DC-Build-Header: canu 1.8+dfsg-2 / 2019-01-09 21:17:52 +0000 DC-Task: type:rebuild-binarch-only source:canu version:1.8+dfsg-2 chroot:unstable esttime:372 logfile:/tmp/canu_1.8+dfsg-2_unstable_clang8.log modes:clang8:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang8 canu_1.8+dfsg-2' sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-4-137.eu-central-1.compute.internal +==============================================================================+ | canu 1.8+dfsg-2 (amd64) Wed, 09 Jan 2019 21:17:52 +0000 | +==============================================================================+ Package: canu Version: 1.8+dfsg-2 Source Version: 1.8+dfsg-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-75cf1cd3-a554-43e9-9441-4bfa8f188d35' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang8 ----------- + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=8 + echo 'Install of clang-8' Install of clang-8 + echo deb http://127.0.0.1:9999/debian experimental main + apt-get update Get:1 http://127.0.0.1:9999/debian sid InRelease [238 kB] Get:2 http://127.0.0.1:9999/debian experimental InRelease [101 kB] Get:3 http://127.0.0.1:9999/debian sid/main Sources.diff/Index [27.9 kB] Get:4 http://127.0.0.1:9999/debian sid/main amd64 Packages.diff/Index [27.9 kB] Get:5 http://127.0.0.1:9999/debian sid/main Sources 2019-01-09-1430.36.pdiff [24.1 kB] Get:5 http://127.0.0.1:9999/debian sid/main Sources 2019-01-09-1430.36.pdiff [24.1 kB] Get:6 http://127.0.0.1:9999/debian sid/main amd64 Packages 2019-01-09-1430.36.pdiff [40.9 kB] Get:6 http://127.0.0.1:9999/debian sid/main amd64 Packages 2019-01-09-1430.36.pdiff [40.9 kB] Get:7 http://127.0.0.1:9999/debian sid/main Translation-en [6275 kB] Get:8 http://127.0.0.1:9999/debian experimental/main amd64 Packages [245 kB] Get:9 http://127.0.0.1:9999/debian experimental/main Translation-en [173 kB] Fetched 7153 kB in 2s (3690 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-8 libomp-8-dev libobjc-8-dev Reading package lists... Building dependency tree... The following additional packages will be installed: lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-8-dev libclang1-8 libedit2 libgc1c2 libllvm8 libobjc4 libomp5-8 Suggested packages: clang-8-doc libomp-8-doc Recommended packages: llvm-8-dev python The following NEW packages will be installed: clang-8 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-8-dev libclang1-8 libedit2 libgc1c2 libllvm8 libobjc-8-dev libobjc4 libomp-8-dev libomp5-8 0 upgraded, 14 newly installed, 0 to remove and 5 not upgraded. Need to get 35.8 MB of archives. After this operation, 191 MB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian sid/main amd64 libbsd0 amd64 0.9.1-1 [99.3 kB] Get:2 http://127.0.0.1:9999/debian sid/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB] Get:3 http://127.0.0.1:9999/debian experimental/main amd64 libllvm8 amd64 1:8~svn350193-1~exp1 [13.8 MB] Get:4 http://127.0.0.1:9999/debian sid/main amd64 libgc1c2 amd64 1:7.6.4-0.4 [224 kB] Get:5 http://127.0.0.1:9999/debian sid/main amd64 libobjc4 amd64 8.2.0-14 [50.4 kB] Get:6 http://127.0.0.1:9999/debian sid/main amd64 libobjc-8-dev amd64 8.2.0-14 [225 kB] Get:7 http://127.0.0.1:9999/debian sid/main amd64 libc6-i386 amd64 2.28-4 [2873 kB] Get:8 http://127.0.0.1:9999/debian sid/main amd64 lib32gcc1 amd64 1:8.2.0-14 [47.9 kB] Get:9 http://127.0.0.1:9999/debian sid/main amd64 lib32stdc++6 amd64 8.2.0-14 [406 kB] Get:10 http://127.0.0.1:9999/debian experimental/main amd64 libclang-common-8-dev amd64 1:8~svn350193-1~exp1 [3350 kB] Get:11 http://127.0.0.1:9999/debian experimental/main amd64 libclang1-8 amd64 1:8~svn350193-1~exp1 [6255 kB] Get:12 http://127.0.0.1:9999/debian experimental/main amd64 clang-8 amd64 1:8~svn350193-1~exp1 [8025 kB] Get:13 http://127.0.0.1:9999/debian experimental/main amd64 libomp5-8 amd64 1:8~svn350193-1~exp1 [328 kB] Get:14 http://127.0.0.1:9999/debian experimental/main amd64 libomp-8-dev amd64 1:8~svn350193-1~exp1 [58.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 35.8 MB in 0s (119 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11802 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../01-libedit2_3.1-20181209-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20181209-1) ... Selecting previously unselected package libllvm8:amd64. Preparing to unpack .../02-libllvm8_1%3a8~svn350193-1~exp1_amd64.deb ... Unpacking libllvm8:amd64 (1:8~svn350193-1~exp1) ... Selecting previously unselected package libgc1c2:amd64. Preparing to unpack .../03-libgc1c2_1%3a7.6.4-0.4_amd64.deb ... Unpacking libgc1c2:amd64 (1:7.6.4-0.4) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../04-libobjc4_8.2.0-14_amd64.deb ... Unpacking libobjc4:amd64 (8.2.0-14) ... Selecting previously unselected package libobjc-8-dev:amd64. Preparing to unpack .../05-libobjc-8-dev_8.2.0-14_amd64.deb ... Unpacking libobjc-8-dev:amd64 (8.2.0-14) ... Selecting previously unselected package libc6-i386. Preparing to unpack .../06-libc6-i386_2.28-4_amd64.deb ... Unpacking libc6-i386 (2.28-4) ... Selecting previously unselected package lib32gcc1. Preparing to unpack .../07-lib32gcc1_1%3a8.2.0-14_amd64.deb ... Unpacking lib32gcc1 (1:8.2.0-14) ... Selecting previously unselected package lib32stdc++6. Preparing to unpack .../08-lib32stdc++6_8.2.0-14_amd64.deb ... Unpacking lib32stdc++6 (8.2.0-14) ... Selecting previously unselected package libclang-common-8-dev. Preparing to unpack .../09-libclang-common-8-dev_1%3a8~svn350193-1~exp1_amd64.deb ... Unpacking libclang-common-8-dev (1:8~svn350193-1~exp1) ... Selecting previously unselected package libclang1-8:amd64. Preparing to unpack .../10-libclang1-8_1%3a8~svn350193-1~exp1_amd64.deb ... Unpacking libclang1-8:amd64 (1:8~svn350193-1~exp1) ... Selecting previously unselected package clang-8. Preparing to unpack .../11-clang-8_1%3a8~svn350193-1~exp1_amd64.deb ... Unpacking clang-8 (1:8~svn350193-1~exp1) ... Selecting previously unselected package libomp5-8:amd64. Preparing to unpack .../12-libomp5-8_1%3a8~svn350193-1~exp1_amd64.deb ... Unpacking libomp5-8:amd64 (1:8~svn350193-1~exp1) ... Selecting previously unselected package libomp-8-dev. Preparing to unpack .../13-libomp-8-dev_1%3a8~svn350193-1~exp1_amd64.deb ... Unpacking libomp-8-dev (1:8~svn350193-1~exp1) ... Setting up libomp5-8:amd64 (1:8~svn350193-1~exp1) ... Setting up libgc1c2:amd64 (1:7.6.4-0.4) ... Setting up libc6-i386 (2.28-4) ... Setting up libbsd0:amd64 (0.9.1-1) ... Setting up libomp-8-dev (1:8~svn350193-1~exp1) ... Processing triggers for libc-bin (2.28-4) ... Setting up lib32gcc1 (1:8.2.0-14) ... Setting up libedit2:amd64 (3.1-20181209-1) ... Setting up libobjc4:amd64 (8.2.0-14) ... Setting up libobjc-8-dev:amd64 (8.2.0-14) ... Setting up libllvm8:amd64 (1:8~svn350193-1~exp1) ... Setting up libclang1-8:amd64 (1:8~svn350193-1~exp1) ... Setting up lib32stdc++6 (8.2.0-14) ... Setting up libclang-common-8-dev (1:8~svn350193-1~exp1) ... Setting up clang-8 (1:8~svn350193-1~exp1) ... Processing triggers for libc-bin (2.28-4) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7 8' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-8 g++-4.6 + ln -s clang-8 gcc-4.6 + ln -s clang-8 cpp-4.6 + ln -s clang-8 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 + 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 + for VERSION in $VERSIONS + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-8 g++-4.7 + ln -s clang-8 gcc-4.7 + ln -s clang-8 cpp-4.7 + ln -s clang-8 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 + 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 + for VERSION in $VERSIONS + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-8 g++-4.8 + ln -s clang-8 gcc-4.8 + ln -s clang-8 cpp-4.8 + ln -s clang-8 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 + 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 + for VERSION in $VERSIONS + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-8 g++-4.9 + ln -s clang-8 gcc-4.9 + ln -s clang-8 cpp-4.9 + ln -s clang-8 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 + 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 + for VERSION in $VERSIONS + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-8 g++-5 + ln -s clang-8 gcc-5 + ln -s clang-8 cpp-5 + ln -s clang-8 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 + 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 + for VERSION in $VERSIONS + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-8 g++-6 + ln -s clang-8 gcc-6 + ln -s clang-8 cpp-6 + ln -s clang-8 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 + 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 + for VERSION in $VERSIONS + rm -f g++-7 gcc-7 cpp-7 gcc + ln -s clang++-8 g++-7 + ln -s clang-8 gcc-7 + ln -s clang-8 cpp-7 + ln -s clang-8 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 + 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 + for VERSION in $VERSIONS + rm -f g++-8 gcc-8 cpp-8 gcc + ln -s clang++-8 g++-8 + ln -s clang-8 gcc-8 + ln -s clang-8 cpp-8 + ln -s clang-8 gcc + echo 'gcc-8 hold' + dpkg --set-selections + echo 'g++-8 hold' + dpkg --set-selections + cd - /build/canu-l8xWt9 + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang I: Finished running '/tmp/clang8'. Finished processing commands. -------------------------------------------------------------------------------- +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:9999/debian sid InRelease Hit:2 http://127.0.0.1:9999/debian experimental InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libmpfr6 libpam-modules libpam-modules-bin libpam-runtime libpam0g 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1519 kB of archives. After this operation, 7168 B of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian sid/main amd64 libpam0g amd64 1.1.8-4 [124 kB] Get:2 http://127.0.0.1:9999/debian sid/main amd64 libpam-modules-bin amd64 1.1.8-4 [106 kB] Get:3 http://127.0.0.1:9999/debian sid/main amd64 libpam-modules amd64 1.1.8-4 [305 kB] Get:4 http://127.0.0.1:9999/debian sid/main amd64 libpam-runtime all 1.1.8-4 [211 kB] Get:5 http://127.0.0.1:9999/debian sid/main amd64 libmpfr6 amd64 4.0.2~rc1-1 [773 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1519 kB in 0s (28.3 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12592 files and directories currently installed.) Preparing to unpack .../libpam0g_1.1.8-4_amd64.deb ... Unpacking libpam0g:amd64 (1.1.8-4) over (1.1.8-3.8) ... Setting up libpam0g:amd64 (1.1.8-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12592 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.1.8-4_amd64.deb ... Unpacking libpam-modules-bin (1.1.8-4) over (1.1.8-3.8) ... Setting up libpam-modules-bin (1.1.8-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12592 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.1.8-4_amd64.deb ... Unpacking libpam-modules:amd64 (1.1.8-4) over (1.1.8-3.8) ... Setting up libpam-modules:amd64 (1.1.8-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12592 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.1.8-4_all.deb ... Unpacking libpam-runtime (1.1.8-4) over (1.1.8-3.8) ... Setting up libpam-runtime (1.1.8-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12592 files and directories currently installed.) Preparing to unpack .../libmpfr6_4.0.2~rc1-1_amd64.deb ... Unpacking libmpfr6:amd64 (4.0.2~rc1-1) over (4.0.1-2) ... Setting up libmpfr6:amd64 (4.0.2~rc1-1) ... Processing triggers for libc-bin (2.28-4) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'canu' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/canu.git Please use: git clone https://salsa.debian.org/med-team/canu.