https://launchpad.net/ubuntu/+source/libstatgen/1.0.15-4/+build/22601457 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-028 4.15.0-163-generic #171-Ubuntu SMP Fri Nov 5 11:55:11 UTC 2021 x86_64 Buildd toolchain package versions: launchpad-buildd_204~508~ubuntu18.04.1 python3-lpbuildd_204~508~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.9 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 8 Dec 05:20:21 ntpdate[1973]: adjust time server 10.211.37.1 offset 0.000339 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22601457 --image-type chroot /home/buildd/filecache-default/b0c128df17a460089eca69348f06144377489985 Creating target for build PACKAGEBUILD-22601457 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22601457 Starting target for build PACKAGEBUILD-22601457 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22601457 'deb http://ftpmaster.internal/ubuntu jammy main universe' 'deb http://ftpmaster.internal/ubuntu jammy-security main universe' 'deb http://ftpmaster.internal/ubuntu jammy-updates main universe' 'deb http://ftpmaster.internal/ubuntu jammy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-22601457 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22601457 Updating target for build PACKAGEBUILD-22601457 Get:1 http://ftpmaster.internal/ubuntu jammy InRelease [270 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed InRelease [121 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main amd64 Packages [1397 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe amd64 Packages [13.3 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5554 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 Packages [150 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [51.0 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 Packages [734 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [346 kB] Fetched 22.6 MB in 26s (859 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libssl1.1 Use 'sudo apt autoremove' to remove it. The following packages will be REMOVED: libsemanage1* The following NEW packages will be installed: libsemanage2 libsepol2 libssl3 The following packages will be upgraded: apt base-files bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils bzip2 ca-certificates cpp-11 dash debconf debianutils dpkg dpkg-dev e2fsprogs g++-11 gcc-11 gcc-11-base gpg gpg-agent gpgconf gpgv grep libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libbinutils libblkid1 libbz2-1.0 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdpkg-perl libext2fs2 libgcc-11-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn2-0 libip4tc2 libisl23 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblsan0 libmount1 libmpc3 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsmartcols1 libsqlite3-0 libss2 libstdc++-11-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mount ncurses-base ncurses-bin openssl passwd pkgbinarymangler sed sensible-utils systemd systemd-sysv systemd-timesyncd tzdata usrmerge util-linux 106 upgraded, 3 newly installed, 1 to remove and 0 not upgraded. Need to get 84.2 MB of archives. After this operation, 354 MB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu jammy/main amd64 debconf all 1.5.79 [126 kB] Get:2 http://ftpmaster.internal/ubuntu jammy/main amd64 libpam0g amd64 1.4.0-10ubuntu2 [61.5 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main amd64 libcrypt-dev amd64 1:4.4.26-1 [112 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main amd64 libcrypt1 amd64 1:4.4.26-1 [82.1 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main amd64 base-files amd64 12ubuntu2 [63.3 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main amd64 debianutils amd64 5.5-1ubuntu1 [107 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main amd64 bash amd64 5.1-5ubuntu1 [771 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main amd64 bsdutils amd64 1:2.37.2-4ubuntu1 [80.9 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main amd64 libgpg-error0 amd64 1.42-3 [68.1 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main amd64 libgcrypt20 amd64 1.9.4-3ubuntu2 [515 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 bzip2 amd64 1.0.8-5 [34.8 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libbz2-1.0 amd64 1.0.8-5 [34.5 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main amd64 libcc1-0 amd64 11.2.0-12ubuntu1 [53.8 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main amd64 gcc-11-base amd64 11.2.0-12ubuntu1 [20.7 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main amd64 libgcc-s1 amd64 11.2.0-12ubuntu1 [45.6 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main amd64 libgomp1 amd64 11.2.0-12ubuntu1 [117 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main amd64 libitm1 amd64 11.2.0-12ubuntu1 [30.0 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main amd64 libatomic1 amd64 11.2.0-12ubuntu1 [9998 B] Get:19 http://ftpmaster.internal/ubuntu jammy/main amd64 libasan6 amd64 11.2.0-12ubuntu1 [2282 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main amd64 liblsan0 amd64 11.2.0-12ubuntu1 [976 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main amd64 libtsan0 amd64 11.2.0-12ubuntu1 [2259 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main amd64 libubsan1 amd64 11.2.0-12ubuntu1 [922 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main amd64 libquadmath0 amd64 11.2.0-12ubuntu1 [154 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main amd64 g++-11 amd64 11.2.0-12ubuntu1 [11.4 MB] Get:25 http://ftpmaster.internal/ubuntu jammy/main amd64 libstdc++-11-dev amd64 11.2.0-12ubuntu1 [2098 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main amd64 libgcc-11-dev amd64 11.2.0-12ubuntu1 [2532 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main amd64 gcc-11 amd64 11.2.0-12ubuntu1 [20.1 MB] Get:28 http://ftpmaster.internal/ubuntu jammy/main amd64 cpp-11 amd64 11.2.0-12ubuntu1 [9962 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main amd64 libstdc++6 amd64 11.2.0-12ubuntu1 [656 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main amd64 libisl23 amd64 0.24-2 [728 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main amd64 libmpc3 amd64 1.2.1-1 [46.9 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main amd64 libzstd1 amd64 1.4.8+dfsg-3 [324 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main amd64 libctf0 amd64 2.37-10ubuntu1 [103 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main amd64 libctf-nobfd0 amd64 2.37-10ubuntu1 [106 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main amd64 libbinutils amd64 2.37-10ubuntu1 [653 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main amd64 binutils-common amd64 2.37-10ubuntu1 [213 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main amd64 binutils amd64 2.37-10ubuntu1 [3192 B] Get:38 http://ftpmaster.internal/ubuntu jammy/main amd64 binutils-x86-64-linux-gnu amd64 2.37-10ubuntu1 [2314 kB] Get:39 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libssl3 amd64 3.0.0-1ubuntu2 [1896 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main amd64 libblkid1 amd64 2.37.2-4ubuntu1 [103 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main amd64 libuuid1 amd64 2.37.2-4ubuntu1 [23.8 kB] Get:42 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libcryptsetup12 amd64 2:2.4.2-1ubuntu3 [208 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main amd64 libidn2-0 amd64 2.3.2-2 [66.5 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main amd64 libp11-kit0 amd64 0.24.0-6 [252 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main amd64 libtasn1-6 amd64 4.18.0-4 [42.9 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main amd64 libgnutls30 amd64 3.7.2-2ubuntu1 [957 kB] Get:47 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 systemd-timesyncd amd64 249.5-2ubuntu1 [31.0 kB] Get:48 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 systemd-sysv amd64 249.5-2ubuntu1 [10.5 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/main amd64 libapparmor1 amd64 3.0.3-0ubuntu4 [37.9 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main amd64 libip4tc2 amd64 1.8.7-1ubuntu4 [19.8 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main amd64 libkmod2 amd64 28-1ubuntu5 [48.0 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main amd64 libpcre2-8-0 amd64 10.39-3 [220 kB] Get:53 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libselinux1 amd64 3.3-1build1 [74.5 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main amd64 libmount1 amd64 2.37.2-4ubuntu1 [122 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main amd64 libseccomp2 amd64 2.5.2-2ubuntu2 [48.3 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main amd64 login amd64 1:4.8.1-2ubuntu1 [188 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main amd64 util-linux amd64 2.37.2-4ubuntu1 [1063 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main amd64 mount amd64 2.37.2-4ubuntu1 [114 kB] Get:59 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 systemd amd64 249.5-2ubuntu1 [4542 kB] Get:60 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libsystemd0 amd64 249.5-2ubuntu1 [319 kB] Get:61 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libudev1 amd64 249.5-2ubuntu1 [78.0 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main amd64 libapt-pkg6.0 amd64 2.3.13 [904 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/main amd64 dpkg amd64 1.20.9ubuntu3 [1266 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/main amd64 dash amd64 0.5.11+git20210903+057cd650a4ed-3 [91.8 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main amd64 grep amd64 3.7-1 [156 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main amd64 libncurses6 amd64 6.3-1 [111 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main amd64 libncursesw6 amd64 6.3-1 [147 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main amd64 libtinfo6 amd64 6.3-1 [104 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main amd64 ncurses-bin amd64 6.3-1 [184 kB] Get:70 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 sed amd64 4.8-1 [188 kB] Get:71 http://ftpmaster.internal/ubuntu jammy/main amd64 ncurses-base all 6.3-1 [19.9 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main amd64 gpgv amd64 2.2.27-2ubuntu1 [137 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main amd64 apt amd64 2.3.13 [1387 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/main amd64 libsepol2 amd64 3.3-1 [281 kB] Get:75 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libsemanage-common all 3.3-1build1 [10.0 kB] Get:76 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libsemanage2 amd64 3.3-1build1 [92.4 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/main amd64 passwd amd64 1:4.8.1-2ubuntu1 [765 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/main amd64 libpam-modules-bin amd64 1.4.0-10ubuntu2 [37.6 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/main amd64 libpam-modules amd64 1.4.0-10ubuntu2 [280 kB] Get:80 http://ftpmaster.internal/ubuntu jammy/main amd64 logsave amd64 1.46.4-1ubuntu1 [10.9 kB] Get:81 http://ftpmaster.internal/ubuntu jammy/main amd64 libext2fs2 amd64 1.46.4-1ubuntu1 [209 kB] Get:82 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lto-disabled-list all 17 [12.1 kB] Get:103 http://ftpmaster.internal/ubuntu jammy/main amd64 gpg amd64 2.2.27-2ubuntu1 [518 kB] Get:104 http://ftpmaster.internal/ubuntu jammy/main amd64 gpgconf amd64 2.2.27-2ubuntu1 [93.9 kB] Get:105 http://ftpmaster.internal/ubuntu jammy/main amd64 gpg-agent amd64 2.2.27-2ubuntu1 [209 kB] Get:106 http://ftpmaster.internal/ubuntu jammy/main amd64 libgdbm-compat4 amd64 1.22-1 [6450 B] Get:107 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 linux-libc-dev amd64 5.15.0-13.13 [1273 kB] Get:108 http://ftpmaster.internal/ubuntu jammy/main amd64 lockfile-progs amd64 0.1.19 [10.0 kB] Get:109 http://ftpmaster.internal/ubuntu jammy/main amd64 pkgbinarymangler all 149 [32.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 84.2 MB in 5s (15.6 MB/s) (Reading database ... 13258 files and directories currently installed.) Preparing to unpack .../debconf_1.5.79_all.deb ... Unpacking debconf (1.5.79) over (1.5.77) ... Setting up debconf (1.5.79) ... (Reading database ... 13257 files and directories currently installed.) Preparing to unpack .../libpam0g_1.4.0-10ubuntu2_amd64.deb ... Unpacking libpam0g:amd64 (1.4.0-10ubuntu2) over (1.3.1-5ubuntu11) ... Setting up libpam0g:amd64 (1.4.0-10ubuntu2) ... Checking for services that may need to be restarted...Checking init scripts... Nothing to restart. (Reading database ... 13257 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.26-1_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.26-1) over (1:4.4.18-4ubuntu2) ... Preparing to unpack .../libcrypt1_1%3a4.4.26-1_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.26-1) over (1:4.4.18-4ubuntu2) ... Setting up libcrypt1:amd64 (1:4.4.26-1) ... (Reading database ... 13257 files and directories currently installed.) Preparing to unpack .../base-files_12ubuntu2_amd64.deb ... 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Setting up systemd (249.5-2ubuntu1) ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/resolved.conf ... Initializing machine ID from random generator. Setting up ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 7 added, 8 removed; done. Setting up systemd-timesyncd (249.5-2ubuntu1) ... Setting up libgdbm-compat4:amd64 (1.22-1) ... Setting up libgcc-11-dev:amd64 (11.2.0-12ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.37-10ubuntu1) ... Setting up systemd-sysv (249.5-2ubuntu1) ... Setting up binutils (2.37-10ubuntu1) ... Setting up dpkg-dev (1.20.9ubuntu3) ... Setting up libstdc++-11-dev:amd64 (11.2.0-12ubuntu1) ... Setting up gcc-11 (11.2.0-12ubuntu1) ... Setting up g++-11 (11.2.0-12ubuntu1) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... 