DC-Build-Header: bedops 2.4.39+dfsg-1 / 2020-05-03 03:53:16 +0000 DC-Task: type:rebuild-binarch-only source:bedops version:2.4.39+dfsg-1 chroot:unstable esttime:901 logfile:/tmp/bedops_2.4.39+dfsg-1_unstable_clang10.log modes:clang10:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --no-run-lintian --chroot-setup-commands=/tmp/clang10 bedops_2.4.39+dfsg-1' sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-7-28.eu-central-1.compute.internal +==============================================================================+ | bedops 2.4.39+dfsg-1 (amd64) Sun, 03 May 2020 03:53:16 +0000 | +==============================================================================+ Package: bedops Version: 2.4.39+dfsg-1 Source Version: 2.4.39+dfsg-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-316cf00e-0b6b-43f4-a668-29ad5b56c583' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang10 ------------ + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=10 + echo 'Install of clang-10' Install of clang-10 + apt-get update Get:1 http://127.0.0.1:12990/debian sid InRelease [146 kB] Get:2 http://127.0.0.1:12990/debian sid/main Sources.diff/Index [27.9 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-0208.16.pdiff [3982 B] Get:5 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-0807.49.pdiff [10.9 kB] Get:6 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-1412.30.pdiff [12.9 kB] Get:7 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-2007.10.pdiff [13.4 kB] Get:8 http://127.0.0.1:12990/debian sid/main Sources 2020-05-03-0208.39.pdiff [9476 B] Get:9 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-0208.16.pdiff [2772 B] Get:10 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-0807.49.pdiff [3238 B] Get:11 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-1412.30.pdiff [7641 B] Get:12 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-2007.10.pdiff [10.5 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-03-0208.39.pdiff [18.4 kB] Get:8 http://127.0.0.1:12990/debian sid/main Sources 2020-05-03-0208.39.pdiff [9476 B] Get:13 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-03-0208.39.pdiff [18.4 kB] Get:14 http://127.0.0.1:12990/debian sid/main Translation-en [6185 kB] Fetched 6480 kB in 2s (3803 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-10 libomp-10-dev libobjc-9-dev Reading package lists... Building dependency tree... The following additional packages will be installed: gcc-10-base lib32gcc-s1 lib32gcc1 lib32stdc++6 libatomic1 libbsd0 libc6-i386 libcc1-0 libclang-common-10-dev libclang-cpp10 libclang1-10 libedit2 libgc1c2 libgcc-s1 libgomp1 libitm1 libllvm10 liblsan0 libobjc4 libomp5-10 libquadmath0 libstdc++6 libtsan0 libubsan1 libz3-4 Suggested packages: clang-10-doc libomp-10-doc Recommended packages: llvm-10-dev python3 The following NEW packages will be installed: clang-10 lib32gcc-s1 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-10-dev libclang-cpp10 libclang1-10 libedit2 libgc1c2 libllvm10 libobjc-9-dev libobjc4 libomp-10-dev libomp5-10 libz3-4 The following packages will be upgraded: gcc-10-base libatomic1 libcc1-0 libgcc-s1 libgomp1 libitm1 liblsan0 libquadmath0 libstdc++6 libtsan0 libubsan1 11 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. Need to get 51.4 MB of archives. After this operation, 259 MB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 libatomic1 amd64 10-20200502-1 [9048 B] Get:2 http://127.0.0.1:12990/debian sid/main amd64 libubsan1 amd64 10-20200502-1 [134 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libtsan0 amd64 10-20200502-1 [313 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 gcc-10-base amd64 10-20200502-1 [197 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libstdc++6 amd64 10-20200502-1 [492 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 libquadmath0 amd64 10-20200502-1 [145 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 liblsan0 amd64 10-20200502-1 [141 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libitm1 amd64 10-20200502-1 [25.7 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libgomp1 amd64 10-20200502-1 [99.3 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 libcc1-0 amd64 10-20200502-1 [39.7 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 libgcc-s1 amd64 10-20200502-1 [41.2 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 libedit2 amd64 3.1-20191231-1 [95.4 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 libz3-4 amd64 4.8.7-4 [6790 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libllvm10 amd64 1:10.0.0-4 [15.5 MB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libclang-cpp10 amd64 1:10.0.0-4 [10.1 MB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 libgc1c2 amd64 1:7.6.4-0.4 [224 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libobjc4 amd64 10-20200502-1 [41.6 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 libobjc-9-dev amd64 9.3.0-11 [218 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libc6-i386 amd64 2.30-4 [2926 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc-s1 amd64 10-20200502-1 [49.4 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc1 amd64 1:10-20200502-1 [1100 B] Get:23 http://127.0.0.1:12990/debian sid/main amd64 lib32stdc++6 amd64 10-20200502-1 [510 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 libclang-common-10-dev amd64 1:10.0.0-4 [5062 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 libclang1-10 amd64 1:10.0.0-4 [7609 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 clang-10 amd64 1:10.0.0-4 [105 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 libomp5-10 amd64 1:10.0.0-4 [338 kB] Get:28 http://127.0.0.1:12990/debian sid/main amd64 libomp-10-dev amd64 1:10.0.0-4 [85.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 51.4 MB in 0s (107 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 ... 12123 files and directories currently installed.) Preparing to unpack .../libatomic1_10-20200502-1_amd64.deb ... Unpacking libatomic1:amd64 (10-20200502-1) over (10-20200418-1) ... Preparing to unpack .../libubsan1_10-20200502-1_amd64.deb ... Unpacking libubsan1:amd64 (10-20200502-1) over (10-20200418-1) ... Preparing to unpack .../libtsan0_10-20200502-1_amd64.deb ... Unpacking libtsan0:amd64 (10-20200502-1) over (10-20200418-1) ... Preparing to unpack .../gcc-10-base_10-20200502-1_amd64.deb ... Unpacking gcc-10-base:amd64 (10-20200502-1) over (10-20200418-1) ... Setting up gcc-10-base:amd64 (10-20200502-1) ... (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 ... 12123 files and directories currently installed.) Preparing to unpack .../libstdc++6_10-20200502-1_amd64.deb ... Unpacking libstdc++6:amd64 (10-20200502-1) over (10-20200418-1) ... Setting up libstdc++6:amd64 (10-20200502-1) ... (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 ... 12123 files and directories currently installed.) Preparing to unpack .../0-libquadmath0_10-20200502-1_amd64.deb ... Unpacking libquadmath0:amd64 (10-20200502-1) over (10-20200418-1) ... Preparing to unpack .../1-liblsan0_10-20200502-1_amd64.deb ... Unpacking liblsan0:amd64 (10-20200502-1) over (10-20200418-1) ... Preparing to unpack .../2-libitm1_10-20200502-1_amd64.deb ... Unpacking libitm1:amd64 (10-20200502-1) over (10-20200418-1) ... Preparing to unpack .../3-libgomp1_10-20200502-1_amd64.deb ... Unpacking libgomp1:amd64 (10-20200502-1) over (10-20200418-1) ... Preparing to unpack .../4-libcc1-0_10-20200502-1_amd64.deb ... Unpacking libcc1-0:amd64 (10-20200502-1) over (10-20200418-1) ... Preparing to unpack .../5-libgcc-s1_10-20200502-1_amd64.deb ... Unpacking libgcc-s1:amd64 (10-20200502-1) over (10-20200418-1) ... Setting up libgcc-s1:amd64 (10-20200502-1) ... 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 ... 12123 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../01-libedit2_3.1-20191231-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20191231-1) ... Selecting previously unselected package libz3-4:amd64. Preparing to unpack .../02-libz3-4_4.8.7-4_amd64.deb ... Unpacking libz3-4:amd64 (4.8.7-4) ... Selecting previously unselected package libllvm10:amd64. Preparing to unpack .../03-libllvm10_1%3a10.0.0-4_amd64.deb ... Unpacking libllvm10:amd64 (1:10.0.0-4) ... Selecting previously unselected package libclang-cpp10. Preparing to unpack .../04-libclang-cpp10_1%3a10.0.0-4_amd64.deb ... Unpacking libclang-cpp10 (1:10.0.0-4) ... Selecting previously unselected package libgc1c2:amd64. Preparing to unpack .../05-libgc1c2_1%3a7.6.4-0.4_amd64.deb ... Unpacking libgc1c2:amd64 (1:7.6.4-0.4) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../06-libobjc4_10-20200502-1_amd64.deb ... Unpacking libobjc4:amd64 (10-20200502-1) ... Selecting previously unselected package libobjc-9-dev:amd64. Preparing to unpack .../07-libobjc-9-dev_9.3.0-11_amd64.deb ... Unpacking libobjc-9-dev:amd64 (9.3.0-11) ... Selecting previously unselected package libc6-i386. Preparing to unpack .../08-libc6-i386_2.30-4_amd64.deb ... Unpacking libc6-i386 (2.30-4) ... Selecting previously unselected package lib32gcc-s1. Preparing to unpack .../09-lib32gcc-s1_10-20200502-1_amd64.deb ... Unpacking lib32gcc-s1 (10-20200502-1) ... Selecting previously unselected package lib32gcc1. Preparing to unpack .../10-lib32gcc1_1%3a10-20200502-1_amd64.deb ... Unpacking lib32gcc1 (1:10-20200502-1) ... Selecting previously unselected package lib32stdc++6. Preparing to unpack .../11-lib32stdc++6_10-20200502-1_amd64.deb ... Unpacking lib32stdc++6 (10-20200502-1) ... Selecting previously unselected package libclang-common-10-dev. Preparing to unpack .../12-libclang-common-10-dev_1%3a10.0.0-4_amd64.deb ... Unpacking libclang-common-10-dev (1:10.0.0-4) ... Selecting previously unselected package libclang1-10. Preparing to unpack .../13-libclang1-10_1%3a10.0.0-4_amd64.deb ... Unpacking libclang1-10 (1:10.0.0-4) ... Selecting previously unselected package clang-10. Preparing to unpack .../14-clang-10_1%3a10.0.0-4_amd64.deb ... Unpacking clang-10 (1:10.0.0-4) ... Selecting previously unselected package libomp5-10:amd64. Preparing to unpack .../15-libomp5-10_1%3a10.0.0-4_amd64.deb ... Unpacking libomp5-10:amd64 (1:10.0.0-4) ... Selecting previously unselected package libomp-10-dev. Preparing to unpack .../16-libomp-10-dev_1%3a10.0.0-4_amd64.deb ... Unpacking libomp-10-dev (1:10.0.0-4) ... Setting up libgc1c2:amd64 (1:7.6.4-0.4) ... Setting up libobjc4:amd64 (10-20200502-1) ... Setting up libgomp1:amd64 (10-20200502-1) ... Setting up libz3-4:amd64 (4.8.7-4) ... Setting up libquadmath0:amd64 (10-20200502-1) ... Setting up libatomic1:amd64 (10-20200502-1) ... Setting up libobjc-9-dev:amd64 (9.3.0-11) ... Setting up libubsan1:amd64 (10-20200502-1) ... Setting up libomp5-10:amd64 (1:10.0.0-4) ... Setting up libc6-i386 (2.30-4) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libcc1-0:amd64 (10-20200502-1) ... Setting up liblsan0:amd64 (10-20200502-1) ... Setting up libitm1:amd64 (10-20200502-1) ... Setting up libtsan0:amd64 (10-20200502-1) ... Setting up libomp-10-dev (1:10.0.0-4) ... Setting up libedit2:amd64 (3.1-20191231-1) ... Setting up libllvm10:amd64 (1:10.0.0-4) ... Setting up lib32gcc-s1 (10-20200502-1) ... Setting up libclang1-10 (1:10.0.0-4) ... Setting up lib32gcc1 (1:10-20200502-1) ... Setting up libclang-cpp10 (1:10.0.0-4) ... Setting up lib32stdc++6 (10-20200502-1) ... Setting up libclang-common-10-dev (1:10.0.0-4) ... Setting up clang-10 (1:10.0.0-4) ... Processing triggers for libc-bin (2.30-4) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7 8 9 10' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-10 g++-4.6 + ln -s clang-10 gcc-4.6 + ln -s clang-10 cpp-4.6 + ln -s clang-10 