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1092 kB of source archives. Get:1 http://127.0.0.1:9999/debian sid/main canu 1.8+dfsg-2 (dsc) [1980 B] Get:2 http://127.0.0.1:9999/debian sid/main canu 1.8+dfsg-2 (tar) [1084 kB] Get:3 http://127.0.0.1:9999/debian sid/main canu 1.8+dfsg-2 (diff) [5904 B] Fetched 1092 kB in 1s (1164 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/canu-l8xWt9/canu-1.8+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/canu-l8xWt9' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-IE3COE/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-IE3COE/apt_archive ./ InRelease Get:2 copy:/<>/resolver-IE3COE/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-IE3COE/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-IE3COE/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-IE3COE/apt_archive ./ Packages [429 B] Fetched 1735 B in 0s (0 B/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-IE3COE/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12592 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 11~), libboost-dev, libmeryl-dev, libfilesys-df-perl, mhap (>= 2.1.3) Filtered Build-Depends: debhelper (>= 11~), libboost-dev, libmeryl-dev, libfilesys-df-perl, mhap (>= 2.1.3) dpkg-deb: building package 'sbuild-build-depends-canu-dummy' in '/<>/resolver-IE3COE/apt_archive/sbuild-build-depends-canu-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-canu-dummy sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-IE3COE/apt_archive ./ InRelease Get:2 copy:/<>/resolver-IE3COE/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-IE3COE/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-IE3COE/apt_archive ./ Sources [520 B] Get:5 copy:/<>/resolver-IE3COE/apt_archive ./ Packages [601 B] Fetched 2084 B in 0s (0 B/s) Reading package lists... Reading package lists... Install canu 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 binfmt-support bsdmainutils ca-certificates ca-certificates-java debhelper default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz fastjar file fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian jaligner jarwrapper java-common libapache-pom-java libarchive-zip-perl libasound2 libasound2-data libatinject-jsr330-api-java libavahi-client3 libavahi-common-data libavahi-common3 libboost-dev libboost1.67-dev libcommons-compress-java libcommons-parent-java libcroco3 libcups2 libdbus-1-3 libelf1 libexpat1 libfastutil-java libfile-stripnondeterminism-perl libfilesys-df-perl libfontconfig1 libfreetype6 libglib2.0-0 libgssapi-krb5-2 libguava-java libicu63 libjpeg62-turbo libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 libmagic-mgc libmagic1 libmeryl-dev libncurses6 libnspr4 libnss3 libpcsclite1 libpipeline1 libpng16-16 libsigsegv2 libsqlite3-0 libssl1.1 libssw-java libtool libuchardet0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxtst6 lsb-base m4 man-db mhap openjdk-11-jre-headless openssl po-debconf sensible-utils ucf x11-common Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make default-jre gettext-doc libasprintf-dev libgettextpo-dev groff libasound2-plugins alsa-utils libatinject-jsr330-api-java-doc libboost-doc libboost1.67-doc libboost-atomic1.67-dev libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev libboost-coroutine1.67-dev libboost-date-time1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev libboost-filesystem1.67-dev libboost-graph1.67-dev libboost-graph-parallel1.67-dev libboost-iostreams1.67-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-program-options1.67-dev libboost-python1.67-dev libboost-random1.67-dev libboost-regex1.67-dev libboost-serialization1.67-dev libboost-signals1.67-dev libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev libxz-java cups-common krb5-doc krb5-user libjsr305-java-doc liblcms2-utils pcscd libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic libmail-box-perl Recommended packages: curl | wget | lynx dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2 libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binfmt-support bsdmainutils ca-certificates ca-certificates-java debhelper default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz fastjar file fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian jaligner jarwrapper java-common libapache-pom-java libarchive-zip-perl libasound2 libasound2-data libatinject-jsr330-api-java libavahi-client3 libavahi-common-data libavahi-common3 libboost-dev libboost1.67-dev libcommons-compress-java libcommons-parent-java libcroco3 libcups2 libdbus-1-3 libelf1 libexpat1 libfastutil-java libfile-stripnondeterminism-perl libfilesys-df-perl libfontconfig1 libfreetype6 libglib2.0-0 libgssapi-krb5-2 libguava-java libicu63 libjpeg62-turbo libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 libmagic-mgc libmagic1 libmeryl-dev libncurses6 libnspr4 libnss3 libpcsclite1 libpipeline1 libpng16-16 libsigsegv2 libsqlite3-0 libssl1.1 libssw-java libtool libuchardet0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxtst6 lsb-base m4 man-db mhap openjdk-11-jre-headless openssl po-debconf sbuild-build-depends-canu-dummy sensible-utils ucf x11-common 0 upgraded, 93 newly installed, 0 to remove and 0 not upgraded. Need to get 92.7 MB of archives. After this operation, 420 MB of additional disk space will be used. Get:1 copy:/<>/resolver-IE3COE/apt_archive ./ sbuild-build-depends-canu-dummy 0.invalid.0 [896 B] Get:2 http://127.0.0.1:9999/debian sid/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:3 http://127.0.0.1:9999/debian sid/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:4 http://127.0.0.1:9999/debian sid/main amd64 groff-base amd64 1.22.4-2 [917 kB] Get:5 http://127.0.0.1:9999/debian sid/main amd64 libpipeline1 amd64 1.5.0-2 [29.5 kB] Get:6 http://127.0.0.1:9999/debian sid/main amd64 man-db amd64 2.8.5-1 [1274 kB] Get:7 http://127.0.0.1:9999/debian sid/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:8 http://127.0.0.1:9999/debian sid/main amd64 libmagic-mgc amd64 1:5.34-2 [239 kB] Get:9 http://127.0.0.1:9999/debian sid/main amd64 libmagic1 amd64 1:5.34-2 [116 kB] Get:10 http://127.0.0.1:9999/debian sid/main amd64 file amd64 1:5.34-2 [65.8 kB] Get:11 http://127.0.0.1:9999/debian sid/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:12 http://127.0.0.1:9999/debian sid/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:13 http://127.0.0.1:9999/debian sid/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:14 http://127.0.0.1:9999/debian sid/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:15 http://127.0.0.1:9999/debian sid/main amd64 autoconf all 2.69-11 [341 kB] Get:16 http://127.0.0.1:9999/debian sid/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:17 http://127.0.0.1:9999/debian sid/main amd64 automake all 1:1.16.1-4 [771 kB] Get:18 http://127.0.0.1:9999/debian sid/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:19 http://127.0.0.1:9999/debian sid/main amd64 lsb-base all 10.2018112800 [28.3 kB] Get:20 http://127.0.0.1:9999/debian sid/main amd64 binfmt-support amd64 2.1.8-2.1 [61.4 kB] Get:21 http://127.0.0.1:9999/debian sid/main amd64 libssl1.1 amd64 1.1.1a-1 [1527 kB] Get:22 http://127.0.0.1:9999/debian sid/main amd64 openssl amd64 1.1.1a-1 [836 kB] Get:23 http://127.0.0.1:9999/debian sid/main amd64 ca-certificates all 20180409 [161 kB] Get:24 http://127.0.0.1:9999/debian sid/main amd64 java-common all 0.71 [14.4 kB] Get:25 http://127.0.0.1:9999/debian sid/main amd64 libavahi-common-data amd64 0.7-4+b1 [122 kB] Get:26 http://127.0.0.1:9999/debian sid/main amd64 libavahi-common3 amd64 0.7-4+b1 [54.6 kB] Get:27 http://127.0.0.1:9999/debian sid/main amd64 libdbus-1-3 amd64 1.12.12-1 [212 kB] Get:28 http://127.0.0.1:9999/debian sid/main amd64 libavahi-client3 amd64 0.7-4+b1 [58.1 kB] Get:29 http://127.0.0.1:9999/debian sid/main amd64 libkeyutils1 amd64 1.5.9-9.3 [13.0 kB] Get:30 http://127.0.0.1:9999/debian sid/main amd64 libkrb5support0 amd64 1.16.2-1 [63.3 kB] Get:31 http://127.0.0.1:9999/debian sid/main amd64 libk5crypto3 amd64 1.16.2-1 [121 kB] Get:32 http://127.0.0.1:9999/debian sid/main amd64 libkrb5-3 amd64 1.16.2-1 [320 kB] Get:33 http://127.0.0.1:9999/debian sid/main amd64 libgssapi-krb5-2 amd64 1.16.2-1 [158 kB] Get:34 http://127.0.0.1:9999/debian sid/main amd64 libcups2 amd64 2.2.10-3 [324 kB] Get:35 http://127.0.0.1:9999/debian sid/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get:36 http://127.0.0.1:9999/debian sid/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+b1 [134 kB] Get:37 http://127.0.0.1:9999/debian sid/main amd64 libexpat1 amd64 2.2.6-1 [105 kB] Get:38 http://127.0.0.1:9999/debian sid/main amd64 libpng16-16 amd64 1.6.36-2 [292 kB] Get:39 http://127.0.0.1:9999/debian sid/main amd64 libfreetype6 amd64 2.9.1-3 [379 kB] Get:40 http://127.0.0.1:9999/debian sid/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:41 http://127.0.0.1:9999/debian sid/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get:42 http://127.0.0.1:9999/debian sid/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get:43 http://127.0.0.1:9999/debian sid/main amd64 libnspr4 amd64 2:4.20-1 [112 kB] Get:44 http://127.0.0.1:9999/debian sid/main amd64 libsqlite3-0 amd64 3.26.0+fossilbc891ac6b-1 [634 kB] Get:45 http://127.0.0.1:9999/debian sid/main amd64 libnss3 amd64 2:3.41-1 [1157 kB] Get:46 http://127.0.0.1:9999/debian sid/main amd64 libasound2-data all 1.1.7-2 [56.6 kB] Get:47 http://127.0.0.1:9999/debian sid/main amd64 libasound2 amd64 1.1.7-2 [362 kB] Get:48 http://127.0.0.1:9999/debian sid/main amd64 libpcsclite1 amd64 1.8.24-1 [58.5 kB] Get:49 http://127.0.0.1:9999/debian sid/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:50 http://127.0.0.1:9999/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:51 http://127.0.0.1:9999/debian sid/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get:52 http://127.0.0.1:9999/debian sid/main amd64 libx11-data all 2:1.6.7-1 [298 kB] Get:53 http://127.0.0.1:9999/debian sid/main amd64 libx11-6 amd64 2:1.6.7-1 [754 kB] Get:54 http://127.0.0.1:9999/debian sid/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:55 http://127.0.0.1:9999/debian sid/main amd64 libxi6 amd64 2:1.7.9-1 [82.6 kB] Get:56 http://127.0.0.1:9999/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:57 http://127.0.0.1:9999/debian sid/main amd64 x11-common all 1:7.7+19 [251 kB] Get:58 http://127.0.0.1:9999/debian sid/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB] Get:59 http://127.0.0.1:9999/debian sid/main amd64 openjdk-11-jre-headless amd64 11.0.1+13-3 [36.9 MB] Get:60 http://127.0.0.1:9999/debian sid/main amd64 default-jre-headless amd64 2:1.11-71 [10.9 kB] Get:61 http://127.0.0.1:9999/debian sid/main amd64 ca-certificates-java all 20180516 [15.5 kB] Get:62 http://127.0.0.1:9999/debian sid/main amd64 libtool all 2.4.6-6 [547 kB] Get:63 http://127.0.0.1:9999/debian sid/main amd64 dh-autoreconf all 19 [16.9 kB] Get:64 http://127.0.0.1:9999/debian sid/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get:65 http://127.0.0.1:9999/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.0.0-1 [19.5 kB] Get:66 http://127.0.0.1:9999/debian sid/main amd64 dh-strip-nondeterminism all 1.0.0-1 [12.5 kB] Get:67 http://127.0.0.1:9999/debian sid/main amd64 libelf1 amd64 0.175-2 [160 kB] Get:68 http://127.0.0.1:9999/debian sid/main amd64 dwz amd64 0.12-3 [78.0 kB] Get:69 http://127.0.0.1:9999/debian sid/main amd64 libglib2.0-0 amd64 2.58.2-3 [1257 kB] Get:70 http://127.0.0.1:9999/debian sid/main amd64 libicu63 amd64 63.1-5 [8293 kB] Get:71 http://127.0.0.1:9999/debian sid/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:72 http://127.0.0.1:9999/debian sid/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get:73 http://127.0.0.1:9999/debian sid/main amd64 libncurses6 amd64 6.1+20181013-1 [102 kB] Get:74 http://127.0.0.1:9999/debian sid/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:75 http://127.0.0.1:9999/debian sid/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:76 http://127.0.0.1:9999/debian sid/main amd64 po-debconf all 1.0.21 [248 kB] Get:77 http://127.0.0.1:9999/debian sid/main amd64 debhelper all 12 [1002 kB] Get:78 http://127.0.0.1:9999/debian sid/main amd64 fastjar amd64 2:0.98-6+b1 [81.0 kB] Get:79 http://127.0.0.1:9999/debian sid/main amd64 jaligner all 1.0+dfsg-6 [131 kB] Get:80 http://127.0.0.1:9999/debian sid/main amd64 jarwrapper all 0.72.1 [20.3 kB] Get:81 http://127.0.0.1:9999/debian sid/main amd64 libapache-pom-java all 18-1 [4676 B] Get:82 http://127.0.0.1:9999/debian sid/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get:83 http://127.0.0.1:9999/debian sid/main amd64 libboost1.67-dev amd64 1.67.0-11 [8386 kB] Get:84 http://127.0.0.1:9999/debian sid/main amd64 libboost-dev amd64 1.67.0.1 [3864 B] Get:85 http://127.0.0.1:9999/debian sid/main amd64 libcommons-parent-java all 43-1 [10.8 kB] Get:86 http://127.0.0.1:9999/debian sid/main amd64 libcommons-compress-java all 1.18-1 [532 kB] Get:87 http://127.0.0.1:9999/debian sid/main amd64 libfastutil-java all 7.1.0-2 [14.4 MB] Get:88 http://127.0.0.1:9999/debian sid/main amd64 libfilesys-df-perl amd64 0.92-6+b4 [12.6 kB] Get:89 http://127.0.0.1:9999/debian sid/main amd64 libjsr305-java all 0.1~+svn49-10 [26.5 kB] Get:90 http://127.0.0.1:9999/debian sid/main amd64 libguava-java all 19.0-1 [2028 kB] Get:91 http://127.0.0.1:9999/debian sid/main amd64 libmeryl-dev amd64 0~20150903+r2013-6 [53.6 kB] Get:92 http://127.0.0.1:9999/debian sid/main amd64 libssw-java amd64 1.1-2 [13.8 kB] Get:93 http://127.0.0.1:9999/debian sid/main amd64 mhap all 2.1.3+dfsg-2 [160 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 92.7 MB in 2s (52.7 MB/s) Selecting previously unselected package bsdmainutils. (Reading database ... 