DC-Build-Header: bedops 2.4.40+dfsg-1 / 2021-10-26 21:20:37 +0000 DC-Task: type:rebuild-binarch-only source:bedops version:2.4.40+dfsg-1 chroot:unstable esttime:496 logfile:/tmp/bedops_2.4.40+dfsg-1_unstable_clang13.log modes:clang13:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --no-run-lintian --chroot-setup-commands=/tmp/clang13 bedops_2.4.40+dfsg-1' sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-12-73.eu-central-1.compute.internal +==============================================================================+ | bedops 2.4.40+dfsg-1 (amd64) Tue, 26 Oct 2021 21:20:37 +0000 | +==============================================================================+ Package: bedops Version: 2.4.40+dfsg-1 Source Version: 2.4.40+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-0f3f9b6f-5df0-4ae1-9ab8-9f617093b38a' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang13 ------------ + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=13 + echo 'Install of clang-13' Install of clang-13 + apt-get update Get:1 http://127.0.0.1:12990/debian sid InRelease [165 kB] Get:2 http://127.0.0.1:12990/debian sid/main Sources.diff/Index [63.6 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://127.0.0.1:12990/debian sid/main Sources T-2021-10-26-2004.40-F-2021-10-26-0202.15.pdiff [47.3 kB] Get:4 http://127.0.0.1:12990/debian sid/main Sources T-2021-10-26-2004.40-F-2021-10-26-0202.15.pdiff [47.3 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 Packages T-2021-10-26-2004.40-F-2021-10-26-0202.15.pdiff [55.9 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 Packages T-2021-10-26-2004.40-F-2021-10-26-0202.15.pdiff [55.9 kB] Get:6 http://127.0.0.1:12990/debian sid/main Translation-en [6586 kB] Fetched 6981 kB in 3s (2791 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-13 libomp-13-dev libobjc-9-dev Reading package lists... Building dependency tree... The following additional packages will be installed: lib32gcc-s1 lib32stdc++6 libasan5 libbsd0 libc6-i386 libclang-common-13-dev libclang-cpp13 libclang1-13 libedit2 libgc1 libgcc-9-dev libicu67 libllvm13 libmd0 libobjc-11-dev libobjc4 libomp5-13 libxml2 libz3-4 Suggested packages: clang-13-doc libomp-13-doc Recommended packages: llvm-13-dev python3 The following NEW packages will be installed: clang-13 lib32gcc-s1 lib32stdc++6 libasan5 libbsd0 libc6-i386 libclang-common-13-dev libclang-cpp13 libclang1-13 libedit2 libgc1 libgcc-9-dev libicu67 libllvm13 libmd0 libobjc-11-dev libobjc-9-dev libobjc4 libomp-13-dev libomp5-13 libxml2 libz3-4 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. Need to get 68.5 MB of archives. After this operation, 379 MB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 libmd0 amd64 1.0.4-1 [29.6 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libedit2 amd64 3.1-20210910-1 [97.5 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libxml2 amd64 2.9.12+dfsg-5 [696 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 libz3-4 amd64 4.8.12-1+b1 [6997 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 libllvm13 amd64 1:13.0.0-8 [19.7 MB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libclang-cpp13 amd64 1:13.0.0-8 [10.5 MB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libgc1 amd64 1:8.0.4-3 [239 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 libobjc4 amd64 11.2.0-10 [43.2 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 libobjc-11-dev amd64 11.2.0-10 [170 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libc6-i386 amd64 2.32-4 [2624 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc-s1 amd64 11.2.0-10 [49.9 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 lib32stdc++6 amd64 11.2.0-10 [601 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libclang-common-13-dev amd64 1:13.0.0-8 [5730 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libclang1-13 amd64 1:13.0.0-8 [6093 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 clang-13 amd64 1:13.0.0-8 [119 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libasan5 amd64 9.4.0-3 [2734 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 libgcc-9-dev amd64 9.4.0-3 [2343 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libobjc-9-dev amd64 9.4.0-3 [219 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 libomp5-13 amd64 1:13.0.0-8 [377 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 libomp-13-dev amd64 1:13.0.0-8 [482 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 68.5 MB in 0s (155 MB/s) Selecting previously unselected package libmd0: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 ... 