev, libbz2-dev, liblzma-dev, rapmap-dev, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [963 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [580 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [664 B]
Fetched 2207 B in 0s (0 B/s)
Reading package lists...
Reading package lists...

Install main 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 ca-certificates cmake
  cmake-data debhelper dh-autoreconf dh-strip-nondeterminism docutils-common
  docutils-doc dwz file fonts-font-awesome fonts-lato fonts-mathjax gettext
  gettext-base groff-base help2man icu-devtools intltool-debian
  libarchive-zip-perl libarchive13 libboost-atomic1.67-dev
  libboost-atomic1.67.0 libboost-chrono1.67-dev libboost-chrono1.67.0
  libboost-date-time1.67-dev libboost-date-time1.67.0 libboost-filesystem-dev
  libboost-filesystem1.67-dev libboost-filesystem1.67.0 libboost-iostreams-dev
  libboost-iostreams1.67-dev libboost-iostreams1.67.0
  libboost-program-options-dev libboost-program-options1.67-dev
  libboost-program-options1.67.0 libboost-regex1.67-dev libboost-regex1.67.0
  libboost-serialization1.67-dev libboost-serialization1.67.0
  libboost-system-dev libboost-system1.67-dev libboost-system1.67.0
  libboost-thread-dev libboost-thread1.67-dev libboost-thread1.67.0
  libboost-timer-dev libboost-timer1.67-dev libboost-timer1.67.0
  libboost1.67-dev libbrotli1 libbwa-dev libbz2-dev libcereal-dev libcroco3
  libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl
  libdivsufsort-dev libdivsufsort3 libeigen3-dev libelf1 libexpat1
  libfile-stripnondeterminism-perl libfmt-dev libgff-dev libglib2.0-0
  libgssapi-krb5-2 libicu-dev libicu63 libjellyfish-2.0-2 libjellyfish-2.0-dev
  libjemalloc-dev libjemalloc2 libjs-jquery libjs-mathjax libjs-modernizr
  libjs-sphinxdoc libjs-underscore libjsoncpp1 libk5crypto3 libkeyutils1
  libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common
  liblocale-gettext-perl liblzma-dev libmagic-mgc libmagic1 libmpdec2
  libncurses6 libnghttp2-14 libpipeline1 libprocps8 libpsl5
  libpthread-stubs0-dev libpython3-stdlib libpython3.8-minimal
  libpython3.8-stdlib libreadline8 librhash0 librtmp1 libsasl2-2
  libsasl2-modules-db libsigsegv2 libsparsehash-dev libspdlog-dev libspdlog1
  libsqlite3-0 libssh2-1 libssl1.1 libstaden-read-dev libstaden-read13
  libsub-override-perl libtbb-dev libtbb2 libtclap-dev libtool libuchardet0
  libuv1 libxml2 m4 man-db mime-support openssl pkg-config po-debconf procps
  python-babel-localedata python3 python3-alabaster python3-babel
  python3-certifi python3-chardet python3-distutils python3-docutils
  python3-idna python3-imagesize python3-jinja2 python3-lib2to3
  python3-markupsafe python3-minimal python3-packaging python3-pkg-resources
  python3-pygments python3-pyparsing python3-requests python3-roman
  python3-six python3-sphinx python3-sphinx-rtd-theme python3-tz
  python3-urllib3 python3.8 python3.8-minimal rapmap-dev readline-common
  sensible-utils sgml-base sphinx-common sphinx-doc sphinx-rtd-theme-common
  xml-core zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation cmake-doc ninja-build dh-make gettext-doc libasprintf-dev
  libgettextpo-dev groff lrzip libboost1.67-doc libboost-container1.67-dev
  libboost-context1.67-dev libboost-contract1.67-dev
  libboost-coroutine1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev
  libboost-graph1.67-dev libboost-graph-parallel1.67-dev
  libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev
  libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev
  libboost-python1.67-dev libboost-random1.67-dev libboost-signals1.67-dev
  libboost-stacktrace1.67-dev libboost-test1.67-dev
  libboost-type-erasure1.67-dev libboost-wave1.67-dev libboost1.67-tools-dev
  libmpfrc++-dev libntl-dev samtools libcurl4-doc libgnutls28-dev libidn11-dev
  libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev libeigen3-doc libfmt-doc
  krb5-doc krb5-user icu-doc fonts-mathjax-extras fonts-stix libjs-mathjax-doc
  liblzma-doc libtbb-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
  m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk
  python3-venv fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french
  texlive-latex-base texlive-latex-recommended python-jinja2-doc
  python3-setuptools python-pygments-doc ttf-bitstream-vera
  python-pyparsing-doc python3-cryptography python3-openssl python3-socks
  python-requests-doc dvipng fonts-freefont-otf imagemagick-6.q16 latexmk
  python3-stemmer texlive-fonts-recommended texlive-latex-extra
  texlive-plain-generic python3.8-venv python3.8-doc binfmt-support
  readline-doc sgml-base-doc
Recommended packages:
  curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data
  shared-mime-info xdg-user-dirs javascript-common krb5-locales libgpm2
  publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl psmisc
  libpaper-utils python3-pil
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils ca-certificates cmake
  cmake-data debhelper dh-autoreconf dh-strip-nondeterminism docutils-common
  docutils-doc dwz file fonts-font-awesome fonts-lato fonts-mathjax gettext
  gettext-base groff-base help2man icu-devtools intltool-debian
  libarchive-zip-perl libarchive13 libboost-atomic1.67-dev
  libboost-atomic1.67.0 libboost-chrono1.67-dev libboost-chrono1.67.0
  libboost-date-time1.67-dev libboost-date-time1.67.0 libboost-filesystem-dev
  libboost-filesystem1.67-dev libboost-filesystem1.67.0 libboost-iostreams-dev
  libboost-iostreams1.67-dev libboost-iostreams1.67.0
  libboost-program-options-dev libboost-program-options1.67-dev
  libboost-program-options1.67.0 libboost-regex1.67-dev libboost-regex1.67.0
  libboost-serialization1.67-dev libboost-serialization1.67.0
  libboost-system-dev libboost-system1.67-dev libboost-system1.67.0
  libboost-thread-dev libboost-thread1.67-dev libboost-thread1.67.0
  libboost-timer-dev libboost-timer1.67-dev libboost-timer1.67.0
  libboost1.67-dev libbrotli1 libbwa-dev libbz2-dev libcereal-dev libcroco3
  libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl
  libdivsufsort-dev libdivsufsort3 libeigen3-dev libelf1 libexpat1
  libfile-stripnondeterminism-perl libfmt-dev libgff-dev libglib2.0-0
  libgssapi-krb5-2 libicu-dev libicu63 libjellyfish-2.0-2 libjellyfish-2.0-dev
  libjemalloc-dev libjemalloc2 libjs-jquery libjs-mathjax libjs-modernizr
  libjs-sphinxdoc libjs-underscore libjsoncpp1 libk5crypto3 libkeyutils1
  libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common
  liblocale-gettext-perl liblzma-dev libmagic-mgc libmagic1 libmpdec2
  libncurses6 libnghttp2-14 libpipeline1 libprocps8 libpsl5
  libpthread-stubs0-dev libpython3-stdlib libpython3.8-minimal
  libpython3.8-stdlib libreadline8 librhash0 librtmp1 libsasl2-2
  libsasl2-modules-db libsigsegv2 libsparsehash-dev libspdlog-dev libspdlog1
  libsqlite3-0 libssh2-1 libssl1.1 libstaden-read-dev libstaden-read13
  libsub-override-perl libtbb-dev libtbb2 libtclap-dev libtool libuchardet0
  libuv1 libxml2 m4 man-db mime-support openssl pkg-config po-debconf procps
  python-babel-localedata python3 python3-alabaster python3-babel
  python3-certifi python3-chardet python3-distutils python3-docutils
  python3-idna python3-imagesize python3-jinja2 python3-lib2to3
  python3-markupsafe python3-minimal python3-packaging python3-pkg-resources
  python3-pygments python3-pyparsing python3-requests python3-roman
  python3-six python3-sphinx python3-sphinx-rtd-theme python3-tz
  python3-urllib3 python3.8 python3.8-minimal rapmap-dev readline-common
  sbuild-build-depends-main-dummy sensible-utils sgml-base sphinx-common
  sphinx-doc sphinx-rtd-theme-common xml-core zlib1g-dev
0 upgraded, 172 newly installed, 0 to remove and 0 not upgraded.
Need to get 90.4 MB of archives.
After this operation, 514 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1092 B]
Get:2 http://127.0.0.1:12990/debian sid/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB]
Get:3 http://127.0.0.1:12990/debian sid/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB]
Get:4 http://127.0.0.1:12990/debian sid/main amd64 groff-base amd64 1.22.4-4 [919 kB]
Get:5 http://127.0.0.1:12990/debian sid/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB]
Get:6 http://127.0.0.1:12990/debian sid/main amd64 man-db amd64 2.9.1-1 [1308 kB]
Get:7 http://127.0.0.1:12990/debian sid/main amd64 fonts-lato all 2.0-2 [2698 kB]
Get:8 http://127.0.0.1:12990/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB]
Get:9 http://127.0.0.1:12990/debian sid/main amd64 libssl1.1 amd64 1.1.1g-1 [1543 kB]
Get:10 http://127.0.0.1:12990/debian sid/main amd64 libpython3.8-minimal amd64 3.8.3~rc1-1 [760 kB]
Get:11 http://127.0.0.1:12990/debian sid/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB]
Get:12 http://127.0.0.1:12990/debian sid/main amd64 python3.8-minimal amd64 3.8.3~rc1-1 [1944 kB]
Get:13 http://127.0.0.1:12990/debian sid/main amd64 python3-minimal amd64 3.8.2-3 [37.6 kB]
Get:14 http://127.0.0.1:12990/debian sid/main amd64 mime-support all 3.64 [37.8 kB]
Get:15 http://127.0.0.1:12990/debian sid/main amd64 libmpdec2 amd64 2.4.2-3 [84.1 kB]
Get:16 http://127.0.0.1:12990/debian sid/main amd64 readline-common all 8.0-4 [72.5 kB]
Get:17 http://127.0.0.1:12990/debian sid/main amd64 libreadline8 amd64 8.0-4 [160 kB]
Get:18 http://127.0.0.1:12990/debian sid/main amd64 libsqlite3-0 amd64 3.31.1-5 [661 kB]
Get:19 http://127.0.0.1:12990/debian sid/main amd64 libpython3.8-stdlib amd64 3.8.3~rc1-1 [1667 kB]
Get:20 http://127.0.0.1:12990/debian sid/main amd64 python3.8 amd64 3.8.3~rc1-1 [415 kB]
Get:21 http://127.0.0.1:12990/debian sid/main amd64 libpython3-stdlib amd64 3.8.2-3 [20.8 kB]
Get:22 http://127.0.0.1:12990/debian sid/main amd64 python3 amd64 3.8.2-3 [63.7 kB]
Get:23 http://127.0.0.1:12990/debian sid/main amd64 sgml-base all 1.30 [15.1 kB]
Get:24 http://127.0.0.1:12990/debian sid/main amd64 libncurses6 amd64 6.2-1 [102 kB]
Get:25 http://127.0.0.1:12990/debian sid/main amd64 libprocps8 amd64 2:3.3.16-4 [62.7 kB]
Get:26 http://127.0.0.1:12990/debian sid/main amd64 procps amd64 2:3.3.16-4 [262 kB]
Get:27 http://127.0.0.1:12990/debian sid/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:28 http://127.0.0.1:12990/debian sid/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB]
Get:29 http://127.0.0.1:12990/debian sid/main amd64 libmagic1 amd64 1:5.38-4 [120 kB]
Get:30 http://127.0.0.1:12990/debian sid/main amd64 file amd64 1:5.38-4 [67.9 kB]
Get:31 http://127.0.0.1:12990/debian sid/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB]
Get:32 http://127.0.0.1:12990/debian sid/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB]
Get:33 http://127.0.0.1:12990/debian sid/main amd64 m4 amd64 1.4.18-4 [203 kB]
Get:34 http://127.0.0.1:12990/debian sid/main amd64 autoconf all 2.69-11.1 [341 kB]
Get:35 http://127.0.0.1:12990/debian sid/main amd64 autotools-dev all 20180224.1 [77.0 kB]
Get:36 http://127.0.0.1:12990/debian sid/main amd64 automake all 1:1.16.2-1 [775 kB]
Get:37 http://127.0.0.1:12990/debian sid/main amd64 autopoint all 0.19.8.1-10 [435 kB]
Get:38 http://127.0.0.1:12990/debian sid/main amd64 openssl amd64 1.1.1g-1 [846 kB]
Get:39 http://127.0.0.1:12990/debian sid/main amd64 ca-certificates all 20190110 [157 kB]
Get:40 http://127.0.0.1:12990/debian sid/main amd64 cmake-data all 3.16.3-2 [1628 kB]
Get:41 http://127.0.0.1:12990/debian sid/main amd64 libicu63 amd64 63.2-3 [8296 kB]
Get:42 http://127.0.0.1:12990/debian sid/main amd64 libxml2 amd64 2.9.10+dfsg-5 [709 kB]
Get:43 http://127.0.0.1:12990/debian sid/main amd64 libarchive13 amd64 3.4.0-2 [335 kB]
Get:44 http://127.0.0.1:12990/debian sid/main amd64 libbrotli1 amd64 1.0.7-6.1 [267 kB]
Get:45 http://127.0.0.1:12990/debian sid/main amd64 libkrb5support0 amd64 1.17-7 [64.4 kB]
Get:46 http://127.0.0.1:12990/debian sid/main amd64 libk5crypto3 amd64 1.17-7 [115 kB]
Get:47 http://127.0.0.1:12990/debian sid/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB]
Get:48 http://127.0.0.1:12990/debian sid/main amd64 libkrb5-3 amd64 1.17-7 [366 kB]
Get:49 http://127.0.0.1:12990/debian sid/main amd64 libgssapi-krb5-2 amd64 1.17-7 [156 kB]