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. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-22601457 amd64 jammy-proposed -c chroot:build-PACKAGEBUILD-22601457 --arch=amd64 --dist=jammy-proposed --nolog -A libstatgen_1.0.15-4.dsc Initiating build PACKAGEBUILD-22601457 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-163-generic #171-Ubuntu SMP Fri Nov 5 11:55:11 UTC 2021 x86_64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on lgw01-amd64-028.buildd +==============================================================================+ | libstatgen 1.0.15-4 (amd64) Wed, 08 Dec 2021 05:23:04 +0000 | +==============================================================================+ Package: libstatgen Version: 1.0.15-4 Source Version: 1.0.15-4 Distribution: jammy-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-22601457/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- libstatgen_1.0.15-4.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/libstatgen-M9OHpd/libstatgen-1.0.15' with '<>' I: NOTICE: Log filtering will replace 'build/libstatgen-M9OHpd' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-nab5BI/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-nab5BI/apt_archive ./ InRelease Get:2 copy:/<>/resolver-nab5BI/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-nab5BI/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-nab5BI/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-nab5BI/apt_archive ./ Packages [434 B] Fetched 1740 B in 0s (48.5 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libssl1.1 systemd-timesyncd Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 652 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-nab5BI/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [652 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 652 B in 0s (40.9 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 13453 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any-amd64 all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), doxygen, libssl-dev, zlib1g-dev, d-shlibs Filtered Build-Depends: debhelper-compat (= 13), doxygen, libssl-dev, zlib1g-dev, d-shlibs dpkg-deb: building package 'sbuild-build-depends-libstatgen-dummy' in '/<>/resolver-nab5BI/apt_archive/sbuild-build-depends-libstatgen-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-libstatgen-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-nab5BI/apt_archive ./ InRelease Get:2 copy:/<>/resolver-nab5BI/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-nab5BI/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-nab5BI/apt_archive ./ Sources [518 B] Get:5 copy:/<>/resolver-nab5BI/apt_archive ./ Packages [602 B] Fetched 2083 B in 0s (36.8 kB/s) Reading package lists... Reading package lists... Install libstatgen build dependencies (apt-based resolver) ---------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libssl1.1 systemd-timesyncd Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils d-shlibs debhelper debugedit dh-autoreconf dh-strip-nondeterminism doxygen dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libclang-cpp12 libclang1-12 libdebhelper-perl libdw1 libedit2 libelf1 libfile-stripnondeterminism-perl libicu67 libllvm12 libmagic-mgc libmagic1 libmd0 libpipeline1 libsigsegv2 libssl-dev libsub-override-perl libtool libuchardet0 libxapian30 libxml2 m4 man-db po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make doxygen-latex doxygen-doc doxygen-gui graphviz gettext-doc libasprintf-dev libgettextpo-dev groff libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk xapian-tools m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils d-shlibs debhelper debugedit dh-autoreconf dh-strip-nondeterminism doxygen dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libclang-cpp12 libclang1-12 libdebhelper-perl libdw1 libedit2 libelf1 libfile-stripnondeterminism-perl libicu67 libllvm12 libmagic-mgc libmagic1 libmd0 libpipeline1 libsigsegv2 libssl-dev libsub-override-perl libtool libuchardet0 libxapian30 libxml2 m4 man-db po-debconf sbuild-build-depends-libstatgen-dummy zlib1g-dev 0 upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 63.6 MB of archives. After this operation, 267 MB of additional disk space will be used. Get:1 copy:/<>/resolver-nab5BI/apt_archive ./ sbuild-build-depends-libstatgen-dummy 0.invalid.0 [690 B] Get:2 http://ftpmaster.internal/ubuntu jammy/main amd64 bsdextrautils amd64 2.37.2-4ubuntu1 [71.1 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main amd64 libuchardet0 amd64 0.0.7-1build1 [76.7 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main amd64 groff-base amd64 1.22.4-7 [956 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main amd64 libpipeline1 amd64 1.5.4-1 [23.6 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main amd64 man-db amd64 2.9.4-2build1 [1180 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main amd64 libmd0 amd64 1.0.4-1 [22.9 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main amd64 libbsd0 amd64 0.11.3-1ubuntu3 [44.7 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main amd64 libelf1 amd64 0.186-1 [51.4 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main amd64 libicu67 amd64 67.1-7ubuntu1 [10.1 MB] Get:11 http://ftpmaster.internal/ubuntu jammy/main amd64 libxml2 amd64 2.9.12+dfsg-5 [761 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main amd64 libmagic-mgc amd64 1:5.41-2 [257 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main amd64 libmagic1 amd64 1:5.41-2 [87.3 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main amd64 file amd64 1:5.41-2 [21.5 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main amd64 gettext-base amd64 0.21-4ubuntu3 [36.6 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main amd64 libedit2 amd64 3.1-20210910-1 [96.5 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main amd64 libsigsegv2 amd64 2.13-1ubuntu2 [14.6 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main amd64 m4 amd64 1.4.18-5ubuntu1 [199 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main amd64 autoconf all 2.71-2 [338 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main amd64 autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main amd64 automake all 1:1.16.5-1.1 [558 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main amd64 autopoint all 0.21-4ubuntu3 [422 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/universe amd64 d-shlibs all 0.104 [10.2 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main amd64 libdebhelper-perl all 13.5.2ubuntu1 [66.0 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main amd64 libtool all 2.4.6-15build1 [164 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main amd64 dh-autoreconf all 20 [16.1 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main amd64 libsub-override-perl all 0.09-2 [9532 B] Get:29 http://ftpmaster.internal/ubuntu jammy/main amd64 libfile-stripnondeterminism-perl all 1.12.1-1 [18.1 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main amd64 dh-strip-nondeterminism all 1.12.1-1 [5200 B] Get:31 http://ftpmaster.internal/ubuntu jammy/main amd64 libdw1 amd64 0.186-1 [251 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main amd64 debugedit amd64 1:5.0-3 [47.0 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main amd64 dwz amd64 0.14-1build1 [104 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main amd64 gettext amd64 0.21-4ubuntu3 [824 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main amd64 debhelper all 13.5.2ubuntu1 [926 kB] Get:38 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libllvm12 amd64 1:12.0.1-17 [21.3 MB] Get:39 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 libclang-cpp12 amd64 1:12.0.1-17 [10.8 MB] Get:40 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 libclang1-12 amd64 1:12.0.1-17 [6186 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/universe amd64 libxapian30 amd64 1.4.18-4 [701 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/universe amd64 doxygen amd64 1.9.1-2ubuntu1 [3942 kB] Get:43 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libssl-dev amd64 3.0.0-1ubuntu2 [2364 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2ubuntu7 [164 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 63.6 MB in 5s (13.8 MB/s) Selecting previously unselected package bsdextrautils. 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Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu7) ... Selecting previously unselected package sbuild-build-depends-libstatgen-dummy. Preparing to unpack .../43-sbuild-build-depends-libstatgen-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-libstatgen-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.4-1) ... Setting up libxapian30:amd64 (1.4.18-4) ... Setting up bsdextrautils (2.37.2-4ubuntu1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7ubuntu1) ... Setting up libmagic-mgc (1:5.41-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.5.2ubuntu1) ... Setting up libmagic1:amd64 (1:5.41-2) ... Setting up gettext-base (0.21-4ubuntu3) ... Setting up file (1:5.41-2) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libsigsegv2:amd64 (2.13-1ubuntu2) ... Setting up libssl-dev:amd64 (3.0.0-1ubuntu2) ... Setting up autopoint (0.21-4ubuntu3) ... Setting up d-shlibs (0.104) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu7) ... Setting up libmd0:amd64 (1.0.4-1) ... Setting up libuchardet0:amd64 (0.0.7-1build1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libbsd0:amd64 (0.11.3-1ubuntu3) ... Setting up libelf1:amd64 (0.186-1) ... Setting up libxml2:amd64 (2.9.12+dfsg-5) ... Setting up libfile-stripnondeterminism-perl (1.12.1-1) ... Setting up libdw1:amd64 (0.186-1) ... Setting up gettext (0.21-4ubuntu3) ... Setting up libtool (2.4.6-15build1) ... Setting up libedit2:amd64 (3.1-20210910-1) ... Setting up m4 (1.4.18-5ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libllvm12:amd64 (1:12.0.1-17) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.12.1-1) ... Setting up dwz (0.14-1build1) ... Setting up groff-base (1.22.4-7) ... Setting up debugedit (1:5.0-3) ... Setting up automake (1:1.16.5-1.1) ... 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 (2.9.4-2build1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libclang1-12 (1:12.0.1-17) ... Setting up dh-autoreconf (20) ... Setting up libclang-cpp12 (1:12.0.1-17) ... Setting up debhelper (13.5.2ubuntu1) ... Setting up doxygen (1.9.1-2ubuntu1) ... Setting up sbuild-build-depends-libstatgen-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-163-generic amd64 (x86_64) Toolchain package versions: binutils_2.37-10ubuntu1 dpkg-dev_1.20.9ubuntu3 g++-11_11.2.0-12ubuntu1 gcc-11_11.2.0-12ubuntu1 libc6-dev_2.34-0ubuntu3 libstdc++-11-dev_11.2.0-12ubuntu1 libstdc++6_11.2.0-12ubuntu1 linux-libc-dev_5.15.0-13.13 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu1 apt_2.3.13 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4ubuntu3 autotools-dev_20180224.1+nmu1 base-files_12ubuntu2 base-passwd_3.5.52 bash_5.1-5ubuntu1 binutils_2.37-10ubuntu1 binutils-common_2.37-10ubuntu1 binutils-x86-64-linux-gnu_2.37-10ubuntu1 bsdextrautils_2.37.2-4ubuntu1 bsdutils_1:2.37.2-4ubuntu1 build-essential_12.9ubuntu2 bzip2_1.0.8-5 ca-certificates_20211016 coreutils_8.32-4ubuntu3 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libuuid1_2.37.2-4ubuntu1 libxapian30_1.4.18-4 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2build1 libzstd1_1.4.8+dfsg-3 linux-libc-dev_5.15.0-13.13 lockfile-progs_0.1.19 login_1:4.8.1-2ubuntu1 logsave_1.46.4-1ubuntu1 lsb-base_11.1.0ubuntu3 lto-disabled-list_17 m4_1.4.18-5ubuntu1 make_4.3-4ubuntu2 man-db_2.9.4-2build1 mawk_1.3.4.20200120-2build1 mount_2.37.2-4ubuntu1 ncurses-base_6.3-1 ncurses-bin_6.3-1 openssl_3.0.0-1ubuntu2 optipng_0.7.7-2 passwd_1:4.8.1-2ubuntu1 patch_2.7.6-7build1 perl_5.32.1-3ubuntu3 perl-base_5.32.1-3ubuntu3 perl-modules-5.32_5.32.1-3ubuntu3 pinentry-curses_1.1.1-1build1 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.17-5ubuntu3 readline-common_8.1-2build1 rpcsvc-proto_1.4.2-0ubuntu5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-libstatgen-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 systemd_249.5-2ubuntu1 systemd-sysv_249.5-2ubuntu1 systemd-timesyncd_249.5-2ubuntu1 sysvinit-utils_2.96-7ubuntu2 tar_1.34+dfsg-1build2 tzdata_2021e-1ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_25ubuntu2 util-linux_2.37.2-4ubuntu1 xz-utils_5.2.5-2build1 zlib1g_1:1.2.11.dfsg-2ubuntu7 zlib1g-dev_1:1.2.11.dfsg-2ubuntu7 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Dec 7 22:05:49 2021 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./libstatgen_1.0.15-4.dsc dpkg-source: info: extracting libstatgen in /<> dpkg-source: info: unpacking libstatgen_1.0.15.orig.tar.gz dpkg-source: info: unpacking libstatgen_1.0.15-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Fix_compilation_flags.patch dpkg-source: info: applying spelling.