12592 files and directories currently installed.) Preparing to unpack .../00-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-2_amd64.deb ... Unpacking groff-base (1.22.4-2) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.0-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.0-2) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.8.5-1_amd64.deb ... Unpacking man-db (2.8.5-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.34-2_amd64.deb ... Unpacking libmagic-mgc (1:5.34-2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../07-libmagic1_1%3a5.34-2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.34-2) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.34-2_amd64.deb ... Unpacking file (1:5.34-2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package ucf. Preparing to unpack .../10-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../11-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package lsb-base. Preparing to unpack .../17-lsb-base_10.2018112800_all.deb ... Unpacking lsb-base (10.2018112800) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../18-binfmt-support_2.1.8-2.1_amd64.deb ... Unpacking binfmt-support (2.1.8-2.1) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../19-libssl1.1_1.1.1a-1_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1a-1) ... Selecting previously unselected package openssl. Preparing to unpack .../20-openssl_1.1.1a-1_amd64.deb ... Unpacking openssl (1.1.1a-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../21-ca-certificates_20180409_all.deb ... Unpacking ca-certificates (20180409) ... Selecting previously unselected package java-common. Preparing to unpack .../22-java-common_0.71_all.deb ... Unpacking java-common (0.71) ... Selecting previously unselected package libavahi-common-data:amd64. Preparing to unpack .../23-libavahi-common-data_0.7-4+b1_amd64.deb ... Unpacking libavahi-common-data:amd64 (0.7-4+b1) ... Selecting previously unselected package libavahi-common3:amd64. Preparing to unpack .../24-libavahi-common3_0.7-4+b1_amd64.deb ... Unpacking libavahi-common3:amd64 (0.7-4+b1) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../25-libdbus-1-3_1.12.12-1_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.12.12-1) ... Selecting previously unselected package libavahi-client3:amd64. Preparing to unpack .../26-libavahi-client3_0.7-4+b1_amd64.deb ... Unpacking libavahi-client3:amd64 (0.7-4+b1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../27-libkeyutils1_1.5.9-9.3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.5.9-9.3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../28-libkrb5support0_1.16.2-1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.16.2-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../29-libk5crypto3_1.16.2-1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.16.2-1) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../30-libkrb5-3_1.16.2-1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.16.2-1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../31-libgssapi-krb5-2_1.16.2-1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.16.2-1) ... Selecting previously unselected package libcups2:amd64. Preparing to unpack .../32-libcups2_2.2.10-3_amd64.deb ... Unpacking libcups2:amd64 (2.2.10-3) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../33-liblcms2-2_2.9-3_amd64.deb ... Unpacking liblcms2-2:amd64 (2.9-3) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../34-libjpeg62-turbo_1%3a1.5.2-2+b1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:1.5.2-2+b1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../35-libexpat1_2.2.6-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-1) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../36-libpng16-16_1.6.36-2_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.36-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../37-libfreetype6_2.9.1-3_amd64.deb ... Unpacking libfreetype6:amd64 (2.9.1-3) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../38-fonts-dejavu-core_2.37-1_all.deb ... Unpacking fonts-dejavu-core (2.37-1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../39-fontconfig-config_2.13.1-2_all.deb ... Unpacking fontconfig-config (2.13.1-2) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../40-libfontconfig1_2.13.1-2_amd64.deb ... Unpacking libfontconfig1:amd64 (2.13.1-2) ... Selecting previously unselected package libnspr4:amd64. Preparing to unpack .../41-libnspr4_2%3a4.20-1_amd64.deb ... Unpacking libnspr4:amd64 (2:4.20-1) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../42-libsqlite3-0_3.26.0+fossilbc891ac6b-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.26.0+fossilbc891ac6b-1) ... Selecting previously unselected package libnss3:amd64. Preparing to unpack .../43-libnss3_2%3a3.41-1_amd64.deb ... Unpacking libnss3:amd64 (2:3.41-1) ... Selecting previously unselected package libasound2-data. Preparing to unpack .../44-libasound2-data_1.1.7-2_all.deb ... Unpacking libasound2-data (1.1.7-2) ... Selecting previously unselected package libasound2:amd64. Preparing to unpack .../45-libasound2_1.1.7-2_amd64.deb ... Unpacking libasound2:amd64 (1.1.7-2) ... Selecting previously unselected package libpcsclite1:amd64. Preparing to unpack .../46-libpcsclite1_1.8.24-1_amd64.deb ... Unpacking libpcsclite1:amd64 (1.8.24-1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../47-libxau6_1%3a1.0.8-1+b2_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.8-1+b2) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../48-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../49-libxcb1_1.13.1-2_amd64.deb ... Unpacking libxcb1:amd64 (1.13.1-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../50-libx11-data_2%3a1.6.7-1_all.deb ... Unpacking libx11-data (2:1.6.7-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../51-libx11-6_2%3a1.6.7-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.6.7-1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../52-libxext6_2%3a1.3.3-1+b2_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.3-1+b2) ... Selecting previously unselected package libxi6:amd64. Preparing to unpack .../53-libxi6_2%3a1.7.9-1_amd64.deb ... Unpacking libxi6:amd64 (2:1.7.9-1) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../54-libxrender1_1%3a0.9.10-1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../55-x11-common_1%3a7.7+19_all.deb ... Unpacking x11-common (1:7.7+19) ... Selecting previously unselected package libxtst6:amd64. Preparing to unpack .../56-libxtst6_2%3a1.2.3-1_amd64.deb ... Unpacking libxtst6:amd64 (2:1.2.3-1) ... Selecting previously unselected package openjdk-11-jre-headless:amd64. Preparing to unpack .../57-openjdk-11-jre-headless_11.0.1+13-3_amd64.deb ... Unpacking openjdk-11-jre-headless:amd64 (11.0.1+13-3) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../58-default-jre-headless_2%3a1.11-71_amd64.deb ... Unpacking default-jre-headless (2:1.11-71) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../59-ca-certificates-java_20180516_all.deb ... Unpacking ca-certificates-java (20180516) ... Selecting previously unselected package libtool. Preparing to unpack .../60-libtool_2.4.6-6_all.deb ... Unpacking libtool (2.4.6-6) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../61-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../62-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../63-libfile-stripnondeterminism-perl_1.0.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.0.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../64-dh-strip-nondeterminism_1.0.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.0.0-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../65-libelf1_0.175-2_amd64.deb ... Unpacking libelf1:amd64 (0.175-2) ... Selecting previously unselected package dwz. Preparing to unpack .../66-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../67-libglib2.0-0_2.58.2-3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.2-3) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../68-libicu63_63.1-5_amd64.deb ... Unpacking libicu63:amd64 (63.1-5) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../69-libxml2_2.9.4+dfsg1-7+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../70-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../71-libncurses6_6.1+20181013-1_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-1) ... Selecting previously unselected package gettext. Preparing to unpack .../72-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../73-intltool-debian_0.35.0+20060710.4_all.deb ... Unpacking intltool-debian (0.35.0+20060710.4) ... Selecting previously unselected package po-debconf. Preparing to unpack .../74-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../75-debhelper_12_all.deb ... Unpacking debhelper (12) ... Selecting previously unselected package fastjar. Preparing to unpack .../76-fastjar_2%3a0.98-6+b1_amd64.deb ... Unpacking fastjar (2:0.98-6+b1) ... Selecting previously unselected package jaligner. Preparing to unpack .../77-jaligner_1.0+dfsg-6_all.deb ... Unpacking jaligner (1.0+dfsg-6) ... Selecting previously unselected package jarwrapper. Preparing to unpack .../78-jarwrapper_0.72.1_all.deb ... Unpacking jarwrapper (0.72.1) ... Selecting previously unselected package libapache-pom-java. Preparing to unpack .../79-libapache-pom-java_18-1_all.deb ... Unpacking libapache-pom-java (18-1) ... Selecting previously unselected package libatinject-jsr330-api-java. Preparing to unpack .../80-libatinject-jsr330-api-java_1.0+ds1-5_all.deb ... Unpacking libatinject-jsr330-api-java (1.0+ds1-5) ... Selecting previously unselected package libboost1.67-dev:amd64. Preparing to unpack .../81-libboost1.67-dev_1.67.0-11_amd64.deb ... Unpacking libboost1.67-dev:amd64 (1.67.0-11) ... Selecting previously unselected package libboost-dev:amd64. Preparing to unpack .../82-libboost-dev_1.67.0.1_amd64.deb ... Unpacking libboost-dev:amd64 (1.67.0.1) ... Selecting previously unselected package libcommons-parent-java. Preparing to unpack .../83-libcommons-parent-java_43-1_all.deb ... Unpacking libcommons-parent-java (43-1) ... Selecting previously unselected package libcommons-compress-java. Preparing to unpack .../84-libcommons-compress-java_1.18-1_all.deb ... Unpacking libcommons-compress-java (1.18-1) ... Selecting previously unselected package libfastutil-java. Preparing to unpack .../85-libfastutil-java_7.1.0-2_all.deb ... Unpacking libfastutil-java (7.1.0-2) ... Selecting previously unselected package libfilesys-df-perl. Preparing to unpack .../86-libfilesys-df-perl_0.92-6+b4_amd64.deb ... Unpacking libfilesys-df-perl (0.92-6+b4) ... Selecting previously unselected package libjsr305-java. Preparing to unpack .../87-libjsr305-java_0.1~+svn49-10_all.deb ... Unpacking libjsr305-java (0.1~+svn49-10) ... Selecting previously unselected package libguava-java. Preparing to unpack .../88-libguava-java_19.0-1_all.deb ... Unpacking libguava-java (19.0-1) ... Selecting previously unselected package libmeryl-dev. Preparing to unpack .../89-libmeryl-dev_0~20150903+r2013-6_amd64.deb ... Unpacking libmeryl-dev (0~20150903+r2013-6) ... Selecting previously unselected package libssw-java. Preparing to unpack .../90-libssw-java_1.1-2_amd64.deb ... Unpacking libssw-java (1.1-2) ... Selecting previously unselected package mhap. Preparing to unpack .../91-mhap_2.1.3+dfsg-2_all.deb ... Unpacking mhap (2.1.3+dfsg-2) ... Selecting previously unselected package sbuild-build-depends-canu-dummy. Preparing to unpack .../92-sbuild-build-depends-canu-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-canu-dummy (0.invalid.0) ... Setting up libssw-java (1.1-2) ... Setting up libfastutil-java (7.1.0-2) ... Setting up libmeryl-dev (0~20150903+r2013-6) ... Setting up libexpat1:amd64 (2.2.6-1) ... Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+b1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libicu63:amd64 (63.1-5) ... Setting up fastjar (2:0.98-6+b1) ... Setting up libpng16-16:amd64 (1.6.36-2) ... Setting up liblcms2-2:amd64 (2.9-3) ... Setting up libpcsclite1:amd64 (1.8.24-1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libelf1:amd64 (0.175-2) ... Setting up libglib2.0-0:amd64 (2.58.2-3) ... No schema files found: doing nothing. Setting up libasound2-data (1.1.7-2) ... Setting up libfilesys-df-perl (0.92-6+b4) ... Setting up java-common (0.71) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libpipeline1:amd64 (1.5.0-2) ... Setting up m4 (1.4.18-2) ... Setting up libnspr4:amd64 (2:4.20-1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libfreetype6:amd64 (2.9.1-3) ... Setting up libmagic-mgc (1:5.34-2) ... Setting up libasound2:amd64 (1.1.7-2) ... Setting up libmagic1:amd64 (1:5.34-2) ... Setting up lsb-base (10.2018112800) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up libjsr305-java (0.1~+svn49-10) ... Setting up sensible-utils (0.0.12) ... Processing triggers for libc-bin (2.28-4) ... Setting up dwz (0.12-3) ... Setting up autotools-dev (20180224.1) ... Setting up libboost1.67-dev:amd64 (1.67.0-11) ... Setting up libssl1.1:amd64 (1.1.1a-1) ... Setting up libapache-pom-java (18-1) ... Setting up openssl (1.1.1a-1) ... Setting up libsqlite3-0:amd64 (3.26.0+fossilbc891ac6b-1) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libboost-dev:amd64 (1.67.0.1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libkeyutils1:amd64 (1.5.9-9.3) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up ca-certificates (20180409) ... Updating certificates in /etc/ssl/certs... 133 added, 0 removed; done. Setting up libncurses6:amd64 (6.1+20181013-1) ... Setting up libx11-data (2:1.6.7-1) ... Setting up libxau6:amd64 (1:1.0.8-1+b2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libdbus-1-3:amd64 (1.12.12-1) ... Setting up libavahi-common-data:amd64 (0.7-4+b1) ... Setting up libfile-stripnondeterminism-perl (1.0.0-1) ... Setting up binfmt-support (2.1.8-2.1) ... invoke-rc.d: could not determine current runlevel All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up gettext (0.19.8.1-9) ... Setting up groff-base (1.22.4-2) ... Setting up libguava-java (19.0-1) ... Setting up libnss3:amd64 (2:3.41-1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.34-2) ... Setting up libkrb5support0:amd64 (1.16.2-1) ... Setting up ucf (3.0038+nmu1) ... Setting up libcommons-parent-java (43-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libcommons-compress-java (1.18-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libavahi-common3:amd64 (0.7-4+b1) ... Setting up jarwrapper (0.72.1) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up libtool (2.4.6-6) ... Setting up libk5crypto3:amd64 (1.16.2-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up po-debconf (1.0.21) ... Setting up libx11-6:amd64 (2:1.6.7-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libavahi-client3:amd64 (0.7-4+b1) ... Setting up libkrb5-3:amd64 (1.16.2-1) ... Setting up libfontconfig1:amd64 (2.13.1-2) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libgssapi-krb5-2:amd64 (1.16.2-1) ... Setting up libcups2:amd64 (2.2.10-3) ... Setting up libxi6:amd64 (2:1.7.9-1) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up dh-autoreconf (19) ... Setting up openjdk-11-jre-headless:amd64 (11.0.1+13-3) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up dh-strip-nondeterminism (1.0.0-1) ... Setting up default-jre-headless (2:1.11-71) ... Setting up debhelper (12) ... Setting up ca-certificates-java (20180516) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:Visa_eCommerce_Root.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:Certigna.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Secure_Global_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:OpenTrust_Root_CA_G3.pem Adding debian:TrustCor_ECA-1.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:EC-ACC.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SecureTrust_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:OpenTrust_Root_CA_G1.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Networking.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:AddTrust_External_Root.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:ISRG_Root_X1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority.pem Warning: there was a problem reading the certificate file /etc/ssl/certs/NetLock_Arany_=Class_Gold=_F?tan?s?tv?ny.pem. Message: /etc/ssl/certs/NetLock_Arany_=Class_Gold=_F?tan?s?tv?ny.pem (No such file or directory) Adding debian:ACCVRAIZ1.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:DST_Root_CA_X3.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certplus_Root_CA_G1.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:Certinomis_-_Root_CA.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Izenpe.com.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:OpenTrust_Root_CA_G2.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Warning: there was a problem reading the certificate file /etc/ssl/certs/T?RKTRUST_Elektronik_Sertifika_Hizmet_Sa?lay?c?s?_H5.pem. Message: /etc/ssl/certs/T?RKTRUST_Elektronik_Sertifika_Hizmet_Sa?lay?c?s?_H5.pem (No such file or directory) Adding debian:TWCA_Global_Root_CA.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Taiwan_GRCA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:Certplus_Root_CA_G2.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:Security_Communication_RootCA2.pem done. Setting up jaligner (1.0+dfsg-6) ... Setting up mhap (2.1.3+dfsg-2) ... Setting up sbuild-build-depends-canu-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.28-4) ... Processing triggers for ca-certificates (20180409) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.31.1-11 dpkg-dev_1.19.2 g++-8_8.2.0-14 gcc-8_8.2.0-14 libc6-dev_2.28-4 libstdc++-8-dev_8.2.0-14 libstdc++6_8.2.0-14 linux-libc-dev_4.19.13-1 Package versions: adduser_3.118 apt_1.8.0~alpha3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1 base-passwd_3.5.45 bash_4.4.18-3.1 binfmt-support_2.1.8-2.1 binutils_2.31.1-11 binutils-common_2.31.1-11 binutils-x86-64-linux-gnu_2.31.1-11 bsdmainutils_11.1.2+b1 bsdutils_1:2.33-0.2 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20180409 ca-certificates-java_20180516 clang-8_1:8~svn350193-1~exp1 coreutils_8.30-1 cpp_4:8.2.0-2 cpp-8_8.2.0-14 dash_0.5.10.2-4 debconf_1.5.69 debhelper_12 debian-archive-keyring_2018.1 debianutils_4.8.6 default-jre-headless_2:1.11-71 dh-autoreconf_19 dh-strip-nondeterminism_1.0.0-1 diffutils_1:3.6-1 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fastjar_2:0.98-6+b1 fdisk_2.33-0.2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 fontconfig-config_2.13.1-2 fonts-dejavu-core_2.37-1 g++_4:8.2.0-2 g++-8_8.2.0-14 gcc_4:8.2.0-2 gcc-8_8.2.0-14 gcc-8-base_8.2.0-14 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.12-1 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 hostname_3.21 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.4 jaligner_1.0+dfsg-6 jarwrapper_0.72.1 java-common_0.71 lib32gcc1_1:8.2.0-14 lib32stdc++6_8.2.0-14 libacl1_2.2.52-3+b1 libapache-pom-java_18-1 libapt-pkg5.0_1.8.0~alpha3 libarchive-zip-perl_1.64-1 libasan5_8.2.0-14 libasound2_1.1.7-2 libasound2-data_1.1.7-2 libatinject-jsr330-api-java_1.0+ds1-5 libatomic1_8.2.0-14 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libavahi-client3_0.7-4+b1 libavahi-common-data_0.7-4+b1 libavahi-common3_0.7-4+b1 libbinutils_2.31.1-11 libblkid1_2.33-0.2 libboost-dev_1.67.0.1 libboost1.67-dev_1.67.0-11 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-4 libc-dev-bin_2.28-4 libc6_2.28-4 libc6-dev_2.28-4 libc6-i386_2.28-4 libcap-ng0_0.7.9-1+b1 libcc1-0_8.2.0-14 libclang-common-8-dev_1:8~svn350193-1~exp1 libclang1-8_1:8~svn350193-1~exp1 libcom-err2_1.44.5-1 libcommons-compress-java_1.18-1 libcommons-parent-java_43-1 libcroco3_0.6.12-3 libcups2_2.2.10-3 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.12-1 libdebconfclient0_0.246 libdpkg-perl_1.19.2 libedit2_3.1-20181209-1 libelf1_0.175-2 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfastutil-java_7.1.0-2 libfdisk1_2.33-0.2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.0.0-1 libfilesys-df-perl_0.92-6+b4 libfontconfig1_2.13.1-2 libfreetype6_2.9.1-3 libgc1c2_1:7.6.4-0.4 libgcc-8-dev_8.2.0-14 libgcc1_1:8.2.0-14 libgcrypt20_1.8.4-4 libgdbm-compat4_1.18.1-2 libgdbm6_1.18.1-2 libglib2.0-0_2.58.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.5-2 libgomp1_8.2.0-14 libgpg-error0_1.33-3 libgssapi-krb5-2_1.16.2-1 libguava-java_19.0-1 libhogweed4_3.4.1~rc1-1 libicu63_63.1-5 libidn2-0_2.0.5-1 libisl19_0.20-2 libitm1_8.2.0-14 libjpeg62-turbo_1:1.5.2-2+b1 libjsr305-java_0.1~+svn49-10 libk5crypto3_1.16.2-1 libkeyutils1_1.5.9-9.3 libkrb5-3_1.16.2-1 libkrb5support0_1.16.2-1 liblcms2-2_2.9-3 libllvm8_1:8~svn350193-1~exp1 liblsan0_8.2.0-14 liblz4-1_1.8.3-1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmeryl-dev_0~20150903+r2013-6 libmount1_2.33-0.2 libmpc3_1.1.0-1 libmpfr6_4.0.2~rc1-1 libmpx2_8.2.0-14 libncurses6_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4.1~rc1-1 libnspr4_2:4.20-1 libnss3_2:3.41-1 libobjc-8-dev_8.2.0-14 libobjc4_8.2.0-14 libomp-8-dev_1:8~svn350193-1~exp1 libomp5-8_1:8~svn350193-1~exp1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-4 libpam-modules-bin_1.1.8-4 libpam-runtime_1.1.8-4 libpam0g_1.1.8-4 libpcre3_2:8.39-11 libpcsclite1_1.8.24-1 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libpng16-16_1.6.36-2 libquadmath0_8.2.0-14 libseccomp2_2.3.3-3 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33-0.2 libsqlite3-0_3.26.0+fossilbc891ac6b-1 libss2_1.44.5-1 libssl1.1_1.1.1a-1 libssw-java_1.1-2 libstdc++-8-dev_8.2.0-14 libstdc++6_8.2.0-14 libsystemd0_240-2 libtasn1-6_4.13-3 libtinfo6_6.1+20181013-1 libtool_2.4.6-6 libtsan0_8.2.0-14 libubsan1_8.2.0-14 libuchardet0_0.0.6-3 libudev1_240-2 libunistring2_0.9.10-1 libuuid1_2.33-0.2 libx11-6_2:1.6.7-1 libx11-data_2:1.6.7-1 libxau6_1:1.0.8-1+b2 libxcb1_1.13.1-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxi6_2:1.7.9-1 libxml2_2.9.4+dfsg1-7+b3 libxrender1_1:0.9.10-1 libxtst6_2:1.2.3-1 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.13-1 login_1:4.5-1.1 lsb-base_10.2018112800 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-1 mawk_1.3.3-17+b3 mhap_2.1.3+dfsg-2 mount_2.33-0.2 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 openjdk-11-jre-headless_11.0.1+13-3 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.28_5.28.1-3 po-debconf_1.0.21 sbuild-build-depends-canu-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-3 tar_1.30+dfsg-4 tzdata_2018i-1 ucf_3.0038+nmu1 util-linux_2.33-0.2 x11-common_1:7.7+19 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon Dec 3 09:35:47 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./canu_1.8+dfsg-2.dsc dpkg-source: info: extracting canu in /<>/canu-1.8+dfsg dpkg-source: info: unpacking canu_1.8+dfsg.orig.tar.gz dpkg-source: info: unpacking canu_1.8+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-debian-mhap-at-runtime.patch dpkg-source: info: applying external-mhap.patch dpkg-source: info: applying tell_version_properly.