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + 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++-10 g++-4.7 + ln -s clang-10 gcc-4.7 + ln -s clang-10 cpp-4.7 + ln -s clang-10 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + 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++-10 g++-4.8 + ln -s clang-10 gcc-4.8 + ln -s clang-10 cpp-4.8 + ln -s clang-10 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + 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++-10 g++-4.9 + ln -s clang-10 gcc-4.9 + ln -s clang-10 cpp-4.9 + ln -s clang-10 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + 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++-10 g++-5 + ln -s clang-10 gcc-5 + ln -s clang-10 cpp-5 + ln -s clang-10 gcc + echo 'gcc-5 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + 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++-10 g++-6 + ln -s clang-10 gcc-6 + ln -s clang-10 cpp-6 + ln -s clang-10 gcc + echo 'gcc-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + 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++-10 g++-7 + ln -s clang-10 gcc-7 + ln -s clang-10 cpp-7 + ln -s clang-10 gcc + echo 'gcc-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + 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++-10 g++-8 + ln -s clang-10 gcc-8 + ln -s clang-10 cpp-8 + ln -s clang-10 gcc + echo 'gcc-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-9 gcc-9 cpp-9 gcc + ln -s clang++-10 g++-9 + ln -s clang-10 gcc-9 + ln -s clang-10 cpp-9 + ln -s clang-10 gcc + echo 'gcc-9 hold' + dpkg --set-selections + echo 'g++-9 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-10 gcc-10 cpp-10 gcc + ln -s clang++-10 g++-10 + ln -s clang-10 gcc-10 + ln -s clang-10 cpp-10 + ln -s clang-10 gcc + echo 'gcc-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-10 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-10 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + cd - /build/bedops-xLS4Uw + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang + cd /usr/bin/ + rm -f clang++ clang + ln -s clang-10 clang++ + ln -s clang-10 clang + clang++ --version clang version 10.0.0-4 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + clang --version clang version 10.0.0-4 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + cd - /build/bedops-xLS4Uw + apt install --yes --no-install-recommends --force-yes qt5-qmake WARNING: apt does not have a stable CLI interface. Use with caution in scripts. Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: qt5-qmake-bin qtchooser The following NEW packages will be installed: qt5-qmake qt5-qmake-bin qtchooser 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 1270 kB of archives. After this operation, 4788 kB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 qt5-qmake-bin amd64 5.12.5+dfsg-10 [1015 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 qtchooser amd64 66-2 [26.3 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 qt5-qmake amd64 5.12.5+dfsg-10 [229 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1270 kB in 0s (19.7 MB/s) Selecting previously unselected package qt5-qmake-bin. (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 ... 12968 files and directories currently installed.) Preparing to unpack .../qt5-qmake-bin_5.12.5+dfsg-10_amd64.deb ... Unpacking qt5-qmake-bin (5.12.5+dfsg-10) ... Selecting previously unselected package qtchooser. Preparing to unpack .../qtchooser_66-2_amd64.deb ... Unpacking qtchooser (66-2) ... Selecting previously unselected package qt5-qmake:amd64. Preparing to unpack .../qt5-qmake_5.12.5+dfsg-10_amd64.deb ... Unpacking qt5-qmake:amd64 (5.12.5+dfsg-10) ... Setting up qt5-qmake-bin (5.12.5+dfsg-10) ... Setting up qtchooser (66-2) ... Setting up qt5-qmake:amd64 (5.12.5+dfsg-10) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + cp /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/qmake.conf /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/qplatformdefs.h /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/ + ls -al /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/ total 16 drwxr-xr-x 2 root root 4096 May 3 03:53 . drwxr-xr-x 75 root root 4096 May 3 03:53 .. -rw-r--r-- 1 root root 276 May 3 03:53 qmake.conf -rw-r--r-- 1 root root 3218 May 3 03:53 qplatformdefs.h + cat /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/qmake.conf # # qmake configuration for linux-clang # MAKEFILE_GENERATOR = UNIX CONFIG += incremental QMAKE_INCREMENTAL_STYLE = sublib include(../common/linux.conf) include(../common/gcc-base-unix.conf) include(../common/clang.conf) QMAKE_LFLAGS += -ccc-gcc-name g++ load(qt_config) + export QMAKESPEC=/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/ + QMAKESPEC=/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/ + sed -i -e 's|compare_problem(2,|compare_problem(0,|g' /usr/bin/dpkg-gensymbols + sed -i -e 's|compare_problem(1,|compare_problem(0,|g' /usr/bin/dpkg-gensymbols + grep 'compare_problem(' /usr/bin/dpkg-gensymbols compare_problem(4, g_('new libraries appeared in the symbols file: %s'), "@libs"); compare_problem(3, g_('some libraries disappeared in the symbols file: %s'), "@libs"); compare_problem(0, g_('some new symbols appeared in the symbols file: %s'), compare_problem(0, g_('some symbols or patterns disappeared in the symbols file: %s'), I: Finished running '/tmp/clang10'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/bedops-xLS4Uw/resolver-nrX3SS' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:12990/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'bedops' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bedops.git Please use: git clone https://salsa.debian.org/med-team/bedops.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 15.3 MB of source archives. Get:1 http://127.0.0.1:12990/debian sid/main bedops 2.4.39+dfsg-1 (dsc) [2147 B] Get:2 http://127.0.0.1:12990/debian sid/main bedops 2.4.39+dfsg-1 (tar) [15.3 MB] Get:3 http://127.0.0.1:12990/debian sid/main bedops 2.4.39+dfsg-1 (diff) [10.6 kB] Fetched 15.3 MB in 0s (99.8 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/bedops-xLS4Uw/bedops-2.4.39+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/bedops-xLS4Uw' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), help2man, libbz2-dev, libjansson-dev, libjs-mathjax, python3-distutils, python3-sphinx, zlib1g-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), help2man, libbz2-dev, libjansson-dev, libjs-mathjax, python3-distutils, python3-sphinx, zlib1g-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [425 B] Get:5 copy:/<>/apt_archive ./ Packages [507 B] Fetched 1889 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils ca-certificates debhelper dh-autoreconf dh-strip-nondeterminism docutils-common dwz file fonts-mathjax gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbz2-dev libcroco3 libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu63 libjansson-dev libjansson4 libjs-jquery libjs-mathjax libjs-sphinxdoc libjs-underscore liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libreadline8 libsigsegv2 libsqlite3-0 libssl1.1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db mime-support openssl po-debconf python-babel-localedata python3 python3-alabaster python3-babel python3-certifi python3-chardet python3-distutils python3-docutils python3-idna python3-imagesize python3-jinja2 python3-lib2to3 python3-markupsafe python3-minimal python3-packaging python3-pkg-resources python3-pygments python3-pyparsing python3-requests python3-roman python3-six python3-sphinx python3-tz python3-urllib3 python3.8 python3.8-minimal readline-common sensible-utils sgml-base sphinx-common xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff fonts-mathjax-extras fonts-stix libjs-mathjax-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base texlive-latex-recommended python-jinja2-doc python3-setuptools python-pygments-doc ttf-bitstream-vera python-pyparsing-doc python3-cryptography python3-openssl python3-socks python-requests-doc dvipng fonts-freefont-otf imagemagick-6.q16 latexmk python3-sphinx-rtd-theme python3-stemmer sphinx-doc texlive-fonts-recommended texlive-latex-extra texlive-plain-generic python3.8-venv python3.8-doc binfmt-support readline-doc sgml-base-doc Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libltdl-dev libmail-sendmail-perl libpaper-utils python3-pil The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils ca-certificates debhelper dh-autoreconf dh-strip-nondeterminism docutils-common dwz file fonts-mathjax gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbz2-dev libcroco3 libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu63 libjansson-dev libjansson4 libjs-jquery libjs-mathjax libjs-sphinxdoc libjs-underscore liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libreadline8 libsigsegv2 libsqlite3-0 libssl1.1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db mime-support openssl po-debconf python-babel-localedata python3 python3-alabaster python3-babel python3-certifi python3-chardet python3-distutils python3-docutils python3-idna python3-imagesize python3-jinja2 python3-lib2to3 python3-markupsafe python3-minimal python3-packaging python3-pkg-resources python3-pygments python3-pyparsing python3-requests python3-roman python3-six python3-sphinx python3-tz python3-urllib3 python3.8 python3.8-minimal readline-common sbuild-build-depends-main-dummy sensible-utils sgml-base sphinx-common xml-core zlib1g-dev 0 upgraded, 87 newly installed, 0 to remove and 0 not upgraded. Need to get 45.2 MB of archives. After this operation, 193 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [932 B] Get:2 http://127.0.0.1:12990/debian sid/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 groff-base amd64 1.22.4-4 [919 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 man-db amd64 2.9.1-1 [1308 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libssl1.1 amd64 1.1.1g-1 [1543 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libpython3.8-minimal amd64 3.8.3~rc1-1 [760 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 python3.8-minimal amd64 3.8.3~rc1-1 [1944 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 python3-minimal amd64 3.8.2-3 [37.6 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 mime-support all 3.64 [37.8 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 libmpdec2 amd64 2.4.2-3 [84.1 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 readline-common all 8.0-4 [72.5 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libreadline8 amd64 8.0-4 [160 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 libsqlite3-0 amd64 3.31.1-5 [661 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libpython3.8-stdlib amd64 3.8.3~rc1-1 [1667 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 python3.8 amd64 3.8.3~rc1-1 [415 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libpython3-stdlib amd64 3.8.2-3 [20.8 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 python3 amd64 3.8.2-3 [63.7 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 sgml-base all 1.30 [15.1 kB] Get:23 http://127.0.0.1:12990/debian sid/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 libmagic1 amd64 1:5.38-4 [120 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 file amd64 1:5.38-4 [67.9 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:28 http://127.0.0.1:12990/debian sid/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:29 http://127.0.0.1:12990/debian sid/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:30 http://127.0.0.1:12990/debian sid/main amd64 autoconf all 2.69-11.1 [341 kB] Get:31 http://127.0.0.1:12990/debian sid/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:32 