12431 files and directories currently installed.) Preparing to unpack .../00-libmd0_1.0.4-1_amd64.deb ... Unpacking libmd0:amd64 (1.0.4-1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../01-libbsd0_0.11.3-1_amd64.deb ... Unpacking libbsd0:amd64 (0.11.3-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../02-libedit2_3.1-20210910-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20210910-1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../03-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../04-libxml2_2.9.12+dfsg-5_amd64.deb ... Unpacking libxml2:amd64 (2.9.12+dfsg-5) ... Selecting previously unselected package libz3-4:amd64. Preparing to unpack .../05-libz3-4_4.8.12-1+b1_amd64.deb ... Unpacking libz3-4:amd64 (4.8.12-1+b1) ... Selecting previously unselected package libllvm13:amd64. Preparing to unpack .../06-libllvm13_1%3a13.0.0-8_amd64.deb ... Unpacking libllvm13:amd64 (1:13.0.0-8) ... Selecting previously unselected package libclang-cpp13. Preparing to unpack .../07-libclang-cpp13_1%3a13.0.0-8_amd64.deb ... Unpacking libclang-cpp13 (1:13.0.0-8) ... Selecting previously unselected package libgc1:amd64. Preparing to unpack .../08-libgc1_1%3a8.0.4-3_amd64.deb ... Unpacking libgc1:amd64 (1:8.0.4-3) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../09-libobjc4_11.2.0-10_amd64.deb ... Unpacking libobjc4:amd64 (11.2.0-10) ... Selecting previously unselected package libobjc-11-dev:amd64. Preparing to unpack .../10-libobjc-11-dev_11.2.0-10_amd64.deb ... Unpacking libobjc-11-dev:amd64 (11.2.0-10) ... Selecting previously unselected package libc6-i386. Preparing to unpack .../11-libc6-i386_2.32-4_amd64.deb ... Unpacking libc6-i386 (2.32-4) ... Selecting previously unselected package lib32gcc-s1. Preparing to unpack .../12-lib32gcc-s1_11.2.0-10_amd64.deb ... Unpacking lib32gcc-s1 (11.2.0-10) ... Selecting previously unselected package lib32stdc++6. Preparing to unpack .../13-lib32stdc++6_11.2.0-10_amd64.deb ... Unpacking lib32stdc++6 (11.2.0-10) ... Selecting previously unselected package libclang-common-13-dev. Preparing to unpack .../14-libclang-common-13-dev_1%3a13.0.0-8_amd64.deb ... Unpacking libclang-common-13-dev (1:13.0.0-8) ... Selecting previously unselected package libclang1-13. Preparing to unpack .../15-libclang1-13_1%3a13.0.0-8_amd64.deb ... Unpacking libclang1-13 (1:13.0.0-8) ... Selecting previously unselected package clang-13. Preparing to unpack .../16-clang-13_1%3a13.0.0-8_amd64.deb ... Unpacking clang-13 (1:13.0.0-8) ... Selecting previously unselected package libasan5:amd64. Preparing to unpack .../17-libasan5_9.4.0-3_amd64.deb ... Unpacking libasan5:amd64 (9.4.0-3) ... Selecting previously unselected package libgcc-9-dev:amd64. Preparing to unpack .../18-libgcc-9-dev_9.4.0-3_amd64.deb ... Unpacking libgcc-9-dev:amd64 (9.4.0-3) ... Selecting previously unselected package libobjc-9-dev:amd64. Preparing to unpack .../19-libobjc-9-dev_9.4.0-3_amd64.deb ... Unpacking libobjc-9-dev:amd64 (9.4.0-3) ... Selecting previously unselected package libomp5-13:amd64. Preparing to unpack .../20-libomp5-13_1%3a13.0.0-8_amd64.deb ... Unpacking libomp5-13:amd64 (1:13.0.0-8) ... Selecting previously unselected package libomp-13-dev. Preparing to unpack .../21-libomp-13-dev_1%3a13.0.0-8_amd64.deb ... Unpacking libomp-13-dev (1:13.0.0-8) ... Setting up libicu67:amd64 (67.1-7) ... Setting up libasan5:amd64 (9.4.0-3) ... Setting up libz3-4:amd64 (4.8.12-1+b1) ... Setting up libgc1:amd64 (1:8.0.4-3) ... Setting up libmd0:amd64 (1.0.4-1) ... Setting up libc6-i386 (2.32-4) ... Setting up libomp5-13:amd64 (1:13.0.0-8) ... Setting up libbsd0:amd64 (0.11.3-1) ... Setting up libxml2:amd64 (2.9.12+dfsg-5) ... Setting up libedit2:amd64 (3.1-20210910-1) ... Setting up libobjc4:amd64 (11.2.0-10) ... Setting up libgcc-9-dev:amd64 (9.4.0-3) ... Setting up lib32gcc-s1 (11.2.0-10) ... Setting up lib32stdc++6 (11.2.0-10) ... Setting up libllvm13:amd64 (1:13.0.0-8) ... Setting up libobjc-9-dev:amd64 (9.4.0-3) ... Setting up libclang-common-13-dev (1:13.0.0-8) ... Setting up libomp-13-dev (1:13.0.0-8) ... Setting up libobjc-11-dev:amd64 (11.2.0-10) ... Setting up libclang1-13 (1:13.0.0-8) ... Setting up libclang-cpp13 (1:13.0.0-8) ... Setting up clang-13 (1:13.0.0-8) ... Processing triggers for libc-bin (2.32-4) ... 