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=sid-amd64-sbuild-75cf1cd3-a554-43e9-9441-4bfa8f188d35 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package canu dpkg-buildpackage: info: source version 1.8+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --sourcedirectory=src/ dh_auto_clean -O--sourcedirectory=src/ cd src && make -j4 clean make[1]: Entering directory '/<>/canu-1.8+dfsg/src' WARNING: WARNING: g++ 4.2.1 detected, disabling stack trace support. Please upgrade to GCC 4.7 or higher. WARNING: Building for 'Linux' '4.9.0-8-amd64' as 'amd64' into '/<>/canu-1.8+dfsg/Linux-amd64/{bin,obj}'. Using '/usr/bin/g++' version '4.2.1'. rm -f /<>/canu-1.8+dfsg/Linux-amd64/lib/libcanu.a /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/AS_global.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-buffered.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-compressed.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-memoryMapped.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/strings.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system-stackTrace.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sequence.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-reader.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-block.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-stream.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-statistics.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-exact.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/bits.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/hexDump.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/md5.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/mt19937ar.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/objectStore.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/speedCounter.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sweatShop.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqLibrary.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStore.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreConstructor.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreInfo.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreEncode.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStorePartition.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovOverlap.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStore.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreWriter.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFilter.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFile.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgStore.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapErrorAdjustment/analyzeAlignment.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/libedlib/edlib.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-addRead.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-appendBases.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-applyAlignment.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-baseCall.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-mergeRefine.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refine.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refreshMultiAlign.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abColumn.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abMultiAlign.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/unitigConsensus.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/gfa.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/bed.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/dumpBlob /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/dumpBlob/stores/dumpBlob.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/ovStoreBuild /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreBuild/stores/ovStoreBuild.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/ovStoreConfig /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreConfig/stores/ovStoreConfig.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/ovStoreBucketizer /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/ovStoreSorter /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreSorter/stores/ovStoreSorter.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/ovStoreIndexer /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/ovStoreDump /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreDump/stores/ovStoreDump.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/ovStoreStats /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreStats/stores/ovStoreStats.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/sqStoreCreate /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreCreate/stores/sqStoreCreate.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/sqStoreCreatePartition /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreCreatePartition/stores/sqStoreCreatePartition.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/sqStoreDumpFASTQ /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/sqStoreDumpMetaData /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/tgStoreCompress /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreCompress/stores/tgStoreCompress.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/tgStoreDump /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgStoreDump.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/tgStoreLoad /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreLoad/stores/tgStoreLoad.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/tgStoreFilter /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreFilter/stores/tgStoreFilter.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/tgStoreCoverageStat /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreCoverageStat/stores/tgStoreCoverageStat.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/tgTigDisplay /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/tgTigDisplay/stores/tgTigDisplay.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/loadCorrectedReads /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/loadTrimmedReads /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/loadErates /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/loadErates/stores/loadErates.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/meryl /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/meryl.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylCountArray.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylInput.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-count.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-countSimple.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-histogram.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-nextMer.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/sequence /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/overlapInCore /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/overlapInCorePartition /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/overlapConvert /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapConvert/overlapInCore/overlapConvert.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/overlapImport /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapImport/overlapInCore/overlapImport.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/overlapPair /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapPair/overlapInCore/overlapPair.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/edalign /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/edalign/overlapInCore/edalign.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/prefixEditDistance-matchLimitGenerate /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/mhapConvert /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/mhapConvert/mhap/mhapConvert.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/mmapConvert /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/mmapConvert/minimap/mmapConvert.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/wtdbgConvert /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/wtdbgConvert/wtdbg/wtdbgConvert.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/filterCorrectionOverlaps /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/generateCorrectionLayouts /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/generateCorrectionLayouts/utgcns/stashContains.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/filterCorrectionLayouts /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/falconsense /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/falconsense/correction/falconsense.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/falconsense/utgcns/stashContains.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/readConsensus /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/readConsensus/correction/readConsensus.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/errorEstimate /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/errorEstimate/correction/errorEstimate.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/splitHaplotype /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/splitHaplotype/haplotyping/splitHaplotype.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/trimReads /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/trimReads/overlapBasedTrimming/trimReads-quality.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/splitReads /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/findErrors /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/findErrors-Dump /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/correctOverlaps /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/bogart /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/bogart.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_CreateUnitigs.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_DropDeadEnds.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Instrumentation.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Logging.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Outputs.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_OverlapCache.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceContains.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_ReadInfo.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigGraph.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_TigVector.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/bogus /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogus/bogus/bogus.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/bogus/bogus/bogusUtil.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/utgcns /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/utgcns.[doP] /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/utgcns/utgcns/stashContains.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/alignGFA /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/alignGFA/gfa/alignGFA.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/fastqAnalyze /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqAnalyze/fastq-utilities/fastqAnalyze.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/fastqSample /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqSample/fastq-utilities/fastqSample.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/fastqSimulate /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqSimulate/fastq-utilities/fastqSimulate.[doP] rm -f /<>/canu-1.8+dfsg/Linux-amd64/bin/fastqSimulate-sort /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/fastqSimulate-sort/fastq-utilities/fastqSimulate-sort.