http://127.0.0.1:12990/debian sid/main amd64 automake all 1:1.16.2-1 [775 kB] Get:33 http://127.0.0.1:12990/debian sid/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:34 http://127.0.0.1:12990/debian sid/main amd64 openssl amd64 1.1.1g-1 [846 kB] Get:35 http://127.0.0.1:12990/debian sid/main amd64 ca-certificates all 20190110 [157 kB] Get:36 http://127.0.0.1:12990/debian sid/main amd64 libtool all 2.4.6-14 [513 kB] Get:37 http://127.0.0.1:12990/debian sid/main amd64 dh-autoreconf all 19 [16.9 kB] Get:38 http://127.0.0.1:12990/debian sid/main amd64 libdebhelper-perl all 13 [184 kB] Get:39 http://127.0.0.1:12990/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:40 http://127.0.0.1:12990/debian sid/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:41 http://127.0.0.1:12990/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.8.0-1 [24.2 kB] Get:42 http://127.0.0.1:12990/debian sid/main amd64 dh-strip-nondeterminism all 1.8.0-1 [14.8 kB] Get:43 http://127.0.0.1:12990/debian sid/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:44 http://127.0.0.1:12990/debian sid/main amd64 dwz amd64 0.13-5 [151 kB] Get:45 http://127.0.0.1:12990/debian sid/main amd64 libglib2.0-0 amd64 2.64.2-1 [1343 kB] Get:46 http://127.0.0.1:12990/debian sid/main amd64 libicu63 amd64 63.2-3 [8296 kB] Get:47 http://127.0.0.1:12990/debian sid/main amd64 libxml2 amd64 2.9.10+dfsg-5 [709 kB] Get:48 http://127.0.0.1:12990/debian sid/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:49 http://127.0.0.1:12990/debian sid/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:50 http://127.0.0.1:12990/debian sid/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:51 http://127.0.0.1:12990/debian sid/main amd64 po-debconf all 1.0.21 [248 kB] Get:52 http://127.0.0.1:12990/debian sid/main amd64 debhelper all 13 [1002 kB] Get:53 http://127.0.0.1:12990/debian sid/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get:54 http://127.0.0.1:12990/debian sid/main amd64 docutils-common all 0.16+dfsg-2 [129 kB] Get:55 http://127.0.0.1:12990/debian sid/main amd64 fonts-mathjax all 2.7.4+dfsg-1 [2209 kB] Get:56 http://127.0.0.1:12990/debian sid/main amd64 help2man amd64 1.47.15 [181 kB] Get:57 http://127.0.0.1:12990/debian sid/main amd64 libbz2-dev amd64 1.0.8-2 [30.1 kB] Get:58 http://127.0.0.1:12990/debian sid/main amd64 libjansson4 amd64 2.12-1 [38.0 kB] Get:59 http://127.0.0.1:12990/debian sid/main amd64 libjansson-dev amd64 2.12-1 [40.5 kB] Get:60 http://127.0.0.1:12990/debian sid/main amd64 libjs-jquery all 3.3.1~dfsg-3 [332 kB] Get:61 http://127.0.0.1:12990/debian sid/main amd64 libjs-mathjax all 2.7.4+dfsg-1 [5658 kB] Get:62 http://127.0.0.1:12990/debian sid/main amd64 libjs-underscore all 1.9.1~dfsg-1 [99.4 kB] Get:63 http://127.0.0.1:12990/debian sid/main amd64 libjs-sphinxdoc all 2.4.3-2 [110 kB] Get:64 http://127.0.0.1:12990/debian sid/main amd64 python-babel-localedata all 2.8.0+dfsg.1-3 [4998 kB] Get:65 http://127.0.0.1:12990/debian sid/main amd64 python3-alabaster all 0.7.8-1.1 [18.6 kB] Get:66 http://127.0.0.1:12990/debian sid/main amd64 python3-pkg-resources all 46.1.3-1 [183 kB] Get:67 http://127.0.0.1:12990/debian sid/main amd64 python3-tz all 2019.3-2 [27.3 kB] Get:68 http://127.0.0.1:12990/debian sid/main amd64 python3-babel all 2.8.0+dfsg.1-3 [99.8 kB] Get:69 http://127.0.0.1:12990/debian sid/main amd64 python3-certifi all 2019.11.28-2 [149 kB] Get:70 http://127.0.0.1:12990/debian sid/main amd64 python3-chardet all 3.0.4-7 [81.1 kB] Get:71 http://127.0.0.1:12990/debian sid/main amd64 python3-lib2to3 all 3.8.2-2 [78.4 kB] Get:72 http://127.0.0.1:12990/debian sid/main amd64 python3-distutils all 3.8.2-2 [145 kB] Get:73 http://127.0.0.1:12990/debian sid/main amd64 python3-roman all 2.0.0-4 [8972 B] Get:74 http://127.0.0.1:12990/debian sid/main amd64 python3-docutils all 0.16+dfsg-2 [383 kB] Get:75 http://127.0.0.1:12990/debian sid/main amd64 python3-idna all 2.9-1 [37.1 kB] Get:76 http://127.0.0.1:12990/debian sid/main amd64 python3-imagesize all 1.2.0-2 [5824 B] Get:77 http://127.0.0.1:12990/debian sid/main amd64 python3-markupsafe amd64 1.1.1-1+b1 [15.2 kB] Get:78 http://127.0.0.1:12990/debian sid/main amd64 python3-jinja2 all 2.11.1-1 [114 kB] Get:79 http://127.0.0.1:12990/debian sid/main amd64 python3-pyparsing all 2.4.7-1 [109 kB] Get:80 http://127.0.0.1:12990/debian sid/main amd64 python3-six all 1.14.0-3 [16.7 kB] Get:81 http://127.0.0.1:12990/debian sid/main amd64 python3-packaging all 20.3-1.2 [29.9 kB] Get:82 http://127.0.0.1:12990/debian sid/main amd64 python3-pygments all 2.3.1+dfsg-3 [596 kB] Get:83 http://127.0.0.1:12990/debian sid/main amd64 python3-urllib3 all 1.25.9-1 [105 kB] Get:84 http://127.0.0.1:12990/debian sid/main amd64 python3-requests all 2.23.0+dfsg-2 [71.4 kB] Get:85 http://127.0.0.1:12990/debian sid/main amd64 sphinx-common all 2.4.3-2 [550 kB] Get:86 http://127.0.0.1:12990/debian sid/main amd64 python3-sphinx all 2.4.3-2 [502 kB] Get:87 http://127.0.0.1:12990/debian sid/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 45.2 MB in 0s (126 MB/s) Selecting previously unselected package bsdmainutils. (Reading database ... 13685 files and directories currently installed.) Preparing to unpack .../0-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-4_amd64.deb ... Unpacking groff-base (1.22.4-4) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../3-libpipeline1_1.5.2-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.2-2) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.1-1_amd64.deb ... Unpacking man-db (2.9.1-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../5-liblocale-gettext-perl_1.07-4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../6-libssl1.1_1.1.1g-1_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1g-1) ... Selecting previously unselected package libpython3.8-minimal:amd64. Preparing to unpack .../7-libpython3.8-minimal_3.8.3~rc1-1_amd64.deb ... Unpacking libpython3.8-minimal:amd64 (3.8.3~rc1-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../8-libexpat1_2.2.9-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.9-1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../9-python3.8-minimal_3.8.3~rc1-1_amd64.deb ... Unpacking python3.8-minimal (3.8.3~rc1-1) ... Setting up libssl1.1:amd64 (1.1.1g-1) ... Setting up libpython3.8-minimal:amd64 (3.8.3~rc1-1) ... Setting up libexpat1:amd64 (2.2.9-1) ... Setting up python3.8-minimal (3.8.3~rc1-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 14648 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.8.2-3_amd64.deb ... Unpacking python3-minimal (3.8.2-3) ... Selecting previously unselected package mime-support. Preparing to unpack .../1-mime-support_3.64_all.deb ... Unpacking mime-support (3.64) ... Selecting previously unselected package libmpdec2:amd64. Preparing to unpack .../2-libmpdec2_2.4.2-3_amd64.deb ... Unpacking libmpdec2:amd64 (2.4.2-3) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.0-4_all.deb ... Unpacking readline-common (8.0-4) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../4-libreadline8_8.0-4_amd64.deb ... Unpacking libreadline8:amd64 (8.0-4) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../5-libsqlite3-0_3.31.1-5_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.31.1-5) ... Selecting previously unselected package libpython3.8-stdlib:amd64. Preparing to unpack .../6-libpython3.8-stdlib_3.8.3~rc1-1_amd64.deb ... Unpacking libpython3.8-stdlib:amd64 (3.8.3~rc1-1) ... Selecting previously unselected package python3.8. Preparing to unpack .../7-python3.8_3.8.3~rc1-1_amd64.deb ... Unpacking python3.8 (3.8.3~rc1-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.8.2-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.8.2-3) ... Setting up python3-minimal (3.8.2-3) ... Selecting previously unselected package python3. (Reading database ... 15082 files and directories currently installed.) Preparing to unpack .../00-python3_3.8.2-3_amd64.deb ... Unpacking python3 (3.8.2-3) ... Selecting previously unselected package sgml-base. Preparing to unpack .../01-sgml-base_1.30_all.deb ... Unpacking sgml-base (1.30) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.12+nmu1_all.deb ... Unpacking sensible-utils (0.0.12+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.38-4_amd64.deb ... Unpacking libmagic-mgc (1:5.38-4) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../04-libmagic1_1%3a5.38-4_amd64.deb ... Unpacking libmagic1:amd64 (1:5.38-4) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.38-4_amd64.deb ... Unpacking file (1:5.38-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.19.8.1-10_amd64.deb ... Unpacking gettext-base (0.19.8.1-10) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../07-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../08-m4_1.4.18-4_amd64.deb ... Unpacking m4 (1.4.18-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../09-autoconf_2.69-11.1_all.deb ... Unpacking autoconf (2.69-11.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../10-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../11-automake_1%3a1.16.2-1_all.deb ... Unpacking automake (1:1.16.2-1) ... Selecting previously unselected package autopoint. Preparing to unpack .../12-autopoint_0.19.8.1-10_all.deb ... Unpacking autopoint (0.19.8.1-10) ... Selecting previously unselected package openssl. Preparing to unpack .../13-openssl_1.1.1g-1_amd64.deb ... Unpacking openssl (1.1.1g-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../14-ca-certificates_20190110_all.deb ... Unpacking ca-certificates (20190110) ... Selecting previously unselected package libtool. Preparing to unpack .../15-libtool_2.4.6-14_all.deb ... Unpacking libtool (2.4.6-14) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../16-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13_all.deb ... Unpacking libdebhelper-perl (13) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.8.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.8.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.8.