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-22601457 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-22601457 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-22601457 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package libstatgen dpkg-buildpackage: info: source version 1.0.15-4 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j4 clean make[1]: Entering directory '/<>' make[2]: Entering directory '/<>/samtools' rm -f ../include/bgzf.h ../include/knetfile.h ../include/khash.h ../include/bam.h ar d ../libStatGen.a obj/bgzf.o obj/knetfile.o ar: creating ../libStatGen.a ranlib ../libStatGen.a ar d ../libStatGen_debug.a obj/debug/bgzf.o obj/debug/knetfile.o ar: creating ../libStatGen_debug.a ranlib ../libStatGen_debug.a ar d ../libStatGen_profile.a obj/profile/bgzf.o obj/profile/knetfile.o ar: creating ../libStatGen_profile.a ranlib ../libStatGen_profile.a rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ make[2]: Leaving directory '/<>/samtools' make[2]: Entering directory '/<>/general' rm -f ../include/BaseAsciiMap.h ../include/BaseQualityHelper.h ../include/BaseUtilities.h ../include/BasicHash.h ../include/BgzfFileType.h ../include/BgzfFileTypeRecovery.h ../include/CharBuffer.h ../include/Chromosome.h ../include/Cigar.h ../include/CigarRoller.h ../include/Error.h ../include/ErrorHandler.h ../include/FileType.h ../include/FortranFormat.h ../include/GenomeSequence.h ../include/GenotypeLists.h ../include/glfHandler.h ../include/GzipFileType.h ../include/GzipHeader.h ../include/Hash.h ../include/IndexBase.h ../include/Input.h ../include/InputFile.h ../include/IntArray.h ../include/IntHash.h ../include/LongLongCounter.h ../include/MapFunction.h ../include/MathMatrix.h ../include/MathVector.h ../include/MemoryAllocators.h ../include/MemoryInfo.h ../include/MemoryMapArray.h ../include/MemoryMap.h ../include/MiniDeflate.h ../include/NonOverlapRegions.h ../include/Parameters.h ../include/PedigreeAlleleFreq.h ../include/Pedigree.h ../include/PedigreeDescription.h ../include/PedigreeFamily.h ../include/PedigreeGlobals.h ../include/PedigreePerson.h ../include/PhoneHome.h ../include/QuickIndex.h ../include/Random.h ../include/ReferenceSequence.h ../include/SmithWaterman.h ../include/Sort.h ../include/STLUtilities.h ../include/StatGenStatus.h ../include/StringAlias.h ../include/StringArray.h ../include/StringBasics.h ../include/StringHash.h ../include/StringMap.h ../include/Tabix.h ../include/UncompressedFileType.h ../include/Constant.h ../include/CSG_MD5.h ../include/Generic.h ../include/GenomeSequenceHelpers.h ../include/GreedyTupleAligner.h ../include/InplaceMerge.h ../include/LongHash.h ../include/LongInt.h ../include/MathConstant.h ../include/PackedVector.h ../include/PedigreeAlleles.h ../include/Performance.h ../include/ReusableVector.h ../include/SimpleStats.h ../include/TrimSequence.h ../include/UnitTest.h ar d ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/PhoneHome.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o ranlib ../libStatGen.a ar d ../libStatGen_debug.a obj/debug/BaseAsciiMap.o obj/debug/BaseQualityHelper.o obj/debug/BaseUtilities.o obj/debug/BasicHash.o obj/debug/BgzfFileType.o obj/debug/BgzfFileTypeRecovery.o obj/debug/CharBuffer.o obj/debug/Chromosome.o obj/debug/Cigar.o obj/debug/CigarRoller.o obj/debug/Error.o obj/debug/ErrorHandler.o obj/debug/FileType.o obj/debug/FortranFormat.o obj/debug/GenomeSequence.o obj/debug/GenotypeLists.o obj/debug/glfHandler.o obj/debug/GzipFileType.o obj/debug/GzipHeader.o obj/debug/Hash.o obj/debug/IndexBase.o obj/debug/Input.o obj/debug/InputFile.o obj/debug/IntArray.o obj/debug/IntHash.o obj/debug/LongLongCounter.o obj/debug/MapFunction.o obj/debug/MathMatrix.o obj/debug/MathVector.o obj/debug/MemoryAllocators.o obj/debug/MemoryInfo.o obj/debug/MemoryMapArray.o obj/debug/MemoryMap.o obj/debug/MiniDeflate.o obj/debug/NonOverlapRegions.o obj/debug/Parameters.o obj/debug/PedigreeAlleleFreq.o obj/debug/Pedigree.o obj/debug/PedigreeDescription.o obj/debug/PedigreeFamily.o obj/debug/PedigreeGlobals.o obj/debug/PedigreePerson.o obj/debug/PhoneHome.o obj/debug/QuickIndex.o obj/debug/Random.o obj/debug/ReferenceSequence.o obj/debug/SmithWaterman.o obj/debug/Sort.o obj/debug/STLUtilities.o obj/debug/StatGenStatus.o obj/debug/StringAlias.o obj/debug/StringArray.o obj/debug/StringBasics.o obj/debug/StringHash.o obj/debug/StringMap.o obj/debug/Tabix.o obj/debug/UncompressedFileType.o obj/debug/PedigreeLoader.o obj/debug/PedigreeTrim.o obj/debug/PedigreeTwin.o ranlib ../libStatGen_debug.a ar d ../libStatGen_profile.a obj/profile/BaseAsciiMap.o obj/profile/BaseQualityHelper.o obj/profile/BaseUtilities.o obj/profile/BasicHash.o obj/profile/BgzfFileType.o obj/profile/BgzfFileTypeRecovery.o obj/profile/CharBuffer.o obj/profile/Chromosome.o obj/profile/Cigar.o obj/profile/CigarRoller.o obj/profile/Error.o obj/profile/ErrorHandler.o obj/profile/FileType.o obj/profile/FortranFormat.o obj/profile/GenomeSequence.o obj/profile/GenotypeLists.o obj/profile/glfHandler.o obj/profile/GzipFileType.o obj/profile/GzipHeader.o obj/profile/Hash.o obj/profile/IndexBase.o obj/profile/Input.o obj/profile/InputFile.o obj/profile/IntArray.o obj/profile/IntHash.o obj/profile/LongLongCounter.o obj/profile/MapFunction.o obj/profile/MathMatrix.o obj/profile/MathVector.o obj/profile/MemoryAllocators.o obj/profile/MemoryInfo.o obj/profile/MemoryMapArray.o obj/profile/MemoryMap.o obj/profile/MiniDeflate.o obj/profile/NonOverlapRegions.o obj/profile/Parameters.o obj/profile/PedigreeAlleleFreq.o obj/profile/Pedigree.o obj/profile/PedigreeDescription.o obj/profile/PedigreeFamily.o obj/profile/PedigreeGlobals.o obj/profile/PedigreePerson.o obj/profile/PhoneHome.o obj/profile/QuickIndex.o obj/profile/Random.o obj/profile/ReferenceSequence.o obj/profile/SmithWaterman.o obj/profile/Sort.o obj/profile/STLUtilities.o obj/profile/StatGenStatus.o obj/profile/StringAlias.o obj/profile/StringArray.o obj/profile/StringBasics.o obj/profile/StringHash.o obj/profile/StringMap.o obj/profile/Tabix.o obj/profile/UncompressedFileType.o obj/profile/PedigreeLoader.o obj/profile/PedigreeTrim.o obj/profile/PedigreeTwin.o ranlib ../libStatGen_profile.a rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ rm -rf obj inputFileTest *~ results/* rm -rf obj cigarRollerTest *~ results/* rm -rf obj memoryMapArrayTest *~ results/* rm -rf obj packedVectorTest *~ results/* rm -rf obj stringTest *~ results/* rm -rf obj referenceSequenceTest *~ results/* rm -rf obj baseUtilitiesTest *~ results/* rm -rf obj nonOverlapRegionsTest *~ results/* rm -rf obj trimSequence *~ results/* rm -rf obj reusableVectorTest *~ results/* # clean current directory rm -f *.o *~ rm -f phiX-bs.umfa phiX-cs.umfa gtest make[2]: Leaving directory '/<>/general' make[2]: Entering directory '/<>/fastq' make[2]: Entering directory '/<>/bam' make[2]: Entering directory '/<>/glf' rm -f ../include/FastQFile.h ../include/BaseCount.h ../include/BaseComposition.h ../include/FastQStatus.h make[2]: Entering directory '/<>/vcf' ar d ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o ranlib ../libStatGen.a ar d ../libStatGen_debug.a obj/debug/FastQFile.o obj/debug/BaseCount.o obj/debug/BaseComposition.o obj/debug/FastQStatus.o rm -f ../include/SamFileHeader.h ../include/SamFile.h ../include/GenericSamInterface.h ../include/SamInterface.h ../include/BamInterface.h ../include/SamRecord.h ../include/BamIndex.h ../include/SamHeaderHD.h ../include/SamHeaderPG.h ../include/SamHeaderRecord.h ../include/SamHeaderSQ.h ../include/SamHeaderRG.h ../include/SamHeaderTag.h ../include/SamValidation.h ../include/SamStatistics.h ../include/SamQuerySeqWithRefHelper.h ../include/SamFilter.h ../include/PileupElement.h ../include/PileupElementBaseQual.h ../include/SamReferenceInfo.h ../include/SamTags.h ../include/PosList.h ../include/CigarHelper.h ../include/SamRecordPool.h ../include/SamCoordOutput.h ../include/SamRecordHelper.h ../include/Pileup.h ../include/SamHelper.h ../include/SamFlag.h ../include/SamStatus.h ranlib ../libStatGen_debug.a ar d ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o rm -f ../include/VcfFile.h ../include/VcfFileReader.h ../include/VcfFileWriter.h ../include/VcfGenotypeField.h ../include/VcfGenotypeFormat.h ../include/VcfGenotypeSample.h ../include/VcfHeader.h ../include/VcfHelper.h ../include/VcfRecord.h ../include/VcfRecordField.h ../include/VcfRecordFilter.h ../include/VcfRecordGenotype.h ../include/VcfRecordInfo.h ../include/VcfSubsetSamples.h ../include/VcfRecordDiscardRules.h ar d ../libStatGen_profile.a obj/profile/FastQFile.o obj/profile/BaseCount.o obj/profile/BaseComposition.o obj/profile/FastQStatus.o ranlib ../libStatGen.a ranlib ../libStatGen_profile.a ar d ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o obj/VcfRecordDiscardRules.o rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ ranlib ../libStatGen.a ar d ../libStatGen_debug.a obj/debug/VcfFile.o obj/debug/VcfFileReader.o obj/debug/VcfFileWriter.o obj/debug/VcfGenotypeField.o obj/debug/VcfGenotypeFormat.o obj/debug/VcfGenotypeSample.o obj/debug/VcfHeader.o obj/debug/VcfHelper.o obj/debug/VcfRecord.o obj/debug/VcfRecordField.o obj/debug/VcfRecordFilter.o obj/debug/VcfRecordGenotype.o obj/debug/VcfRecordInfo.o obj/debug/VcfSubsetSamples.o obj/debug/VcfRecordDiscardRules.o ar d ../libStatGen_debug.a obj/debug/SamFileHeader.o obj/debug/SamFile.o obj/debug/GenericSamInterface.o obj/debug/SamInterface.o obj/debug/BamInterface.o obj/debug/SamRecord.o obj/debug/BamIndex.o obj/debug/SamHeaderHD.o obj/debug/SamHeaderPG.o obj/debug/SamHeaderRecord.o obj/debug/SamHeaderSQ.o obj/debug/SamHeaderRG.o obj/debug/SamHeaderTag.o obj/debug/SamValidation.o obj/debug/SamStatistics.o obj/debug/SamQuerySeqWithRefHelper.o obj/debug/SamFilter.o obj/debug/PileupElement.o obj/debug/PileupElementBaseQual.o obj/debug/SamReferenceInfo.o obj/debug/SamTags.o obj/debug/PosList.o obj/debug/CigarHelper.o obj/debug/SamRecordPool.o obj/debug/SamCoordOutput.o obj/debug/SamRecordHelper.o ranlib ../libStatGen_debug.a ranlib ../libStatGen_debug.a rm -f ../include/GlfException.h ../include/GlfFile.h ../include/GlfHeader.h ../include/GlfRecord.h ../include/GlfRefSection.h ../include/GlfStatus.h ar d ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o ranlib ../libStatGen.a ar d ../libStatGen_debug.a obj/debug/GlfException.o obj/debug/GlfFile.o obj/debug/GlfHeader.o obj/debug/GlfRecord.o obj/debug/GlfRefSection.o obj/debug/GlfStatus.o ranlib ../libStatGen_debug.a ar d ../libStatGen_profile.a obj/profile/SamFileHeader.o obj/profile/SamFile.o obj/profile/GenericSamInterface.o obj/profile/SamInterface.o obj/profile/BamInterface.o obj/profile/SamRecord.o obj/profile/BamIndex.o obj/profile/SamHeaderHD.o obj/profile/SamHeaderPG.o obj/profile/SamHeaderRecord.o obj/profile/SamHeaderSQ.o obj/profile/SamHeaderRG.o obj/profile/SamHeaderTag.o obj/profile/SamValidation.o obj/profile/SamStatistics.o obj/profile/SamQuerySeqWithRefHelper.o obj/profile/SamFilter.o obj/profile/PileupElement.o obj/profile/PileupElementBaseQual.o obj/profile/SamReferenceInfo.o obj/profile/SamTags.o obj/profile/PosList.o obj/profile/CigarHelper.o obj/profile/SamRecordPool.o obj/profile/SamCoordOutput.o obj/profile/SamRecordHelper.o ranlib ../libStatGen_profile.a ar d ../libStatGen_profile.a obj/profile/GlfException.o obj/profile/GlfFile.o obj/profile/GlfHeader.o obj/profile/GlfRecord.o obj/profile/GlfRefSection.o obj/profile/GlfStatus.o ranlib ../libStatGen_profile.a rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ rm -rf obj fastqTest *~ results/* ar d ../libStatGen_profile.a obj/profile/VcfFile.o obj/profile/VcfFileReader.o obj/profile/VcfFileWriter.o obj/profile/VcfGenotypeField.o obj/profile/VcfGenotypeFormat.o obj/profile/VcfGenotypeSample.o obj/profile/VcfHeader.o obj/profile/VcfHelper.o obj/profile/VcfRecord.o obj/profile/VcfRecordField.o obj/profile/VcfRecordFilter.o obj/profile/VcfRecordGenotype.o obj/profile/VcfRecordInfo.o obj/profile/VcfSubsetSamples.o obj/profile/VcfRecordDiscardRules.o make[2]: Leaving directory '/<>/fastq' ranlib ../libStatGen_profile.a rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ rm -rf obj samTest *~ results/* rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ rm -rf obj vcfTest *~ results/* make[2]: Leaving directory '/<>/bam' rm -rf obj glfTest *~ results/* make[2]: Leaving directory '/<>/vcf' make[2]: Leaving directory '/<>/glf' rm -f libStatGen.a rm -f libStatGen_debug.a rm -f libStatGen_profile.a make[1]: Leaving directory '/<>' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>' make[3]: Entering directory '/<>/samtools' ln -s ../samtools/bgzf.h ../include/bgzf.h ln -s ../samtools/knetfile.h ../include/knetfile.h ln -s ../samtools/khash.h ../include/khash.h ln -s ../samtools/bam.h ../include/bam.h mkdir -p obj gcc -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/bgzf.o -c bgzf.c gcc -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/knetfile.o -c knetfile.c ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/<>/samtools' make[3]: Entering directory '/<>/general' ln -s ../general/BaseAsciiMap.h ../include/BaseAsciiMap.h ln -s ../general/BaseQualityHelper.h ../include/BaseQualityHelper.h ln -s ../general/BaseUtilities.h ../include/BaseUtilities.h ln -s ../general/BasicHash.h ../include/BasicHash.h ln -s ../general/BgzfFileType.h ../include/BgzfFileType.h ln -s ../general/BgzfFileTypeRecovery.h ../include/BgzfFileTypeRecovery.h ln -s ../general/CharBuffer.h ../include/CharBuffer.h ln -s ../general/Chromosome.h ../include/Chromosome.h ln -s ../general/Cigar.h ../include/Cigar.h ln -s ../general/CigarRoller.h ../include/CigarRoller.h ln -s ../general/Error.h ../include/Error.h ln -s ../general/ErrorHandler.h ../include/ErrorHandler.h ln -s ../general/FileType.h ../include/FileType.h ln -s ../general/FortranFormat.h ../include/FortranFormat.h ln -s ../general/GenomeSequence.h ../include/GenomeSequence.h ln -s ../general/GenotypeLists.h ../include/GenotypeLists.h ln -s ../general/glfHandler.h ../include/glfHandler.h ln -s ../general/GzipFileType.h ../include/GzipFileType.h ln -s ../general/GzipHeader.h ../include/GzipHeader.h ln -s ../general/Hash.h ../include/Hash.h ln -s ../general/IndexBase.h ../include/IndexBase.h ln -s ../general/Input.h ../include/Input.h ln -s ../general/InputFile.h ../include/InputFile.h ln -s ../general/IntArray.h ../include/IntArray.h ln -s ../general/IntHash.h ../include/IntHash.h ln -s ../general/LongLongCounter.h ../include/LongLongCounter.h ln -s ../general/MapFunction.h ../include/MapFunction.h ln -s ../general/MathMatrix.h ../include/MathMatrix.h ln -s ../general/MathVector.h ../include/MathVector.h ln -s ../general/MemoryAllocators.h ../include/MemoryAllocators.h ln -s ../general/MemoryInfo.h ../include/MemoryInfo.h