[doP] make[1]: Leaving directory '/<>/canu-1.8+dfsg/src' dh_autoreconf_clean -O--sourcedirectory=src/ dh_clean -O--sourcedirectory=src/ debian/rules build-arch dh build-arch --sourcedirectory=src/ dh_update_autotools_config -a -O--sourcedirectory=src/ dh_autoreconf -a -O--sourcedirectory=src/ dh_auto_configure -a -O--sourcedirectory=src/ debian/rules override_dh_auto_build make[1]: Entering directory '/<>/canu-1.8+dfsg' dh_auto_build cd src && make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/canu-1.8+dfsg/src' WARNING: WARNING: g++ 4.2.1 detected, disabling stack trace support. Please upgrade to GCC 4.7 or higher. WARNING: Building for 'Linux' '4.9.0-8-amd64' as 'amd64' into '/<>/canu-1.8+dfsg/Linux-amd64/{bin,obj}'. Using '/usr/bin/g++' version '4.2.1'. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/files.C g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-buffered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/files-buffered.C g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-compressed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/files-compressed.C Building release v1.8 g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/files-memoryMapped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/files-memoryMapped.C clangclang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] : warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/strings.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/strings.C g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/system.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: -O4 is equivalent to -O3 [-Wdeprecated]clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/system-stackTrace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/system-stackTrace.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/sequence.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-reader.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-reader.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-writer.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] utility/sequence.C:226:38: warning: unused parameter 'name' [-Wunused-parameter] dnaSeqFile::findSequence(const char *name) { ^ g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-block.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-writer-block.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] utility/kmers-writer.C:58:2: warning: how to set prefix size for streaming operations? [-W#warnings] #warning how to set prefix size for streaming operations? ^ g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer-stream.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-writer-stream.C 1 warning generated. clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-statistics.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-statistics.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/kmers-exact.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-exact.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/bits.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/bits.C g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/hexDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/hexDump.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/md5.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/md5.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] utility/bits.Cg++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/mt19937ar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/mt19937ar.C :224:50: warning: unused parameter 'length' [-Wunused-parameter] stuffedBits::setPosition(uint64 position, uint64 length) { ^ utility/bits.C:413:41: warning: unused parameter 'number' [-Wunused-parameter] stuffedBits::getGeneralizedUnary(uint64 number, uint64 *values) { ^ utility/bits.C:421:41: warning: unused parameter 'value' [-Wunused-parameter] stuffedBits::setGeneralizedUnary(uint64 value) { ^ utility/bits.C:427:41: warning: unused parameter 'number' [-Wunused-parameter] stuffedBits::setGeneralizedUnary(uint64 number, uint64 *values) { ^ utility/bits.C:427:57: warning: unused parameter 'values' [-Wunused-parameter] stuffedBits::setGeneralizedUnary(uint64 number, uint64 *values) { ^ clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/objectStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/objectStore.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 5 warnings generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/speedCounter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/speedCounter.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utility/sweatShop.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/sweatShop.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap correction/computeGlobalScore.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap correction/falconConsensus.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] In file included from correction/computeGlobalScore.C:38: In file included from correction/computeGlobalScore.H:42: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqLibrary.C correction/computeGlobalScore.C:154:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 2 warnings generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqStore.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqStoreConstructor.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqStoreInfo.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreEncode.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqStoreEncode.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/sqStorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqStorePartition.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovOverlap.C g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStore.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStoreWriter.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] In file included from In file included from stores/ovStore.C:55: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ stores/ovOverlap.C:34: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ stores/ovOverlap.C:75:15: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] dat.ovl.ahg5, dat.ovl.ahg3, ^~~~~~~~~~~~ stores/ovOverlap.C:75:29: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] dat.ovl.ahg5, dat.ovl.ahg3, ^~~~~~~~~~~~ stores/ovOverlap.C:76:15: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] dat.ovl.bhg5, dat.ovl.bhg3, ^~~~~~~~~~~~ stores/ovOverlap.C:76:29: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] dat.ovl.bhg5, dat.ovl.bhg3, ^~~~~~~~~~~~ stores/ovOverlap.C:184:2: warning: NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-W#warnings] #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING ^ g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStoreFilter.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] In file included from stores/ovStoreWriter.C:54: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ stores/ovStoreWriter.C:69:2: warning: not failing if a valid store [-W#warnings] #warning not failing if a valid store ^ 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStoreFile.C 6 warnings generated. clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStoreHistogram.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 2 warnings generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgStore.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] In file included from stores/ovStoreFilter.C:54: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ stores/ovStoreFilter.C:291:34: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if ((foverlap.dat.ovl.forDUP == true)) { ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ stores/ovStoreFilter.C:291:34: note: remove extraneous parentheses around the comparison to silence this warning if ((foverlap.dat.ovl.forDUP == true)) { ~ ^ ~ stores/ovStoreFilter.C:291:34: note: use '=' to turn this equality comparison into an assignment if ((foverlap.dat.ovl.forDUP == true)) { ^~ = stores/ovStoreFilter.C:296:34: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if ((roverlap.dat.ovl.forDUP == true)) { ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ stores/ovStoreFilter.C:296:34: note: remove extraneous parentheses around the comparison to silence this warning if ((roverlap.dat.ovl.forDUP == true)) { ~ ^ ~ stores/ovStoreFilter.C:296:34: note: use '=' to turn this equality comparison into an assignment if ((roverlap.dat.ovl.forDUP == true)) { ^~ = In file included from stores/ovStoreFile.C:47: In file included from stores/ovStore.H:42: stores/ovOverlap.H3 warnings generated. :244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgTig.C In file included from stores/ovStoreHistogram.C:30: In file included from stores/ovStoreHistogram.H:35: In file included from stores/ovStoreFile.H:44: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] stores/ovStoreHistogram.C:403:35: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, ^~~~~~~~~~~~~~~~~~~~~ stores/ovStoreHistogram.C:403:58: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, ^~~~~~~~~~~~~~~~~~~~~ stores/ovStoreHistogram.C:404:35: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] overlap->b_iid, blen, overlap->dat.ovl.bhg5, overlap->dat.ovl.bhg3, ^~~~~~~~~~~~~~~~~~~~~ stores/ovStoreHistogram.C:404:58: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] overlap->b_iid, blen, overlap->dat.ovl.bhg5, overlap->dat.ovl.bhg3, ^~~~~~~~~~~~~~~~~~~~~ 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 5 warnings generated. stores/tgTig.C:673:9: warning: variable 'pos' is incremented both in the loop header and in the loop body [-Wfor-loop-analysis] pos++; ^ stores/tgTig.C:661:49: note: incremented here for (uint32 pos=10; (pos < W.numWords()); pos++) { ^ g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] stores/libsnappy/snappy-sinksource.cc:39:36: warning: unused parameter 'length' [-Wunused-parameter] char* Sink::GetAppendBuffer(size_t length, char* scratch) { ^ stores/libsnappy/snappy-sinksource.cc:44:14: warning: unused parameter 'min_size' [-Wunused-parameter] size_t min_size, size_t desired_size_hint, char* scratch, ^ stores/libsnappy/snappy-sinksource.cc:44:31: warning: unused parameter 'desired_size_hint' [-Wunused-parameter] size_t min_size, size_t desired_size_hint, char* scratch, ^ stores/libsnappy/snappy-sinksource.cc:82:54: warning: unused parameter 'len' [-Wunused-parameter] char* UncheckedByteArraySink::GetAppendBuffer(size_t len, char* scratch) { ^ stores/libsnappy/snappy-sinksource.cc:82:65: warning: unused parameter 'scratch' [-Wunused-parameter] char* UncheckedByteArraySink::GetAppendBuffer(size_t len, char* scratch) { ^ stores/libsnappy/snappy-sinksource.cc:98:14: warning: unused parameter 'min_size' [-Wunused-parameter] size_t min_size, size_t desired_size_hint, char* scratch, ^ stores/libsnappy/snappy-sinksource.cc:98:56: warning: unused parameter 'scratch' [-Wunused-parameter] size_t min_size, size_t desired_size_hint, char* scratch, ^ stores/libsnappy/snappy-sinksource.cc:99:14: warning: unused parameter 'scratch_size' [-Wunused-parameter] size_t scratch_size, size_t* allocated_size) { ^ 8 warnings generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapErrorAdjustment/analyzeAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapErrorAdjustment/analyzeAlignment.