Get:50 http://127.0.0.1:12990/debian sid/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2 [69.0 kB]
Get:51 http://127.0.0.1:12990/debian sid/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2 [106 kB]
Get:52 http://127.0.0.1:12990/debian sid/main amd64 libldap-common all 2.4.50+dfsg-1 [92.9 kB]
Get:53 http://127.0.0.1:12990/debian sid/main amd64 libldap-2.4-2 amd64 2.4.50+dfsg-1 [228 kB]
Get:54 http://127.0.0.1:12990/debian sid/main amd64 libnghttp2-14 amd64 1.40.0-1 [85.0 kB]
Get:55 http://127.0.0.1:12990/debian sid/main amd64 libpsl5 amd64 0.21.0-1 [55.1 kB]
Get:56 http://127.0.0.1:12990/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b1 [60.8 kB]
Get:57 http://127.0.0.1:12990/debian sid/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB]
Get:58 http://127.0.0.1:12990/debian sid/main amd64 libcurl4 amd64 7.68.0-1 [321 kB]
Get:59 http://127.0.0.1:12990/debian sid/main amd64 libjsoncpp1 amd64 1.7.4-3.1 [77.6 kB]
Get:60 http://127.0.0.1:12990/debian sid/main amd64 librhash0 amd64 1.3.9-1 [123 kB]
Get:61 http://127.0.0.1:12990/debian sid/main amd64 libuv1 amd64 1.35.0-2 [128 kB]
Get:62 http://127.0.0.1:12990/debian sid/main amd64 cmake amd64 3.16.3-2 [3675 kB]
Get:63 http://127.0.0.1:12990/debian sid/main amd64 libtool all 2.4.6-14 [513 kB]
Get:64 http://127.0.0.1:12990/debian sid/main amd64 dh-autoreconf all 19 [16.9 kB]
Get:65 http://127.0.0.1:12990/debian sid/main amd64 libdebhelper-perl all 13 [184 kB]
Get:66 http://127.0.0.1:12990/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:67 http://127.0.0.1:12990/debian sid/main amd64 libsub-override-perl all 0.09-2 [10.2 kB]
Get:68 http://127.0.0.1:12990/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.8.0-1 [24.2 kB]
Get:69 http://127.0.0.1:12990/debian sid/main amd64 dh-strip-nondeterminism all 1.8.0-1 [14.8 kB]
Get:70 http://127.0.0.1:12990/debian sid/main amd64 libelf1 amd64 0.176-1.1 [161 kB]
Get:71 http://127.0.0.1:12990/debian sid/main amd64 dwz amd64 0.13-5 [151 kB]
Get:72 http://127.0.0.1:12990/debian sid/main amd64 libglib2.0-0 amd64 2.64.2-1 [1343 kB]
Get:73 http://127.0.0.1:12990/debian sid/main amd64 libcroco3 amd64 0.6.13-1 [146 kB]
Get:74 http://127.0.0.1:12990/debian sid/main amd64 gettext amd64 0.19.8.1-10 [1303 kB]
Get:75 http://127.0.0.1:12990/debian sid/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:76 http://127.0.0.1:12990/debian sid/main amd64 po-debconf all 1.0.21 [248 kB]
Get:77 http://127.0.0.1:12990/debian sid/main amd64 debhelper all 13 [1002 kB]
Get:78 http://127.0.0.1:12990/debian sid/main amd64 xml-core all 0.18+nmu1 [23.8 kB]
Get:79 http://127.0.0.1:12990/debian sid/main amd64 docutils-common all 0.16+dfsg-2 [129 kB]
Get:80 http://127.0.0.1:12990/debian sid/main amd64 docutils-doc all 0.16+dfsg-2 [932 kB]
Get:81 http://127.0.0.1:12990/debian sid/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-1 [515 kB]
Get:82 http://127.0.0.1:12990/debian sid/main amd64 fonts-mathjax all 2.7.4+dfsg-1 [2209 kB]
Get:83 http://127.0.0.1:12990/debian sid/main amd64 help2man amd64 1.47.15 [181 kB]
Get:84 http://127.0.0.1:12990/debian sid/main amd64 icu-devtools amd64 63.2-3 [189 kB]
Get:85 http://127.0.0.1:12990/debian sid/main amd64 libboost1.67-dev amd64 1.67.0-17+b1 [8389 kB]
Get:86 http://127.0.0.1:12990/debian sid/main amd64 libboost-atomic1.67.0 amd64 1.67.0-17+b1 [226 kB]
Get:87 http://127.0.0.1:12990/debian sid/main amd64 libboost-atomic1.67-dev amd64 1.67.0-17+b1 [225 kB]
Get:88 http://127.0.0.1:12990/debian sid/main amd64 libboost-system1.67.0 amd64 1.67.0-17+b1 [230 kB]
Get:89 http://127.0.0.1:12990/debian sid/main amd64 libboost-chrono1.67.0 amd64 1.67.0-17+b1 [234 kB]
Get:90 http://127.0.0.1:12990/debian sid/main amd64 libboost-chrono1.67-dev amd64 1.67.0-17+b1 [237 kB]
Get:91 http://127.0.0.1:12990/debian sid/main amd64 libboost-date-time1.67.0 amd64 1.67.0-17+b1 [239 kB]
Get:92 http://127.0.0.1:12990/debian sid/main amd64 libboost-serialization1.67.0 amd64 1.67.0-17+b1 [317 kB]
Get:93 http://127.0.0.1:12990/debian sid/main amd64 libboost-serialization1.67-dev amd64 1.67.0-17+b1 [358 kB]
Get:94 http://127.0.0.1:12990/debian sid/main amd64 libboost-date-time1.67-dev amd64 1.67.0-17+b1 [248 kB]
Get:95 http://127.0.0.1:12990/debian sid/main amd64 libboost-filesystem1.67.0 amd64 1.67.0-17+b1 [261 kB]
Get:96 http://127.0.0.1:12990/debian sid/main amd64 libboost-system1.67-dev amd64 1.67.0-17+b1 [232 kB]
Get:97 http://127.0.0.1:12990/debian sid/main amd64 libboost-filesystem1.67-dev amd64 1.67.0-17+b1 [269 kB]
Get:98 http://127.0.0.1:12990/debian sid/main amd64 libboost-filesystem-dev amd64 1.67.0.2+b1 [4312 B]
Get:99 http://127.0.0.1:12990/debian sid/main amd64 libboost-regex1.67.0 amd64 1.67.0-17+b1 [513 kB]
Get:100 http://127.0.0.1:12990/debian sid/main amd64 libicu-dev amd64 63.2-3 [9184 kB]
Get:101 http://127.0.0.1:12990/debian sid/main amd64 libboost-regex1.67-dev amd64 1.67.0-17+b1 [568 kB]
Get:102 http://127.0.0.1:12990/debian sid/main amd64 libboost-iostreams1.67.0 amd64 1.67.0-17+b1 [250 kB]
Get:103 http://127.0.0.1:12990/debian sid/main amd64 libboost-iostreams1.67-dev amd64 1.67.0-17+b1 [256 kB]
Get:104 http://127.0.0.1:12990/debian sid/main amd64 libboost-iostreams-dev amd64 1.67.0.2+b1 [4260 B]
Get:105 http://127.0.0.1:12990/debian sid/main amd64 libboost-program-options1.67.0 amd64 1.67.0-17+b1 [356 kB]
Get:106 http://127.0.0.1:12990/debian sid/main amd64 libboost-program-options1.67-dev amd64 1.67.0-17+b1 [381 kB]
Get:107 http://127.0.0.1:12990/debian sid/main amd64 libboost-program-options-dev amd64 1.67.0.2+b1 [4288 B]
Get:108 http://127.0.0.1:12990/debian sid/main amd64 libboost-system-dev amd64 1.67.0.2+b1 [4416 B]
Get:109 http://127.0.0.1:12990/debian sid/main amd64 libboost-thread1.67.0 amd64 1.67.0-17+b1 [270 kB]
Get:110 http://127.0.0.1:12990/debian sid/main amd64 libboost-thread1.67-dev amd64 1.67.0-17+b1 [272 kB]
Get:111 http://127.0.0.1:12990/debian sid/main amd64 libboost-thread-dev amd64 1.67.0.2+b1 [4308 B]
Get:112 http://127.0.0.1:12990/debian sid/main amd64 libboost-timer1.67.0 amd64 1.67.0-17+b1 [232 kB]
Get:113 http://127.0.0.1:12990/debian sid/main amd64 libboost-timer1.67-dev amd64 1.67.0-17+b1 [232 kB]
Get:114 http://127.0.0.1:12990/debian sid/main amd64 libboost-timer-dev amd64 1.67.0.2+b1 [4404 B]
Get:115 http://127.0.0.1:12990/debian sid/main amd64 libbwa-dev amd64 0.7.17-5 [146 kB]
Get:116 http://127.0.0.1:12990/debian sid/main amd64 libbz2-dev amd64 1.0.8-2 [30.1 kB]
Get:117 http://127.0.0.1:12990/debian sid/main amd64 libcereal-dev all 1.3.0-3 [299 kB]
Get:118 http://127.0.0.1:12990/debian sid/main amd64 libcurl3-gnutls amd64 7.68.0-1 [319 kB]
Get:119 http://127.0.0.1:12990/debian sid/main amd64 libcurl4-gnutls-dev amd64 7.68.0-1 [408 kB]
Get:120 http://127.0.0.1:12990/debian sid/main amd64 libdivsufsort3 amd64 2.0.1-4 [44.5 kB]
Get:121 http://127.0.0.1:12990/debian sid/main amd64 libdivsufsort-dev amd64 2.0.1-4 [27.4 kB]
Get:122 http://127.0.0.1:12990/debian sid/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB]
Get:123 http://127.0.0.1:12990/debian sid/main amd64 libeigen3-dev all 3.3.7-2 [850 kB]
Get:124 http://127.0.0.1:12990/debian sid/main amd64 libfmt-dev amd64 6.1.2+ds-2 [186 kB]
Get:125 http://127.0.0.1:12990/debian sid/main amd64 libgff-dev amd64 1.0-2 [138 kB]
Get:126 http://127.0.0.1:12990/debian sid/main amd64 libjellyfish-2.0-2 amd64 2.3.0-4+b1 [64.1 kB]
Get:127 http://127.0.0.1:12990/debian sid/main amd64 libjellyfish-2.0-dev amd64 2.3.0-4+b1 [134 kB]
Get:128 http://127.0.0.1:12990/debian sid/main amd64 libjemalloc2 amd64 5.2.1-1 [259 kB]
Get:129 http://127.0.0.1:12990/debian sid/main amd64 libjemalloc-dev amd64 5.2.1-1 [452 kB]
Get:130 http://127.0.0.1:12990/debian sid/main amd64 libjs-jquery all 3.3.1~dfsg-3 [332 kB]
Get:131 http://127.0.0.1:12990/debian sid/main amd64 libjs-mathjax all 2.7.4+dfsg-1 [5658 kB]
Get:132 http://127.0.0.1:12990/debian sid/main amd64 libjs-modernizr all 2.6.2+ds1-3 [46.7 kB]
Get:133 http://127.0.0.1:12990/debian sid/main amd64 libjs-underscore all 1.9.1~dfsg-1 [99.4 kB]
Get:134 http://127.0.0.1:12990/debian sid/main amd64 libjs-sphinxdoc all 2.4.3-2 [110 kB]
Get:135 http://127.0.0.1:12990/debian sid/main amd64 liblzma-dev amd64 5.2.4-1+b1 [211 kB]
Get:136 http://127.0.0.1:12990/debian sid/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B]
Get:137 http://127.0.0.1:12990/debian sid/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB]
Get:138 http://127.0.0.1:12990/debian sid/main amd64 libspdlog1 amd64 1:1.5.0+ds-3 [168 kB]
Get:139 http://127.0.0.1:12990/debian sid/main amd64 libspdlog-dev amd64 1:1.5.0+ds-3 [166 kB]
Get:140 http://127.0.0.1:12990/debian sid/main amd64 libstaden-read13 amd64 1.14.11-6 [280 kB]
Get:141 http://127.0.0.1:12990/debian sid/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB]
Get:142 http://127.0.0.1:12990/debian sid/main amd64 libstaden-read-dev amd64 1.14.11-6 [361 kB]
Get:143 http://127.0.0.1:12990/debian sid/main amd64 libtbb2 amd64 2020.2-2 [160 kB]
Get:144 http://127.0.0.1:12990/debian sid/main amd64 libtbb-dev amd64 2020.2-2 [312 kB]
Get:145 http://127.0.0.1:12990/debian sid/main amd64 libtclap-dev amd64 1.2.2-1+b1 [139 kB]
Get:146 http://127.0.0.1:12990/debian sid/main amd64 python-babel-localedata all 2.8.0+dfsg.1-3 [4998 kB]
Get:147 http://127.0.0.1:12990/debian sid/main amd64 python3-alabaster all 0.7.8-1.1 [18.6 kB]
Get:148 http://127.0.0.1:12990/debian sid/main amd64 python3-pkg-resources all 46.1.3-1 [183 kB]
Get:149 http://127.0.0.1:12990/debian sid/main amd64 python3-tz all 2019.3-2 [27.3 kB]
Get:150 http://127.0.0.1:12990/debian sid/main amd64 python3-babel all 2.8.0+dfsg.1-3 [99.8 kB]
Get:151 http://127.0.0.1:12990/debian sid/main amd64 python3-certifi all 2019.11.28-2 [149 kB]
Get:152 http://127.0.0.1:12990/debian sid/main amd64 python3-chardet all 3.0.4-7 [81.1 kB]
Get:153 http://127.0.0.1:12990/debian sid/main amd64 python3-lib2to3 all 3.8.2-2 [78.4 kB]
Get:154 http://127.0.0.1:12990/debian sid/main amd64 python3-distutils all 3.8.2-2 [145 kB]
Get:155 http://127.0.0.1:12990/debian sid/main amd64 python3-roman all 2.0.0-4 [8972 B]
Get:156 http://127.0.0.1:12990/debian sid/main amd64 python3-docutils all 0.16+dfsg-2 [383 kB]
Get:157 http://127.0.0.1:12990/debian sid/main amd64 python3-idna all 2.9-1 [37.1 kB]
Get:158 http://127.0.0.1:12990/debian sid/main amd64 python3-imagesize all 1.2.0-2 [5824 B]
Get:159 http://127.0.0.1:12990/debian sid/main amd64 python3-markupsafe amd64 1.1.1-1+b1 [15.2 kB]
Get:160 http://127.0.0.1:12990/debian sid/main amd64 python3-jinja2 all 2.11.1-1 [114 kB]
Get:161 http://127.0.0.1:12990/debian sid/main amd64 python3-pyparsing all 2.4.7-1 [109 kB]
Get:162 http://127.0.0.1:12990/debian sid/main amd64 python3-six all 1.14.0-3 [16.7 kB]
Get:163 http://127.0.0.1:12990/debian sid/main amd64 python3-packaging all 20.3-1.2 [29.9 kB]
Get:164 http://127.0.0.1:12990/debian sid/main amd64 python3-pygments all 2.3.1+dfsg-3 [596 kB]
Get:165 http://127.0.0.1:12990/debian sid/main amd64 python3-urllib3 all 1.25.9-1 [105 kB]
Get:166 http://127.0.0.1:12990/debian sid/main amd64 python3-requests all 2.23.0+dfsg-2 [71.4 kB]
Get:167 http://127.0.0.1:12990/debian sid/main amd64 sphinx-common all 2.4.3-2 [550 kB]
Get:168 http://127.0.0.1:12990/debian sid/main amd64 python3-sphinx all 2.4.3-2 [502 kB]
Get:169 http://127.0.0.1:12990/debian sid/main amd64 sphinx-rtd-theme-common all 0.4.3+dfsg-3 [993 kB]
Get:170 http://127.0.0.1:12990/debian sid/main amd64 python3-sphinx-rtd-theme all 0.4.3+dfsg-3 [9928 B]
Get:171 http://127.0.0.1:12990/debian sid/main amd64 rapmap-dev all 0.15.0+dfsg-1 [194 kB]
Get:172 http://127.0.0.1:12990/debian sid/main amd64 sphinx-doc all 2.4.3-2 [1898 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libexpat1:amd64 (2.2.9-1) ...
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Setting up python3-sphinx (2.4.3-2) ...
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update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-quickstart to provide /usr/bin/sphinx-quickstart (sphinx-quickstart) in auto mode
Setting up python3-sphinx-rtd-theme (0.4.3+dfsg-3) ...
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Processing triggers for ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.