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.8.0-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../22-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.13-5_amd64.deb ... Unpacking dwz (0.13-5) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../24-libglib2.0-0_2.64.2-1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.64.2-1) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../25-libicu63_63.2-3_amd64.deb ... Unpacking libicu63:amd64 (63.2-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../26-libxml2_2.9.10+dfsg-5_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-5) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../27-libcroco3_0.6.13-1_amd64.deb ... Unpacking libcroco3:amd64 (0.6.13-1) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.19.8.1-10_amd64.deb ... Unpacking gettext (0.19.8.1-10) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13_all.deb ... Unpacking debhelper (13) ... Selecting previously unselected package xml-core. Preparing to unpack .../32-xml-core_0.18+nmu1_all.deb ... Unpacking xml-core (0.18+nmu1) ... Selecting previously unselected package docutils-common. Preparing to unpack .../33-docutils-common_0.16+dfsg-2_all.deb ... Unpacking docutils-common (0.16+dfsg-2) ... Selecting previously unselected package fonts-mathjax. Preparing to unpack .../34-fonts-mathjax_2.7.4+dfsg-1_all.deb ... Unpacking fonts-mathjax (2.7.4+dfsg-1) ... Selecting previously unselected package help2man. Preparing to unpack .../35-help2man_1.47.15_amd64.deb ... Unpacking help2man (1.47.15) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../36-libbz2-dev_1.0.8-2_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.8-2) ... Selecting previously unselected package libjansson4:amd64. Preparing to unpack .../37-libjansson4_2.12-1_amd64.deb ... Unpacking libjansson4:amd64 (2.12-1) ... Selecting previously unselected package libjansson-dev:amd64. Preparing to unpack .../38-libjansson-dev_2.12-1_amd64.deb ... Unpacking libjansson-dev:amd64 (2.12-1) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../39-libjs-jquery_3.3.1~dfsg-3_all.deb ... Unpacking libjs-jquery (3.3.1~dfsg-3) ... Selecting previously unselected package libjs-mathjax. Preparing to unpack .../40-libjs-mathjax_2.7.4+dfsg-1_all.deb ... Unpacking libjs-mathjax (2.7.4+dfsg-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../41-libjs-underscore_1.9.1~dfsg-1_all.deb ... Unpacking libjs-underscore (1.9.1~dfsg-1) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../42-libjs-sphinxdoc_2.4.3-2_all.deb ... Unpacking libjs-sphinxdoc (2.4.3-2) ... Selecting previously unselected package python-babel-localedata. Preparing to unpack .../43-python-babel-localedata_2.8.0+dfsg.1-3_all.deb ... Unpacking python-babel-localedata (2.8.0+dfsg.1-3) ... Selecting previously unselected package python3-alabaster. Preparing to unpack .../44-python3-alabaster_0.7.8-1.1_all.deb ... Unpacking python3-alabaster (0.7.8-1.1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../45-python3-pkg-resources_46.1.3-1_all.deb ... Unpacking python3-pkg-resources (46.1.3-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../46-python3-tz_2019.3-2_all.deb ... Unpacking python3-tz (2019.3-2) ... Selecting previously unselected package python3-babel. Preparing to unpack .../47-python3-babel_2.8.0+dfsg.1-3_all.deb ... Unpacking python3-babel (2.8.0+dfsg.1-3) ... Selecting previously unselected package python3-certifi. Preparing to unpack .../48-python3-certifi_2019.11.28-2_all.deb ... Unpacking python3-certifi (2019.11.28-2) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../49-python3-chardet_3.0.4-7_all.deb ... Unpacking python3-chardet (3.0.4-7) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../50-python3-lib2to3_3.8.2-2_all.deb ... Unpacking python3-lib2to3 (3.8.2-2) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../51-python3-distutils_3.8.2-2_all.deb ... Unpacking python3-distutils (3.8.2-2) ... Selecting previously unselected package python3-roman. Preparing to unpack .../52-python3-roman_2.0.0-4_all.deb ... Unpacking python3-roman (2.0.0-4) ... Selecting previously unselected package python3-docutils. Preparing to unpack .../53-python3-docutils_0.16+dfsg-2_all.deb ... Unpacking python3-docutils (0.16+dfsg-2) ... Selecting previously unselected package python3-idna. Preparing to unpack .../54-python3-idna_2.9-1_all.deb ... Unpacking python3-idna (2.9-1) ... Selecting previously unselected package python3-imagesize. Preparing to unpack .../55-python3-imagesize_1.2.0-2_all.deb ... Unpacking python3-imagesize (1.2.0-2) ... Selecting previously unselected package python3-markupsafe. Preparing to unpack .../56-python3-markupsafe_1.1.1-1+b1_amd64.deb ... Unpacking python3-markupsafe (1.1.1-1+b1) ... Selecting previously unselected package python3-jinja2. Preparing to unpack .../57-python3-jinja2_2.11.1-1_all.deb ... Unpacking python3-jinja2 (2.11.1-1) ... Selecting previously unselected package python3-pyparsing. Preparing to unpack .../58-python3-pyparsing_2.4.7-1_all.deb ... Unpacking python3-pyparsing (2.4.7-1) ... Selecting previously unselected package python3-six. Preparing to unpack .../59-python3-six_1.14.0-3_all.deb ... Unpacking python3-six (1.14.0-3) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../60-python3-packaging_20.3-1.2_all.deb ... Unpacking python3-packaging (20.3-1.2) ... Selecting previously unselected package python3-pygments. Preparing to unpack .../61-python3-pygments_2.3.1+dfsg-3_all.deb ... Unpacking python3-pygments (2.3.1+dfsg-3) ... Selecting previously unselected package python3-urllib3. Preparing to unpack .../62-python3-urllib3_1.25.9-1_all.deb ... Unpacking python3-urllib3 (1.25.9-1) ... Selecting previously unselected package python3-requests. Preparing to unpack .../63-python3-requests_2.23.0+dfsg-2_all.deb ... Unpacking python3-requests (2.23.0+dfsg-2) ... Selecting previously unselected package sphinx-common. Preparing to unpack .../64-sphinx-common_2.4.3-2_all.deb ... Unpacking sphinx-common (2.4.3-2) ... Selecting previously unselected package python3-sphinx. Preparing to unpack .../65-python3-sphinx_2.4.3-2_all.deb ... Unpacking python3-sphinx (2.4.3-2) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../66-zlib1g-dev_1%3a1.2.11.dfsg-2_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../67-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.2-2) ... Setting up fonts-mathjax (2.7.4+dfsg-1) ... Setting up mime-support (3.64) ... Setting up libjs-mathjax (2.7.4+dfsg-1) ... Setting up libmagic-mgc (1:5.38-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.64.2-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13) ... Setting up libsqlite3-0:amd64 (3.31.1-5) ... Setting up libmagic1:amd64 (1:5.38-4) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-4) ... Setting up libicu63:amd64 (63.2-3) ... Setting up python-babel-localedata (2.8.0+dfsg.1-3) ... Setting up libjansson4:amd64 (2.12-1) ... Setting up autotools-dev (20180224.1) ... Setting up libsigsegv2:amd64 (2.12-2) ... 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 autopoint (0.19.8.1-10) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up sgml-base (1.30) ... Setting up libmpdec2:amd64 (2.4.2-3) ... Setting up libjs-jquery (3.3.1~dfsg-3) ... Setting up openssl (1.1.1g-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up readline-common (8.0-4) ... Setting up libxml2:amd64 (2.9.10+dfsg-5) ... Setting up libjansson-dev:amd64 (2.12-1) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up libjs-underscore (1.9.1~dfsg-1) ... Setting up libbz2-dev:amd64 (1.0.8-2) ... Setting up libfile-stripnondeterminism-perl (1.8.0-1) ... Setting up libtool (2.4.6-14) ... Setting up libreadline8:amd64 (8.0-4) ... Setting up m4 (1.4.18-4) ... Setting up help2man (1.47.15) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up libcroco3:amd64 (0.6.13-1) ... Setting up libjs-sphinxdoc (2.4.3-2) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.8.0-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up xml-core (0.18+nmu1) ... Setting up libpython3.8-stdlib:amd64 (3.8.3~rc1-1) ... Setting up python3.8 (3.8.3~rc1-1) ... Setting up libpython3-stdlib:amd64 (3.8.2-3) ... Setting up automake (1:1.16.2-1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10) ... Setting up python3 (3.8.2-3) ... Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (1.1.1-1+b1) ... Setting up python3-tz (2019.3-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-six (1.14.0-3) ... Setting up python3-roman (2.0.0-4) ... Setting up python3-jinja2 (2.11.1-1) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-certifi (2019.11.28-2) ... Setting up sphinx-common (2.4.3-2) ... Setting up python3-idna (2.9-1) ... Setting up python3-urllib3 (1.25.9-1) ... Setting up python3-lib2to3 (3.8.2-2) ... Setting up python3-imagesize (1.2.0-2) ... Setting up python3-pkg-resources (46.1.3-1) ... Setting up python3-distutils (3.8.2-2) ... Setting up python3-babel (2.8.0+dfsg.1-3) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-alabaster (0.7.8-1.1) ... Setting up po-debconf (1.0.21) ... Setting up python3-pygments (2.3.1+dfsg-3) ... Setting up python3-packaging (20.3-1.2) ... Setting up python3-chardet (3.0.4-7) ... Setting up python3-requests (2.23.0+dfsg-2) ... Setting up dh-autoreconf (19) ... Setting up debhelper (13) ... Processing triggers for libc-bin (2.30-4) ... Processing triggers for sgml-base (1.30) ... Setting up docutils-common (0.16+dfsg-2) ... Processing triggers for sgml-base (1.30) ... Setting up python3-docutils (0.16+dfsg-2) ... update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python3-sphinx (2.4.3-2) ... update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-apidoc to provide /usr/bin/sphinx-apidoc (sphinx-apidoc) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-autogen to provide /usr/bin/sphinx-autogen (sphinx-autogen) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-build to provide /usr/bin/sphinx-build (sphinx-build) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-quickstart to provide /usr/bin/sphinx-quickstart (sphinx-quickstart) in auto mode Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-6-cloud-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) amd64 (x86_64) Toolchain package versions: binutils_2.34-6 dpkg-dev_1.19.7 g++-9_9.3.0-11 gcc-9_9.3.0-11 libc6-dev_2.30-4 libstdc++-9-dev_9.3.0-11 libstdc++6_10-20200502-1 linux-libc-dev_5.6.7-1 Package versions: adduser_3.118 apt_2.0.2 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-6 binutils-common_2.34-6 binutils-x86-64-linux-gnu_2.34-6 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 ca-certificates_20190110 clang-10_1:10.0.0-4 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-9_9.3.0-11 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.8.0-1 diffutils_1:3.7-3 docutils-common_0.16+dfsg-2 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 fonts-mathjax_2.7.4+dfsg-1 g++_4:9.2.1-3.1 g++-9_9.3.0-11 gcc_4:9.2.1-3.1 gcc-10-base_10-20200502-1 gcc-9_9.3.0-11 gcc-9-base_9.3.0-11 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-2 help2man_1.47.15 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 lib32gcc-s1_10-20200502-1 lib32gcc1_1:10-20200502-1 lib32stdc++6_10-20200502-1 libacl1_2.2.53-8 libapt-pkg6.0_2.0.2 libarchive-zip-perl_1.68-1 libasan5_9.3.0-11 libatomic1_10-20200502-1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3+b1 libbinutils_2.34-6 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libbz2-dev_1.0.8-2 libc-bin_2.30-4 libc-dev-bin_2.30-4 libc6_2.30-4 libc6-dev_2.30-4 libc6-i386_2.30-4 libcap-ng0_0.7.9-2.1+b2 libcc1-0_10-20200502-1 libclang-common-10-dev_1:10.0.0-4 libclang-cpp10_1:10.0.0-4 libclang1-10_1:10.0.0-4 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-6 libctf0_2.34-6 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_13 libdpkg-perl_1.19.7 libedit2_3.1-20191231-1 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.0-1 libgc1c2_1:7.6.4-0.4 libgcc-9-dev_9.3.0-11 libgcc-s1_10-20200502-1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.2-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10-20200502-1 libgpg-error0_1.37-1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libitm1_10-20200502-1 libjansson-dev_2.12-1 libjansson4_2.12-1 libjs-jquery_3.3.1~dfsg-3 libjs-mathjax_2.7.4+dfsg-1 libjs-sphinxdoc_2.4.3-2 libjs-underscore_1.9.1~dfsg-1 libllvm10_1:10.0.0-4 liblocale-gettext-perl_1.07-4 liblsan0_10-20200502-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-3 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libobjc-9-dev_9.3.0-11 libobjc4_10-20200502-1 libomp-10-dev_1:10.0.0-4 libomp5-10_1:10.0.0-4 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12+b1 libperl5.30_5.30.0-10 libpipeline1_1.5.2-2 libpython3-stdlib_3.8.2-3 libpython3.8-minimal_3.8.3~rc1-1 libpython3.8-stdlib_3.8.3~rc1-1 libquadmath0_10-20200502-1 libreadline8_8.0-4 libseccomp2_2.4.3-1+b1 libselinux1_3.0-1+b3 libsemanage-common_3.0-1 libsemanage1_3.0-1+b3 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.1-5 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-11 libstdc++6_10-20200502-1 libsub-override-perl_0.09-2 libsystemd0_245.5-2 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libtsan0_10-20200502-1 libubsan1_10-20200502-1 libuchardet0_0.0.6-3 libudev1_245.5-2 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.10+dfsg-5 libz3-4_4.8.7-4 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.6.7-1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-1.3 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.2-1 ncurses-bin_6.2-1 openssl_1.1.1g-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-10 perl-base_5.30.0-10 perl-modules-5.30_5.30.0-10 po-debconf_1.0.21 python-babel-localedata_2.8.0+dfsg.1-3 python3_3.8.2-3 python3-alabaster_0.7.8-1.1 python3-babel_2.8.0+dfsg.1-3 python3-certifi_2019.11.28-2 python3-chardet_3.0.4-7 python3-distutils_3.8.2-2 python3-docutils_0.16+dfsg-2 python3-idna_2.9-1 python3-imagesize_1.2.0-2 python3-jinja2_2.11.1-1 python3-lib2to3_3.8.2-2 python3-markupsafe_1.1.1-1+b1 python3-minimal_3.8.2-3 python3-packaging_20.3-1.2 python3-pkg-resources_46.1.3-1 python3-pygments_2.3.1+dfsg-3 python3-pyparsing_2.4.7-1 python3-requests_2.23.0+dfsg-2 python3-roman_2.0.0-4 python3-six_1.14.0-3 python3-sphinx_2.4.3-2 python3-tz_2019.3-2 python3-urllib3_1.25.9-1 python3.8_3.8.3~rc1-1 python3.8-minimal_3.8.3~rc1-1 qt5-qmake_5.12.5+dfsg-10 qt5-qmake-bin_5.12.5+dfsg-10 qtchooser_66-2 readline-common_8.0-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sgml-base_1.30 sphinx-common_2.4.3-2 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.34-0.1 xml-core_0.18+nmu1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: bedops Binary: bedops, bedops-doc Architecture: any all Version: 2.4.39+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou Homepage: https://github.com/bedops/bedops Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/bedops Vcs-Git: https://salsa.debian.org/med-team/bedops.