ln -s ../general/MemoryMapArray.h ../include/MemoryMapArray.h ln -s ../general/MemoryMap.h ../include/MemoryMap.h ln -s ../general/MiniDeflate.h ../include/MiniDeflate.h ln -s ../general/NonOverlapRegions.h ../include/NonOverlapRegions.h ln -s ../general/Parameters.h ../include/Parameters.h ln -s ../general/PedigreeAlleleFreq.h ../include/PedigreeAlleleFreq.h ln -s ../general/Pedigree.h ../include/Pedigree.h ln -s ../general/PedigreeDescription.h ../include/PedigreeDescription.h ln -s ../general/PedigreeFamily.h ../include/PedigreeFamily.h ln -s ../general/PedigreeGlobals.h ../include/PedigreeGlobals.h ln -s ../general/PedigreePerson.h ../include/PedigreePerson.h ln -s ../general/PhoneHome.h ../include/PhoneHome.h ln -s ../general/QuickIndex.h ../include/QuickIndex.h ln -s ../general/Random.h ../include/Random.h ln -s ../general/ReferenceSequence.h ../include/ReferenceSequence.h ln -s ../general/SmithWaterman.h ../include/SmithWaterman.h ln -s ../general/Sort.h ../include/Sort.h ln -s ../general/STLUtilities.h ../include/STLUtilities.h ln -s ../general/StatGenStatus.h ../include/StatGenStatus.h ln -s ../general/StringAlias.h ../include/StringAlias.h ln -s ../general/StringArray.h ../include/StringArray.h ln -s ../general/StringBasics.h ../include/StringBasics.h ln -s ../general/StringHash.h ../include/StringHash.h ln -s ../general/StringMap.h ../include/StringMap.h ln -s ../general/Tabix.h ../include/Tabix.h ln -s ../general/UncompressedFileType.h ../include/UncompressedFileType.h ln -s ../general/Constant.h ../include/Constant.h ln -s ../general/CSG_MD5.h ../include/CSG_MD5.h ln -s ../general/Generic.h ../include/Generic.h ln -s ../general/GenomeSequenceHelpers.h ../include/GenomeSequenceHelpers.h ln -s ../general/GreedyTupleAligner.h ../include/GreedyTupleAligner.h ln -s ../general/InplaceMerge.h ../include/InplaceMerge.h ln -s ../general/LongHash.h ../include/LongHash.h ln -s ../general/LongInt.h ../include/LongInt.h ln -s ../general/MathConstant.h ../include/MathConstant.h ln -s ../general/PackedVector.h ../include/PackedVector.h ln -s ../general/PedigreeAlleles.h ../include/PedigreeAlleles.h ln -s ../general/Performance.h ../include/Performance.h ln -s ../general/ReusableVector.h ../include/ReusableVector.h ln -s ../general/SimpleStats.h ../include/SimpleStats.h ln -s ../general/TrimSequence.h ../include/TrimSequence.h ln -s ../general/UnitTest.h ../include/UnitTest.h g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BgzfFileType.o -c BgzfFileType.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Error.o -c Error.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Input.o -c Input.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PhoneHome.o -c PhoneHome.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Random.o -c Random.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/PhoneHome.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/<>/general' make[3]: Entering directory '/<>/fastq' make[3]: Entering directory '/<>/bam' make[3]: Entering directory '/<>/vcf' make[3]: Entering directory '/<>/glf' ln -s ../fastq/FastQFile.h ../include/FastQFile.h ln -s ../fastq/BaseCount.h ../include/BaseCount.h ln -s ../fastq/BaseComposition.h ../include/BaseComposition.h ln -s ../fastq/FastQStatus.h ../include/FastQStatus.h mkdir -p obj ln -s ../bam/SamFileHeader.h ../include/SamFileHeader.h ln -s ../vcf/VcfFile.h ../include/VcfFile.h ln -s ../bam/SamFile.h ../include/SamFile.h ln -s ../bam/GenericSamInterface.h ../include/GenericSamInterface.h ln -s ../bam/SamInterface.h ../include/SamInterface.h ln -s ../glf/GlfException.h ../include/GlfException.h ln -s ../glf/GlfFile.h ../include/GlfFile.h g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\"" ln -s ../glf/GlfHeader.h ../include/GlfHeader.h ln -s ../glf/GlfRecord.h ../include/GlfRecord.h ln -s ../bam/BamInterface.h ../include/BamInterface.h ln -s ../vcf/VcfFileReader.h ../include/VcfFileReader.h ln -s ../vcf/VcfFileWriter.h ../include/VcfFileWriter.h ln -s ../vcf/VcfGenotypeField.h ../include/VcfGenotypeField.h ln -s ../vcf/VcfGenotypeFormat.h ../include/VcfGenotypeFormat.h ln -s ../glf/GlfRefSection.h ../include/GlfRefSection.h ln -s ../bam/SamRecord.h ../include/SamRecord.h ln -s ../glf/GlfStatus.h ../include/GlfStatus.h ln -s ../vcf/VcfGenotypeSample.h ../include/VcfGenotypeSample.h mkdir -p obj ln -s ../bam/BamIndex.h ../include/BamIndex.h ln -s ../vcf/VcfHeader.h ../include/VcfHeader.h ln -s ../bam/SamHeaderHD.h ../include/SamHeaderHD.h ln -s ../vcf/VcfHelper.h ../include/VcfHelper.h ln -s ../bam/SamHeaderPG.h ../include/SamHeaderPG.h ln -s ../bam/SamHeaderRecord.h ../include/SamHeaderRecord.h ln -s ../vcf/VcfRecord.h ../include/VcfRecord.h ln -s ../bam/SamHeaderSQ.h ../include/SamHeaderSQ.h ln -s ../vcf/VcfRecordField.h ../include/VcfRecordField.h g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\"" ln -s ../bam/SamHeaderRG.h ../include/SamHeaderRG.h ln -s ../vcf/VcfRecordFilter.h ../include/VcfRecordFilter.h ln -s ../vcf/VcfRecordGenotype.h ../include/VcfRecordGenotype.h ln -s ../bam/SamHeaderTag.h ../include/SamHeaderTag.h ln -s ../bam/SamValidation.h ../include/SamValidation.h ln -s ../bam/SamStatistics.h ../include/SamStatistics.h ln -s ../vcf/VcfRecordInfo.h ../include/VcfRecordInfo.h ln -s ../bam/SamQuerySeqWithRefHelper.h ../include/SamQuerySeqWithRefHelper.h ln -s ../bam/SamFilter.h ../include/SamFilter.h ln -s ../vcf/VcfSubsetSamples.h ../include/VcfSubsetSamples.h ln -s ../bam/PileupElement.h ../include/PileupElement.h ln -s ../vcf/VcfRecordDiscardRules.h ../include/VcfRecordDiscardRules.h ln -s ../bam/PileupElementBaseQual.h ../include/PileupElementBaseQual.h mkdir -p obj g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\"" ln -s ../bam/SamReferenceInfo.h ../include/SamReferenceInfo.h ln -s ../bam/SamTags.h ../include/SamTags.h ln -s ../bam/PosList.h ../include/PosList.h ln -s ../bam/CigarHelper.h ../include/CigarHelper.h ln -s ../bam/SamRecordPool.h ../include/SamRecordPool.h ln -s ../bam/SamCoordOutput.h ../include/SamCoordOutput.h ln -s ../bam/SamRecordHelper.h ../include/SamRecordHelper.h ln -s ../bam/Pileup.h ../include/Pileup.h ln -s ../bam/SamHelper.h ../include/SamHelper.h ln -s ../bam/SamFlag.h ../include/SamFlag.h ln -s ../bam/SamStatus.h ../include/SamStatus.h mkdir -p obj g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/<>/fastq' g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/<>/glf' g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordDiscardRules.o -c VcfRecordDiscardRules.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o obj/VcfRecordDiscardRules.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/<>/vcf' g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamReferenceInfo.o -c SamReferenceInfo.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamTags.o -c SamTags.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PosList.o -c PosList.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CigarHelper.o -c CigarHelper.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamRecordPool.o -c SamRecordPool.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamCoordOutput.o -c SamCoordOutput.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/<>/bam' make[2]: Leaving directory '/<>' # Build the shared library x86_64-linux-gnu-g++ -shared -o libStatGen.so.1 */obj/*.o -fPIC -Wl,-soname,libStatGen.so.1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now # Build doxygen doc doxygen warning: Tag 'DETAILS_AT_TOP' at line 163 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'SYMBOL_CACHE_SIZE' at line 296 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'SHOW_DIRECTORIES' at line 484 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'COLS_IN_ALPHA_INDEX' at line 755 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'HTML_ALIGN_MEMBERS' at line 810 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'USE_INLINE_TREES' at line 963 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'XML_SCHEMA' at line 1156 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'XML_DTD' at line 1162 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'PERL_PATH' at line 1327 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 1349 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: doxygen no longer ships with the FreeSans font. You may want to clear or change DOT_FONTNAME. Otherwise you run the risk that the wrong font is being used for dot generated graphs. Adding custom extension mapping: 'h' will be treated as language 'c++' Doxygen version used: 1.9.1 Notice: Output directory 'dox' does not exist. I have created it for you. Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching for files in directory /<>/include Searching for files in directory /<>/copyrights Searching for files in directory /<>/dox Searching for files in directory /<>/dox/html Searching for files in directory /<>/dox/man Searching INPUT for files to process... Searching for files in directory /<>/bam Searching for files in directory /<>/bam/examples Searching for files in directory /<>/bam/examples/pileup Searching for files in directory /<>/bam/examples/printRefPositions Searching for files in directory /<>/bam/examples/printRefPositions/expected Searching for files in directory /<>/bam/obj Searching for files in directory /<>/bam/test Searching for files in directory /<>/bam/test/expected Searching for files in directory /<>/bam/test/expected/noZlib Searching for files in directory /<>/bam/test/results Searching for files in directory /<>/bam/test/testFiles Searching for files in directory /<>/fastq Searching for files in directory /<>/fastq/obj Searching for files in directory /<>/fastq/test Searching for files in directory /<>/fastq/test/expectedResults Searching for files in directory /<>/general Searching for files in directory /<>/general/obj Searching for files in directory /<>/general/test Searching for files in directory /<>/general/test/baseUtilitiesTest Searching for files in directory /<>/general/test/cigar Searching for files in directory /<>/general/test/dbsnp Searching for files in directory /<>/general/test/dbsnp/expected Searching for files in directory /<>/general/test/dbsnp/testFiles Searching for files in directory /<>/general/test/inputFileTest Searching for files in directory /<>/general/test/inputFileTest/data Searching for files in directory /<>/general/test/inputFileTest/expected Searching for files in directory /<>/general/test/memoryMapArrayTest Searching for files in directory /<>/general/test/nonOverlapRegions Searching for files in directory /<>/general/test/nonOverlapRegions/results Searching for files in directory /<>/general/test/packedVectorTest Searching for files in directory /<>/general/test/referenceSequenceTest Searching for files in directory /<>/general/test/reusableVector Searching for files in directory /<>/general/test/string Searching for files in directory /<>/general/test/string/testFiles Searching for files in directory /<>/general/test/trimSequence Searching for files in directory /<>/glf Searching for files in directory /<>/glf/obj Searching for files in directory /<>/glf/test Searching for files in directory /<>/glf/test/results Searching for files in directory /<>/glf/test/testFiles Searching for files in directory /<>/samtools Searching for files in directory /<>/samtools/obj Searching for files in directory /<>/Makefiles Reading and parsing tag files Parsing files Preprocessing /<>/bam/BamIndex.cpp... Parsing file /<>/bam/BamIndex.cpp... Preprocessing /<>/bam/BamIndex.h... Parsing file /<>/bam/BamIndex.h... Preprocessing /<>/bam/BamInterface.cpp... Parsing file /<>/bam/BamInterface.cpp... Preprocessing /<>/bam/BamInterface.h... Parsing file /<>/bam/BamInterface.h... Preprocessing /<>/bam/CigarHelper.cpp... Parsing file /<>/bam/CigarHelper.cpp... Preprocessing /<>/bam/CigarHelper.h... Parsing file /<>/bam/CigarHelper.h... Preprocessing /<>/bam/examples/pileup/Main.cpp... Parsing file /<>/bam/examples/pileup/Main.cpp... Preprocessing /<>/bam/examples/printRefPositions/Main.cpp... Parsing file /<>/bam/examples/printRefPositions/Main.cpp... Preprocessing /<>/bam/examples/printRefPositions/PrintRefPositions.cpp... Parsing file /<>/bam/examples/printRefPositions/PrintRefPositions.cpp... Preprocessing /<>/bam/examples/printRefPositions/PrintRefPositions.h... Parsing file /<>/bam/examples/printRefPositions/PrintRefPositions.h... Preprocessing /<>/bam/GenericSamInterface.cpp... Parsing file /<>/bam/GenericSamInterface.cpp... Preprocessing /<>/bam/GenericSamInterface.h... Parsing file /<>/bam/GenericSamInterface.h... Preprocessing /<>/bam/Pileup.h... Parsing file /<>/bam/Pileup.h... Preprocessing /<>/bam/PileupElement.cpp... Parsing file /<>/bam/PileupElement.cpp... Preprocessing /<>/bam/PileupElement.h... Parsing file /<>/bam/PileupElement.h... Preprocessing /<>/bam/PileupElementBaseQual.cpp... Parsing file /<>/bam/PileupElementBaseQual.cpp... Preprocessing /<>/bam/PileupElementBaseQual.h... Parsing file /<>/bam/PileupElementBaseQual.h... Preprocessing /<>/bam/PosList.cpp... Parsing file /<>/bam/PosList.cpp... Preprocessing /<>/bam/PosList.h... Parsing file /<>/bam/PosList.h... Preprocessing /<>/bam/SamCoordOutput.cpp... Parsing file /<>/bam/SamCoordOutput.cpp... Preprocessing /<>/bam/SamCoordOutput.h... Parsing file /<>/bam/SamCoordOutput.h... Preprocessing /<>/bam/SamFile.cpp... Parsing file /<>/bam/SamFile.cpp... Preprocessing /<>/bam/SamFile.h... Parsing file /<>/bam/SamFile.h... Preprocessing /<>/bam/SamFileHeader.cpp... Parsing file /<>/bam/SamFileHeader.cpp... Preprocessing /<>/bam/SamFileHeader.h... Parsing file /<>/bam/SamFileHeader.h... Preprocessing /<>/bam/SamFilter.cpp... Parsing file /<>/bam/SamFilter.cpp... Preprocessing /<>/bam/SamFilter.h... Parsing file /<>/bam/SamFilter.h... Preprocessing /<>/bam/SamFlag.h... Parsing file /<>/bam/SamFlag.h... Preprocessing /<>/bam/SamHeaderHD.cpp... Parsing file /<>/bam/SamHeaderHD.cpp... Preprocessing /<>/bam/SamHeaderHD.h... Parsing file /<>/bam/SamHeaderHD.h... Preprocessing /<>/bam/SamHeaderPG.cpp... Parsing file /<>/bam/SamHeaderPG.cpp... Preprocessing /<>/bam/SamHeaderPG.h... Parsing file /<>/bam/SamHeaderPG.h... Preprocessing /<>/bam/SamHeaderRecord.cpp... Parsing file /<>/bam/SamHeaderRecord.cpp... Preprocessing /<>/bam/SamHeaderRecord.h... Parsing file /<>/bam/SamHeaderRecord.h... Preprocessing /<>/bam/SamHeaderRG.cpp... Parsing file /<>/bam/SamHeaderRG.cpp... Preprocessing /<>/bam/SamHeaderRG.h... Parsing file /<>/bam/SamHeaderRG.h... Preprocessing /<>/bam/SamHeaderSQ.cpp... Parsing file /<>/bam/SamHeaderSQ.cpp... Preprocessing /<>/bam/SamHeaderSQ.h... Parsing file /<>/bam/SamHeaderSQ.h... Preprocessing /<>/bam/SamHeaderTag.cpp... Parsing file /<>/bam/SamHeaderTag.cpp... Preprocessing /<>/bam/SamHeaderTag.h... Parsing file /<>/bam/SamHeaderTag.h... Preprocessing /<>/bam/SamHelper.h... Parsing file /<>/bam/SamHelper.h... Preprocessing /<>/bam/SamInterface.cpp... Parsing file /<>/bam/SamInterface.cpp... Preprocessing /<>/bam/SamInterface.h... Parsing file /<>/bam/SamInterface.h... Preprocessing /<>/bam/SamQuerySeqWithRefHelper.cpp... Parsing file /<>/bam/SamQuerySeqWithRefHelper.cpp... Preprocessing /<>/bam/SamQuerySeqWithRefHelper.h... Parsing file /<>/bam/SamQuerySeqWithRefHelper.h... Preprocessing /<>/bam/SamRecord.cpp... Parsing file /<>/bam/SamRecord.cpp... Preprocessing /<>/bam/SamRecord.h... Parsing file /<>/bam/SamRecord.h... Preprocessing /<>/bam/SamRecordHelper.cpp... Parsing file /<>/bam/SamRecordHelper.cpp... Preprocessing /<>/bam/SamRecordHelper.h... Parsing file /<>/bam/SamRecordHelper.h... Preprocessing /<>/bam/SamRecordPool.cpp... Parsing file /<>/bam/SamRecordPool.cpp... Preprocessing /<>/bam/SamRecordPool.h... Parsing file /<>/bam/SamRecordPool.h... Preprocessing /<>/bam/SamReferenceInfo.cpp... Parsing file /<>/bam/SamReferenceInfo.cpp... Preprocessing /<>/bam/SamReferenceInfo.h... Parsing file /<>/bam/SamReferenceInfo.h... Preprocessing /<>/bam/SamStatistics.cpp... Parsing file /<>/bam/SamStatistics.cpp... Preprocessing /<>/bam/SamStatistics.h... Parsing file /<>/bam/SamStatistics.h... Preprocessing /<>/bam/SamStatus.h... Parsing file /<>/bam/SamStatus.h... Preprocessing /<>/bam/SamTags.cpp... Parsing file /<>/bam/SamTags.cpp... Preprocessing /<>/bam/SamTags.h... Parsing file /<>/bam/SamTags.h... Preprocessing /<>/bam/SamValidation.cpp... Parsing file /<>/bam/SamValidation.cpp... Preprocessing /<>/bam/SamValidation.h... Parsing file /<>/bam/SamValidation.h... Preprocessing /<>/bam/test/BamIndexTest.cpp... Parsing file /<>/bam/test/BamIndexTest.cpp... Preprocessing /<>/bam/test/BamIndexTest.h... Parsing file /<>/bam/test/BamIndexTest.h... Preprocessing /<>/bam/test/Main.cpp... Parsing file /<>/bam/test/Main.cpp... Preprocessing /<>/bam/test/Modify.cpp... Parsing file /<>/bam/test/Modify.cpp... Preprocessing /<>/bam/test/Modify.h... Parsing file /<>/bam/test/Modify.h... Preprocessing /<>/bam/test/ModifyVar.cpp... Parsing file /<>/bam/test/ModifyVar.cpp... Preprocessing /<>/bam/test/ModifyVar.h... Parsing file /<>/bam/test/ModifyVar.h... Preprocessing /<>/bam/test/ReadFiles.cpp... Parsing file /<>/bam/test/ReadFiles.cpp... Preprocessing /<>/bam/test/ReadFiles.h... Parsing file /<>/bam/test/ReadFiles.h... Preprocessing /<>/bam/test/SamFileTest.cpp... Parsing file /<>/bam/test/SamFileTest.cpp... Preprocessing /<>/bam/test/SamFileTest.h... Parsing file /<>/bam/test/SamFileTest.h... Preprocessing /<>/bam/test/ShiftIndels.cpp... Parsing file /<>/bam/test/ShiftIndels.cpp... Preprocessing /<>/bam/test/ShiftIndels.h... Parsing file /<>/bam/test/ShiftIndels.h... Preprocessing /<>/bam/test/TestCigarHelper.cpp... Parsing file /<>/bam/test/TestCigarHelper.cpp... Preprocessing /<>/bam/test/TestCigarHelper.h... Parsing file /<>/bam/test/TestCigarHelper.h... Preprocessing /<>/bam/test/TestEquals.cpp... Parsing file /<>/bam/test/TestEquals.cpp... Preprocessing /<>/bam/test/TestEquals.h... Parsing file /<>/bam/test/TestEquals.h... Preprocessing /<>/bam/test/TestFilter.cpp... Parsing file /<>/bam/test/TestFilter.cpp... Preprocessing /<>/bam/test/TestFilter.h... Parsing file /<>/bam/test/TestFilter.h... Preprocessing /<>/bam/test/TestPileup.cpp... Parsing file /<>/bam/test/TestPileup.cpp... Preprocessing /<>/bam/test/TestPileup.h... Parsing file /<>/bam/test/TestPileup.h... Preprocessing /<>/bam/test/TestPosList.cpp... Parsing file /<>/bam/test/TestPosList.cpp... Preprocessing /<>/bam/test/TestPosList.h... Parsing file /<>/bam/test/TestPosList.h... Preprocessing /<>/bam/test/TestSamCoordOutput.cpp... Parsing file /<>/bam/test/TestSamCoordOutput.cpp... Preprocessing /<>/bam/test/TestSamCoordOutput.h... Parsing file /<>/bam/test/TestSamCoordOutput.h... Preprocessing /<>/bam/test/TestSamRecordHelper.cpp... Parsing file /<>/bam/test/TestSamRecordHelper.cpp... Preprocessing /<>/bam/test/TestSamRecordHelper.h... Parsing file /<>/bam/test/TestSamRecordHelper.h... Preprocessing /<>/bam/test/TestSamRecordPool.cpp... Parsing file /<>/bam/test/TestSamRecordPool.cpp... Preprocessing /<>/bam/test/TestSamRecordPool.h... Parsing file /<>/bam/test/TestSamRecordPool.h... Preprocessing /<>/bam/test/TestValidate.cpp... Parsing file /<>/bam/test/TestValidate.cpp... Preprocessing /<>/bam/test/TestValidate.h... Parsing file /<>/bam/test/TestValidate.h... Preprocessing /<>/bam/test/ValidationTest.cpp... Parsing file /<>/bam/test/ValidationTest.cpp... Preprocessing /<>/bam/test/ValidationTest.h... Parsing file /<>/bam/test/ValidationTest.h... Preprocessing /<>/bam/test/WriteFiles.cpp... Parsing file /<>/bam/test/WriteFiles.cpp... Preprocessing /<>/bam/test/WriteFiles.h... Parsing file /<>/bam/test/WriteFiles.h... Preprocessing /<>/fastq/BaseComposition.cpp... Parsing file /<>/fastq/BaseComposition.cpp... Preprocessing /<>/fastq/BaseComposition.h... Parsing file /<>/fastq/BaseComposition.h... Preprocessing /<>/fastq/BaseCount.cpp... Parsing file /<>/fastq/BaseCount.cpp... Preprocessing /<>/fastq/BaseCount.h... Parsing file /<>/fastq/BaseCount.h... Preprocessing /<>/fastq/FastQFile.cpp... Parsing file /<>/fastq/FastQFile.cpp... Preprocessing /<>/fastq/FastQFile.h... Parsing file /<>/fastq/FastQFile.h... Preprocessing /<>/fastq/FastQStatus.cpp... Parsing file /<>/fastq/FastQStatus.cpp... Preprocessing /<>/fastq/FastQStatus.h... Parsing file /<>/fastq/FastQStatus.h... Preprocessing /<>/fastq/test/FastQFileTest.cpp... Parsing file /<>/fastq/test/FastQFileTest.cpp... Preprocessing /<>/general/BaseAsciiMap.cpp... Parsing file /<>/general/BaseAsciiMap.cpp... Preprocessing /<>/general/BaseAsciiMap.h... Parsing file /<>/general/BaseAsciiMap.h... Preprocessing /<>/general/BaseQualityHelper.cpp... Parsing file /<>/general/BaseQualityHelper.cpp... Preprocessing /<>/general/BaseQualityHelper.h... Parsing file /<>/general/BaseQualityHelper.h... Preprocessing /<>/general/BaseUtilities.cpp... Parsing file /<>/general/BaseUtilities.cpp... Preprocessing /<>/general/BaseUtilities.h... Parsing file /<>/general/BaseUtilities.h... Preprocessing /<>/general/BasicHash.cpp... Parsing file /<>/general/BasicHash.cpp... Preprocessing /<>/general/BasicHash.h... Parsing file /<>/general/BasicHash.h... Preprocessing /<>/general/BgzfFileType.cpp... Parsing file /<>/general/BgzfFileType.cpp... Preprocessing /<>/general/BgzfFileType.h... Parsing file /<>/general/BgzfFileType.h... Preprocessing /<>/general/BgzfFileTypeRecovery.cpp... Parsing file /<>/general/BgzfFileTypeRecovery.cpp... Preprocessing /<>/general/BgzfFileTypeRecovery.h... Parsing file /<>/general/BgzfFileTypeRecovery.h... Preprocessing /<>/general/CharBuffer.cpp... Parsing file /<>/general/CharBuffer.cpp... Preprocessing /<>/general/CharBuffer.h... Parsing file /<>/general/CharBuffer.h... Preprocessing /<>/general/Chromosome.cpp... Parsing file /<>/general/Chromosome.cpp... Preprocessing /<>/general/Chromosome.h... Parsing file /<>/general/Chromosome.h... Preprocessing /<>/general/Cigar.cpp... Parsing file /<>/general/Cigar.cpp... Preprocessing /<>/general/Cigar.h... Parsing file /<>/general/Cigar.h... Preprocessing /<>/general/CigarRoller.cpp... Parsing file /<>/general/CigarRoller.cpp... Preprocessing /<>/general/CigarRoller.h... Parsing file /<>/general/CigarRoller.h... Preprocessing /<>/general/Constant.h... Parsing file /<>/general/Constant.h... Preprocessing /<>/general/CSG_MD5.h... Parsing file /<>/general/CSG_MD5.h... Preprocessing /<>/general/Error.cpp... Parsing file /<>/general/Error.cpp... Preprocessing /<>/general/Error.h... Parsing file /<>/general/Error.h... Preprocessing /<>/general/ErrorHandler.cpp... Parsing file /<>/general/ErrorHandler.cpp... Preprocessing /<>/general/ErrorHandler.h... Parsing file /<>/general/ErrorHandler.h... Preprocessing /<>/general/FileType.cpp... Parsing file /<>/general/FileType.cpp... Preprocessing /<>/general/FileType.h... Parsing file /<>/general/FileType.h... Preprocessing /<>/general/FortranFormat.cpp... Parsing file /<>/general/FortranFormat.cpp... Preprocessing /<>/general/FortranFormat.h... Parsing file /<>/general/FortranFormat.h... Preprocessing /<>/general/Generic.cpp... Parsing file /<>/general/Generic.cpp... Preprocessing /<>/general/Generic.h... Parsing file /<>/general/Generic.h... Preprocessing /<>/general/GenomeSequence.cpp... Parsing file /<>/general/GenomeSequence.cpp... Preprocessing /<>/general/GenomeSequence.h... Parsing file /<>/general/GenomeSequence.h... Preprocessing /<>/general/GenomeSequenceHelpers.h... Parsing file /<>/general/GenomeSequenceHelpers.h... Preprocessing /<>/general/GenotypeLists.cpp... Parsing file /<>/general/GenotypeLists.cpp... Preprocessing /<>/general/GenotypeLists.h... Parsing file /<>/general/GenotypeLists.h... Preprocessing /<>/general/glfHandler.cpp... Parsing file /<>/general/glfHandler.cpp... Preprocessing /<>/general/glfHandler.h... Parsing file /<>/general/glfHandler.h... Preprocessing /<>/general/GreedyTupleAligner.h... Parsing file /<>/general/GreedyTupleAligner.h... Preprocessing /<>/general/GzipFileType.cpp... Parsing file /<>/general/GzipFileType.cpp... Preprocessing /<>/general/GzipFileType.h... Parsing file /<>/general/GzipFileType.h... Preprocessing /<>/general/GzipHeader.cpp... Parsing file /<>/general/GzipHeader.cpp... Preprocessing /<>/general/GzipHeader.h... Parsing file /<>/general/GzipHeader.h... Preprocessing /<>/general/Hash.cpp... Parsing file /<>/general/Hash.cpp... Preprocessing /<>/general/Hash.h... Parsing file /<>/general/Hash.h... Preprocessing /<>/general/IndexBase.cpp... Parsing file /<>/general/IndexBase.cpp... Preprocessing /<>/general/IndexBase.h... Parsing file /<>/general/IndexBase.h... Preprocessing /<>/general/InplaceMerge.cpp... Parsing file /<>/general/InplaceMerge.cpp... Preprocessing /<>/general/InplaceMerge.h... Parsing file /<>/general/InplaceMerge.h... Preprocessing /<>/general/Input.cpp... Parsing file /<>/general/Input.cpp... Preprocessing /<>/general/Input.h... Parsing file /<>/general/Input.h... Preprocessing /<>/general/InputFile.cpp... Parsing file /<>/general/InputFile.cpp... Preprocessing /<>/general/InputFile.h... Parsing file /<>/general/InputFile.h... Preprocessing /<>/general/IntArray.cpp... Parsing file /<>/general/IntArray.cpp... Preprocessing /<>/general/IntArray.h... Parsing file /<>/general/IntArray.h... Preprocessing /<>/general/IntHash.cpp... Parsing file /<>/general/IntHash.cpp... Preprocessing /<>/general/IntHash.h... Parsing file /<>/general/IntHash.h... Preprocessing /<>/general/LongHash.h... Parsing file /<>/general/LongHash.h... Preprocessing /<>/general/LongInt.h... Parsing file /<>/general/LongInt.h... Preprocessing /<>/general/LongLongCounter.cpp... Parsing file /<>/general/LongLongCounter.cpp... Preprocessing /<>/general/LongLongCounter.h... Parsing file /<>/general/LongLongCounter.h... Preprocessing /<>/general/MapFunction.cpp... Parsing file /<>/general/MapFunction.cpp... Preprocessing /<>/general/MapFunction.h... Parsing file /<>/general/MapFunction.h... Preprocessing /<>/general/MathConstant.h... Parsing file /<>/general/MathConstant.h... Preprocessing /<>/general/MathMatrix.cpp... Parsing file /<>/general/MathMatrix.cpp... Preprocessing /<>/general/MathMatrix.h... Parsing file /<>/general/MathMatrix.h... Preprocessing /<>/general/MathVector.cpp... Parsing file /<>/general/MathVector.cpp... Preprocessing /<>/general/MathVector.h... Parsing file /<>/general/MathVector.h... Preprocessing /<>/general/MemoryAllocators.cpp... Parsing file /<>/general/MemoryAllocators.cpp... Preprocessing /<>/general/MemoryAllocators.h... Parsing file /<>/general/MemoryAllocators.h... Preprocessing /<>/general/MemoryInfo.cpp... Parsing file /<>/general/MemoryInfo.cpp... Preprocessing /<>/general/MemoryInfo.h... Parsing file /<>/general/MemoryInfo.h... Preprocessing /<>/general/MemoryMap.cpp... Parsing file /<>/general/MemoryMap.cpp... Preprocessing /<>/general/MemoryMap.h... Parsing file /<>/general/MemoryMap.h... Preprocessing /<>/general/MemoryMapArray.cpp... Parsing file /<>/general/MemoryMapArray.cpp... Preprocessing /<>/general/MemoryMapArray.h... Parsing file /<>/general/MemoryMapArray.h... Preprocessing /<>/general/MiniDeflate.cpp... Parsing file /<>/general/MiniDeflate.cpp... Preprocessing /<>/general/MiniDeflate.h... Parsing file /<>/general/MiniDeflate.h... Preprocessing /<>/general/NonOverlapRegions.cpp... Parsing file /<>/general/NonOverlapRegions.cpp... Preprocessing /<>/general/NonOverlapRegions.h... Parsing file /<>/general/NonOverlapRegions.h... Preprocessing /<>/general/PackedVector.h... Parsing file /<>/general/PackedVector.h... Preprocessing /<>/general/Parameters.cpp... Parsing file /<>/general/Parameters.cpp... Preprocessing /<>/general/Parameters.h... Parsing file /<>/general/Parameters.h... Preprocessing /<>/general/Pedigree.cpp... Parsing