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

Arch check ok (amd64 included in any)

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

Kernel: Linux 4.19.0-6-cloud-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) amd64 (x86_64)
Toolchain package versions: binutils_2.34-6 dpkg-dev_1.19.7 g++-9_9.3.0-11 gcc-9_9.3.0-11 libc6-dev_2.30-4 libstdc++-9-dev_9.3.0-11 libstdc++6_10-20200418-1 linux-libc-dev_5.6.7-1
Package versions: adduser_3.118 apt_2.0.2 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-6 binutils-common_2.34-6 binutils-x86-64-linux-gnu_2.34-6 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 ca-certificates_20190110 clang-10_1:10.0.0-4 cmake_3.16.3-2 cmake-data_3.16.3-2 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-9_9.3.0-11 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.8.0-1 diffutils_1:3.7-3 docutils-common_0.16+dfsg-2 docutils-doc_0.16+dfsg-2 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 fonts-font-awesome_5.0.10+really4.7.0~dfsg-1 fonts-lato_2.0-2 fonts-mathjax_2.7.4+dfsg-1 g++_4:9.2.1-3.1 g++-9_9.3.0-11 gcc_4:9.2.1-3.1 gcc-10-base_10-20200418-1 gcc-9_9.3.0-11 gcc-9-base_9.3.0-11 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libboost-program-options-dev_1.67.0.2+b1 libboost-program-options1.67-dev_1.67.0-17+b1 libboost-program-options1.67.0_1.67.0-17+b1 libboost-regex1.67-dev_1.67.0-17+b1 libboost-regex1.67.0_1.67.0-17+b1 libboost-serialization1.67-dev_1.67.0-17+b1 libboost-serialization1.67.0_1.67.0-17+b1 libboost-system-dev_1.67.0.2+b1 libboost-system1.67-dev_1.67.0-17+b1 libboost-system1.67.0_1.67.0-17+b1 libboost-thread-dev_1.67.0.2+b1 libboost-thread1.67-dev_1.67.0-17+b1 libboost-thread1.67.0_1.67.0-17+b1 libboost-timer-dev_1.67.0.2+b1 libboost-timer1.67-dev_1.67.0-17+b1 libboost-timer1.67.0_1.67.0-17+b1 libboost1.67-dev_1.67.0-17+b1 libbrotli1_1.0.7-6.1 libbsd0_0.10.0-1 libbwa-dev_0.7.17-5 libbz2-1.0_1.0.8-2 libbz2-dev_1.0.8-2 libc-bin_2.30-4 libc-dev-bin_2.30-4 libc6_2.30-4 libc6-dev_2.30-4 libc6-i386_2.30-4 libcap-ng0_0.7.9-2.1+b2 libcc1-0_10-20200418-1 libcereal-dev_1.3.0-3 libclang-common-10-dev_1:10.0.0-4 libclang-cpp10_1:10.0.0-4 libclang1-10_1:10.0.0-4 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-6 libctf0_2.34-6 libcurl3-gnutls_7.68.0-1 libcurl4_7.68.0-1 libcurl4-gnutls-dev_7.68.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_13 libdivsufsort-dev_2.0.1-4 libdivsufsort3_2.0.1-4 libdpkg-perl_1.19.7 libedit2_3.1-20191231-1 libeigen3-dev_3.3.7-2 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.0-1 libfmt-dev_6.1.2+ds-2 libgc1c2_1:7.6.4-0.4 libgcc-9-dev_9.3.0-11 libgcc-s1_10-20200418-1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgff-dev_1.0-2 libglib2.0-0_2.64.2-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10-20200418-1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-7 libhogweed5_3.5.1+really3.5.1-2 libicu-dev_63.2-3 libicu63_63.2-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libitm1_10-20200418-1 libjellyfish-2.0-2_2.3.0-4+b1 libjellyfish-2.0-dev_2.3.0-4+b1 libjemalloc-dev_5.2.1-1 libjemalloc2_5.2.1-1 libjs-jquery_3.3.1~dfsg-3 libjs-mathjax_2.7.4+dfsg-1 libjs-modernizr_2.6.2+ds1-3 libjs-sphinxdoc_2.4.3-2 libjs-underscore_1.9.1~dfsg-1 libjsoncpp1_1.7.4-3.1 libk5crypto3_1.17-7 libkeyutils1_1.6.1-2 libkrb5-3_1.17-7 libkrb5support0_1.17-7 libldap-2.4-2_2.4.50+dfsg-1 libldap-common_2.4.50+dfsg-1 libllvm10_1:10.0.0-4 liblocale-gettext-perl_1.07-4 liblsan0_10-20200418-1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1+b1 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-3 libmpfr6_4.0.2-1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libobjc-9-dev_9.3.0-11 libobjc4_10-20200418-1 libomp-10-dev_1:10.0.0-4 libomp5-10_1:10.0.0-4 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12+b1 libperl5.30_5.30.0-10 libpipeline1_1.5.2-2 libprocps8_2:3.3.16-4 libpsl5_0.21.0-1 libpthread-stubs0-dev_0.4-1 libpython3-stdlib_3.8.2-3 libpython3.8-minimal_3.8.3~rc1-1 libpython3.8-stdlib_3.8.3~rc1-1 libquadmath0_10-20200418-1 libreadline8_8.0-4 librhash0_1.3.9-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+b1 libselinux1_3.0-1+b3 libsemanage-common_3.0-1 libsemanage1_3.0-1+b3 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsparsehash-dev_2.0.3-2 libspdlog-dev_1:1.5.0+ds-3 libspdlog1_1:1.5.0+ds-3 libsqlite3-0_3.31.1-5 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1g-1 libstaden-read-dev_1.14.11-6 libstaden-read13_1.14.11-6 libstdc++-9-dev_9.3.0-11 libstdc++6_10-20200418-1 libsub-override-perl_0.09-2 libsystemd0_245.5-2 libtasn1-6_4.16.0-2 libtbb-dev_2020.2-2 libtbb2_2020.2-2 libtclap-dev_1.2.2-1+b1 libtinfo6_6.2-1 libtool_2.4.6-14 libtsan0_10-20200418-1 libubsan1_10-20200418-1 libuchardet0_0.0.6-3 libudev1_245.5-2 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libuv1_1.35.0-2 libxml2_2.9.10+dfsg-5 libz3-4_4.8.7-4 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.6.7-1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-1.3 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.2-1 ncurses-bin_6.2-1 openssl_1.1.1g-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-10 perl-base_5.30.0-10 perl-modules-5.30_5.30.0-10 pkg-config_0.29.2-1 po-debconf_1.0.21 procps_2:3.3.16-4 python-babel-localedata_2.8.0+dfsg.1-3 python3_3.8.2-3 python3-alabaster_0.7.8-1.1 python3-babel_2.8.0+dfsg.1-3 python3-certifi_2019.11.28-2 python3-chardet_3.0.4-7 python3-distutils_3.8.2-2 python3-docutils_0.16+dfsg-2 python3-idna_2.9-1 python3-imagesize_1.2.0-2 python3-jinja2_2.11.1-1 python3-lib2to3_3.8.2-2 python3-markupsafe_1.1.1-1+b1 python3-minimal_3.8.2-3 python3-packaging_20.3-1.2 python3-pkg-resources_46.1.3-1 python3-pygments_2.3.1+dfsg-3 python3-pyparsing_2.4.7-1 python3-requests_2.23.0+dfsg-2 python3-roman_2.0.0-4 python3-six_1.14.0-3 python3-sphinx_2.4.3-2 python3-sphinx-rtd-theme_0.4.3+dfsg-3 python3-tz_2019.3-2 python3-urllib3_1.25.9-1 python3.8_3.8.3~rc1-1 python3.8-minimal_3.8.3~rc1-1 qt5-qmake_5.12.5+dfsg-10 qt5-qmake-bin_5.12.5+dfsg-10 qtchooser_66-2 rapmap-dev_0.15.0+dfsg-1 readline-common_8.0-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sgml-base_1.30 sphinx-common_2.4.3-2 sphinx-doc_2.4.3-2 sphinx-rtd-theme-common_0.4.3+dfsg-3 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.34-0.1 xml-core_0.18+nmu1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2