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 11' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-13 g++-4.6 + ln -s clang-13 gcc-4.6 + ln -s clang-13 cpp-4.6 + ln -s clang-13 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++-13 g++-4.7 + ln -s clang-13 gcc-4.7 + ln -s clang-13 cpp-4.7 + ln -s clang-13 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++-13 g++-4.8 + ln -s clang-13 gcc-4.8 + ln -s clang-13 cpp-4.8 + ln -s clang-13 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++-13 g++-4.9 + ln -s clang-13 gcc-4.9 + ln -s clang-13 cpp-4.9 + ln -s clang-13 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++-13 g++-5 + ln -s clang-13 gcc-5 + ln -s clang-13 cpp-5 + ln -s clang-13 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++-13 g++-6 + ln -s clang-13 gcc-6 + ln -s clang-13 cpp-6 + ln -s clang-13 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++-13 g++-7 + ln -s clang-13 gcc-7 + ln -s clang-13 cpp-7 + ln -s clang-13 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++-13 g++-8 + ln -s clang-13 gcc-8 + ln -s clang-13 cpp-8 + ln -s clang-13 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++-13 g++-9 + ln -s clang-13 gcc-9 + ln -s clang-13 cpp-9 + ln -s clang-13 gcc + echo 'gcc-9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-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++-9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-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++-10 gcc-10 cpp-10 gcc + ln -s clang++-13 g++-10 + ln -s clang-13 gcc-10 + ln -s clang-13 cpp-10 + ln -s clang-13 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 + for VERSION in $VERSIONS + rm -f g++-11 gcc-11 cpp-11 gcc + ln -s clang++-13 g++-11 + ln -s clang-13 gcc-11 + ln -s clang-13 cpp-11 + ln -s clang-13 gcc + echo 'gcc-11 hold' + dpkg --set-selections + echo 'g++-11 hold' + dpkg --set-selections + cd - /build/bedops-liyHit + 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-13 clang++ + ln -s clang-13 clang + clang++ --version Debian clang version 13.0.0-8 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + clang --version Debian clang version 13.0.0-8 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + cd - /build/bedops-liyHit + 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 1322 kB of archives. After this operation, 4914 kB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 qt5-qmake-bin amd64 5.15.2+dfsg-12 [1046 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 5.15.2+dfsg-12 [249 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1322 kB in 0s (57.8 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 ... 13528 files and directories currently installed.) Preparing to unpack .../qt5-qmake-bin_5.15.2+dfsg-12_amd64.deb ... Unpacking qt5-qmake-bin (5.15.2+dfsg-12) ... 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_5.15.2+dfsg-12_amd64.deb ... Unpacking qt5-qmake:amd64 (5.15.2+dfsg-12) ... Setting up qt5-qmake-bin (5.15.2+dfsg-12) ... Setting up qtchooser (66-2) ... Setting up qt5-qmake:amd64 (5.15.2+dfsg-12) ... 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 Oct 26 21:20 . drwxr-xr-x 76 root root 4096 Oct 26 21:20 .. -rw-r--r-- 1 root root 276 Oct 26 21:20 qmake.conf -rw-r--r-- 1 root root 3218 Oct 26 21:20 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/clang13'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/bedops-liyHit/resolver-ppOeP3' 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 13.5 MB of source archives. Get:1 http://127.0.0.1:12990/debian sid/main bedops 2.4.40+dfsg-1 (dsc) [2178 B] Get:2 http://127.0.0.1:12990/debian sid/main bedops 2.4.40+dfsg-1 (tar) [13.4 MB] Get:3 http://127.0.0.1:12990/debian sid/main bedops 2.4.40+dfsg-1 (diff) [10.3 kB] Fetched 13.5 MB in 0s (104 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/bedops-liyHit/bedops-2.4.40+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/bedops-liyHit' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), help2man, libbz2-dev, libjansson-dev, python3-distutils, zlib1g-dev, build-essential, fakeroot, sphinx-common, libjs-mathjax, python3-sphinx Filtered Build-Depends: debhelper-compat (= 12), help2man, libbz2-dev, libjansson-dev, python3-distutils, zlib1g-dev, build-essential, fakeroot, sphinx-common, libjs-mathjax, python3-sphinx 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 [439 B] Get:5 copy:/<>/apt_archive ./ Packages [516 B] Fetched 1912 B in 0s (187 kB/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 bsdextrautils 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 libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl libjansson-dev libjansson4 libjs-jquery libjs-mathjax libjs-sphinxdoc libjs-underscore liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec3 libncursesw6 libpipeline1 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 libsigsegv2 libsqlite3-0 libsub-override-perl