file /<>/general/Pedigree.cpp... Preprocessing /<>/general/Pedigree.h... Parsing file /<>/general/Pedigree.h... Preprocessing /<>/general/PedigreeAlleleFreq.cpp... Parsing file /<>/general/PedigreeAlleleFreq.cpp... Preprocessing /<>/general/PedigreeAlleleFreq.h... Parsing file /<>/general/PedigreeAlleleFreq.h... Preprocessing /<>/general/PedigreeAlleles.h... Parsing file /<>/general/PedigreeAlleles.h... Preprocessing /<>/general/PedigreeDescription.cpp... Parsing file /<>/general/PedigreeDescription.cpp... Preprocessing /<>/general/PedigreeDescription.h... Parsing file /<>/general/PedigreeDescription.h... Preprocessing /<>/general/PedigreeFamily.cpp... Parsing file /<>/general/PedigreeFamily.cpp... Preprocessing /<>/general/PedigreeFamily.h... Parsing file /<>/general/PedigreeFamily.h... Preprocessing /<>/general/PedigreeGlobals.cpp... Parsing file /<>/general/PedigreeGlobals.cpp... Preprocessing /<>/general/PedigreeGlobals.h... Parsing file /<>/general/PedigreeGlobals.h... Preprocessing /<>/general/PedigreeLoader.cpp... Parsing file /<>/general/PedigreeLoader.cpp... Preprocessing /<>/general/PedigreePerson.cpp... Parsing file /<>/general/PedigreePerson.cpp... Preprocessing /<>/general/PedigreePerson.h... Parsing file /<>/general/PedigreePerson.h... Preprocessing /<>/general/PedigreeTrim.cpp... Parsing file /<>/general/PedigreeTrim.cpp... Preprocessing /<>/general/PedigreeTwin.cpp... Parsing file /<>/general/PedigreeTwin.cpp... Preprocessing /<>/general/Performance.h... Parsing file /<>/general/Performance.h... Preprocessing /<>/general/PhoneHome.cpp... Parsing file /<>/general/PhoneHome.cpp... Preprocessing /<>/general/PhoneHome.h... Parsing file /<>/general/PhoneHome.h... Preprocessing /<>/general/QuickIndex.cpp... Parsing file /<>/general/QuickIndex.cpp... Preprocessing /<>/general/QuickIndex.h... Parsing file /<>/general/QuickIndex.h... Preprocessing /<>/general/Random.cpp... Parsing file /<>/general/Random.cpp... Preprocessing /<>/general/Random.h... Parsing file /<>/general/Random.h... Preprocessing /<>/general/ReferenceSequence.cpp... Parsing file /<>/general/ReferenceSequence.cpp... Preprocessing /<>/general/ReferenceSequence.h... Parsing file /<>/general/ReferenceSequence.h... Preprocessing /<>/general/ReusableVector.h... Parsing file /<>/general/ReusableVector.h... Preprocessing /<>/general/SimpleStats.h... Parsing file /<>/general/SimpleStats.h... Preprocessing /<>/general/SmithWaterman.cpp... Parsing file /<>/general/SmithWaterman.cpp... Preprocessing /<>/general/SmithWaterman.h... Parsing file /<>/general/SmithWaterman.h... Preprocessing /<>/general/Sort.cpp... Parsing file /<>/general/Sort.cpp... Preprocessing /<>/general/Sort.h... Parsing file /<>/general/Sort.h... Preprocessing /<>/general/StatGenStatus.cpp... Parsing file /<>/general/StatGenStatus.cpp... Preprocessing /<>/general/StatGenStatus.h... Parsing file /<>/general/StatGenStatus.h... Preprocessing /<>/general/STLUtilities.cpp... Parsing file /<>/general/STLUtilities.cpp... Preprocessing /<>/general/STLUtilities.h... Parsing file /<>/general/STLUtilities.h... Preprocessing /<>/general/String.cpp... Parsing file /<>/general/String.cpp... Preprocessing /<>/general/StringAlias.cpp... Parsing file /<>/general/StringAlias.cpp... Preprocessing /<>/general/StringAlias.h... Parsing file /<>/general/StringAlias.h... Preprocessing /<>/general/StringArray.cpp... Parsing file /<>/general/StringArray.cpp... Preprocessing /<>/general/StringArray.h... Parsing file /<>/general/StringArray.h... Preprocessing /<>/general/StringBasics.cpp... Parsing file /<>/general/StringBasics.cpp... Preprocessing /<>/general/StringBasics.h... Parsing file /<>/general/StringBasics.h... Preprocessing /<>/general/StringHash.cpp... Parsing file /<>/general/StringHash.cpp... Preprocessing /<>/general/StringHash.h... Parsing file /<>/general/StringHash.h... Preprocessing /<>/general/StringMap.cpp... Parsing file /<>/general/StringMap.cpp... Preprocessing /<>/general/StringMap.h... Parsing file /<>/general/StringMap.h... Preprocessing /<>/general/Tabix.cpp... Parsing file /<>/general/Tabix.cpp... Preprocessing /<>/general/Tabix.h... Parsing file /<>/general/Tabix.h... Preprocessing /<>/general/test/baseUtilitiesTest/BaseUtilitiesTest.cpp... Parsing file /<>/general/test/baseUtilitiesTest/BaseUtilitiesTest.cpp... Preprocessing /<>/general/test/baseUtilitiesTest/BaseUtilitiesTest.h... Parsing file /<>/general/test/baseUtilitiesTest/BaseUtilitiesTest.h... Preprocessing /<>/general/test/Chromosome_test.cpp... Parsing file /<>/general/test/Chromosome_test.cpp... Preprocessing /<>/general/test/cigar/CigarRollerTest.cpp... Parsing file /<>/general/test/cigar/CigarRollerTest.cpp... Preprocessing /<>/general/test/cigar/CigarRollerTest.h... Parsing file /<>/general/test/cigar/CigarRollerTest.h... Preprocessing /<>/general/test/dbsnp/Main.cpp... Parsing file /<>/general/test/dbsnp/Main.cpp... Preprocessing /<>/general/test/GenomeSequence_test.cpp... Parsing file /<>/general/test/GenomeSequence_test.cpp... Preprocessing /<>/general/test/GreedyTupleAligner_test.cpp... Parsing file /<>/general/test/GreedyTupleAligner_test.cpp... Preprocessing /<>/general/test/gtest.cpp... Parsing file /<>/general/test/gtest.cpp... Preprocessing /<>/general/test/inputFileTest/InputFileTest.cpp... Parsing file /<>/general/test/inputFileTest/InputFileTest.cpp... Preprocessing /<>/general/test/inputFileTest/InputFileTest.h... Parsing file /<>/general/test/inputFileTest/InputFileTest.h... Preprocessing /<>/general/test/memoryMapArrayTest/MemoryMapArrayTest.cpp... Parsing file /<>/general/test/memoryMapArrayTest/MemoryMapArrayTest.cpp... Preprocessing /<>/general/test/memoryMapArrayTest/MemoryMapArrayTest.h... Parsing file /<>/general/test/memoryMapArrayTest/MemoryMapArrayTest.h... Preprocessing /<>/general/test/nonOverlapRegions/NonOverlapRegionsTest.cpp... Parsing file /<>/general/test/nonOverlapRegions/NonOverlapRegionsTest.cpp... Preprocessing /<>/general/test/nonOverlapRegions/NonOverlapRegionsTest.h... Parsing file /<>/general/test/nonOverlapRegions/NonOverlapRegionsTest.h... Preprocessing /<>/general/test/packedVectorTest/PackedVectorTest.cpp... Parsing file /<>/general/test/packedVectorTest/PackedVectorTest.cpp... Preprocessing /<>/general/test/packedVectorTest/PackedVectorTest.h... Parsing file /<>/general/test/packedVectorTest/PackedVectorTest.h... Preprocessing /<>/general/test/referenceSequenceTest/ReferenceSequenceTest.cpp... Parsing file /<>/general/test/referenceSequenceTest/ReferenceSequenceTest.cpp... Preprocessing /<>/general/test/referenceSequenceTest/ReferenceSequenceTest.h... Parsing file /<>/general/test/referenceSequenceTest/ReferenceSequenceTest.h... Preprocessing /<>/general/test/reusableVector/ReusableVectorTest.cpp... Parsing file /<>/general/test/reusableVector/ReusableVectorTest.cpp... Preprocessing /<>/general/test/reusableVector/ReusableVectorTest.h... Parsing file /<>/general/test/reusableVector/ReusableVectorTest.h... Preprocessing /<>/general/test/STLUtilities_test.cpp... Parsing file /<>/general/test/STLUtilities_test.cpp... Preprocessing /<>/general/test/string/StringTest.cpp... Parsing file /<>/general/test/string/StringTest.cpp... Preprocessing /<>/general/test/string/StringTest.h... Parsing file /<>/general/test/string/StringTest.h... Preprocessing /<>/general/test/trimSequence/TrimSequence.cpp... Parsing file /<>/general/test/trimSequence/TrimSequence.cpp... Preprocessing /<>/general/test/TrimSequence_test.cpp... Parsing file /<>/general/test/TrimSequence_test.cpp... Preprocessing /<>/general/TrimSequence.h... Parsing file /<>/general/TrimSequence.h... Preprocessing /<>/general/UncompressedFileType.cpp... Parsing file /<>/general/UncompressedFileType.cpp... Preprocessing /<>/general/UncompressedFileType.h... Parsing file /<>/general/UncompressedFileType.h... Preprocessing /<>/general/UnitTest.h... Parsing file /<>/general/UnitTest.h... Preprocessing /<>/glf/GlfException.cpp... Parsing file /<>/glf/GlfException.cpp... Preprocessing /<>/glf/GlfException.h... Parsing file /<>/glf/GlfException.h... Preprocessing /<>/glf/GlfFile.cpp... Parsing file /<>/glf/GlfFile.cpp... Preprocessing /<>/glf/GlfFile.h... Parsing file /<>/glf/GlfFile.h... Preprocessing /<>/glf/GlfHeader.cpp... Parsing file /<>/glf/GlfHeader.cpp... Preprocessing /<>/glf/GlfHeader.h... Parsing file /<>/glf/GlfHeader.h... Preprocessing /<>/glf/GlfRecord.cpp... Parsing file /<>/glf/GlfRecord.cpp... Preprocessing /<>/glf/GlfRecord.h... Parsing file /<>/glf/GlfRecord.h... Preprocessing /<>/glf/GlfRefSection.cpp... Parsing file /<>/glf/GlfRefSection.cpp... Preprocessing /<>/glf/GlfRefSection.h... Parsing file /<>/glf/GlfRefSection.h... Preprocessing /<>/glf/GlfStatus.cpp... Parsing file /<>/glf/GlfStatus.cpp... Preprocessing /<>/glf/GlfStatus.h... Parsing file /<>/glf/GlfStatus.h... Preprocessing /<>/glf/test/Main.cpp... Parsing file /<>/glf/test/Main.cpp... Preprocessing /<>/glf/test/ReadFiles.cpp... Parsing file /<>/glf/test/ReadFiles.cpp... Preprocessing /<>/glf/test/ReadFiles.h... Parsing file /<>/glf/test/ReadFiles.h... Preprocessing /<>/glf/test/Validate.cpp... Parsing file /<>/glf/test/Validate.cpp... Preprocessing /<>/glf/test/Validate.h... Parsing file /<>/glf/test/Validate.h... Preprocessing /<>/glf/test/WriteFiles.cpp... Parsing file /<>/glf/test/WriteFiles.cpp... Preprocessing /<>/glf/test/WriteFiles.h... Parsing file /<>/glf/test/WriteFiles.h... Preprocessing /<>/samtools/bam.h... Parsing file /<>/samtools/bam.h... Preprocessing /<>/samtools/bgzf.c... Parsing file /<>/samtools/bgzf.c... Preprocessing /<>/samtools/bgzf.h... Parsing file /<>/samtools/bgzf.h... Preprocessing /<>/samtools/khash.h... Parsing file /<>/samtools/khash.h... Preprocessing /<>/samtools/knetfile.c... Parsing file /<>/samtools/knetfile.c... Preprocessing /<>/samtools/knetfile.h... Parsing file /<>/samtools/knetfile.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Computing nesting relations for classes... Associating documentation with classes... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file bam/BamIndex.cpp... Generating code for file bam/BamIndex.h... Generating code for file bam/BamInterface.cpp... Generating code for file bam/BamInterface.h... Generating code for file bam/CigarHelper.cpp... Generating code for file bam/CigarHelper.h... Generating code for file bam/examples/pileup/Main.cpp... Generating code for file bam/examples/printRefPositions/Main.cpp... Generating code for file bam/test/Main.cpp... Generating code for file general/test/dbsnp/Main.cpp... Generating code for file glf/test/Main.cpp... Generating code for file bam/examples/printRefPositions/PrintRefPositions.cpp... Generating code for file bam/examples/printRefPositions/PrintRefPositions.h... Generating code for file bam/GenericSamInterface.cpp... Generating code for file bam/GenericSamInterface.h... Generating code for file bam/Pileup.h... Generating code for file bam/PileupElement.cpp... Generating code for file bam/PileupElement.h... Generating code for file bam/PileupElementBaseQual.cpp... Generating code for file bam/PileupElementBaseQual.h... Generating code for file bam/PosList.cpp... Generating code for file bam/PosList.h... Generating code for file bam/SamCoordOutput.cpp... Generating code for file bam/SamCoordOutput.h... Generating code for file bam/SamFile.cpp... Generating code for file bam/SamFile.h... Generating code for file bam/SamFileHeader.cpp... Generating code for file bam/SamFileHeader.h... Generating code for file bam/SamFilter.cpp... Generating code for file bam/SamFilter.h... Generating code for file bam/SamFlag.h... Generating code for file bam/SamHeaderHD.cpp... Generating code for file bam/SamHeaderHD.h... Generating code for file bam/SamHeaderPG.cpp... Generating code for file bam/SamHeaderPG.h... Generating code for file bam/SamHeaderRecord.cpp... Generating code for file bam/SamHeaderRecord.h... Generating code for file bam/SamHeaderRG.cpp... Generating code for file bam/SamHeaderRG.h... Generating code for file bam/SamHeaderSQ.cpp... Generating code for file bam/SamHeaderSQ.h... Generating code for file bam/SamHeaderTag.cpp... Generating code for file bam/SamHeaderTag.h... Generating code for file bam/SamHelper.h... Generating code for file bam/SamInterface.cpp... Generating code for file bam/SamInterface.h... Generating code for file bam/SamQuerySeqWithRefHelper.cpp... Generating code for file bam/SamQuerySeqWithRefHelper.h... Generating code for file bam/SamRecord.cpp... Generating code for file bam/SamRecord.h... Generating code for file bam/SamRecordHelper.cpp... Generating code for file bam/SamRecordHelper.h... Generating code for file bam/SamRecordPool.cpp... Generating code for file bam/SamRecordPool.h... Generating code for file bam/SamReferenceInfo.cpp... Generating code for file bam/SamReferenceInfo.h... Generating code for file bam/SamStatistics.cpp... Generating code for file bam/SamStatistics.h... Generating code for file bam/SamStatus.h... Generating code for file bam/SamTags.cpp... Generating code for file bam/SamTags.h... Generating code for file bam/SamValidation.cpp... Generating code for file bam/SamValidation.h... Generating code for file bam/test/BamIndexTest.cpp... Generating code for file bam/test/BamIndexTest.h... Generating code for file bam/test/Modify.cpp... Generating code for file bam/test/Modify.h... Generating code for file bam/test/ModifyVar.cpp... Generating code for file bam/test/ModifyVar.h... Generating code for file bam/test/ReadFiles.cpp... Generating code for file glf/test/ReadFiles.cpp... Generating code for file bam/test/ReadFiles.h... Generating code for file glf/test/ReadFiles.h... Generating code for file bam/test/SamFileTest.cpp... Generating code for file bam/test/SamFileTest.h... Generating code for file bam/test/ShiftIndels.cpp... Generating code