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


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

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 3.0 (quilt)
Source: salmon
Binary: salmon
Architecture: any
Version: 1.2.1+ds1-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>, Kevin Murray <spam@kdmurray.id.au>
Homepage: https://github.com/COMBINE-lab/salmon
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/salmon
Vcs-Git: https://salsa.debian.org/med-team/salmon.git
Build-Depends: debhelper-compat (= 12), cmake, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, libboost-thread-dev, libboost-program-options-dev, libboost-timer-dev, libjellyfish-2.0-dev (>> 2.2.3-2), libpthread-stubs0-dev, libsparsehash-dev, libdivsufsort-dev, libbwa-dev, pkg-config, libjemalloc-dev, libcereal-dev, libtbb-dev, libgff-dev, libstaden-read-dev, libspdlog-dev, libtclap-dev, help2man, sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, zlib1g-dev, libeigen3-dev, libbz2-dev, liblzma-dev, rapmap-dev
Package-List:
 salmon deb science optional arch=any
Checksums-Sha1:
 b70add6ddb0be7493f7a4bd6391d688e10574b4d 5501960 salmon_1.2.1+ds1.orig.tar.xz
 5c0d88920eb10021e02326de430679be52fc5330 955148 salmon_1.2.1+ds1-1.debian.tar.xz
Checksums-Sha256:
 547f6522186f7609fe752363f61520df5050febeebbd004122cebf925d477607 5501960 salmon_1.2.1+ds1.orig.tar.xz
 2d3bba60728fe981f4a4667d081901f1b8434fa23c5752ab8ae97010b09a4ccf 955148 salmon_1.2.1+ds1-1.debian.tar.xz
Files:
 35d6ddd50ad4f04560242c75c99ac383 5501960 salmon_1.2.1+ds1.orig.tar.xz
 74a4ab58021353b9ba9314aa1835e542 955148 salmon_1.2.1+ds1-1.debian.tar.xz

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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Apr 23 10:13:34 2020 UTC
gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./salmon_1.2.1+ds1-1.dsc
dpkg-source: info: extracting salmon in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking salmon_1.2.1+ds1.orig.tar.xz
dpkg-source: info: unpacking salmon_1.2.1+ds1-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use_debian_packaged_libs.patch
dpkg-source: info: applying pufferfish
dpkg-source: info: applying disable-version-check.patch
dpkg-source: info: applying spelling
dpkg-source: info: applying kseq

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

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=C.UTF-8
LC_ALL=C.UTF-8
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-71766ce7-a336-4c91-a413-5bd5febeba3b
SCHROOT_UID=1001
SCHROOT_USER=user42
SHELL=/bin/sh
USER=user42

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

Command: dpkg-buildpackage -us -uc -b -rfakeroot
dpkg-buildpackage: info: source package salmon
dpkg-buildpackage: info: source version 1.2.1+ds1-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Michael R. Crusoe <michael.crusoe@gmail.com>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean --with sphinxdoc
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
rm -rf external
rm -f debian/*.1
rm -Rf sample_data
cd doc && /usr/bin/make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/doc'
rm -rf build/*
make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc'
rm -rf tests/unitTests
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_clean
 debian/rules binary
dh binary --with sphinxdoc
   dh_update_autotools_config
   dh_autoreconf
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# See here
#    https://github.com/COMBINE-lab/salmon/issues/87
# for a discussion with upstream why it is necessary to include rapmap source
mkdir -p /<<PKGBUILDDIR>>/external/install/src/rapmap
cp -av /usr/share/rapmap/src/* /<<PKGBUILDDIR>>/external/install/src/rapmap
'/usr/share/rapmap/src/HitManager.cpp' -> '/<<PKGBUILDDIR>>/external/install/src/rapmap/HitManager.cpp'
'/usr/share/rapmap/src/RapMapFileSystem.cpp' -> '/<<PKGBUILDDIR>>/external/install/src/rapmap/RapMapFileSystem.cpp'
'/usr/share/rapmap/src/RapMapSAIndex.cpp' -> '/<<PKGBUILDDIR>>/external/install/src/rapmap/RapMapSAIndex.cpp'
'/usr/share/rapmap/src/RapMapSAIndexer.cpp' -> '/<<PKGBUILDDIR>>/external/install/src/rapmap/RapMapSAIndexer.cpp'
'/usr/share/rapmap/src/RapMapUtils.cpp' -> '/<<PKGBUILDDIR>>/external/install/src/rapmap/RapMapUtils.cpp'
'/usr/share/rapmap/src/bit_array.c' -> '/<<PKGBUILDDIR>>/external/install/src/rapmap/bit_array.c'
'/usr/share/rapmap/src/rank9b.cpp' -> '/<<PKGBUILDDIR>>/external/install/src/rapmap/rank9b.cpp'
dh_auto_configure -- -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE -DCMAKE_BUILD_TYPE=Release -DUSE_SHARED_LIBS=TRUE
	cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_AUTOGEN_VERBOSE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE -DCMAKE_BUILD_TYPE=Release -DUSE_SHARED_LIBS=TRUE ..
CC: gcc
CC version: 
-- The C compiler identification is Clang 10.0.0
-- The CXX compiler identification is Clang 10.0.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
version: 1.2.1
-- CMAKE_BUILD_TYPE = Release
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Found Threads: TRUE  
Building with CONDA_BUILD flag
-- Performing Test HAVE_LIBCPP
-- Performing Test HAVE_LIBCPP - Success
It appears that you're compiling with clang and that libc++ is available, so I'll use that
Making Release build
not setting -DHAVE_NUMERIC_LIMITS128
running cd "/<<PKGBUILDDIR>>" && cp -r ./debian/external ./  2>&1
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") 
-- Performing Test Iconv_IS_BUILT_IN
-- Performing Test Iconv_IS_BUILT_IN - Success
-- Found Iconv: /usr/lib/x86_64-linux-gnu/libc.so  
-- Found LibLZMA: lzma (found version "5.2.4") 
Found liblzma library: lzma
===========================================
-- Found BZip2: -lbz2 (found version "1.0.8") 
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
Found libbz2 library: -lbz2
===========================================
-- Found Boost: /usr/include (found suitable version "1.67.0", minimum required is "1.59.0") found components: iostreams filesystem system timer chrono program_options regex 
BOOST_INCLUDEDIR = 
BOOST_LIBRARYDIR = 
Boost_FOUND = TRUE
BOOST ROOT = 
BOOST INCLUDE DIR = /usr/include
BOOST INCLUDE DIRS = /usr/include
BOOST LIB DIR = /usr/lib/x86_64-linux-gnu
BOOST LIBRARIES = /usr/lib/x86_64-linux-gnu/libboost_iostreams.so;/usr/lib/x86_64-linux-gnu/libboost_filesystem.so;/usr/lib/x86_64-linux-gnu/libboost_system.so;/usr/lib/x86_64-linux-gnu/libboost_timer.so;/usr/lib/x86_64-linux-gnu/libboost_chrono.so;/usr/lib/x86_64-linux-gnu/libboost_program_options.so;/usr/lib/x86_64-linux-gnu/libboost_regex.so
-- Found Cereal: /usr/include  
-- Cereal found (include: /usr/include)
FOUND SUITABLE TBB VERSION : 2019.0
TBB_LIBRARIES = 
-- Found libgff: /usr/include  
-- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.68.0")  
-- Found libstadenio: /usr/lib/x86_64-linux-gnu/libstaden-read.so  
-- Staden IOLib found (include: /usr/include)
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") 
-- Found Jemalloc: /usr/lib/x86_64-linux-gnu/libjemalloc.so (found version "5.2.1-0-gea6b3e973b477b8061e0076bb257dbd7f3faa756") 
Found Jemalloc library --- using this memory allocator
CPACK_SOURCE_IGNORE_FILES = /src/PCA.cpp;/src/PCAUtils.cpp;/build/;/scripts/AggregateToGeneLevel.py;/scripts/ExpressionTools.py;/scripts/GenerateExpressionFiles.sh;/scripts/ParseSoftFile.py;/scripts/PlotCorrelation.py;/scripts/junk;/scripts/sfstrace.log;/scripts/SFPipeline.py;/bin/;/lib/;/sample_data/;PublishREADMEToWebsite.sh;/external/;/src/obsolete/;/include/obsolete/;WebsiteHeader.txt;/experimental_configs/;.git/
CC: /usr/bin/cc
CC version: 
version: 1.0.0
Building basic pufferfish components for salmon
not setting -DHAVE_NUMERIC_LIMITS128
NO_IPO = FALSE
TBB_LIBRARIES = 
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_AUTOGEN_VERBOSE
    CMAKE_EXPORT_NO_PACKAGE_REGISTRY
    CMAKE_INSTALL_LIBDIR
    CMAKE_INSTALL_LOCALSTATEDIR
    CMAKE_INSTALL_RUNSTATEDIR
    CMAKE_INSTALL_SYSCONFDIR
    FETCHED_RAPMAP