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] In file included from overlapInCore/overlapReadCache.C:30: In file included from overlapInCore/overlapReadCache.H:36: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ stores/libsnappy/snappy.cc:588:39: warning: unused parameter 'algorithm' [-Wunused-parameter] static inline void Report(const char *algorithm, size_t compressed_size, ^ stores/libsnappy/snappy.cc:588:57: warning: unused parameter 'compressed_size' [-Wunused-parameter] static inline void Report(const char *algorithm, size_t compressed_size, ^ stores/libsnappy/snappy.cc:589:34: warning: unused parameter 'uncompressed_size' [-Wunused-parameter] size_t uncompressed_size) {} ^ overlapErrorAdjustment/analyzeAlignment.C:302:11: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] _vote[j].confirmed, ^~~~~~~~~~~~~~~~~~ overlapErrorAdjustment/analyzeAlignment.C:303:11: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] _vote[j].deletes, ^~~~~~~~~~~~~~~~ overlapErrorAdjustment/analyzeAlignment.C:304:11: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] _vote[j].a_subst, ^~~~~~~~~~~~~~~~ overlapErrorAdjustment/analyzeAlignment.C:305:11: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] _vote[j].c_subst, ^~~~~~~~~~~~~~~~ overlapErrorAdjustment/analyzeAlignment.C:306:11: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] _vote[j].g_subst, ^~~~~~~~~~~~~~~~ overlapErrorAdjustment/analyzeAlignment.C:307:11: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] _vote[j].t_subst, ^~~~~~~~~~~~~~~~ overlapErrorAdjustment/analyzeAlignment.C:308:11: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] _vote[j].no_insert, ^~~~~~~~~~~~~~~~~~ overlapErrorAdjustment/analyzeAlignment.C:309:11: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] _vote[j].a_insert, ^~~~~~~~~~~~~~~~~ overlapErrorAdjustment/analyzeAlignment.C:310:11: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] _vote[j].c_insert, ^~~~~~~~~~~~~~~~~ overlapErrorAdjustment/analyzeAlignment.C:311:11: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] _vote[j].g_insert, ^~~~~~~~~~~~~~~~~ overlapErrorAdjustment/analyzeAlignment.C:312:11: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] _vote[j].t_insert); ^~~~~~~~~~~~~~~~~ stores/libsnappy/snappy.cc:1266:34: warning: unused parameter 'ip' [-Wunused-parameter] inline bool Append(const char* ip, size_t len) { ^ stores/libsnappy/snappy.cc:1270:41: warning: unused parameter 'ip' [-Wunused-parameter] inline bool TryFastAppend(const char* ip, size_t available, size_t length) { ^ stores/libsnappy/snappy.cc:1270:52: overlapErrorAdjustment/analyzeAlignment.C:440:74: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] fprintf(stderr, "INDET confirmed = " F_U64 " max = " F_U64 "\n", _vote[j].confirmed, max);warning: unused parameter 'available' [-Wunused-parameter] inline bool TryFastAppend(const char* ip, size_t available, size_t length) { ~~~~~ ^~~~~~~~~~~~~~~~~~ ^ stores/libsnappy/snappy.cc:1270:70: warning: unused parameter 'length' [-Wunused-parameter] inline bool TryFastAppend(const char* ip, size_t available, size_t length) { ^ overlapErrorAdjustment/analyzeAlignment.C:511:78: warning: format specifies type 'unsigned long' but the argument has type 'int' [-Wformat] fprintf(stderr, "INDET no_insert = " F_U64 " ins_max = " F_U64 "\n", _vote[j].no_insert, ins_max); ~~~~~ ^~~~~~~~~~~~~~~~~~ stores/libsnappy/snappy.cc:1506:29: warning: unused parameter 'arg' [-Wunused-parameter] static void Deleter(void* arg, const char* bytes, size_t size) { ^ stores/libsnappy/snappy.cc:1506:60: warning: unused parameter 'size' [-Wunused-parameter] static void Deleter(void* arg, const char* bytes, size_t size) { ^ g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 13 warnings generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] In file included from overlapInCore/liboverlap/prefixEditDistance-extend.C:69: In file included from overlapInCore/overlapInCore.H:66: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/libedlib/edlib.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/libedlib/edlib.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 9 warnings generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] In file included from utgcns/libNDalign/NDalign.C:34: In file included from utgcns/libNDalign/NDalign.H:39: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] overlapInCore/libedlib/edlib.C:566:71: warning: unused parameter 'query' [-Wunused-parameter] const unsigned char* const query, const int queryLength, ^ overlapInCore/libedlib/edlib.C:568:54: warning: unused parameter 'alphabetLength' [-Wunused-parameter] const int alphabetLength, int k, const EdlibAlignMode mode, ^ overlapInCore/libedlib/edlib.C:750:63: warning: unused parameter 'query' [-Wunused-parameter] const unsigned char* const query, const int queryLength, ^ overlapInCore/libedlib/edlib.C:752:46: warning: unused parameter 'alphabetLength' [-Wunused-parameter] const int alphabetLength, int k, int* const bestScore_, ^ g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] utgcns/libNDalign/NDalgorithm-forward.C:235:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-forward.C:235:84: note: place parentheses around the '+' expression to silence this warning Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:235:84: note: place parentheses around the '?:' expression to evaluate it first Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:236:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Err = Edit_Array_Lazy[ei-1][d-1].errs + (gapCost == PEDFREEGAP) ? 0 : 0; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-forward.C:236:84: note: place parentheses around the '+' expression to silence this warning Err = Edit_Array_Lazy[ei-1][d-1].errs + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:236:84: note: place parentheses around the '?:' expression to evaluate it first Err = Edit_Array_Lazy[ei-1][d-1].errs + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:260:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-forward.C:260:84: note: place parentheses around the '+' expression to silence this warning Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:260:84: note: place parentheses around the '?:' expression to evaluate it first Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:261:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-forward.C:261:84: note: place parentheses around the '+' expression to silence this warning Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-forward.C:261:84: note: place parentheses around the '?:' expression to evaluate it first Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:236:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-reverse.C:236:84: note: place parentheses around the '+' expression to silence this warning Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:236:84: note: place parentheses around the '?:' expression to evaluate it first Dst = Edit_Array_Lazy[ei-1][d-1].dist + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:237:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Err = Edit_Array_Lazy[ei-1][d-1].errs + (gapCost == PEDFREEGAP) ? 0 : 0; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-reverse.C:237:84: note: place parentheses around the '+' expression to silence this warning Err = Edit_Array_Lazy[ei-1][d-1].errs + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:237:84: note: place parentheses around the '?:' expression to evaluate it first Err = Edit_Array_Lazy[ei-1][d-1].errs + (gapCost == PEDFREEGAP) ? 0 : 0; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:260:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-reverse.C:260:84: note: place parentheses around the '+' expression to silence this warning Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:260:84: note: place parentheses around the '?:' expression to evaluate it first Dst = Edit_Array_Lazy[ei-1][d+1].dist + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:261:84: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses] Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ utgcns/libNDalign/NDalgorithm-reverse.C:261:84: note: place parentheses around the '+' expression to silence this warning Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) utgcns/libNDalign/NDalgorithm-reverse.C:261:84: note: place parentheses around the '?:' expression to evaluate it first Err = Edit_Array_Lazy[ei-1][d+1].errs + (gapCost == PEDFREEGAP) ? 0 : 1; ^ ( ) 4 warnings generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-addRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-addRead.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 4 warnings generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-appendBases.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-appendBases.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-applyAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-applyAlignment.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 4 warnings generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-baseCall.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-baseCall.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-mergeRefine.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-mergeRefine.C g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refine.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-refine.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refreshMultiAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-refreshMultiAlign.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] utgcns/libcns/abAbacus-refine.C:1018:37: warning: unused parameter 'abacus' [-Wunused-parameter] abAbacusWork::applyAbacus(abAbacus *abacus) { ^ utgcns/libcns/abAbacus-refine.C:1326:2: warning: SKIPPING ALL REFINEMENTS [-W#warnings] #warning SKIPPING ALL REFINEMENTS ^ 2 warnings generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abColumn.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abColumn.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abMultiAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abMultiAlign.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/unitigConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/unitigConsensus.C g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/gfa.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap gfa/gfa.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/lib/libcanu.a/gfa/bed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap gfa/bed.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/dumpBlob.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/ovStoreBuild.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/ovStoreConfig.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] In file included from stores/ovStoreBuild.C:45: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ In file included from stores/ovStoreConfig.C:31: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/ovStoreBucketizer.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/ovStoreSorter.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] In file included from utgcns/libcns/unitigConsensus.C:80: In file included from utgcns/libNDalign/NDalign.H:39: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ In file included from stores/ovStoreBucketizer.C:45: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ In file included from stores/ovStoreSorter.C:41: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/ovStoreIndexer.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/ovStoreDump.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] In file included from stores/ovStoreIndexer.C:41: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/ovStoreStats.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/sqStoreCreate.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] In file included from stores/ovStoreDump.C:55: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ In file included from stores/ovStoreStats.C:33: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreCreatePartition/stores/sqStoreCreatePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/sqStoreCreatePartition.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] stores/sqStoreDumpFASTQ.C:503:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ stores/sqStoreDumpFASTQ.C:514:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/sqStoreDumpMetaData.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 2 warnings generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/tgStoreCompress.C g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/tgStoreDump.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/tgTigSizeAnalysis.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] stores/tgStoreDump.C:677:2: warning: replace this with genericStatistics [-W#warnings] #warning replace this with genericStatistics ^ g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/tgStoreLoad.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreFilter/stores/tgStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/tgStoreFilter.