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12), help2man, libbz2-dev, libjansson-dev, libjs-mathjax, python3-distutils, python3-sphinx, zlib1g-dev Package-List: bedops deb science optional arch=any bedops-doc deb doc optional arch=all Checksums-Sha1: 02550945736d47c22f2f56a798020d76c267c146 15286132 bedops_2.4.39+dfsg.orig.tar.xz 185ab05efb904802f2a5605f2a9e6f5f96c77e68 10580 bedops_2.4.39+dfsg-1.debian.tar.xz Checksums-Sha256: 84e921aa3bf319964c3cb2843a31bcfdaa5cf5b4c6729a8f44afebb02a3b302a 15286132 bedops_2.4.39+dfsg.orig.tar.xz 33ab41186dd584b0ff738de46a4a1719f69d045b1f58f2b77b660854f80e2043 10580 bedops_2.4.39+dfsg-1.debian.tar.xz Files: 4ad7fb6b051cabd5916d476bb55d3f9e 15286132 bedops_2.4.39+dfsg.orig.tar.xz 870b34e8fa765540077f965f72b2ebbe 10580 bedops_2.4.39+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJHBAEBCAAxFiEEhMGXeonn7+0+XKYuL9i+2sAg7tEFAl6m6CUTHG1vZWxsZXJA ZGViaWFuLm9yZwAKCRAv2L7awCDu0WbCEAC96st3uqhNCV5eECTHLIIV2NbUosK+ ZU85EL+PKt4CEU5NyVcc1Y1u50P0WgvaoHzvB5ALUTCzUCCxlP4wl/KJ3GcSBgo2 u99JLsF7hcPy+Gc6HB6p898ZtI1IsVbjPhjtd2zz6xqEM9AoYYji7nJdYCdRyGlN 4qOomCjebcmflbh4+PwAebYFlFonJ3VceLpWatXq5CAuYyB7x8RiaqrlgILlUj+j cnVd3hpk9BC1qjb3t+UkFrjRu/lA4vlzui7ehoqmIe5z93VVGvX4S63yRVFLFpjD /SdD2ZllbR4fm3yWxQmlk0BGi1qp8eri1XMY+QiKehNyIxQaAyvHX6e7OuaxOMNP nk5lzs/7fzkZMiM6BO35vqMv0sXMfadDCzr7qO8IvfEYnOZGH4bQ9nx1EPRNSlHK L0wt1+yXGQebInSgWyunGcVc07x9t66CCeOM5a0WA51tffzPf6y0X8TWAAyoO89n mqkDsW1Oq0ckzyZsT+/lxbLzY8iG4Mi0hvHlNSEIYnqMVh8S9hBqE/e93UylTpGV ylOeBG9sgdRH3o9f5PKIVhzlmZl3YBRXG6wU4bvEvVWiyaJ68dGsdTTGVfPxygtu omTDtypWuRl2E2bU1SQvqU1iW+cpiEupKGEsj5QWX8QPBaeLadLnOicP0O5Vacn1 +N8jO7Dtf3qr/g== =Nmhu -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon Apr 27 14:11:49 2020 UTC gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bedops_2.4.39+dfsg-1.dsc dpkg-source: info: extracting bedops in /<> dpkg-source: info: unpacking bedops_2.4.39+dfsg.orig.tar.xz dpkg-source: info: unpacking bedops_2.4.39+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tests_use_installed_binaries.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying use_debian_libs dpkg-source: info: applying hardening.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=sid-amd64-sbuild-316cf00e-0b6b-43f4-a668-29ad5b56c583 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -b -rfakeroot dpkg-buildpackage: info: source package bedops dpkg-buildpackage: info: source version 2.4.39+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with sphinxdoc debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean make -j4 clean make[2]: Entering directory '/<>' make clean -j 8 -f system.mk/Makefile.linux make[3]: Entering directory '/<>' make[3]: warning: -j8 forced in submake: resetting jobserver mode. rm -rf bin rm -rf bin rm -rf bin make -C applications/bed/bedmap/src -f Makefile clean make -C applications/bed/sort-bed/src -f Makefile clean make -C applications/bed/bedops/src -f Makefile clean rm -rf modules make[4]: Entering directory '/<>/applications/bed/sort-bed/src' make -C applications/bed/closestfeats/src -f Makefile clean make[4]: Entering directory '/<>/applications/bed/bedmap/src' rm -rf objects_typical make -C applications/bed/bedextract/src -f Makefile clean make -C applications/bed/starch/src -f Makefile clean rm -rf ../bin make -C applications/bed/conversion/src -f Makefile clean make[4]: Entering directory '/<>/applications/bed/bedops/src' rm -rf objects_typical rm -rf objects-typical make[4]: Entering directory '/<>/applications/bed/closestfeats/src' rm -rf objects_typical make[4]: Entering directory '/<>/applications/bed/starch/src' rm -rf ../lib make[4]: Entering directory '/<>/applications/bed/bedextract/src' rm -rf objects_typical rm -rf ../bin rm -rf ../bin make[4]: Leaving directory '/<>/applications/bed/bedmap/src' rm -rf ../bin rm -f ../lib/libstarch_debug.a rm -rf ../bin make[4]: Leaving directory '/<>/applications/bed/sort-bed/src' rm -f ../lib/libstarch_gprof.a make[4]: Leaving directory '/<>/applications/bed/bedextract/src' make[4]: Entering directory '/<>/applications/bed/conversion/src' rm -rf ../bin make[4]: Leaving directory '/<>/applications/bed/bedops/src' rm -rf objects make[4]: Leaving directory '/<>/applications/bed/closestfeats/src' rm -rf objects rm -rf ../bin rm -rf *.so *~ make[4]: Leaving directory '/<>/applications/bed/starch/src' make[4]: Leaving directory '/<>/applications/bed/conversion/src' rm -rf third-party/bzip2-1.0.6 rm -f third-party/bzip2 rm -rf third-party/jansson-2.6 rm -f third-party/jansson rm -rf third-party/zlib-1.2.7 rm -f third-party/zlib rm -rf bin make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' rm -rf docs/_build/ make[1]: Leaving directory '/<>' dh_clean debian/rules build dh build --with sphinxdoc dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' make -j 8 -f system.mk/Makefile.linux make[2]: Entering directory '/<>' make[2]: warning: -j8 forced in submake: resetting jobserver mode. #bzcat | tar -x -C third-party #cd third-party/jansson-2.6 && ./configure --prefix=/<>/third-party/jansson-2.6 && make && make install && cd /<> && rm -f jansson && ln -sf jansson-2.6 third-party/jansson #bzcat | tar -x -C third-party #cd third-party/bzip2-1.0.6 && make libbz2.a && cd /<> && rm -f bzip2 && ln -sf bzip2-1.0.6 third-party/bzip2 #bzcat | tar -x -C third-party #cd third-party/zlib-1.2.7 && ./configure --static && make && cd /<> && rm -f zlib && ln -sf zlib-1.2.7 third-party/zlib make build -f /<>/system.mk/Makefile.linux make[3]: Entering directory '/<>' make -C applications/bed/bedmap/src -f Makefile build make -C applications/bed/sort-bed/src -f Makefile build make -C applications/bed/bedops/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/sort-bed/src' make -C applications/bed/closestfeats/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/bedmap/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers make -C applications/bed/bedextract/src -f Makefile build mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/<>/applications/bed/bedops/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/<>/applications/bed/closestfeats/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects-typical/starchConstants.o -iquote../../../../interfaces/general-headers make -C applications/bed/starch/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/bedextract/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/<>/applications/bed/starch/src' mkdir -p objects g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchConstants.c -o objects/starchConstants.o -iquote../../../../interfaces/general-headers -iquote../../../.. clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clangclang: clang: warningwarning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] : treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] : warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: argument unused during compilation: '-s' [-Wunused-command-line-argument] mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects-typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers make -C applications/bed/conversion/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/conversion/src' mkdir -p ../bin && gcc -Wall -Wextra -pedantic -std=c99 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -O3 -iquote"/<>/applications/bed/conversion/src" -iquote"../../../../interfaces/general-headers" convert2bed.c -o ../bin/convert2bed-typical -lpthread mkdir -p objects g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects/unstarchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers clangclang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] : warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: argument unused during compilation: '-s' [-Wunused-command-line-argument] clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects-typical/starchHelpers.o -iquote../../../../interfaces/general-headers convert2bed.c:3540:78: warning: format specifies type 'unsigned long long' but the argument has type 'uint64_t' (aka 'unsigned long') [-Wformat] fprintf(stderr, "Error: Invalid query coordinates at line [%llu]\n", c2b_globals.rmsk->line); ~~~~ ^~~~~~~~~~~~~~~~~~~~~~ %lu clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] mkdir -p objects g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchHelpers.c -o objects/starchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: argument unused during compilation: '-s' [-Wunused-command-line-argument] mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] ../../../../interfaces/src/data/starch/starchSha1Digest.c:279:10: warning: keyword is hidden by macro definition [-Wkeyword-macro] # define alignof(type) offsetof (struct offset_test, x) ^ mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects-typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] mkdir -p objects g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: argument unused during compilation: '-s' [-Wunused-command-line-argument] mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects-typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 1 warning generated. mkdir -p ../bin && g++ -o ../bin/bedmap-typical -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 Bedmap.cpp mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers clangclang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] : warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] ../../../../interfaces/src/data/starch/starchSha1Digest.c:279:10: warning: keyword is hidden by macro definition [-Wkeyword-macro] # define alignof(type) offsetof (struct offset_test, x) ^ mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects-typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] ../../../../interfaces/src/data/starch/starchSha1Digest.c:279:10: warning: keyword is hidden by macro definition [-Wkeyword-macro] # define alignof(type) offsetof (struct offset_test, x) ^ mkdir -p objects 1 warning generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects/starchFileHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers rm -rf objects make[4]: Leaving directory '/<>/applications/bed/conversion/src' mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 SortDetails.cpp -o objects-typical/SortDetails.o -iquote../../../../interfaces/general-headers clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: argument unused during compilation: '-s' [-Wunused-command-line-argument] clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] mkdir -p objects g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects/starchSha1Digest.o -iquote../../../../interfaces/general-headers -iquote../../../.. clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: argument unused during compilation: '-s' [-Wunused-command-line-argument] mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 Sort.cpp -o objects-typical/Sort.