-- Build files have been written to: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
	cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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make -f CMakeFiles/Makefile2 all
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build.make external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/depend
make -f external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build.make external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/depend
make -f external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/depend
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make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/external/pufferfish/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake --color=
Scanning dependencies of target ntcard
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[  1%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/external/ntcard/Common  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -O3 -std=c++14 -o CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/external/ntcard/Common/SignalHandler.cpp
[  2%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<<PKGBUILDDIR>>/external/pufferfish/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o   -c /<<PKGBUILDDIR>>/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c
[  3%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/graphdump.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphdump/../common -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphdump/.  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -std=c++14 -o CMakeFiles/graphdump.dir/graphdump.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphdump/graphdump.cpp
[  4%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor/../common  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -std=c++14 -o CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/common/dnachar.cpp
[  5%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor/../common  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -std=c++14 -o CMakeFiles/twopaco.dir/constructor.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp
[  6%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/external/ntcard/Common  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -O3 -std=c++14 -o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/external/ntcard/Common/Fcontrol.cpp
[  8%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o
[  8%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/external/ntcard/Common  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -O3 -std=c++14 -o CMakeFiles/ntcard.dir/nthll.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/external/ntcard/nthll.cpp
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<<PKGBUILDDIR>>/external/pufferfish/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o   -c /<<PKGBUILDDIR>>/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c
[  9%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<<PKGBUILDDIR>>/external/pufferfish/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o   -c /<<PKGBUILDDIR>>/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c
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[  9%] Built target ksw2pp_sse4
make -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/external/pufferfish/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 10%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<<PKGBUILDDIR>>/external/pufferfish/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o   -c /<<PKGBUILDDIR>>/external/pufferfish/src/ksw2pp/kalloc.c
[ 11%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<<PKGBUILDDIR>>/external/pufferfish/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o   -c /<<PKGBUILDDIR>>/external/pufferfish/src/ksw2pp/ksw2_extd.c
[ 12%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<<PKGBUILDDIR>>/external/pufferfish/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o   -c /<<PKGBUILDDIR>>/external/pufferfish/src/ksw2pp/ksw2_extz.c
[ 13%] Linking CXX static library libntcard.a
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -P CMakeFiles/ntcard.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -E cmake_link_script CMakeFiles/ntcard.dir/link.txt --verbose=1
/usr/bin/ar qc libntcard.a  CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o CMakeFiles/ntcard.dir/nthll.cpp.o
/usr/bin/ranlib libntcard.a
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cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/external/pufferfish/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/<<PKGBUILDDIR>>/external/pufferfish/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -O3 -msse -msse2 -mno-sse4.1 -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o   -c /<<PKGBUILDDIR>>/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c
[ 15%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<<PKGBUILDDIR>>/external/pufferfish/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o   -c /<<PKGBUILDDIR>>/external/pufferfish/src/ksw2pp/ksw2_gg.c
[ 16%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<<PKGBUILDDIR>>/external/pufferfish/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o   -c /<<PKGBUILDDIR>>/external/pufferfish/src/ksw2pp/ksw2_gg2.c
[ 17%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/<<PKGBUILDDIR>>/external/pufferfish/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -O3 -msse -msse2 -mno-sse4.1 -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o   -c /<<PKGBUILDDIR>>/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c
[ 18%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<<PKGBUILDDIR>>/external/pufferfish/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o   -c /<<PKGBUILDDIR>>/external/pufferfish/src/ksw2pp/ksw2_gg2_sse.c
[ 18%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/<<PKGBUILDDIR>>/external/pufferfish/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -O3 -msse -msse2 -mno-sse4.1 -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o   -c /<<PKGBUILDDIR>>/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c
[ 19%] Building CXX object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<<PKGBUILDDIR>>/external/pufferfish/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -std=c++14 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp
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[ 19%] Built target ksw2pp_sse2
make -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/external/pufferfish/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/DependInfo.cmake --color=
Scanning dependencies of target puffer
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make -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 20%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndexer.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 20%] Built target ksw2pp_basic
make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/CMakeFiles/salmon_core.dir/DependInfo.cmake --color=
Scanning dependencies of target salmon_core
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 21%] Building CXX object src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++  -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/<<PKGBUILDDIR>>/include -I/usr/include/eigen3 -I/<<PKGBUILDDIR>>/external -I/<<PKGBUILDDIR>>/external/cereal/include -I/<<PKGBUILDDIR>>/external/install/include -I/<<PKGBUILDDIR>>/external/install/include/pufferfish -I/<<PKGBUILDDIR>>/external/install/include/pufferfish/digestpp  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -stdlib=libc++ -DBOOST_HAS_INT128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -c /<<PKGBUILDDIR>>/src/jellyfish/mer_dna.cc
In file included from /<<PKGBUILDDIR>>/src/jellyfish/mer_dna.cc:18:
/<<PKGBUILDDIR>>/include/jellyfish/mer_dna.hpp:27:10: fatal error: 'iostream' file not found
#include <iostream>
         ^~~~~~~~~~
1 error generated.
make[4]: *** [src/CMakeFiles/salmon_core.dir/build.make:66: src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:566: src/CMakeFiles/salmon_core.dir/all] Error 2
make[3]: *** Waiting for unfinished jobs....
[ 22%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBaseIndex.cpp
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndexer.cpp:16:
/<<PKGBUILDDIR>>/external/pufferfish/include/ghc/filesystem.hpp:2467:37: warning: loop variable 's' has type 'const ghc::filesystem::path::string_type &' (aka 'const basic_string<char> &') but is initialized with type 'const ghc::filesystem::path' resulting in a copy [-Wrange-loop-construct]
            for (const string_type& s : input_iterator_range<iterator>(begin(), --end())) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/ghc/filesystem.hpp:2467:18: note: use non-reference type 'ghc::filesystem::path::string_type' (aka 'basic_string<char>') to keep the copy or type 'const ghc::filesystem::path &' to prevent copying
            for (const string_type& s : input_iterator_range<iterator>(begin(), --end())) {
                 ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/external/pufferfish/include/ghc/filesystem.hpp:2577:29: warning: loop variable 's' has type 'const ghc::filesystem::path::string_type &' (aka 'const basic_string<char> &') but is initialized with type 'const ghc::filesystem::path' resulting in a copy [-Wrange-loop-construct]
    for (const string_type& s : *this) {
                            ^
/<<PKGBUILDDIR>>/external/pufferfish/include/ghc/filesystem.hpp:2577:10: note: use non-reference type 'ghc::filesystem::path::string_type' (aka 'basic_string<char>') to keep the copy or type 'const ghc::filesystem::path &' to prevent copying
    for (const string_type& s : *this) {
         ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/external/pufferfish/include/ghc/filesystem.hpp:3331:35: warning: loop variable 'part' has type 'const path::string_type &' (aka 'const basic_string<char> &') but is initialized with type 'const ghc::filesystem::path' resulting in a copy [-Wrange-loop-construct]
    for (const path::string_type& part : p) {
                                  ^
/<<PKGBUILDDIR>>/external/pufferfish/include/ghc/filesystem.hpp:3331:10: note: use non-reference type 'path::string_type' (aka 'basic_string<char>') to keep the copy or type 'const ghc::filesystem::path &' to prevent copying
    for (const path::string_type& part : p) {
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBaseIndex.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishBaseIndex.hpp:9:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter]
  Derived& operator=(std::nullptr_t p) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator==(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator!=(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter]
bool operator==(std::nullptr_t lfs, const common<D, I, B, W, U>& rhs) {
                               ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter]
  iterator(W* p, unsigned b, unsigned o)
                          ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBaseIndex.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishBaseIndex.hpp:13:
/<<PKGBUILDDIR>>/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
                               ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndexer.cpp:20:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter]
  Derived& operator=(std::nullptr_t p) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator==(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator!=(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter]
bool operator==(std::nullptr_t lfs, const common<D, I, B, W, U>& rhs) {
                               ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter]
  iterator(W* p, unsigned b, unsigned o)
                          ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndexer.cpp:22:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishIndex.hpp:9:
/<<PKGBUILDDIR>>/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
                               ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndexer.cpp:27:
/<<PKGBUILDDIR>>/external/pufferfish/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter]
  mer_base_static(unsigned int k, const char* s) : super(k_) {
                               ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndexer.cpp:20:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long, 2, unsigned long, false, 64>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
  lhs_setter& operator=(const lhs_setter& rhs) {
              ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndexer.cpp:250:14: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long, 2, unsigned long, false, 64>' first required here
    auto c = seqVec[i];
             ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBaseIndex.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishBaseIndex.hpp:9:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long, 0, unsigned long, false, 64>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
  lhs_setter& operator=(const lhs_setter& rhs) {
              ^
/<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishBaseIndex.hpp:26:19: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long, 0, unsigned long, false, 64>' first required here
      auto spos = underlying().contigOffsets_[contigRank];
                  ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBaseIndex.cpp:335:17: note: in instantiation of member function 'PufferfishBaseIndex<PufferfishIndex>::contigRange' requested here
template class  PufferfishBaseIndex<PufferfishIndex>;
                ^
[ 23%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor/../common  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -std=c++14 -o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.cpp
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndexer.cpp:20:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9:
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > >, spp::sparsegroup<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > >, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > > *, std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > *, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
    Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
                                ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2816:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > >, spp::sparsegroup<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > >, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > > *, std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > *, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >' first required here
        for (destructive_iterator it = ht.destructive_begin();
                                       ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2947:9: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > >, unsigned long, spp::spp_hash<uint64_t>, spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::SelectKey, spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::SetKey, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::_move_from' requested here
        _move_from(mover, ht, min_buckets_wanted);
        ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2744:26: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > >, unsigned long, spp::spp_hash<uint64_t>, spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::SelectKey, spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::SetKey, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::sparse_hashtable' requested here
        sparse_hashtable tmp(MoveDontCopy, *this, resize_to);
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:3277:21: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > >, unsigned long, spp::spp_hash<uint64_t>, spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::SelectKey, spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::SetKey, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::_resize_delta' requested here
                if (_resize_delta(1))
                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:3808:29: note: in instantiation of function template specialization 'spp::sparse_hashtable<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > >, unsigned long, spp::spp_hash<uint64_t>, spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::SelectKey, spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::SetKey, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::find_or_insert<spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::DefaultValue, unsigned long &>' requested here
        return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
                            ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:17: note: in instantiation of function template specialization 'spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::operator[]<unsigned long &>' requested here
            path[ref_cnt].resize(contigCntPerPath);
                ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndexer.cpp:20:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long, 8, unsigned long, false, 64>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
  lhs_setter& operator=(const lhs_setter& rhs) {
              ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:162:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long, 8, unsigned long, false, 64>' first required here
                       ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB)
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:195:63: note: in instantiation of member function 'compact::vector_imp::vector<compact::vector<unsigned long, 8, unsigned long, std::allocator<unsigned long> >, unsigned long, 8, unsigned long, std::allocator<unsigned long>, 64, false>::operator[]' requested here
            for (uint64_t i = 0; i < contigCntr; i++) edgeVec_[i] = 0;
                                                              ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndexer.cpp:20:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long, 0, unsigned long, false, 64>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
  lhs_setter& operator=(const lhs_setter& rhs) {
              ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:162:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long, 0, unsigned long, false, 64>' first required here
                       ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB)
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:310:24: note: in instantiation of member function 'compact::vector_imp::vector<compact::vector_imp::vector_dyn<unsigned long, unsigned long, std::allocator<unsigned long>, 64, false>, unsigned long, 0, unsigned long, std::allocator<unsigned long>, 64, false>::operator[]' requested here
        (*cpos_offsets)[0] = 0;
                       ^
[ 24%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor/../common  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -std=c++14 -o CMakeFiles/twopaco.dir/compressedstring.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor/compressedstring.cpp
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndexer.cpp:20:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9:
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > > *, std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> *, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
    Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
                                ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2816:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > > *, std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> *, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >' first required here
        for (destructive_iterator it = ht.destructive_begin();
                                       ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2947:9: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int>, std::vector<unsigned int, std::allocator<unsigned int> >, VecHasher, spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::SelectKey, spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::SetKey, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::_move_from' requested here
        _move_from(mover, ht, min_buckets_wanted);
        ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2744:26: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int>, std::vector<unsigned int, std::allocator<unsigned int> >, VecHasher, spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::SelectKey, spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::SetKey, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::sparse_hashtable' requested here
        sparse_hashtable tmp(MoveDontCopy, *this, resize_to);