for file bam/test/ShiftIndels.h... Generating code for file bam/test/TestCigarHelper.cpp... Generating code for file bam/test/TestCigarHelper.h... Generating code for file bam/test/TestEquals.cpp... Generating code for file bam/test/TestEquals.h... Generating code for file bam/test/TestFilter.cpp... Generating code for file bam/test/TestFilter.h... Generating code for file bam/test/TestPileup.cpp... Generating code for file bam/test/TestPileup.h... Generating code for file bam/test/TestPosList.cpp... Generating code for file bam/test/TestPosList.h... Generating code for file bam/test/TestSamCoordOutput.cpp... Generating code for file bam/test/TestSamCoordOutput.h... Generating code for file bam/test/TestSamRecordHelper.cpp... Generating code for file bam/test/TestSamRecordHelper.h... Generating code for file bam/test/TestSamRecordPool.cpp... Generating code for file bam/test/TestSamRecordPool.h... Generating code for file bam/test/TestValidate.cpp... Generating code for file bam/test/TestValidate.h... Generating code for file bam/test/ValidationTest.cpp... Generating code for file bam/test/ValidationTest.h... Generating code for file bam/test/WriteFiles.cpp... Generating code for file glf/test/WriteFiles.cpp... Generating code for file bam/test/WriteFiles.h... Generating code for file glf/test/WriteFiles.h... Generating code for file fastq/BaseComposition.cpp... Generating code for file fastq/BaseComposition.h... Generating code for file fastq/BaseCount.cpp... Generating code for file fastq/BaseCount.h... Generating code for file fastq/FastQFile.cpp... Generating code for file fastq/FastQFile.h... Generating code for file fastq/FastQStatus.cpp... Generating code for file fastq/FastQStatus.h... Generating code for file fastq/test/FastQFileTest.cpp... Generating code for file general/BaseAsciiMap.cpp... Generating code for file general/BaseAsciiMap.h... Generating code for file general/BaseQualityHelper.cpp... Generating code for file general/BaseQualityHelper.h... Generating code for file general/BaseUtilities.cpp... Generating code for file general/BaseUtilities.h... Generating code for file general/BasicHash.cpp... Generating code for file general/BasicHash.h... Generating code for file general/BgzfFileType.cpp... Generating code for file general/BgzfFileType.h... Generating code for file general/BgzfFileTypeRecovery.cpp... Generating code for file general/BgzfFileTypeRecovery.h... Generating code for file general/CharBuffer.cpp... Generating code for file general/CharBuffer.h... Generating code for file general/Chromosome.cpp... Generating code for file general/Chromosome.h... Generating code for file general/Cigar.cpp... Generating code for file general/Cigar.h... Generating code for file general/CigarRoller.cpp... Generating code for file general/CigarRoller.h... Generating code for file general/Constant.h... Generating code for file general/CSG_MD5.h... Generating code for file general/Error.cpp... Generating code for file general/Error.h... Generating code for file general/ErrorHandler.cpp... Generating code for file general/ErrorHandler.h... Generating code for file general/FileType.cpp... Generating code for file general/FileType.h... Generating code for file general/FortranFormat.cpp... Generating code for file general/FortranFormat.h... Generating code for file general/Generic.cpp... Generating code for file general/Generic.h... Generating code for file general/GenomeSequence.cpp... Generating code for file general/GenomeSequence.h... Generating code for file general/GenomeSequenceHelpers.h... Generating code for file general/GenotypeLists.cpp... Generating code for file general/GenotypeLists.h... Generating code for file general/glfHandler.cpp... Generating code for file general/glfHandler.h... Generating code for file general/GreedyTupleAligner.h... Generating code for file general/GzipFileType.cpp... Generating code for file general/GzipFileType.h... Generating code for file general/GzipHeader.cpp... Generating code for file general/GzipHeader.h... Generating code for file general/Hash.cpp... Generating code for file general/Hash.h... Generating code for file general/IndexBase.cpp... Generating code for file general/IndexBase.h... Generating code for file general/InplaceMerge.cpp... Generating code for file general/InplaceMerge.h... Generating code for file general/Input.cpp... Generating code for file general/Input.h... Generating code for file general/InputFile.cpp... Generating code for file general/InputFile.h... Generating code for file general/IntArray.cpp... Generating code for file general/IntArray.h... Generating code for file general/IntHash.cpp... Generating code for file general/IntHash.h... Generating code for file general/LongHash.h... Generating code for file general/LongInt.h... Generating code for file general/LongLongCounter.cpp... Generating code for file general/LongLongCounter.h... Generating code for file general/MapFunction.cpp... Generating code for file general/MapFunction.h... Generating code for file general/MathConstant.h... Generating code for file general/MathMatrix.cpp... Generating code for file general/MathMatrix.h... Generating code for file general/MathVector.cpp... Generating code for file general/MathVector.h... Generating code for file general/MemoryAllocators.cpp... Generating code for file general/MemoryAllocators.h... Generating code for file general/MemoryInfo.cpp... Generating code for file general/MemoryInfo.h... Generating code for file general/MemoryMap.cpp... Generating code for file general/MemoryMap.h... Generating code for file general/MemoryMapArray.cpp... Generating code for file general/MemoryMapArray.h... Generating code for file general/MiniDeflate.cpp... Generating code for file general/MiniDeflate.h... Generating code for file general/NonOverlapRegions.cpp... Generating code for file general/NonOverlapRegions.h... Generating code for file general/PackedVector.h... Generating code for file general/Parameters.cpp... Generating code for file general/Parameters.h... Generating code for file general/Pedigree.cpp... Generating code for file general/Pedigree.h... Generating code for file general/PedigreeAlleleFreq.cpp... Generating code for file general/PedigreeAlleleFreq.h... Generating code for file general/PedigreeAlleles.h... Generating code for file general/PedigreeDescription.cpp... Generating code for file general/PedigreeDescription.h... Generating code for file general/PedigreeFamily.cpp... Generating code for file general/PedigreeFamily.h... Generating code for file general/PedigreeGlobals.cpp... Generating code for file general/PedigreeGlobals.h... Generating code for file general/PedigreeLoader.cpp... Generating code for file general/PedigreePerson.cpp... Generating code for file general/PedigreePerson.h... Generating code for file general/PedigreeTrim.cpp... Generating code for file general/PedigreeTwin.cpp... Generating code for file general/Performance.h... Generating code for file general/PhoneHome.cpp... Generating code for file general/PhoneHome.h... Generating code for file general/QuickIndex.cpp... Generating code for file general/QuickIndex.h... Generating code for file general/Random.cpp... Generating code for file general/Random.h... Generating code for file general/ReferenceSequence.cpp... Generating code for file general/ReferenceSequence.h... Generating code for file general/ReusableVector.h... Generating code for file general/SimpleStats.h... Generating code for file general/SmithWaterman.cpp... Generating code for file general/SmithWaterman.h... Generating code for file general/Sort.cpp... Generating code for file general/Sort.h... Generating code for file general/StatGenStatus.cpp... Generating code for file general/StatGenStatus.h... Generating code for file general/STLUtilities.cpp... Generating code for file general/STLUtilities.h... Generating code for file general/String.cpp... Generating code for file general/StringAlias.cpp... Generating code for file general/StringAlias.h... Generating code for file general/StringArray.cpp... Generating code for file general/StringArray.h... Generating code for file general/StringBasics.cpp... Generating code for file general/StringBasics.h... Generating code for file general/StringHash.cpp... Generating code for file general/StringHash.h... Generating code for file general/StringMap.cpp... Generating code for file general/StringMap.h... Generating code for file general/Tabix.cpp... Generating code for file general/Tabix.h... Generating code for file general/test/baseUtilitiesTest/BaseUtilitiesTest.cpp... Generating code for file general/test/baseUtilitiesTest/BaseUtilitiesTest.h... Generating code for file general/test/Chromosome_test.cpp... Generating code for file general/test/cigar/CigarRollerTest.cpp... Generating code for file general/test/cigar/CigarRollerTest.h... Generating code for file general/test/GenomeSequence_test.cpp... Generating code for file general/test/GreedyTupleAligner_test.cpp... Generating code for file general/test/gtest.cpp... Generating code for file general/test/inputFileTest/InputFileTest.cpp... Generating code for file general/test/inputFileTest/InputFileTest.h... Generating code for file general/test/memoryMapArrayTest/MemoryMapArrayTest.cpp... Generating code for file general/test/memoryMapArrayTest/MemoryMapArrayTest.h... Generating code for file general/test/nonOverlapRegions/NonOverlapRegionsTest.cpp... Generating code for file general/test/nonOverlapRegions/NonOverlapRegionsTest.h... Generating code for file general/test/packedVectorTest/PackedVectorTest.cpp... Generating code for file general/test/packedVectorTest/PackedVectorTest.h... Generating code for file general/test/referenceSequenceTest/ReferenceSequenceTest.cpp... Generating code for file general/test/referenceSequenceTest/ReferenceSequenceTest.h... Generating code for file general/test/reusableVector/ReusableVectorTest.cpp... Generating code for file general/test/reusableVector/ReusableVectorTest.h... Generating code for file general/test/STLUtilities_test.cpp... Generating code for file general/test/string/StringTest.cpp... Generating code for file general/test/string/StringTest.h... Generating code for file general/test/trimSequence/TrimSequence.cpp... Generating code for file general/test/TrimSequence_test.cpp... Generating code for file general/TrimSequence.h... Generating code for file general/UncompressedFileType.cpp... Generating code for file general/UncompressedFileType.h... Generating code for file general/UnitTest.h... Generating code for file glf/GlfException.cpp... Generating code for file glf/GlfException.h... Generating code for file glf/GlfFile.cpp... Generating code for file glf/GlfFile.h... Generating code for file glf/GlfHeader.cpp... Generating code for file glf/GlfHeader.h... Generating code for file glf/GlfRecord.cpp... Generating code for file glf/GlfRecord.h... Generating code for file glf/GlfRefSection.cpp... Generating code for file glf/GlfRefSection.h... Generating code for file glf/GlfStatus.cpp... Generating code for file glf/GlfStatus.h... Generating code for file glf/test/Validate.cpp... Generating code for file glf/test/Validate.h... Generating code for file samtools/bam.h... Generating code for file samtools/bgzf.c... Generating code for file samtools/bgzf.h... Generating code for file samtools/khash.h... Generating code for file samtools/knetfile.c... Generating code for file samtools/knetfile.h... Generating file documentation... Generating docs for file general/InputFile.h... Generating page documentation... Generating group documentation... Generating class documentation... Generating docs for compound __kstring_t... Generating docs for compound Alleles... Generating docs for compound AnalyzeClass... Generating docs for compound BamIndex... Generating docs for compound BamIndexFileTest... Generating docs for compound BamInterface... Generating docs for compound bamRecordStruct... Generating docs for compound BaseAsciiMap... Generating docs for compound BaseComposition... Generating docs for compound BaseCount... Generating docs for compound baseQualityConvertor... Generating docs for compound BaseUtilities... Generating docs for compound BasicHash... Generating docs for compound BGZF... Generating docs for compound CharBuffer... Generating docs for compound Chromosome... Generating docs for compound ChromosomeInfo... Generating docs for compound Chunk... Generating docs for compound Cigar... Generating docs for nested compound Cigar::CigarOperator... Generating docs for compound CigarHelper... Generating docs for compound CigarHelperTest... Generating docs for compound CigarRoller... Generating docs for compound CigarRollerTest... Generating docs for compound ColumnExtras... Generating docs for compound defaultPileup... Generating docs for compound DoubleParameter... Generating docs for compound emptyGenericHeader... Generating docs for compound EqualsTest... Generating docs for compound ErrorHandler... Generating docs for compound Family... Generating docs for compound FastQFile... Generating docs for compound FastQStatus... Generating docs for compound FileType... Generating docs for compound FilterTest... Generating docs for compound FortranFormat... Generating docs for compound GenericSamInterface... Generating docs for compound GenomeSequence... Generating docs for compound genomeSequenceMmapHeader... Generating docs for compound GenotypeList... Generating docs for compound glfEntry... Generating docs for compound GlfException... Generating docs for compound GlfFile... Generating docs for compound GlfFileReader... Generating docs for compound GlfFileWriter... Generating docs for compound glfHandler... Generating docs for compound GlfHeader... Generating docs for compound glfIndel... Generating docs for compound GlfRecord... Generating