libtool libuchardet0 m4 man-db media-types 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-snowballstemmer python3-sphinx python3-tz python3-urllib3 python3.9 python3.9-minimal readline-common sensible-utils sgml-base sphinx-common xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc 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 python3-stemmer dvipng fonts-freefont-otf imagemagick-6.q16 latexmk python3-sphinx-rtd-theme sphinx-doc tex-gyre texlive-fonts-recommended texlive-latex-extra texlive-plain-generic python3.9-venv python3.9-doc binfmt-support readline-doc sgml-base-doc Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl javascript-common libgpm2 libltdl-dev libmail-sendmail-perl libpaper-utils python3-pil The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils 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 libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl libjansson-dev libjansson4 libjs-jquery libjs-mathjax libjs-sphinxdoc libjs-underscore liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec3 libncursesw6 libpipeline1 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 libsigsegv2 libsqlite3-0 libsub-override-perl libtool libuchardet0 m4 man-db media-types 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-snowballstemmer python3-sphinx python3-tz python3-urllib3 python3.9 python3.9-minimal readline-common sbuild-build-depends-main-dummy sensible-utils sgml-base sphinx-common xml-core zlib1g-dev 0 upgraded, 84 newly installed, 0 to remove and 0 not upgraded. Need to get 34.1 MB of archives. After this operation, 153 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [944 B] Get:2 http://127.0.0.1:12990/debian sid/main amd64 bsdextrautils amd64 2.37.2-4 [143 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 groff-base amd64 1.22.4-7 [935 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-4+b1 [19.0 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libpython3.9-minimal amd64 3.9.7-4 [804 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libexpat1 amd64 2.4.1-3 [104 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 python3.9-minimal amd64 3.9.7-4 [1963 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get:12 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1.16.0-2 [17.5 kB] Get:79 http://127.0.0.1:12990/debian sid/main amd64 python3-urllib3 all 1.26.5-1~exp1 [114 kB] Get:80 http://127.0.0.1:12990/debian sid/main amd64 python3-requests all 2.25.1+dfsg-2 [69.3 kB] Get:81 http://127.0.0.1:12990/debian sid/main amd64 python3-snowballstemmer all 2.1.0-2 [58.8 kB] Get:82 http://127.0.0.1:12990/debian sid/main amd64 sphinx-common all 4.2.0-5 [623 kB] Get:83 http://127.0.0.1:12990/debian sid/main amd64 python3-sphinx all 4.2.0-5 [529 kB] Get:84 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 34.1 MB in 0s (145 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 14273 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.37.2-4_amd64.deb ... Unpacking bsdextrautils (2.37.2-4) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-7_amd64.deb ... Unpacking groff-base (1.22.4-7) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../3-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../5-liblocale-gettext-perl_1.07-4+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... 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Setting up autopoint (0.21-4) ... Setting up libncursesw6:amd64 (6.2+20210905-1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.17) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libmpdec3:amd64 (2.5.1-2) ... Setting up libsub-override-perl (0.09-2) ... Setting up sgml-base (1.30) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-8) ... Setting up openssl (1.1.1l-1) ... Setting up libelf1:amd64 (0.185-2) ... Setting up readline-common (8.1-2) ... Setting up libjansson-dev:amd64 (2.13.1-1.1) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libjs-underscore (1.9.1~dfsg-4) ... Setting up libbz2-dev:amd64 (1.0.8-4) ... Setting up libfile-stripnondeterminism-perl (1.12.0-2) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libreadline8:amd64 (8.1-2) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.5) ... Setting up ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 127 added, 0 removed; done. Setting up libjs-sphinxdoc (4.2.0-5) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.12.0-2) ... Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-7) ... Setting up xml-core (0.18+nmu1) ... Setting up libpython3.9-stdlib:amd64 (3.9.7-4) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up automake (1:1.16.5-1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up sphinx-common (4.2.0-5) ... Setting up python3.9 (3.9.7-4) ... Setting up debhelper (13.5.2) ... Setting up python3 (3.9.2-3) ... Setting up python3-markupsafe (2.0.1-2) ... Setting up python3-tz (2021.3-1) ... Setting up python3-six (1.16.0-2) ... Setting up python3-roman (3.3-1) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-certifi (2020.6.20-1) ... Setting up python3-snowballstemmer (2.1.0-2) ... Setting up python3-idna (2.10-1) ... Setting up python3-urllib3 (1.26.5-1~exp1) ... Setting up python3-lib2to3 (3.9.7-1) ... Setting up python3-imagesize (1.2.0-2) ... Setting up python3-pkg-resources (58.2.0-1) ... Setting up python3-distutils (3.9.7-1) ... Setting up python3-babel (2.8.0+dfsg.1-7) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-alabaster (0.7.12-1) ... Setting up python3-jinja2 (3.0.1-2) ... Setting up python3-pygments (2.7.1+dfsg-2.1) ... Setting up python3-packaging (21.0-1) ... Setting up python3-chardet (4.0.0-1) ... Setting up python3-requests (2.25.1+dfsg-2) ... Processing triggers for libc-bin (2.32-4) ... Processing triggers for sgml-base (1.30) ... Setting up docutils-common (0.17.1+dfsg-2) ... Processing triggers for sgml-base (1.30) ... Setting up python3-docutils (0.17.1+dfsg-2) ... Setting up python3-sphinx (4.2.0-5) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for ca-certificates (20211016) ... 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_2.37-7 dpkg-dev_1.20.9 g++-11_11.2.0-10 gcc-11_11.2.0-10 libc6-dev_2.32-4 libstdc++-11-dev_11.2.0-10 libstdc++6_11.2.0-10 linux-libc-dev_5.14.12-1 Package versions: adduser_3.118 apt_2.3.11 autoconf_2.71-2 automake_1:1.16.5-1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12 base-passwd_3.5.52 bash_5.1-3+b2 binutils_2.37-7 binutils-common_2.37-7 binutils-x86-64-linux-gnu_2.37-7 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 ca-certificates_20211016 clang-13_1:13.0.0-8 coreutils_8.32-4+b1 cpp_4:11.2.0-2 cpp-11_11.2.0-10 dash_0.5.11+git20210120+802ebd4-2 debconf_1.5.78 debhelper_13.5.2 debian-archive-keyring_2021.1.1 debianutils_5.5-1 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-2 diffutils_1:3.7-5 docutils-common_0.17.1+dfsg-2 dpkg_1.20.9 dpkg-dev_1.20.9 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.26-1 file_1:5.39-3 findutils_4.8.0-1 fonts-mathjax_2.7.9+dfsg-1 g++_4:11.2.0-2 g++-11_11.2.0-10 gcc_4:11.2.0-2 gcc-10-base_10.3.0-11 gcc-11_11.2.0-10 gcc-11-base_11.2.0-10 gcc-9-base_9.4.0-3 gettext_0.21-4 gettext-base_0.21-4 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 help2man_1.48.5 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 lib32gcc-s1_11.2.0-10 lib32stdc++6_11.2.0-10 libacl1_2.3.1-1 libapt-pkg6.0_2.3.11 libarchive-zip-perl_1.68-1 libasan5_9.4.0-3 libasan6_11.2.0-10 libatomic1_11.2.0-10 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbinutils_2.37-7 libblkid1_2.37.2-4 libbsd0_0.11.3-1 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.32-4 libc-dev-bin_2.32-4 libc6_2.32-4 libc6-dev_2.32-4 libc6-i386_2.32-4 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-10 libclang-common-13-dev_1:13.0.0-8 libclang-cpp13_1:13.0.0-8 libclang1-13_1:13.0.0-8 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-7 libctf0_2.37-7 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9 libedit2_3.1-20210910-1 libelf1_0.185-2 libexpat1_2.4.1-3 libext2fs2_1.46.4-1 libfakeroot_1.26-1 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.12.0-2 libgc1_1:8.0.4-3 libgcc-11-dev_11.2.0-10 libgcc-9-dev_9.4.0-3 libgcc-s1_11.2.0-10 libgcrypt20_1.9.4-3+b1 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-10 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.24-2 libitm1_11.2.0-10 libjansson-dev_2.13.1-1.1 libjansson4_2.13.1-1.1 libjs-jquery_3.5.1+dfsg+~3.5.5-8 libjs-mathjax_2.7.9+dfsg-1 libjs-sphinxdoc_4.2.0-5 libjs-underscore_1.9.1~dfsg-4 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libllvm13_1:13.0.0-8 liblocale-gettext-perl_1.07-4+b1 liblsan0_11.2.0-10 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmd0_1.0.4-1 libmount1_2.37.2-4 libmpc3_1.2.1-1 libmpdec3_2.5.1-2 libmpfr6_4.1.0-3 libncursesw6_6.2+20210905-1 libnettle8_3.7.3-1 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libobjc-11-dev_11.2.0-10 libobjc-9-dev_9.4.0-3 libobjc4_11.2.0-10 libomp-13-dev_1:13.0.0-8 libomp5-13_1:13.0.0-8 libp11-kit0_0.24.0-5 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libpipeline1_1.5.3-1 libpython3-stdlib_3.9.2-3 libpython3.9-minimal_3.9.7-4 libpython3.9-stdlib_3.9.7-4 libquadmath0_11.2.0-10 