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/tgStoreCoverageStat/stores/tgStoreCoverageStat.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/tgStoreCoverageStat.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/tgTigDisplay.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/loadCorrectedReads.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Istores -Iutility -IoverlapBasedTrimming stores/loadTrimmedReads.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility stores/loadErates.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/<>/canu-1.8+dfsg/src -Iutility -Istores meryl/meryl.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] In file included from stores/loadErates.C:45: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/<>/canu-1.8+dfsg/src -Iutility -Istores meryl/merylCountArray.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] meryl/meryl.C:265:2: warning: HARD CODED NUMBER OF FILES! [-W#warnings] #warning HARD CODED NUMBER OF FILES! ^ 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/<>/canu-1.8+dfsg/src -Iutility -Istores meryl/merylInput.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-count.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/<>/canu-1.8+dfsg/src -Iutility -Istores meryl/merylOp-count.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-countSimple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/<>/canu-1.8+dfsg/src -Iutility -Istores meryl/merylOp-countSimple.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] meryl/merylOp-count.C:266:32: warning: unused parameter 'nKmerEstimate' [-Wunused-parameter] reportNumberOfOutputs(uint64 nKmerEstimate, ^ meryl/merylOp-count.C:331:44: warning: unused parameter 'useSimple_' [-Wunused-parameter] bool &useSimple_, // Output: algorithm to use ^ g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/<>/canu-1.8+dfsg/src -Iutility -Istores meryl/merylOp-histogram.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp-nextMer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/<>/canu-1.8+dfsg/src -Iutility -Istores meryl/merylOp-nextMer.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 2 warnings generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/meryl/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Imeryl -I/<>/canu-1.8+dfsg/src -Iutility -Istores meryl/merylOp.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/sequence/sequence/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -DCANU -Isequence -I/<>/canu-1.8+dfsg/src -Iutility sequence/sequence.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] meryl/merylOp-nextMer.C:98:2: warning: "need to decide whic direction we're going?" [-W#warnings] #warning "need to decide whic direction we're going?" ^ meryl/merylOp-nextMer.C:116:2: warning: "rounding issues in word-frequency!" [-W#warnings] #warning "rounding issues in word-frequency!" ^ sequence/sequence.C:836:28: warning: unused parameter 'inputs' [-Wunused-parameter] doSimulate(vector &inputs) { ^ sequence/sequence.C:867:35: warning: unused parameter 'numBasesTotal' [-Wunused-parameter] uint64 numBasesTotal, ^ In file included from overlapInCore/overlapInCore.C:51: In file included from overlapInCore/overlapInCore.H:66: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] 2 warnings generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C 1 warning generated. clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] In file included from overlapInCore/overlapInCore-Build_Hash_Index.C:67: In file included from overlapInCore/overlapInCore.H:66: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ In file included from overlapInCore/overlapInCore-Find_Overlaps.C:71: In file included from overlapInCore/overlapInCore.H:66: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ In file included from overlapInCore/overlapInCore-Output.C:67: In file included from overlapInCore/overlapInCore.H:66: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ 1 warning generated. 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C 1 warning generated. g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] g++ -o /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/canu-1.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<>/canu-1.8+dfsg/src -Iutility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] clang: warning: -O4 is equivalent to -O3 [-Wdeprecated] clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument] In file included from overlapInCore/overlapInCore-Process_String_Overlaps.C:72: In file included from overlapInCore/overlapInCore.H:63: In file included from /<>/canu-1.8+dfsg/src/AS_global.H:113: In file included from utility/arrays.H:33: In file included from /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/algorithm:62: /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/bits/stl_algo.h:3451:15: error: no member named 'min_element' in namespace 'std'; did you mean '__cxx1998::min_element'? { return *std::min_element(__l.begin(), __l.end()); } ^~~~~ /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/bits/algorithmfwd.h:702:5: note: '__cxx1998::min_element' declared here min_element(_FIter, _FIter); ^ In file included from overlapInCore/overlapInCore-Process_String_Overlaps.C:72: In file included from overlapInCore/overlapInCore.H:63: In file included from /<>/canu-1.8+dfsg/src/AS_global.H:113: In file included from utility/arrays.H:33: In file included from /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/algorithm:62: /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/bits/stl_algo.h:3457:15: error: no member named 'min_element' in namespace 'std'; did you mean '__cxx1998::min_element'? { return *std::min_element(__l.begin(), __l.end(), __comp); } ^~~~~ /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/bits/algorithmfwd.h:702:5: note: '__cxx1998::min_element' declared here min_element(_FIter, _FIter); ^ In file included from overlapInCore/overlapInCore-Process_String_Overlaps.C:72: In file included from overlapInCore/overlapInCore.H:63: In file included from /<>/canu-1.8+dfsg/src/AS_global.H:113: In file included from utility/arrays.H:33: In file included from /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/algorithm:62: /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/bits/stl_algo.h:3463:15: error: no member named 'max_element' in namespace 'std'; did you mean '__cxx1998::max_element'? { return *std::max_element(__l.begin(), __l.end()); } ^~~~~ /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/bits/algorithmfwd.h:683:5: note: '__cxx1998::max_element' declared here max_element(_FIter, _FIter); ^ In file included from overlapInCore/overlapInCore-Process_String_Overlaps.C:72: In file included from overlapInCore/overlapInCore.H:63: In file included from /<>/canu-1.8+dfsg/src/AS_global.H:113: In file included from utility/arrays.H:33: In file included from /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/algorithm:62: /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/bits/stl_algo.h:3469:15: error: no member named 'max_element' in namespace 'std'; did you mean '__cxx1998::max_element'? { return *std::max_element(__l.begin(), __l.end(), __comp); } ^~~~~ /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/bits/algorithmfwd.h:683:5: note: '__cxx1998::max_element' declared here max_element(_FIter, _FIter); ^ In file included from overlapInCore/overlapInCore-Process_String_Overlaps.C:72: In file included from overlapInCore/overlapInCore.H:65: In file included from stores/sqStore.H:38: In file included from utility/files.H:36: In file included from /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/vector:64: /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/bits/stl_vector.h:1755:11: error: no member named 'equal' in namespace 'std'; did you mean '__cxx1998::equal'? && std::equal(__x.begin(), __x.end(), __y.begin())); } ^~~~~ /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/bits/algorithmfwd.h:638:5: note: '__cxx1998::equal' declared here equal(_IIter1, _IIter1, _IIter2); ^ In file included from overlapInCore/overlapInCore-Process_String_Overlaps.C:72: In file included from overlapInCore/overlapInCore.H:65: In file included from stores/sqStore.H:38: In file included from utility/files.H:36: In file included from /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/vector:64: /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/bits/stl_vector.h:1771:14: error: no member named 'lexicographical_compare' in namespace 'std'; did you mean '__cxx1998::lexicographical_compare'? { return std::lexicographical_compare(__x.begin(), __x.end(), ^~~~~ /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/bits/algorithmfwd.h:674:5: note: '__cxx1998::lexicographical_compare' declared here lexicographical_compare(_IIter1, _IIter1, _IIter2, _IIter2); ^ In file included from overlapInCore/overlapInCore-Process_Overlaps.C:71: In file included from overlapInCore/overlapInCore.H:66: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ In file included from overlapInCore/overlapInCore-Process_String_Overlaps.C:72: In file included from overlapInCore/overlapInCore.H:66: In file included from stores/ovStore.H:42: In file included from stores/ovOverlap.H:41: In file included from utility/strings.H:37: In file included from /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/set:60: /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/bits/stl_tree.h:1553:10: error: no member named 'equal' in namespace 'std'; did you mean '__cxx1998::equal'? && std::equal(__x.begin(), __x.end(), __y.begin()); ^~~~~ /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/bits/algorithmfwd.h:638:5: note: '__cxx1998::equal' declared here equal(_IIter1, _IIter1, _IIter2); ^ In file included from overlapInCore/overlapInCore-Process_String_Overlaps.C:72: In file included from overlapInCore/overlapInCore.H:66: In file included from stores/ovStore.H:42: In file included from stores/ovOverlap.H:41: In file included from utility/strings.H:37: In file included from /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/set:60: /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/bits/stl_tree.h:1562:14: error: no member named 'lexicographical_compare' in namespace 'std'; did you mean '__cxx1998::lexicographical_compare'? return std::lexicographical_compare(__x.begin(), __x.end(), ^~~~~ /usr/bin/../lib/gcc/x86_64-linux-gnu/8/../../../../include/c++/8/bits/algorithmfwd.h:674:5: note: '__cxx1998::lexicographical_compare' declared here lexicographical_compare(_IIter1, _IIter1, _IIter2, _IIter2); ^ In file included from overlapInCore/overlapInCore-Process_String_Overlaps.C:72: In file included from overlapInCore/overlapInCore.H:66: In file included from stores/ovStore.H:42: stores/ovOverlap.H:244:35: warning: unused parameter 'v' [-Wunused-parameter] uint32 a_bgn(sqRead_version v=sqRead_defaultVersion) const { return(dat.ovl.ahg5); }; ^ 1 warning and 8 errors generated. make[2]: *** [Makefile:707: /<>/canu-1.8+dfsg/Linux-amd64/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o] Error 1 make[2]: *** Waiting for unfinished jobs.... 1 warning generated. 2 warnings generated. make[2]: Leaving directory '/<>/canu-1.8+dfsg/src' dh_auto_build: cd src && make -j4 "INSTALL=install --strip-program=true" returned exit code 2 make[1]: *** [debian/rules:16: override_dh_auto_build] Error 2 make[1]: Leaving directory '/<>/canu-1.8+dfsg' make: *** [debian/rules:13: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2019-01-09T21:18:48Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 27516 Build-Time: 21 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 21 Job: canu_1.8+dfsg-2 Machine Architecture: amd64 Package: canu Package-Time: 56 Source-Version: 1.8+dfsg-2 Space: 27516 Status: attempted Version: 1.8+dfsg-2 -------------------------------------------------------------------------------- Finished at 2019-01-09T21:18:48Z Build needed 00:00:56, 27516k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 56.490516876s DC-Time-Estimation: 56.490516876 versus expected 372 (r/m: 5.585176071526515 ; m: 56.490516876)