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] ../../../../interfaces/src/data/starch/starchSha1Digest.c:279:10: warning: keyword is hidden by macro definition [-Wkeyword-macro] # define alignof(type) offsetof (struct offset_test, x) ^ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] ../../../../interfaces/src/data/starch/starchSha1Digest.c:279:10: warning: keyword is hidden by macro definition [-Wkeyword-macro] # define alignof(type) offsetof (struct offset_test, x) ^ mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 CheckSort.cpp -o objects-typical/CheckSort.o -iquote../../../../interfaces/general-headers In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27: In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:36: In file included from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:36: 1 warning generated. In file included from ../../../../interfaces/general-headers/utility/PooledMemory.hpp:33: ../../../../interfaces/general-headers/utility/BitMonitor.hpp:89:19: error: cannot assign to non-static data member within const member function 'next_set' _open = bin*BASE+i; ~~~~~ ^ ../../../../interfaces/general-headers/utility/BitMonitor.hpp:81:24: note: member function 'Ext::BSet::next_set' is declared const here inline std::size_t next_set(std::size_t start) const { ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/utility/BitMonitor.hpp:99:21: error: cannot assign to non-static data member within const member function 'next_set' _open = bin*BASE+i; ~~~~~ ^ ../../../../interfaces/general-headers/utility/BitMonitor.hpp:81:24: note: member function 'Ext::BSet::next_set' is declared const here inline std::size_t next_set(std::size_t start) const { ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] mkdir -p ../bin && g++ -o ../bin/closest-features-typical -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 ClosestFeature.cpp In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:29: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:416:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:454:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:30: ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:413:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:451:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. mkdir -p ../bin && cp update-sort-bed-slurm.py ../bin/update-sort-bed-slurm-typical mkdir -p ../bin && cp update-sort-bed-starch-slurm.py ../bin/update-sort-bed-starch-slurm-typical mkdir -p ../bin && cp update-sort-bed-migrate-candidates.py ../bin/update-sort-bed-migrate-candidates-typical mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers 1 warning generated. mkdir -p objects g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects/starchBase64Coding.o -iquote../../../../interfaces/general-headers -iquote../../../.. clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: argument unused during compilation: '-s' [-Wunused-command-line-argument] mkdir -p ../bin cp starchcluster_gnuParallel.tcsh ../bin/starchcluster_gnuParallel-typical mkdir -p ../bin cp starchcluster_sge.tcsh ../bin/starchcluster_sge-typical mkdir -p ../bin cp starchcluster_slurm.tcsh ../bin/starchcluster_slurm-typical mkdir -p ../bin cp starch-diff.py ../bin/starch-diff-typical 1 warning generated. mkdir -p ../bin && g++ -o ../bin/bedextract-typical -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 ExtractRows.cpp mkdir -p ../bin && g++ -o ../bin/bedops-typical -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 Bedops.cpp mkdir -p ../lib ar rcs ../lib/libstarch.a objects/starchConstants.o objects/unstarchHelpers.o objects/starchHelpers.o objects/starchMetadataHelpers.o objects/starchFileHelpers.o objects/starchSha1Digest.o objects/starchBase64Coding.o mkdir -p ../bin mkdir -p ../bin g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starch.c -o objects/starch.o -iquote../../../../interfaces/general-headers -iquote../../../.. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c unstarch.c -o objects/unstarch.o -iquote../../../../interfaces/general-headers -iquote../../../.. In file included from In file included from CheckSort.cpp:28: In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41: In file included from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:36: In file included from ../../../../interfaces/general-headers/utility/PooledMemory.hpp:33: ../../../../interfaces/general-headers/utility/BitMonitor.hpp:89:19: error: cannot assign to non-static data member within const member function 'next_set' _open = bin*BASE+i; ~~~~~ ^ ../../../../interfaces/general-headers/utility/BitMonitor.hpp:81:24: note: member function 'Ext::BSet::next_set' is declared const here inline std::size_t next_set(std::size_t start) const { ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/utility/BitMonitor.hpp:99:21: error: cannot assign to non-static data member within const member function 'next_set' _open = bin*BASE+i; ~~~~~ ^ ../../../../interfaces/general-headers/utility/BitMonitor.hpp:81:24: note: member function 'Ext::BSet::next_set' is declared const here inline std::size_t next_set(std::size_t start) const { ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ClosestFeature.cpp:38: In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:37: In file included from ../../../../interfaces/general-headers/utility/PooledMemory.hpp:33: ../../../../interfaces/general-headers/utility/BitMonitor.hpp:89:19: error: cannot assign to non-static data member within const member function 'next_set' _open = bin*BASE+i; ~~~~~ ^ ../../../../interfaces/general-headers/utility/BitMonitor.hpp:81:24: note: member function 'Ext::BSet::next_set' is declared const here inline std::size_t next_set(std::size_t start) const { ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/utility/BitMonitor.hpp:99:21: error: cannot assign to non-static data member within const member function 'next_set' _open = bin*BASE+i; ~~~~~ ^ ../../../../interfaces/general-headers/utility/BitMonitor.hpp:81:24: note: member function 'Ext::BSet::next_set' is declared const here inline std::size_t next_set(std::size_t start) const { ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ clangclang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: argument unused during compilation: '-s' [-Wunused-command-line-argument] : warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: argument unused during compilation: '-s' [-Wunused-command-line-argument] In file included from ClosestFeature.cpp:39: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:416:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:454:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:416:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:454:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:29: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:416:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:102:20: note: in instantiation of member function 'Bed::bed_check_iterator *, 512>::check' requested here while ( !check(bl) ) { ^ Bedmap.cpp:276:53: note: in instantiation of member function 'Bed::bed_check_iterator *, 512>::bed_check_iterator' requested here Bed::bed_check_iterator refFileI(std::cin, refFileName, mem1, chrom, nestCheck); ^ Bedmap.cpp:903:9: note: in instantiation of function template specialization 'BedMap::runSweep, Bed::BasicCoords >, Bed::Overlapping, Bed::PercentOverlapMapping>' requested here runSweep(st, dt, refFileName, errorCheck, nestCheck, ^ Bedmap.cpp:985:9: note: in instantiation of function template specialization 'BedMap::callSweep' requested here callSweep(st, dt, refFileName, minRefFields, errorCheck, nestCheck, colSep, multivalColSep, onEmptyMap, ^ Bedmap.cpp:127:15: note: in instantiation of function template specialization 'BedMap::selectSweep' requested here BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_, ^ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:29: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:454:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starch.o -o ../bin/starch-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:30: ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:413:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:100:20: note: in instantiation of member function 'Bed::bed_check_iterator_mm *>::check' requested here while ( !check(bl) ) { ^ Bedmap.cpp:283:48: note: in instantiation of member function 'Bed::bed_check_iterator_mm *>::bed_check_iterator_mm' requested here Bed::bed_check_iterator_mm refFileI(std::cin, refFileName, chrom, nestCheck); ^ Bedmap.cpp:903:9: note: in instantiation of function template specialization 'BedMap::runSweep, Bed::BasicCoords >, Bed::Overlapping, Bed::PercentOverlapMapping>' requested here runSweep(st, dt, refFileName, errorCheck, nestCheck, ^ Bedmap.cpp:985:9: note: in instantiation of function template specialization 'BedMap::callSweep' requested here callSweep(st, dt, refFileName, minRefFields, errorCheck, nestCheck, colSep, multivalColSep, onEmptyMap, ^ Bedmap.cpp:127:15: note: in instantiation of function template specialization 'BedMap::selectSweep' requested here BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_, ^ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:30: ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:451:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:416:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:102:20: note: in instantiation of member function 'Bed::bed_check_iterator *, 512>::check' requested here while ( !check(bl) ) { ^ ClosestFeature.cpp:169:19: note: in instantiation of member function 'Bed::bed_check_iterator *, 512>::bed_check_iterator' requested here IterType1 fileI(std::cin, "stdin", mem1, input.Chrome()); ^ ClosestFeature.cpp:243:35: note: in instantiation of member function 'FeatDist::createWork, Bed::BasicCoords >::run' requested here createWork::run(input); ^ In file included from ClosestFeature.cpp:39: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:454:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p ../bin ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:416:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:102:20: note: in instantiation of member function 'Bed::bed_check_iterator *, 16>::check' requested here while ( !check(bl) ) { ^ CheckSort.cpp:48:16: note: in instantiation of member function 'Bed::bed_check_iterator *, 16>::bed_check_iterator' requested here IterType start((std::strcmp(bedFileNames[i], "-") == 0) ? std::cin : infile, ^ In file included from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:454:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starchcat.c -o objects/starchcat.o -iquote../../../../interfaces/general-headers -iquote../../../.. clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: argument unused during compilation: '-s' [-Wunused-command-line-argument] ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:308:10: warning: definition of implicit copy constructor for 'bed_check_iterator *, 16>' is deprecated because it has a user-declared copy assignment operator [-Wdeprecated-copy] bool operator=(const bed_check_iterator& b); ^ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:268:20: note: in implicit copy constructor for 'Bed::bed_check_iterator *, 16>' first required here auto __tmp = *this; ^ CheckSort.cpp:51:28: note: in instantiation of member function 'Bed::bed_check_iterator *, 16>::operator++' requested here pool.release(*start++); ^ 5 warnings and 2 errors generated. make[4]: *** [Makefile:88: objects-typical/CheckSort.o] Error 1 make[4]: *** Waiting for unfinished jobs.... mkdir -p ../bin In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:29: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:416:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:102:20: note: in instantiation of member function 'Bed::bed_check_iterator *, 512>::check' requested here while ( !check(bl) ) { ^ Bedmap.cpp:276:53: note: in instantiation of member function 'Bed::bed_check_iterator *, 512>::bed_check_iterator' requested here Bed::bed_check_iterator refFileI(std::cin, refFileName, mem1, chrom, nestCheck); ^ Bedmap.cpp:911:9: note: in instantiation of function template specialization 'BedMap::runSweep, Bed::NoPool::BasicCoords >, Bed::Overlapping, Bed::PercentOverlapMapping>' requested here runSweep(st, dt, refFileName, errorCheck, nestCheck, ^ Bedmap.cpp:985:9: note: in instantiation of function template specialization 'BedMap::callSweep' requested here callSweep(st, dt, refFileName, minRefFields, errorCheck, nestCheck, colSep, multivalColSep, onEmptyMap, ^ Bedmap.cpp:127:15: note: in instantiation of function template specialization 'BedMap::selectSweep' requested here BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_, ^ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starchstrip.c -o objects/starchstrip.o -iquote../../../../interfaces/general-headers -iquote../../../.. : In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:29: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:454:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/unstarch.o -o ../bin/unstarch-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:30: ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:413:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:100:20: note: in instantiation of member function 'Bed::bed_check_iterator_mm *>::check' requested here while ( !check(bl) ) { ^ Bedmap.cpp:283:48: note: in instantiation of member function 'Bed::bed_check_iterator_mm *>::bed_check_iterator_mm' requested here Bed::bed_check_iterator_mm refFileI(std::cin, refFileName, chrom, nestCheck); ^ Bedmap.cpp:911:9: note: in instantiation of function template specialization 'BedMap::runSweep, Bed::NoPool::BasicCoords >, Bed::Overlapping, Bed::PercentOverlapMapping>' requested here runSweep(st, dt, refFileName, errorCheck, nestCheck, ^ Bedmap.cpp:985:9: note: in instantiation of function template specialization 'BedMap::callSweep' requested here callSweep(st, dt, refFileName, minRefFields, errorCheck, nestCheck, colSep, multivalColSep, onEmptyMap, ^ Bedmap.cpp:127:15: note: in instantiation of function template specialization 'BedMap::selectSweep' requested here BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_, ^ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:30: ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:451:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4 warnings and 2 errors generated. make[4]: *** [Makefile:50: ../bin/closest-features-typical] Error 1 make[4]: Leaving directory '/<>/applications/bed/closestfeats/src' make[3]: *** [/<>/system.mk/Makefile.linux:25: applications/bed/closestfeats/src] Error 2 make[3]: *** Waiting for unfinished jobs.... clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clang: warning: argument unused during compilation: '-s' [-Wunused-command-line-argument] make[4]: Leaving directory '/<>/applications/bed/sort-bed/src' make[3]: *** [/<>/system.mk/Makefile.linux:25: applications/bed/sort-bed/src] Error 2 In file included from ExtractRows.cpp:40: In file included from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:36: In file included from ../../../../interfaces/general-headers/utility/PooledMemory.hpp:33: ../../../../interfaces/general-headers/utility/BitMonitor.hpp:89:19: error: cannot assign to non-static data member within const member function 'next_set' _open = bin*BASE+i; ~~~~~ ^ ../../../../interfaces/general-headers/utility/BitMonitor.hpp:81:24: note: member function 'Ext::BSet::next_set' is declared const here inline std::size_t next_set(std::size_t start) const { ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/utility/BitMonitor.hpp:99:21: error: cannot assign to non-static data member within const member function 'next_set' _open = bin*BASE+i; ~~~~~ ^ ../../../../interfaces/general-headers/utility/BitMonitor.hpp:81:24: note: member function 'Ext::BSet::next_set' is declared const here inline std::size_t next_set(std::size_t start) const { ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:29: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:416:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:102:20: note: in instantiation of member function 'Bed::bed_check_iterator, true> *, 512>::check' requested here while ( !check(bl) ) { ^ Bedmap.cpp:276:53: note: in instantiation of member function 'Bed::bed_check_iterator, true> *, 512>::bed_check_iterator' requested here Bed::bed_check_iterator refFileI(std::cin, refFileName, mem1, chrom, nestCheck); ^ Bedmap.cpp:921:9: note: in instantiation of function template specialization 'BedMap::runSweep, true>, Bed::Bed4, true> >, Bed::Overlapping, Bed::PercentOverlapMapping>' requested here runSweep(st, dt, refFileName, errorCheck, nestCheck, ^ Bedmap.cpp:985:9: note: in instantiation of function template specialization 'BedMap::callSweep' requested here callSweep(st, dt, refFileName, minRefFields, errorCheck, nestCheck, colSep, multivalColSep, onEmptyMap, ^ Bedmap.cpp:127:15: note: in instantiation of function template specialization 'BedMap::selectSweep' requested here BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_, ^ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:29: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:454:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:416:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:454:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ExtractRows.cpp:80:33: error: cannot assign to non-static data member within const member function 'Clear' void Clear() const { empty_ = true; } ~~~~~~ ^ ExtractRows.cpp:80:10: note: member function '(anonymous namespace)::Cache::Clear' is declared const here void Clear() const { empty_ = true; } ~~~~~^~~~~~~~~~~~~ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:30: ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:413:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:100:20: note: in instantiation of member function 'Bed::bed_check_iterator_mm, true> *>::check' requested here while ( !check(bl) ) { ^ Bedmap.cpp:283:48: note: in instantiation of member function 'Bed::bed_check_iterator_mm, true> *>::bed_check_iterator_mm' requested here Bed::bed_check_iterator_mm refFileI(std::cin, refFileName, chrom, nestCheck); ^ Bedmap.cpp:921:9: note: in instantiation of function template specialization 'BedMap::runSweep, true>, Bed::Bed4, true> >, Bed::Overlapping, Bed::PercentOverlapMapping>' requested here runSweep(st, dt, refFileName, errorCheck, nestCheck, ^ Bedmap.cpp:985:9: note: in instantiation of function template specialization 'BedMap::callSweep' requested here callSweep(st, dt, refFileName, minRefFields, errorCheck, nestCheck, colSep, multivalColSep, onEmptyMap, ^ Bedmap.cpp:127:15: note: in instantiation of function template specialization 'BedMap::selectSweep' requested here BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_, ^ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:30: ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:451:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Bedops.cpp:41: In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:37: In file included from ../../../../interfaces/general-headers/utility/PooledMemory.hpp:33: ../../../../interfaces/general-headers/utility/BitMonitor.hpp:89:19: error: cannot assign to non-static data member within const member function 'next_set' _open = bin*BASE+i; ~~~~~ ^ ../../../../interfaces/general-headers/utility/BitMonitor.hpp:81:24: note: member function 'Ext::BSet::next_set' is declared const here inline std::size_t next_set(std::size_t start) const { ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/utility/BitMonitor.hpp:99:21: error: cannot assign to non-static data member within const member function 'next_set' _open = bin*BASE+i; ~~~~~ ^ ../../../../interfaces/general-headers/utility/BitMonitor.hpp:81:24: note: member function 'Ext::BSet::next_set' is declared const here inline std::size_t next_set(std::size_t start) const { ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starchstrip.o -o ../bin/starchstrip-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now In file included from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:416:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:102:20: note: in instantiation of member function 'Bed::bed_check_iterator *, 16>::check' requested here while ( !check(bl) ) { ^ ExtractRows.cpp:267:57: note: in instantiation of member function 'Bed::bed_check_iterator *, 16>::bed_check_iterator' requested here Bed::bed_check_iterator titer(std::cin, input.File2Name(), mem), teof; ^ In file included from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:454:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Bedops.cpp:42: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:416:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:454:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:29: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:416:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:102:20: note: in instantiation of member function 'Bed::bed_check_iterator, true> *, 512>::check' requested here while ( !check(bl) ) { ^ Bedmap.cpp:276:53: note: in instantiation of member function 'Bed::bed_check_iterator, true> *, 512>::bed_check_iterator' requested here Bed::bed_check_iterator refFileI(std::cin, refFileName, mem1, chrom, nestCheck); ^ Bedmap.cpp:929:9: note: in instantiation of function template specialization 'BedMap::runSweep, true>, Bed::NoPool::Bed4, true> >, Bed::Overlapping, Bed::PercentOverlapMapping>' requested here runSweep(st, dt, refFileName, errorCheck, nestCheck, ^ Bedmap.cpp:985:9: note: in instantiation of function template specialization 'BedMap::callSweep' requested here callSweep(st, dt, refFileName, minRefFields, errorCheck, nestCheck, colSep, multivalColSep, onEmptyMap, ^ Bedmap.cpp:127:15: note: in instantiation of function template specialization 'BedMap::selectSweep' requested here BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_, ^ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:29: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:454:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4 warnings and 3 errors generated. make[4]: *** [Makefile:51: ../bin/bedextract-typical] Error 1 make[4]: Leaving directory '/<>/applications/bed/bedextract/src' make[3]: *** [/<>/system.mk/Makefile.linux:25: applications/bed/bedextract/src] Error 2 In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:30: ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:413:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:100:20: note: in instantiation of member function 'Bed::bed_check_iterator_mm, true> *>::check' requested here while ( !check(bl) ) { ^ Bedmap.cpp:283:48: note: in instantiation of member function 'Bed::bed_check_iterator_mm, true> *>::bed_check_iterator_mm' requested here Bed::bed_check_iterator_mm refFileI(std::cin, refFileName, chrom, nestCheck); ^ Bedmap.cpp:929:9: note: in instantiation of function template specialization 'BedMap::runSweep, true>, Bed::NoPool::Bed4, true> >, Bed::Overlapping, Bed::PercentOverlapMapping>' requested here runSweep(st, dt, refFileName, errorCheck, nestCheck, ^ Bedmap.cpp:985:9: note: in instantiation of function template specialization 'BedMap::callSweep' requested here callSweep(st, dt, refFileName, minRefFields, errorCheck, nestCheck, colSep, multivalColSep, onEmptyMap, ^ Bedmap.cpp:127:15: note: in instantiation of function template specialization 'BedMap::selectSweep' requested here BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_, ^ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:30: ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:451:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:416:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:102:20: note: in instantiation of member function 'Bed::bed_check_iterator *, 512>::check' requested here while ( !check(bl) ) { ^ Bedops.cpp:435:18: note: in instantiation of member function 'Bed::bed_check_iterator *, 512>::bed_check_iterator' requested here IterType fileI(std::cin, "stdin", mem, input.Chrom()); ^ Bedops.cpp:470:64: note: in instantiation of member function 'BedOperations::createWork *, 512>, Bed::bed_check_iterator *, 512> >::run' requested here createWork< Bed::bed_check_iterator >::run(input); ^ In file included from Bedops.cpp:42: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:454:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:29: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:416:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:102:20: note: in instantiation of member function 'Bed::bed_check_iterator, true>, double, true> *, 512>::check' requested here while ( !check(bl) ) { ^ Bedmap.cpp:276:53: note: in instantiation of member function 'Bed::bed_check_iterator, true>, double, true> *, 512>::bed_check_iterator' requested here Bed::bed_check_iterator refFileI(std::cin, refFileName, mem1, chrom, nestCheck); ^ Bedmap.cpp:939:9: note: in instantiation of function template specialization 'BedMap::runSweep, true>, double, true>, Bed::Bed5, true>, double, true> >, Bed::Overlapping, Bed::PercentOverlapMapping>' requested here runSweep(st, dt, refFileName, errorCheck, nestCheck, ^ Bedmap.cpp:985:9: note: in instantiation of function template specialization 'BedMap::callSweep' requested here callSweep(st, dt, refFileName, minRefFields, errorCheck, nestCheck, colSep, multivalColSep, onEmptyMap, ^ Bedmap.cpp:127:15: note: in instantiation of function template specialization 'BedMap::selectSweep' requested here BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_, ^ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:29: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:454:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:416:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:102:20: note: in instantiation of member function 'Bed::bed_check_iterator *, 512>::check' requested here while ( !check(bl) ) { ^ Bedops.cpp:386:21: note: in instantiation of member function 'Bed::bed_check_iterator *, 512>::bed_check_iterator' requested here IterType2 fileI(std::cin, "stdin", mem2, input.Chrom()); ^ Bedops.cpp:479:65: note: in instantiation of member function 'BedOperations::createWork *, 512>, Bed::bed_check_iterator *, 512> >::run' requested here Bed::bed_check_iterator >::run(input); ^ In file included from Bedops.cpp:42: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:454:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:30: ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:413:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:100:20: note: in instantiation of member function 'Bed::bed_check_iterator_mm, true>, double, true> *>::check' requested here while ( !check(bl) ) { ^ Bedmap.cpp:283:48: note: in instantiation of member function 'Bed::bed_check_iterator_mm, true>, double, true> *>::bed_check_iterator_mm' requested here Bed::bed_check_iterator_mm refFileI(std::cin, refFileName, chrom, nestCheck); ^ Bedmap.cpp:939:9: note: in instantiation of function template specialization 'BedMap::runSweep, true>, double, true>, Bed::Bed5, true>, double, true> >, Bed::Overlapping, Bed::PercentOverlapMapping>' requested here runSweep(st, dt, refFileName, errorCheck, nestCheck, ^ Bedmap.cpp:985:9: note: in instantiation of function template specialization 'BedMap::callSweep' requested here callSweep(st, dt, refFileName, minRefFields, errorCheck, nestCheck, colSep, multivalColSep, onEmptyMap, ^ Bedmap.cpp:127:15: note: in instantiation of function template specialization 'BedMap::selectSweep' requested here BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_, ^ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:30: ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:451:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Bedops.cpp:608:32: warning: unused variable 'r' [-Wunused-variable] std::pair r; ^ Bedops.cpp:1674:7: note: in instantiation of function template specialization 'BedOperations::doElementOf *, 512> >, std::vector *, 512> > *, std::allocator *, 512> > *> > >' requested here doElementOf(refFile, nonRefFiles, input.Threshold(), input.UsePercentage(), noInvert); ^ Bedops.cpp:398:7: note: in instantiation of function template specialization 'BedOperations::selectWork *, 512> >, std::vector *, 512> > *, std::allocator *, 512> > *> > >' requested here selectWork(input, *refFile, bedFiles); ^ Bedops.cpp:479:65: note: in instantiation of member function 'BedOperations::createWork *, 512>, Bed::bed_check_iterator *, 512> >::run' requested here Bed::bed_check_iterator >::run(input); ^ Bedops.cpp:608:32: warning: unused variable 'r' [-Wunused-variable] std::pair r; ^ Bedops.cpp:1674:7: note: in instantiation of function template specialization 'BedOperations::doElementOf *, 512> >, std::vector *, 512> > *, std::allocator *, 512> > *> > >' requested here doElementOf(refFile, nonRefFiles, input.Threshold(), input.UsePercentage(), noInvert); ^ Bedops.cpp:297:7: note: in instantiation of function template specialization 'BedOperations::selectWork *, 512> >, std::vector *, 512> > *, std::allocator *, 512> > *> > >' requested here selectWork(input, *refFile, bedFiles); ^ Bedops.cpp:482:75: note: in instantiation of member function 'BedOperations::createWork *, 512>, Bed::allocate_iterator_starch_bed *, 512> >::run' requested here Bed::allocate_iterator_starch_bed >::run(input); ^ 8 warnings and 2 errors generated. make[4]: *** [Makefile:52: ../bin/bedops-typical] Error 1 make[4]: Leaving directory '/<>/applications/bed/bedops/src' make[3]: *** [/<>/system.mk/Makefile.linux:25: applications/bed/bedops/src] Error 2 g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starchcat.o -o ../bin/starchcat-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:29: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:416:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:102:20: note: in instantiation of member function 'Bed::bed_check_iterator, true>, double, true> *, 512>::check' requested here while ( !check(bl) ) { ^ Bedmap.cpp:276:53: note: in instantiation of member function 'Bed::bed_check_iterator, true>, double, true> *, 512>::bed_check_iterator' requested here Bed::bed_check_iterator refFileI(std::cin, refFileName, mem1, chrom, nestCheck); ^ Bedmap.cpp:947:9: note: in instantiation of function template specialization 'BedMap::runSweep, true>, double, true>, Bed::NoPool::Bed5, true>, double, true> >, Bed::Overlapping, Bed::PercentOverlapMapping>' requested here runSweep(st, dt, refFileName, errorCheck, nestCheck, ^ Bedmap.cpp:985:9: note: in instantiation of function template specialization 'BedMap::callSweep' requested here callSweep(st, dt, refFileName, minRefFields, errorCheck, nestCheck, colSep, multivalColSep, onEmptyMap, ^ Bedmap.cpp:127:15: note: in instantiation of function template specialization 'BedMap::selectSweep' requested here BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_, ^ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:29: ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:454:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:30: ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:413:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:100:20: note: in instantiation of member function 'Bed::bed_check_iterator_mm, true>, double, true> *>::check' requested here while ( !check(bl) ) { ^ Bedmap.cpp:283:48: note: in instantiation of member function 'Bed::bed_check_iterator_mm, true>, double, true> *>::bed_check_iterator_mm' requested here Bed::bed_check_iterator_mm refFileI(std::cin, refFileName, chrom, nestCheck); ^ Bedmap.cpp:947:9: note: in instantiation of function template specialization 'BedMap::runSweep, true>, double, true>, Bed::NoPool::Bed5, true>, double, true> >, Bed::Overlapping, Bed::PercentOverlapMapping>' requested here runSweep(st, dt, refFileName, errorCheck, nestCheck, ^ Bedmap.cpp:985:9: note: in instantiation of function template specialization 'BedMap::callSweep' requested here callSweep(st, dt, refFileName, minRefFields, errorCheck, nestCheck, colSep, multivalColSep, onEmptyMap, ^ Bedmap.cpp:127:15: note: in instantiation of function template specialization 'BedMap::selectSweep' requested here BedMap::selectSweep(sweepDist, bedDist, input.refFileName_, input.mapFileName_, ^ In file included from Bedmap.cpp:37: In file included from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27: In file included from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31: In file included from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91: In file included from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:30: ../../../../interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:451:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rm -rf objects make[4]: Leaving directory '/<>/applications/bed/starch/src' 28 warnings and 2 errors generated. make[4]: *** [Makefile:51: ../bin/bedmap-typical] Error 1 make[4]: Leaving directory '/<>/applications/bed/bedmap/src' make[3]: *** [/<>/system.mk/Makefile.linux:25: applications/bed/bedmap/src] Error 2 make[3]: Leaving directory '/<>' make[2]: *** [system.mk/Makefile.linux:17: default] Error 2 make[2]: Leaving directory '/<>' make[1]: *** [Makefile:31: default] Error 2 make[1]: Leaving directory '/<>' dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" returned exit code 2 make: *** [debian/rules:25: build] Error 25 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-05-03T03:54:01Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 37840 Build-Time: 13 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 15 Job: bedops_2.4.39+dfsg-1 Machine Architecture: amd64 Package: bedops Package-Time: 45 Source-Version: 2.4.39+dfsg-1 Space: 37840 Status: attempted Version: 2.4.39+dfsg-1 -------------------------------------------------------------------------------- Finished at 2020-05-03T03:54:01Z Build needed 00:00:45, 37840k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 45.891493817s DC-Time-Estimation: 45.891493817 versus expected 901 (r/m: 18.633268064728686 ; m: 45.891493817)