libreadline8_8.1-2 libseccomp2_2.5.2-2 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b2 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-4 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-11-dev_11.2.0-10 libstdc++6_11.2.0-10 libsub-override-perl_0.09-2 libsystemd0_249.5-1 libtasn1-6_4.17.0-2 libtinfo6_6.2+20210905-1 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libtsan0_11.2.0-10 libubsan1_11.2.0-10 libuchardet0_0.0.7-1 libudev1_249.5-1 libunistring2_0.9.10-6 libuuid1_2.37.2-4 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2 libz3-4_4.8.12-1+b1 libzstd1_1.4.8+dfsg-3 linux-libc-dev_5.14.12-1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.37.2-4 ncurses-base_6.2+20210905-1 ncurses-bin_6.2+20210905-1 openssl_1.1.1l-1 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 po-debconf_1.0.21+nmu1 python-babel-localedata_2.8.0+dfsg.1-7 python3_3.9.2-3 python3-alabaster_0.7.12-1 python3-babel_2.8.0+dfsg.1-7 python3-certifi_2020.6.20-1 python3-chardet_4.0.0-1 python3-distutils_3.9.7-1 python3-docutils_0.17.1+dfsg-2 python3-idna_2.10-1 python3-imagesize_1.2.0-2 python3-jinja2_3.0.1-2 python3-lib2to3_3.9.7-1 python3-markupsafe_2.0.1-2 python3-minimal_3.9.2-3 python3-packaging_21.0-1 python3-pkg-resources_58.2.0-1 python3-pygments_2.7.1+dfsg-2.1 python3-pyparsing_2.4.7-1 python3-requests_2.25.1+dfsg-2 python3-roman_3.3-1 python3-six_1.16.0-2 python3-snowballstemmer_2.1.0-2 python3-sphinx_4.2.0-5 python3-tz_2021.3-1 python3-urllib3_1.26.5-1~exp1 python3.9_3.9.7-4 python3.9-minimal_3.9.7-4 qt5-qmake_5.15.2+dfsg-12 qt5-qmake-bin_5.15.2+dfsg-12 qtchooser_66-2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.30 sphinx-common_4.2.0-5 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021e-1 util-linux_2.37.2-4 xml-core_0.18+nmu1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bedops Binary: bedops, bedops-doc Architecture: any all Version: 2.4.40+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, python3-distutils, zlib1g-dev Build-Depends-Indep: sphinx-common, libjs-mathjax, python3-sphinx Package-List: bedops deb science optional arch=any bedops-doc deb doc optional arch=all Checksums-Sha1: d2819342382ce8a8d9519971bd5f6f09b46e53f6 13444448 bedops_2.4.40+dfsg.orig.tar.xz b87353f93d1ef742f06ad98e360a6dfa65d2f4ef 10264 bedops_2.4.40+dfsg-1.debian.tar.xz Checksums-Sha256: 014839e322e14715da2b8b6d879ed9600ef6b558c0bf860c04c64d49328dfc71 13444448 bedops_2.4.40+dfsg.orig.tar.xz 81af8570785380e094f2aaaef9f742f3404b70f01980a1d990de2be391633c1c 10264 bedops_2.4.40+dfsg-1.debian.tar.xz Files: e811a862f0a3c82ee3c4285ebec8393a 13444448 bedops_2.4.40+dfsg.orig.tar.xz 6cf3c54a2b54a622c50c2e42bdb0fe6f 10264 bedops_2.4.40+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmF1G4oSHG5pbGVzaEBk ZWJpYW4ub3JnAAoJEAC650s0M2nxXgcQAJ4ugqYcEIJUI28KOfybiurOgzRjrR8u aq/V8bdyuKIVylcZTPfhttXBSANEZX00gYIOgLFd1l7yUuOzwdBBoh+HTBjn5GIi otGGxkGbkLSrV+AoAsXskEaAGtC4tU6yGTmP5Q9ChMH/38SEnG3iTdm4YS5v4bKz DSoxDBqNA8QNssnU1haJkSSDN3dnhFJR4W6XOzyeO3tiQ5XneyLhDAqH82JEAXs4 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bedops_2.4.40+dfsg.orig.tar.xz dpkg-source: info: unpacking bedops_2.4.40+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 parallel.patch dpkg-source: info: applying adapt_to_new_sphinx.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-0f3f9b6f-5df0-4ae1-9ab8-9f617093b38a 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 2.4.40+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean make -j4 clean make[2]: Entering directory '/<>' make clean -f system.mk/Makefile.linux make[3]: Entering directory '/<>' rm -rf bin rm -rf bin rm -rf bin make -C applications/bed/bedextract/src -f Makefile clean make -C applications/bed/bedmap/src -f Makefile clean make -C applications/bed/bedops/src -f Makefile clean rm -rf modules make[4]: Entering directory '/<>/applications/bed/bedextract/src' rm -rf objects_typical make[4]: Entering directory '/<>/applications/bed/bedmap/src' rm -rf objects_typical make -C applications/bed/closestfeats/src -f Makefile clean make[4]: Entering directory '/<>/applications/bed/bedops/src' rm -rf ../bin rm -rf objects_typical rm -rf ../bin make[4]: Leaving directory '/<>/applications/bed/bedextract/src' make -C applications/bed/conversion/src -f Makefile clean rm -rf ../bin make[4]: Entering directory '/<>/applications/bed/closestfeats/src' rm -rf objects_typical make[4]: Leaving directory '/<>/applications/bed/bedops/src' make -C applications/bed/sort-bed/src -f Makefile clean make[4]: Entering directory '/<>/applications/bed/conversion/src' make[4]: Leaving directory '/<>/applications/bed/bedmap/src' rm -rf ../bin make -C applications/bed/starch/src -f Makefile clean rm -rf ../bin make[4]: Entering directory '/<>/applications/bed/sort-bed/src' rm -rf objects make[4]: Leaving directory '/<>/applications/bed/closestfeats/src' make[4]: Entering directory '/<>/applications/bed/starch/src' rm -rf ../lib rm -rf objects-typical rm -rf *.so *~ rm -rf ../bin rm -f ../lib/libstarch_debug.a make[4]: Leaving directory '/<>/applications/bed/sort-bed/src' rm -f ../lib/libstarch_gprof.a make[4]: Leaving directory '/<>/applications/bed/conversion/src' rm -rf objects rm -rf ../bin make[4]: Leaving directory '/<>/applications/bed/starch/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 dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' make -f system.mk/Makefile.linux make[2]: Entering directory '/<>' #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/bedextract/src -f Makefile build make -C applications/bed/bedmap/src -f Makefile build make -C applications/bed/bedops/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/bedextract/src' mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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/closestfeats/src -f Makefile build make[4]: Entering directory '/<>/applications/bed/bedmap/src' mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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/bedops/src' mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers clangclang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] clangclang: : warning: warning: 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] mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers clangclangclangclang: : : warning: warning: warning: 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]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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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] clang: 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: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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] clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -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] 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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -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] mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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] 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 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchSha1Digest.c:279:10: ../../../../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) ^ warning: keyword is hidden by macro definition [-Wkeyword-macro] # define alignof(type) offsetof (struct offset_test, x) ^ ../../../../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) ^ 11 warning generated. warning generated. mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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_typical && g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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] 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] 1 warning generated. mkdir -p objects_typical && g++ -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-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 -ljansson -lz -lbz2 ClosestFeature.cpp mkdir -p ../bin && g++ -o ../bin/bedextract-typical -g -O2 -ffile-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 -ljansson -lz -lbz2 ExtractRows.cpp mkdir -p ../bin && g++ -o ../bin/bedmap-typical -g -O2 -ffile-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 -ljansson -lz -lbz2 Bedmap.cpp mkdir -p ../bin && g++ -o ../bin/bedops-typical -g -O2 -ffile-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 -ljansson -lz -lbz2 Bedops.cpp In file included from 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 { ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: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: 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 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 { ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-const-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-const-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 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-const-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-const-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-const-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-const-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-const-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-const-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-const-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-const-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-const-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-const-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-const-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-const-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:29: applications/bed/bedextract/src] Error 2 make[3]: *** Waiting for unfinished jobs.... 