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:3277:21: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int>, std::vector<unsigned int, std::allocator<unsigned int> >, VecHasher, spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::SelectKey, spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::SetKey, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::_resize_delta' requested here
                if (_resize_delta(1))
                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:3808:29: note: in instantiation of function template specialization 'spp::sparse_hashtable<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int>, std::vector<unsigned int, std::allocator<unsigned int> >, VecHasher, spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::SelectKey, spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::SetKey, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::find_or_insert<spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::DefaultValue, std::vector<unsigned int, std::allocator<unsigned int> > &>' requested here
        return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
                            ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:37: note: in instantiation of function template specialization 'spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::operator[]<std::vector<unsigned int, std::allocator<unsigned int> > &>' requested here
                        eqID = eqMap[tlist];
                                    ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndexer.cpp:20:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long, 1, unsigned long, false, 64>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
  lhs_setter& operator=(const lhs_setter& rhs) {
              ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:162:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long, 1, unsigned long, false, 64>' first required here
                       ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB)
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndexer.cpp:120:20: note: in instantiation of member function 'compact::vector_imp::vector<compact::vector<unsigned long, 1, unsigned long, std::allocator<unsigned long> >, unsigned long, 1, unsigned long, std::allocator<unsigned long>, 64, false>::operator[]' requested here
          return ((*rank_)[endPos] == 1);
                          ^
[ 25%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor/../common  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -std=c++14 -o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/common/streamfastaparser.cpp
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndexer.cpp:20:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long, 0, unsigned long, true, 64>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
  lhs_setter& operator=(const lhs_setter& rhs) {
              ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:162:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long, 0, unsigned long, true, 64>' first required here
                       ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB)
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndexer.cpp:729:17: note: in instantiation of member function 'compact::vector_imp::vector<compact::vector_imp::vector_dyn<unsigned long, unsigned long, std::allocator<unsigned long>, 64, true>, unsigned long, 0, unsigned long, std::allocator<unsigned long>, 64, true>::operator[]' requested here
          posVec[idx] = kb1.pos();
                ^
[ 26%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor/../common  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -std=c++14 -o CMakeFiles/twopaco.dir/test.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor/test.cpp
9 warnings generated.
[ 27%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndex.cpp
[ 28%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphdump/../common -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphdump/.  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -std=c++14 -o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/common/dnachar.cpp
[ 29%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphdump/../common -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphdump/.  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -std=c++14 -o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/common/streamfastaparser.cpp
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndex.cpp:9:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishIndex.hpp:9:
/<<PKGBUILDDIR>>/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
                               ^
[ 30%] Linking CXX static library libgraphdump.a
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/cmake -P CMakeFiles/graphdump.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphdump.dir/link.txt --verbose=1
/usr/bin/ar qc libgraphdump.a  CMakeFiles/graphdump.dir/graphdump.cpp.o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o
/usr/bin/ranlib libgraphdump.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 30%] Built target graphdump
[ 31%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishSparseIndex.cpp
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndex.cpp:9:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishIndex.hpp:12:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter]
  Derived& operator=(std::nullptr_t p) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator==(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator!=(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter]
bool operator==(std::nullptr_t lfs, const common<D, I, B, W, U>& rhs) {
                               ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter]
  iterator(W* p, unsigned b, unsigned o)
                          ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndex.cpp:13:
/<<PKGBUILDDIR>>/external/pufferfish/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter]
  mer_base_static(unsigned int k, const char* s) : super(k_) {
                               ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishSparseIndex.cpp:10:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishSparseIndex.hpp:12:
/<<PKGBUILDDIR>>/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
                               ^
[ 32%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor/../common  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -std=c++14 -o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishSparseIndex.cpp:10:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishSparseIndex.hpp:13:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter]
  Derived& operator=(std::nullptr_t p) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator==(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator!=(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter]
bool operator==(std::nullptr_t lfs, const common<D, I, B, W, U>& rhs) {
                               ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter]
  iterator(W* p, unsigned b, unsigned o)
                          ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndex.cpp:9:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishIndex.hpp:12:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long, 0, unsigned long, false, 64>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
  lhs_setter& operator=(const lhs_setter& rhs) {
              ^
/<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishBaseIndex.hpp:26:19: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long, 0, unsigned long, false, 64>' first required here
      auto spos = underlying().contigOffsets_[contigRank];
                  ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishIndex.cpp:191:30: note: in instantiation of member function 'PufferfishBaseIndex<PufferfishIndex>::contigRange' requested here
      auto contigIterRange = contigRange(rank);
                             ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long, 0, unsigned long, false, 64>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
  lhs_setter& operator=(const lhs_setter& rhs) {
              ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishSparseIndex.cpp:433:23: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long, 0, unsigned long, false, 64>' first required here
    auto sampledPos = sampledPos_[currRank];
                      ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishSparseIndex.cpp:10:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishSparseIndex.hpp:13:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long, 1, unsigned long, false, 64>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
  lhs_setter& operator=(const lhs_setter& rhs) {
              ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:162:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long, 1, unsigned long, false, 64>' first required here
                       ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB)
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishSparseIndex.cpp:369:19: note: in instantiation of member function 'compact::vector_imp::vector<compact::vector<unsigned long, 1, unsigned long, std::allocator<unsigned long> >, unsigned long, 1, unsigned long, std::allocator<unsigned long>, 64, false>::operator[]' requested here
  if (presenceVec_[idx] == 1) {
                  ^
10 warnings generated.
[ 33%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishLossyIndex.cpp
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishLossyIndex.cpp:7:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishLossyIndex.hpp:11:
/<<PKGBUILDDIR>>/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
                               ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishLossyIndex.cpp:7:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishLossyIndex.hpp:12:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter]
  Derived& operator=(std::nullptr_t p) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator==(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator!=(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter]
bool operator==(std::nullptr_t lfs, const common<D, I, B, W, U>& rhs) {
                               ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter]
  iterator(W* p, unsigned b, unsigned o)
                          ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
10 warnings generated.
[ 34%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/edlib.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/edlib.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/edlib.cpp
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long, 1, unsigned long, false, 64>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
  lhs_setter& operator=(const lhs_setter& rhs) {
              ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:162:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long, 1, unsigned long, false, 64>' first required here
                       ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB)
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishLossyIndex.cpp:159:39: note: in instantiation of member function 'compact::vector_imp::vector<compact::vector<unsigned long, 1, unsigned long, std::allocator<unsigned long> >, unsigned long, 1, unsigned long, std::allocator<unsigned long>, 64, false>::operator[]' requested here
  if (res < numKmers_ and presenceVec_[res] == 1) {
                                      ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishLossyIndex.cpp:7:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishLossyIndex.hpp:12:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long, 0, unsigned long, false, 64>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
  lhs_setter& operator=(const lhs_setter& rhs) {
              ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:162:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long, 0, unsigned long, false, 64>' first required here
                       ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB)
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishLossyIndex.cpp:162:22: note: in instantiation of member function 'compact::vector_imp::vector<compact::vector_imp::vector_dyn<unsigned long, unsigned long, std::allocator<unsigned long>, 64, false>, unsigned long, 0, unsigned long, std::allocator<unsigned long>, 64, false>::operator[]' requested here
    pos = sampledPos_[currRank];
                     ^
[ 35%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/Util.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/Util.cpp
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/Util.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter]
  Derived& operator=(std::nullptr_t p) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator==(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator!=(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter]
bool operator==(std::nullptr_t lfs, const common<D, I, B, W, U>& rhs) {
                               ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter]
  iterator(W* p, unsigned b, unsigned o)
                          ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
19 warnings generated.
[ 36%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9sel.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/rank9sel.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/rank9sel.cpp
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/rank9sel.cpp:29:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/rank9sel.hpp:27:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter]
  Derived& operator=(std::nullptr_t p) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator==(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator!=(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter]
bool operator==(std::nullptr_t lfs, const common<D, I, B, W, U>& rhs) {
                               ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter]
  iterator(W* p, unsigned b, unsigned o)
                          ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
10 warnings generated.
[ 37%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/rank9b.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/rank9b.cpp
[ 38%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishValidate.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishValidate.cpp
7 warnings generated.
[ 38%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishStats.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishStats.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishStats.cpp
7 warnings generated.
[ 39%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishTestLookup.cpp
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishValidate.cpp:14:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter]
  Derived& operator=(std::nullptr_t p) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator==(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator!=(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter]
bool operator==(std::nullptr_t lfs, const common<D, I, B, W, U>& rhs) {
                               ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter]
  iterator(W* p, unsigned b, unsigned o)
                          ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishValidate.cpp:15:
/<<PKGBUILDDIR>>/external/pufferfish/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter]
  mer_base_static(unsigned int k, const char* s) : super(k_) {
                               ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishStats.cpp:16:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter]
  Derived& operator=(std::nullptr_t p) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator==(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator!=(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter]
bool operator==(std::nullptr_t lfs, const common<D, I, B, W, U>& rhs) {
                               ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter]
  iterator(W* p, unsigned b, unsigned o)
                          ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishStats.cpp:17:
/<<PKGBUILDDIR>>/external/pufferfish/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter]
  mer_base_static(unsigned int k, const char* s) : super(k_) {
                               ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishTestLookup.cpp:13:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter]
  Derived& operator=(std::nullptr_t p) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator==(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator!=(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter]
bool operator==(std::nullptr_t lfs, const common<D, I, B, W, U>& rhs) {
                               ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter]
  iterator(W* p, unsigned b, unsigned o)
                          ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishValidate.cpp:18:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishIndex.hpp:9:
/<<PKGBUILDDIR>>/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
                               ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishTestLookup.cpp:14:
/<<PKGBUILDDIR>>/external/pufferfish/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter]
  mer_base_static(unsigned int k, const char* s) : super(k_) {
                               ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishStats.cpp:20:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishIndex.hpp:9:
/<<PKGBUILDDIR>>/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
                               ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishTestLookup.cpp:18:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishIndex.hpp:9:
/<<PKGBUILDDIR>>/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
                               ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishValidate.cpp:14:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long, 2, unsigned long, false, 64>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
  lhs_setter& operator=(const lhs_setter& rhs) {
              ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:162:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long, 2, unsigned long, false, 64>' first required here
                       ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB)
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishValidate.cpp:141:35: note: in instantiation of member function 'compact::vector_imp::vector<compact::vector<unsigned long, 2, unsigned long, std::allocator<unsigned long> >, unsigned long, 2, unsigned long, std::allocator<unsigned long>, 64, false>::operator[]' requested here
      kb.shiftFw(static_cast<int>(refSeq[gpos]));
                                  ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishValidate.cpp:465:14: note: in instantiation of function template specialization 'doPufferfishInternalValidate<PufferfishSparseIndex>' requested here
      return doPufferfishInternalValidate(pi, validateOpts);
             ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishStats.cpp:16:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long, 1, unsigned long, false, 64>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
  lhs_setter& operator=(const lhs_setter& rhs) {
              ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:162:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long, 1, unsigned long, false, 64>' first required here
                       ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB)
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishStats.cpp:53:24: note: in instantiation of member function 'compact::vector_imp::vector<compact::vector<unsigned long, 1, unsigned long, std::allocator<unsigned long> >, unsigned long, 1, unsigned long, std::allocator<unsigned long>, 64, false>::operator[]' requested here
        if (not visited[v]) {
                       ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishStats.cpp:16:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long, 0, unsigned long, false, 64>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
  lhs_setter& operator=(const lhs_setter& rhs) {
              ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:162:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long, 0, unsigned long, false, 64>' first required here
                       ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB)
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishStats.cpp:141:162: note: in instantiation of member function 'compact::vector_imp::vector<compact::vector_imp::vector_dyn<unsigned long, unsigned long, std::allocator<unsigned long>, 64, false>, unsigned long, 0, unsigned long, std::allocator<unsigned long>, 64, false>::operator[]' requested here
              << " contigOffsets size: " << contigOffsets_.size() << ", bpe: " << bits_per_element << " , total elements in the contig table: " << contigOffsets_[contigOffsets_.size()-1] << "\n";
                                                                                                                                                                 ^
11 warnings generated.
[ 40%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishExamine.cpp
9 warnings generated.
[ 41%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/FastxParser.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/FastxParser.cpp
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishExamine.cpp:2:
/<<PKGBUILDDIR>>/external/pufferfish/include/ghc/filesystem.hpp:2467:37: warning: loop variable 's' has type 'const ghc::filesystem::path::string_type &' (aka 'const basic_string<char> &') but is initialized with type 'const ghc::filesystem::path' resulting in a copy [-Wrange-loop-construct]
            for (const string_type& s : input_iterator_range<iterator>(begin(), --end())) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/ghc/filesystem.hpp:2467:18: note: use non-reference type 'ghc::filesystem::path::string_type' (aka 'basic_string<char>') to keep the copy or type 'const ghc::filesystem::path &' to prevent copying
            for (const string_type& s : input_iterator_range<iterator>(begin(), --end())) {
                 ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/external/pufferfish/include/ghc/filesystem.hpp:2577:29: warning: loop variable 's' has type 'const ghc::filesystem::path::string_type &' (aka 'const basic_string<char> &') but is initialized with type 'const ghc::filesystem::path' resulting in a copy [-Wrange-loop-construct]
    for (const string_type& s : *this) {
                            ^
/<<PKGBUILDDIR>>/external/pufferfish/include/ghc/filesystem.hpp:2577:10: note: use non-reference type 'ghc::filesystem::path::string_type' (aka 'basic_string<char>') to keep the copy or type 'const ghc::filesystem::path &' to prevent copying
    for (const string_type& s : *this) {
         ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/external/pufferfish/include/ghc/filesystem.hpp:3331:35: warning: loop variable 'part' has type 'const path::string_type &' (aka 'const basic_string<char> &') but is initialized with type 'const ghc::filesystem::path' resulting in a copy [-Wrange-loop-construct]
    for (const path::string_type& part : p) {
                                  ^
/<<PKGBUILDDIR>>/external/pufferfish/include/ghc/filesystem.hpp:3331:10: note: use non-reference type 'path::string_type' (aka 'basic_string<char>') to keep the copy or type 'const ghc::filesystem::path &' to prevent copying
    for (const path::string_type& part : p) {
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishExamine.cpp:6:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PuffAligner.hpp:8:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter]
  Derived& operator=(std::nullptr_t p) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator==(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator!=(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter]
bool operator==(std::nullptr_t lfs, const common<D, I, B, W, U>& rhs) {
                               ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter]
  iterator(W* p, unsigned b, unsigned o)
                          ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishExamine.cpp:8:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishIndex.hpp:9:
/<<PKGBUILDDIR>>/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
                               ^
10 warnings generated.
[ 42%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter]
  Derived& operator=(std::nullptr_t p) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator==(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator!=(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter]
bool operator==(std::nullptr_t lfs, const common<D, I, B, W, U>& rhs) {
                               ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter]
  iterator(W* p, unsigned b, unsigned o)
                          ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long, 2, unsigned long, false, 64>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
  lhs_setter& operator=(const lhs_setter& rhs) {
              ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:162:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long, 2, unsigned long, false, 64>' first required here
                       ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB)
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:109:15: note: in instantiation of member function 'compact::vector_imp::vector<compact::vector<unsigned long, 2, unsigned long, std::allocator<unsigned long> >, unsigned long, 2, unsigned long, std::allocator<unsigned long>, 64, false>::operator[]' requested here
        seqVec[offset + i] = c;
              ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9:
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > >, spp::sparsegroup<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > >, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > > *, std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > *, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
    Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
                                ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2816:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > >, spp::sparsegroup<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > >, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > > *, std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > *, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >' first required here
        for (destructive_iterator it = ht.destructive_begin();
                                       ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2947:9: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > >, unsigned long, spp::spp_hash<uint64_t>, spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::SelectKey, spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::SetKey, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::_move_from' requested here
        _move_from(mover, ht, min_buckets_wanted);
        ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2744:26: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > >, unsigned long, spp::spp_hash<uint64_t>, spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::SelectKey, spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::SetKey, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::sparse_hashtable' requested here
        sparse_hashtable tmp(MoveDontCopy, *this, resize_to);
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:3277:21: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > >, unsigned long, spp::spp_hash<uint64_t>, spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::SelectKey, spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::SetKey, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::_resize_delta' requested here
                if (_resize_delta(1))
                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:3808:29: note: in instantiation of function template specialization 'spp::sparse_hashtable<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > >, unsigned long, spp::spp_hash<uint64_t>, spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::SelectKey, spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::SetKey, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::find_or_insert<spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::DefaultValue, unsigned long &>' requested here
        return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
                            ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:17: note: in instantiation of function template specialization 'spp::sparse_hash_map<unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::pair<unsigned long, bool>, std::allocator<std::pair<unsigned long, bool> > > > > >::operator[]<unsigned long &>' requested here
            path[ref_cnt].resize(contigCntPerPath);
                ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long, 8, unsigned long, false, 64>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
  lhs_setter& operator=(const lhs_setter& rhs) {
              ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:162:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long, 8, unsigned long, false, 64>' first required here
                       ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB)
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:195:63: note: in instantiation of member function 'compact::vector_imp::vector<compact::vector<unsigned long, 8, unsigned long, std::allocator<unsigned long> >, unsigned long, 8, unsigned long, std::allocator<unsigned long>, 64, false>::operator[]' requested here
            for (uint64_t i = 0; i < contigCntr; i++) edgeVec_[i] = 0;
                                                              ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:636:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long, 0, unsigned long, false, 64>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
  lhs_setter& operator=(const lhs_setter& rhs) {
              ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:162:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long, 0, unsigned long, false, 64>' first required here
                       ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB)
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:310:24: note: in instantiation of member function 'compact::vector_imp::vector<compact::vector_imp::vector_dyn<unsigned long, unsigned long, std::allocator<unsigned long>, 64, false>, unsigned long, 0, unsigned long, std::allocator<unsigned long>, 64, false>::operator[]' requested here
        (*cpos_offsets)[0] = 0;
                       ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9:
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > > *, std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> *, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
    Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
                                ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2816:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > > *, std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> *, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >' first required here
        for (destructive_iterator it = ht.destructive_begin();
                                       ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2947:9: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int>, std::vector<unsigned int, std::allocator<unsigned int> >, VecHasher, spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::SelectKey, spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::SetKey, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::_move_from' requested here
        _move_from(mover, ht, min_buckets_wanted);
        ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2744:26: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int>, std::vector<unsigned int, std::allocator<unsigned int> >, VecHasher, spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::SelectKey, spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::SetKey, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::sparse_hashtable' requested here
        sparse_hashtable tmp(MoveDontCopy, *this, resize_to);
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:3277:21: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int>, std::vector<unsigned int, std::allocator<unsigned int> >, VecHasher, spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::SelectKey, spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::SetKey, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::_resize_delta' requested here
                if (_resize_delta(1))
                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:3808:29: note: in instantiation of function template specialization 'spp::sparse_hashtable<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int>, std::vector<unsigned int, std::allocator<unsigned int> >, VecHasher, spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::SelectKey, spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::SetKey, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::find_or_insert<spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::DefaultValue, std::vector<unsigned int, std::allocator<unsigned int> > &>' requested here
        return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
                            ^
/<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:37: note: in instantiation of function template specialization 'spp::sparse_hash_map<std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int, VecHasher, std::equal_to<std::vector<unsigned int, std::allocator<unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int, std::allocator<unsigned int> >, unsigned int> > >::operator[]<std::vector<unsigned int, std::allocator<unsigned int> > &>' requested here
                        eqID = eqMap[tlist];
                                    ^
[ 43%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferFS.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/PufferFS.cpp
[ 44%] Building C object external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc  -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -o CMakeFiles/puffer.dir/xxhash.c.o   -c /<<PKGBUILDDIR>>/external/pufferfish/src/xxhash.c
[ 45%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/FixFasta.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/FixFasta.cpp
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/FixFasta.cpp:2:
/<<PKGBUILDDIR>>/external/pufferfish/include/jellyfish/mer_dna.hpp:647:32: warning: unused parameter 'k' [-Wunused-parameter]
  mer_base_static(unsigned int k, const char* s) : super(k_) {
                               ^
11 warnings generated.
[ 46%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/MemCollector.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/MemCollector.cpp
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/FixFasta.cpp:27:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/digestpp.hpp:19:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/algorithm/k12m14.hpp:9:
/<<PKGBUILDDIR>>/external/pufferfish/include/digestpp/algorithm/detail/k12m14_provider.hpp:86:77: warning: unused parameter 'reallen' [-Wunused-parameter]
        inline void transform(const unsigned char* data, uint64_t num_blks, size_t reallen)
                                                                                   ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/FixFasta.cpp:28:
/<<PKGBUILDDIR>>/external/pufferfish/include/ghc/filesystem.hpp:2467:37: warning: loop variable 's' has type 'const ghc::filesystem::path::string_type &' (aka 'const basic_string<char> &') but is initialized with type 'const ghc::filesystem::path' resulting in a copy [-Wrange-loop-construct]
            for (const string_type& s : input_iterator_range<iterator>(begin(), --end())) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/ghc/filesystem.hpp:2467:18: note: use non-reference type 'ghc::filesystem::path::string_type' (aka 'basic_string<char>') to keep the copy or type 'const ghc::filesystem::path &' to prevent copying
            for (const string_type& s : input_iterator_range<iterator>(begin(), --end())) {
                 ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/external/pufferfish/include/ghc/filesystem.hpp:2577:29: warning: loop variable 's' has type 'const ghc::filesystem::path::string_type &' (aka 'const basic_string<char> &') but is initialized with type 'const ghc::filesystem::path' resulting in a copy [-Wrange-loop-construct]
    for (const string_type& s : *this) {
                            ^
/<<PKGBUILDDIR>>/external/pufferfish/include/ghc/filesystem.hpp:2577:10: note: use non-reference type 'ghc::filesystem::path::string_type' (aka 'basic_string<char>') to keep the copy or type 'const ghc::filesystem::path &' to prevent copying
    for (const string_type& s : *this) {
         ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/external/pufferfish/include/ghc/filesystem.hpp:3331:35: warning: loop variable 'part' has type 'const path::string_type &' (aka 'const basic_string<char> &') but is initialized with type 'const ghc::filesystem::path' resulting in a copy [-Wrange-loop-construct]
    for (const path::string_type& part : p) {
                                  ^
/<<PKGBUILDDIR>>/external/pufferfish/include/ghc/filesystem.hpp:3331:10: note: use non-reference type 'path::string_type' (aka 'basic_string<char>') to keep the copy or type 'const ghc::filesystem::path &' to prevent copying
    for (const path::string_type& part : p) {
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/MemCollector.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/MemCollector.hpp:6:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishIndex.hpp:9:
/<<PKGBUILDDIR>>/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
                               ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/MemCollector.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/MemCollector.hpp:6:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishIndex.hpp:12:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter]
  Derived& operator=(std::nullptr_t p) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator==(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator!=(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter]
bool operator==(std::nullptr_t lfs, const common<D, I, B, W, U>& rhs) {
                               ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter]
  iterator(W* p, unsigned b, unsigned o)
                          ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/FixFasta.cpp:4:
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > >, spp::sparsegroup<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > >, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > > > *, std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > *, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > > >' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
    Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
                                ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2816:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > >, spp::sparsegroup<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > >, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > > > *, std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > *, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > > >' first required here
        for (destructive_iterator it = ht.destructive_begin();
                                       ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2947:9: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > >, unsigned long, spp::spp_hash<uint64_t>, spp::sparse_hash_map<unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > > >::SelectKey, spp::sparse_hash_map<unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > > >::SetKey, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > > >::_move_from' requested here
        _move_from(mover, ht, min_buckets_wanted);
        ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2744:26: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > >, unsigned long, spp::spp_hash<uint64_t>, spp::sparse_hash_map<unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > > >::SelectKey, spp::sparse_hash_map<unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > > >::SetKey, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > > >::sparse_hashtable' requested here
        sparse_hashtable tmp(MoveDontCopy, *this, resize_to);
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:3277:21: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > >, unsigned long, spp::spp_hash<uint64_t>, spp::sparse_hash_map<unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > > >::SelectKey, spp::sparse_hash_map<unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > > >::SetKey, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > > >::_resize_delta' requested here
                if (_resize_delta(1))
                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:3808:29: note: in instantiation of function template specialization 'spp::sparse_hashtable<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > >, unsigned long, spp::spp_hash<uint64_t>, spp::sparse_hash_map<unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > > >::SelectKey, spp::sparse_hash_map<unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > > >::SetKey, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > > >::find_or_insert<spp::sparse_hash_map<unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > > >::DefaultValue, unsigned long &>' requested here