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:29: applications/bed/closestfeats/src] Error 2 ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:416:69: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-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>>::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-const-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-const-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::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-const-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-const-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::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-const-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-const-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-const-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>> *>>' 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>> *>>' 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); ^ 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-const-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::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-const-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-const-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::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-const-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>> *>>' 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>> *>>' 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:29: applications/bed/bedops/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: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-const-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::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-const-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-const-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::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-const-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-const-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::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-const-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-const-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::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-const-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-const-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::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-const-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-const-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::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-const-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-const-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::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-const-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-const-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::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-const-int-float-conversion] else if ( std::atof(bl.substr(pos, marker-pos).c_str()) > std::numeric_limits::max() ) ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:29: applications/bed/bedmap/src] Error 2 make[3]: Leaving directory '/<>' make[2]: *** [system.mk/Makefile.linux:21: 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 2021-10-26T21:21:28Z 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: 24000 Build-Time: 11 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 18 Job: bedops_2.4.40+dfsg-1 Machine Architecture: amd64 Package: bedops Package-Time: 51 Source-Version: 2.4.40+dfsg-1 Space: 24000 Status: attempted Version: 2.4.40+dfsg-1 -------------------------------------------------------------------------------- Finished at 2021-10-26T21:21:28Z Build needed 00:00:51, 24000k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 52.585656706s DC-Time-Estimation: 52.585656706 versus expected 496 (r/m: 8.43222983356613 ; m: 52.585656706)