        return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
                            ^
/<<PKGBUILDDIR>>/external/pufferfish/src/FixFasta.cpp:261:33: note: in instantiation of function template specialization 'spp::sparse_hash_map<unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, spp::spp_hash<uint64_t>, std::equal_to<unsigned long>, spp::libc_allocator<std::pair<const unsigned long, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > > > >::operator[]<unsigned long &>' requested here
                  duplicateNames[dupInfo.txId].push_back(processedName);
                                ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/FixFasta.cpp:4:
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator<std::__cxx11::basic_string<char>, spp::sparsegroup<std::__cxx11::basic_string<char>, spp::libc_allocator<std::__cxx11::basic_string<char> > > *, std::__cxx11::basic_string<char> *, std::input_iterator_tag, spp::libc_allocator<std::__cxx11::basic_string<char> > >' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
    Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
                                ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2816:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator<std::__cxx11::basic_string<char>, spp::sparsegroup<std::__cxx11::basic_string<char>, spp::libc_allocator<std::__cxx11::basic_string<char> > > *, std::__cxx11::basic_string<char> *, std::input_iterator_tag, spp::libc_allocator<std::__cxx11::basic_string<char> > >' first required here
        for (destructive_iterator it = ht.destructive_begin();
                                       ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2947:9: note: in instantiation of member function 'spp::sparse_hashtable<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char>, spp::spp_hash<std::__cxx11::basic_string<char> >, spp::sparse_hash_set<std::__cxx11::basic_string<char>, spp::spp_hash<std::__cxx11::basic_string<char> >, std::equal_to<std::__cxx11::basic_string<char> >, spp::libc_allocator<std::__cxx11::basic_string<char> > >::Identity, spp::sparse_hash_set<std::__cxx11::basic_string<char>, spp::spp_hash<std::__cxx11::basic_string<char> >, std::equal_to<std::__cxx11::basic_string<char> >, spp::libc_allocator<std::__cxx11::basic_string<char> > >::SetKey, std::equal_to<std::__cxx11::basic_string<char> >, spp::libc_allocator<std::__cxx11::basic_string<char> > >::_move_from' requested here
        _move_from(mover, ht, min_buckets_wanted);
        ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2744:26: note: in instantiation of member function 'spp::sparse_hashtable<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char>, spp::spp_hash<std::__cxx11::basic_string<char> >, spp::sparse_hash_set<std::__cxx11::basic_string<char>, spp::spp_hash<std::__cxx11::basic_string<char> >, std::equal_to<std::__cxx11::basic_string<char> >, spp::libc_allocator<std::__cxx11::basic_string<char> > >::Identity, spp::sparse_hash_set<std::__cxx11::basic_string<char>, spp::spp_hash<std::__cxx11::basic_string<char> >, std::equal_to<std::__cxx11::basic_string<char> >, spp::libc_allocator<std::__cxx11::basic_string<char> > >::SetKey, std::equal_to<std::__cxx11::basic_string<char> >, spp::libc_allocator<std::__cxx11::basic_string<char> > >::sparse_hashtable' requested here
        sparse_hashtable tmp(MoveDontCopy, *this, resize_to);
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:3233:9: note: in instantiation of member function 'spp::sparse_hashtable<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char>, spp::spp_hash<std::__cxx11::basic_string<char> >, spp::sparse_hash_set<std::__cxx11::basic_string<char>, spp::spp_hash<std::__cxx11::basic_string<char> >, std::equal_to<std::__cxx11::basic_string<char> >, spp::libc_allocator<std::__cxx11::basic_string<char> > >::Identity, spp::sparse_hash_set<std::__cxx11::basic_string<char>, spp::spp_hash<std::__cxx11::basic_string<char> >, std::equal_to<std::__cxx11::basic_string<char> >, spp::libc_allocator<std::__cxx11::basic_string<char> > >::SetKey, std::equal_to<std::__cxx11::basic_string<char> >, spp::libc_allocator<std::__cxx11::basic_string<char> > >::_resize_delta' requested here
        _resize_delta(1);                      // adding an object, grow if need be
        ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:4220:67: note: in instantiation of function template specialization 'spp::sparse_hashtable<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char>, spp::spp_hash<std::__cxx11::basic_string<char> >, spp::sparse_hash_set<std::__cxx11::basic_string<char>, spp::spp_hash<std::__cxx11::basic_string<char> >, std::equal_to<std::__cxx11::basic_string<char> >, spp::libc_allocator<std::__cxx11::basic_string<char> > >::Identity, spp::sparse_hash_set<std::__cxx11::basic_string<char>, spp::spp_hash<std::__cxx11::basic_string<char> >, std::equal_to<std::__cxx11::basic_string<char> >, spp::libc_allocator<std::__cxx11::basic_string<char> > >::SetKey, std::equal_to<std::__cxx11::basic_string<char> >, spp::libc_allocator<std::__cxx11::basic_string<char> > >::insert<std::__cxx11::basic_string<char> &>' requested here
    std::pair<iterator, bool> insert(P&& obj)        { return rep.insert(std::forward<P>(obj)); }
                                                                  ^
/<<PKGBUILDDIR>>/external/pufferfish/src/FixFasta.cpp:487:20: note: in instantiation of function template specialization 'spp::sparse_hash_set<std::__cxx11::basic_string<char>, spp::spp_hash<std::__cxx11::basic_string<char> >, std::equal_to<std::__cxx11::basic_string<char> >, spp::libc_allocator<std::__cxx11::basic_string<char> > >::insert<std::__cxx11::basic_string<char> &>' requested here
    auto it = dset.insert(dname);
                   ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/FixFasta.cpp:3:
/<<PKGBUILDDIR>>/external/pufferfish/include/clipp.h:5211:9: warning: private field 'exclusive_' is not used [-Wunused-private-field]
    tri exclusive_  = tri::either;
        ^
12 warnings generated.
[ 47%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/MemChainer.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/MemChainer.cpp
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/MemChainer.cpp:2:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/MemChainer.hpp:8:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishIndex.hpp:9:
/<<PKGBUILDDIR>>/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
                               ^
8 warnings generated.
[ 48%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PuffAligner.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/PuffAligner.cpp
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/MemChainer.cpp:2:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/MemChainer.hpp:8:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishIndex.hpp:12:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter]
  Derived& operator=(std::nullptr_t p) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator==(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator!=(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter]
bool operator==(std::nullptr_t lfs, const common<D, I, B, W, U>& rhs) {
                               ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter]
  iterator(W* p, unsigned b, unsigned o)
                          ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PuffAligner.cpp:2:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PuffAligner.hpp:8:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter]
  Derived& operator=(std::nullptr_t p) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator==(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator!=(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter]
bool operator==(std::nullptr_t lfs, const common<D, I, B, W, U>& rhs) {
                               ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter]
  iterator(W* p, unsigned b, unsigned o)
                          ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PuffAligner.cpp:2:
/<<PKGBUILDDIR>>/external/pufferfish/include/PuffAligner.hpp:70:12: warning: private field 'k' is not used [-Wunused-private-field]
  uint32_t k;
           ^
8 warnings generated.
[ 49%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishAligner.cpp
8 warnings generated.
[ 50%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/RefSeqConstructor.cpp
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/RefSeqConstructor.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/RefSeqConstructor.hpp:7:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter]
  Derived& operator=(std::nullptr_t p) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator==(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator!=(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter]
bool operator==(std::nullptr_t lfs, const common<D, I, B, W, U>& rhs) {
                               ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter]
  iterator(W* p, unsigned b, unsigned o)
                          ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishAligner.cpp:45:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/SelectiveAlignmentUtils.hpp:4:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PuffAligner.hpp:8:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:348:37: warning: unused parameter 'p' [-Wunused-parameter]
  Derived& operator=(std::nullptr_t p) {
                                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:367:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator==(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:371:34: warning: unused parameter 'p' [-Wunused-parameter]
  bool operator!=(std::nullptr_t p) {
                                 ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:582:32: warning: unused parameter 'lfs' [-Wunused-parameter]
bool operator==(std::nullptr_t lfs, const common<D, I, B, W, U>& rhs) {
                               ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:785:27: warning: unused parameter 'b' [-Wunused-parameter]
  iterator(W* p, unsigned b, unsigned o)
                          ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:806:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:845:22: warning: unused parameter 'b' [-Wunused-parameter]
  void bits(unsigned b) { } // NOOP
                     ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/PufferfishAligner.cpp:48:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishIndex.hpp:9:
/<<PKGBUILDDIR>>/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
                               ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/RefSeqConstructor.cpp:2:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/PufferfishIndex.hpp:9:
/<<PKGBUILDDIR>>/external/pufferfish/include/BooPHF.hpp:4:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
                               ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/RefSeqConstructor.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/RefSeqConstructor.hpp:5:
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:946:33: warning: definition of implicit copy constructor for 'Two_d_destructive_iterator<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::sparsegroup<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > > *, std::pair<const unsigned int, pufferfish::util::ContigBlock> *, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
    Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
                                ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2816:40: note: in implicit copy constructor for 'spp::Two_d_destructive_iterator<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::sparsegroup<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > > *, std::pair<const unsigned int, pufferfish::util::ContigBlock> *, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >' first required here
        for (destructive_iterator it = ht.destructive_begin();
                                       ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2947:9: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const unsigned int, pufferfish::util::ContigBlock>, unsigned int, spp::spp_hash<uint32_t>, spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock, spp::spp_hash<uint32_t>, std::equal_to<unsigned int>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::SelectKey, spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock, spp::spp_hash<uint32_t>, std::equal_to<unsigned int>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::SetKey, std::equal_to<unsigned int>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::_move_from' requested here
        _move_from(mover, ht, min_buckets_wanted);
        ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:2744:26: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const unsigned int, pufferfish::util::ContigBlock>, unsigned int, spp::spp_hash<uint32_t>, spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock, spp::spp_hash<uint32_t>, std::equal_to<unsigned int>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::SelectKey, spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock, spp::spp_hash<uint32_t>, std::equal_to<unsigned int>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::SetKey, std::equal_to<unsigned int>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::sparse_hashtable' requested here
        sparse_hashtable tmp(MoveDontCopy, *this, resize_to);
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:3277:21: note: in instantiation of member function 'spp::sparse_hashtable<std::pair<const unsigned int, pufferfish::util::ContigBlock>, unsigned int, spp::spp_hash<uint32_t>, spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock, spp::spp_hash<uint32_t>, std::equal_to<unsigned int>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::SelectKey, spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock, spp::spp_hash<uint32_t>, std::equal_to<unsigned int>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::SetKey, std::equal_to<unsigned int>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::_resize_delta' requested here
                if (_resize_delta(1))
                    ^
/<<PKGBUILDDIR>>/external/pufferfish/include/sparsepp/spp.h:3808:29: note: in instantiation of function template specialization 'spp::sparse_hashtable<std::pair<const unsigned int, pufferfish::util::ContigBlock>, unsigned int, spp::spp_hash<uint32_t>, spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock, spp::spp_hash<uint32_t>, std::equal_to<unsigned int>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::SelectKey, spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock, spp::spp_hash<uint32_t>, std::equal_to<unsigned int>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::SetKey, std::equal_to<unsigned int>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::find_or_insert<spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock, spp::spp_hash<uint32_t>, std::equal_to<unsigned int>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::DefaultValue, unsigned long &>' requested here
        return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
                            ^
/<<PKGBUILDDIR>>/external/pufferfish/src/RefSeqConstructor.cpp:143:47: note: in instantiation of function template specialization 'spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock, spp::spp_hash<uint32_t>, std::equal_to<unsigned int>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::operator[]<unsigned long &>' requested here
          pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid];
                                              ^
In file included from /<<PKGBUILDDIR>>/external/pufferfish/src/RefSeqConstructor.cpp:1:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/RefSeqConstructor.hpp:7:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/Util.hpp:23:
In file included from /<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:10:
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_iterator.hpp:657:15: warning: definition of implicit copy constructor for 'lhs_setter<unsigned long, 8, unsigned long, false, 64>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy]
  lhs_setter& operator=(const lhs_setter& rhs) {
              ^
/<<PKGBUILDDIR>>/external/pufferfish/include/compact_vector/compact_vector.hpp:162:26: note: in implicit copy constructor for 'compact::iterator_imp::lhs_setter<unsigned long, 8, unsigned long, false, 64>' first required here
                       ? typename iterator::lhs_setter_type(m_mem + (i * BITS) / UB, BITS, (i * BITS) % UB)
                         ^
/<<PKGBUILDDIR>>/external/pufferfish/src/RefSeqConstructor.cpp:338:23: note: in instantiation of member function 'compact::vector_imp::vector<compact::vector<unsigned long, 8, unsigned long, std::allocator<unsigned long> >, unsigned long, 8, unsigned long, std::allocator<unsigned long>, 64, false>::operator[]' requested here
    uint8_t edgeVec = edges[contig.contigIdx_] ;
                      ^
10 warnings generated.
[ 51%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/src/metro/metrohash64.cpp
8 warnings generated.
[ 52%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/include -I/<<PKGBUILDDIR>>/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -c /<<PKGBUILDDIR>>/src/LibraryFormat.cpp
[ 53%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor/../common  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -std=c++14 -o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp
[ 54%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++   -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor -I/<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor/../common  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -std=c++14 -o CMakeFiles/twopaco.dir/common.cpp.o -c /<<PKGBUILDDIR>>/external/pufferfish/external/twopaco/graphconstructor/common.cpp
8 warnings generated.
[ 55%] Linking CXX static library libpuffer.a
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/puffer.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/puffer.dir/link.txt --verbose=1
/usr/bin/ar qc libpuffer.a  CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o CMakeFiles/puffer.dir/edlib.cpp.o CMakeFiles/puffer.dir/Util.cpp.o CMakeFiles/puffer.dir/rank9sel.cpp.o CMakeFiles/puffer.dir/rank9b.cpp.o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o CMakeFiles/puffer.dir/PufferfishStats.cpp.o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o CMakeFiles/puffer.dir/FastxParser.cpp.o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o CMakeFiles/puffer.dir/PufferFS.cpp.o CMakeFiles/puffer.dir/xxhash.c.o CMakeFiles/puffer.dir/FixFasta.cpp.o CMakeFiles/puffer.dir/MemCollector.cpp.o CMakeFiles/puffer.dir/MemChainer.cpp.o CMakeFiles/puffer.dir/PuffAligner.cpp.o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o
/usr/bin/ranlib libpuffer.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 55%] Built target puffer
[ 56%] Linking CXX static library libtwopaco.a
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/cmake -P CMakeFiles/twopaco.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/cmake -E cmake_link_script CMakeFiles/twopaco.dir/link.txt --verbose=1
/usr/bin/ar qc libtwopaco.a  CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o CMakeFiles/twopaco.dir/constructor.cpp.o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o CMakeFiles/twopaco.dir/compressedstring.cpp.o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o CMakeFiles/twopaco.dir/test.cpp.o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o CMakeFiles/twopaco.dir/common.cpp.o
/usr/bin/ranlib libtwopaco.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 56%] Built target twopaco
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:166: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" returned exit code 2
make[1]: *** [debian/rules:37: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:26: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2020-05-03T02:19:12Z

Finished
--------


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

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

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

Build Architecture: amd64
Build Type: binary
Build-Space: 255892
Build-Time: 259
Distribution: unstable
Fail-Stage: build
Host Architecture: amd64
Install-Time: 106
Job: salmon_1.2.1+ds1-1
Machine Architecture: amd64
Package: salmon
Package-Time: 380
Source-Version: 1.2.1+ds1-1
Space: 255892
Status: attempted
Version: 1.2.1+ds1-1
--------------------------------------------------------------------------------
Finished at 2020-05-03T02:19:12Z
Build needed 00:06:20, 255892k disk space
E: Build failure (dpkg-buildpackage died)
DC-Status: Failed 381.983378733s
DC-Time-Estimation: 381.983378733 versus expected 1 (r/m: 380.983378733 ; m: 1.0)