docs for compound GlfRefSection... Generating docs for compound GlfStatus... Generating docs for compound GlobalTestEnvironment... Generating docs for compound GreedyTupleAligner... Generating docs for compound GzipHeader... Generating docs for compound HiddenDouble... Generating docs for compound HiddenInteger... Generating docs for compound HiddenString... Generating docs for compound HiddenSwitch... Generating docs for compound IFILE_Test... Generating docs for compound IndexBase... Generating docs for nested compound IndexBase::Bin... Generating docs for nested compound IndexBase::Reference... Generating docs for compound InputFile... Generating docs for compound IntArray... Generating docs for compound IntHash... Generating docs for compound IntParameter... Generating docs for compound knetFile_s... Generating docs for compound ListParameter... Generating docs for compound LongCounter... Generating docs for compound LongHash... Generating docs for compound LongParamContainer... Generating docs for compound LongParameterList... Generating docs for compound LongParameters... Generating docs for compound MarkerInfo... Generating docs for compound Matrix... Generating docs for compound MD5_CTX... Generating docs for compound MemoryMap... Generating docs for compound MemoryMapArray... Generating docs for compound MemoryMapArrayHeader... Generating docs for compound MemoryMapArrayTest... Generating docs for compound MemoryMapGenericHeader... Generating docs for compound MiniDeflate... Generating docs for compound MockGenomeSequence... Generating docs for compound modify... Generating docs for compound modifyVar... Generating docs for compound NonOverlapRegionPos... Generating docs for compound NonOverlapRegions... Generating docs for compound NonOverlapRegionsTest... Generating docs for compound OptionList... Generating docs for compound PackedArrayTest... Generating docs for compound PackedRead... Generating docs for compound PackedSequenceData... Generating docs for compound PackedVector... Generating docs for compound Parameter... Generating docs for compound ParameterList... Generating docs for compound Pedigree... Generating docs for compound PedigreeDescription... Generating docs for compound PedigreeGlobals... Generating docs for compound PedigreeKey... Generating docs for compound Person... Generating docs for compound PhoneHome... Generating docs for compound Pileup... Generating docs for compound PileupElement... Generating docs for compound PileupElementBaseQual... Generating docs for compound PileupHelper... Generating docs for compound PosList... Generating docs for compound QuickIndex... Generating docs for compound Random... Generating docs for compound ReferenceSequenceTest... Generating docs for compound ReusableVector... Generating docs for compound ReusableVectorTest... Generating docs for compound ReusableVectorTestDataType... Generating docs for compound RunningStat... Generating docs for compound SamCoordOutput... Generating docs for compound SamCoordOutputTest... Generating docs for compound SamFile... Generating docs for compound SamFileHeader... Generating docs for compound SamFileReader... Generating docs for compound SamFileWriter... Generating docs for compound SamFilter... Generating docs for compound SamFlag... Generating docs for compound SamHeaderHD... Generating docs for compound SamHeaderPG... Generating docs for compound SamHeaderRecord... Generating docs for compound SamHeaderRG... Generating docs for compound SamHeaderSQ... Generating docs for compound SamHeaderTag... Generating docs for compound SamHelper... Generating docs for compound SamInterface... Generating docs for compound SamQuerySeqWithRef... Generating docs for compound SamQuerySeqWithRefIter... Generating docs for compound SamRecord... Generating docs for compound SamRecordHelper... Generating docs for compound SamRecordHelperTest... Generating docs for compound SamRecordPool... Generating docs for compound SamRecordPoolTest... Generating docs for compound SamReferenceInfo... Generating docs for compound SamSingleBaseMatchInfo... Generating docs for compound SamStatistics... Generating docs for compound SamTags... Generating docs for compound SamValidationError... Generating docs for compound SamValidationErrors... Generating docs for compound SamValidator... Generating docs for compound SetParameter... Generating docs for compound Ssh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: sh: 1: dot: not found dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found hiftIndelsTest... Generating docs for compound SmithWaterman... Generating docs for nested compound SmithWaterman::weight... Generating docs for compound SortedChunkList... Generating docs for compound StatGenStatus... Generating docs for compound String... Generating docs for compound StringAlias... Generating docs for compound StringArray... Generating docs for compound StringDoubleHash... Generating docs for compound StringHash... Generating docs for compound StringHashBase... Generating docs for compound StringIntHash... Generating docs for compound StringIntMap... Generating docs for compound StringMap... Generating docs for compound StringParameter... Generating docs for compound SwitchParameter... Generating docs for compound Tabix... Generating docs for compound TestPileup... Generating docs for compound TestPileupElement... Generating docs for compound TestPosList... Generating docs for compound TestValidate... Generating docs for compound TestWrite... Generating docs for compound Timing... Generating docs for compound UncompressedFileType... Generating docs for compound UnitTest... Generating docs for compound Vector... Generating docs for compound VectorFunc... Generating docs for compound Weight... Generating namespace index... Generating docs for namespace STLUtilities Generating graph info page... Generating directory documentation... Generating dependency graph for directory bam Generating dependency graph for directory general/test/dbsnp Generating dependency graph for directory fastq Generating dependency graph for directory glf Generating dependency graph for directory general/test/inputFileTest Generating dependency graph for directory general/test Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating graphical class hierarchy... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... Running dot... Generating dot graphs using 5 parallel threads... 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77/98 Patching output file 78/98 Patching output file 79/98 Patching output file 80/98 Patching output file 81/98 Patching output file 82/98 Patching output file 83/98 Patching output file 84/98 Patching output file 85/98 Patching output file 86/98 Patching output file 87/98 Patching output file 88/98 Patching output file 89/98 Patching output file 90/98 Patching output file 91/98 Patching output file 92/98 Patching output file 93/98 Patching output file 94/98 Patching output file 95/98 Patching output file 96/98 Patching output file 97/98 Patching output file 98/98 lookup cache used 9569/65536 hits=87373 misses=10083 finished... make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' echo "Build time test is not run here." Build time test is not run here. make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/<>' mkdir -p debian/libstatgen-dev/usr/include/libStatGen/ cp -L include/* debian/libstatgen-dev/usr/include/libStatGen/ ln -s libStatGen.so.1 libStatGen.so d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-a \ libStatGen.so Library package automatic movement utility set -e install -d -m 755 debian/libstatgen-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libstatgen1/usr/lib/x86_64-linux-gnu mv ./libStatGen.la debian/libstatgen-dev/usr/lib/x86_64-linux-gnu || true mv ./libStatGen.so debian/libstatgen-dev/usr/lib/x86_64-linux-gnu mv /<>/libStatGen.so.1 debian/libstatgen1/usr/lib/x86_64-linux-gnu PKGDEV=libstatgen-dev PKGSHL=libstatgen1 mv: cannot stat './libStatGen.la': No such file or directory make[1]: Leaving directory '/<>' dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a 942a3430ce087e80d940b0c5e92838ac2eac7c61 dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: symbol inflateEnd used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzseek64 used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol deflateInit2_ used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol deflate used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gztell64 used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol crc32 used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol inflate used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzdopen used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzrewind used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzclose used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing libstatgen1 (in debian/libstatgen1); do_strip: , oemstrip: INFO: pkgstriptranslations version 149 pkgstriptranslations: processing libstatgen-dev (in debian/libstatgen-dev); do_strip: , oemstrip: pkgstriptranslations: processing libstatgen-doc (in debian/libstatgen-doc); do_strip: , oemstrip: INFO: pkgstriptranslations version 149 pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstriptranslations: processing libstatgen1-dbgsym (in debian/.debhelper/libstatgen1/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libstatgen1/DEBIAN/control, package libstatgen1, directory debian/libstatgen1 pkgstripfiles: Truncating usr/share/doc/libstatgen1/changelog.Debian.gz to topmost ten records pkgstripfiles: processing control file: debian/libstatgen-dev/DEBIAN/control, package libstatgen-dev, directory debian/libstatgen-dev pkgstripfiles: Running PNG optimization (using 4 cpus) for package libstatgen1 ... pkgstripfiles: No PNG files. INFO: pkgstripfiles: waiting for lock (libstatgen-dev) ... dpkg-deb: building package 'libstatgen1' in '../libstatgen1_1.0.15-4_amd64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libstatgen-doc/DEBIAN/control, package libstatgen-doc, directory debian/libstatgen-doc INFO: pkgstripfiles: waiting for lock (libstatgen-doc) ... pkgstripfiles: processing control file: debian/.debhelper/libstatgen1/dbgsym-root/DEBIAN/control, package libstatgen1-dbgsym, directory debian/.debhelper/libstatgen1/dbgsym-root dpkg-deb: building package 'libstatgen1-dbgsym' in 'debian/.debhelper/scratch-space/build-libstatgen1/libstatgen1-dbgsym_1.0.15-4_amd64.deb'. Searching for duplicated docs in dependency libstatgen1... symlinking changelog.Debian.gz in libstatgen-dev to file in libstatgen1 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libstatgen-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libstatgen-dev' in '../libstatgen-dev_1.0.15-4_amd64.deb'. pkgstripfiles: Truncating usr/share/doc/libstatgen-doc/changelog.Debian.gz to topmost ten records pkgstripfiles: Disabled PNG optimization for -doc package libstatgen-doc (to save build time) dpkg-deb: building package 'libstatgen-doc' in '../libstatgen-doc_1.0.15-4_all.deb'. Renaming libstatgen1-dbgsym_1.0.15-4_amd64.deb to libstatgen1-dbgsym_1.0.15-4_amd64.ddeb dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../libstatgen_1.0.15-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2021-12-08T05:27:54Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ libstatgen_1.0.15-4_amd64.changes: ---------------------------------- Format: 1.8 Date: Tue, 07 Dec 2021 22:54:22 +0100 Source: libstatgen Binary: libstatgen-dev libstatgen-doc libstatgen1 Built-For-Profiles: noudeb Architecture: amd64 all Version: 1.0.15-4 Distribution: jammy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Étienne Mollier Description: libstatgen-dev - development files for the libStatGen libstatgen-doc - documentation files for the libStatGen libstatgen1 - processing and analyzing next generation sequencing and genotypin Changes: libstatgen (1.0.15-4) unstable; urgency=medium . * Team upload. * Source only upload. 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c5f39316123c02f0e465a0321bf0b795 122854 libdevel optional libstatgen-dev_1.0.15-4_amd64.deb 08f9a2e39d5237daddfa6d92b78ecc05 1171924 doc optional libstatgen-doc_1.0.15-4_all.deb 739e86abcdcee2af7f6b32b194499365 2711840 debug optional libstatgen1-dbgsym_1.0.15-4_amd64.ddeb a37c6ac3f00723e68f40771d4605de77 343634 libs optional libstatgen1_1.0.15-4_amd64.deb fb2c1b85e1a1aa548ff58415a98315bd 7078 science optional libstatgen_1.0.15-4_amd64.buildinfo +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: libstatgen Binary: libstatgen-dev libstatgen-doc libstatgen1 libstatgen1-dbgsym Architecture: all amd64 Version: 1.0.15-4 Checksums-Md5: c5f39316123c02f0e465a0321bf0b795 122854 libstatgen-dev_1.0.15-4_amd64.deb 08f9a2e39d5237daddfa6d92b78ecc05 1171924 libstatgen-doc_1.0.15-4_all.deb 739e86abcdcee2af7f6b32b194499365 2711840 libstatgen1-dbgsym_1.0.15-4_amd64.ddeb a37c6ac3f00723e68f40771d4605de77 343634 libstatgen1_1.0.15-4_amd64.deb Checksums-Sha1: 3a19bff6f3ee8ce99f60ae51eb8c824e8bb4346c 122854 libstatgen-dev_1.0.15-4_amd64.deb a7f51060789c08baaa5e9c432ee6ed0c80d19913 1171924 libstatgen-doc_1.0.15-4_all.deb 162673141445eefd064997e26f53a555125b2c19 2711840 libstatgen1-dbgsym_1.0.15-4_amd64.ddeb 41f8e25919b76f0bc2570c7f5801558cfbb027ef 343634 libstatgen1_1.0.15-4_amd64.deb Checksums-Sha256: bd44680bd662c382c4137cabc4e5f78c51f10443f0d9a19c0a6495133090312c 122854 libstatgen-dev_1.0.15-4_amd64.deb 0dd8ad1c80eac7e4d8794ada62b3e440d9a710d8fa57b1b8fa1e5bfd129b5cfe 1171924 libstatgen-doc_1.0.15-4_all.deb 0568ab4e4aec7a4c2c5d6e14ed8218828edec8018c792f2e0a89655dd6acfc62 2711840 libstatgen1-dbgsym_1.0.15-4_amd64.ddeb 76c5d1dbb08051f8a79e9e9ef15f533d0fe59ac4784ffa6ef7df234d6fc70cc6 343634 libstatgen1_1.0.15-4_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Wed, 08 Dec 2021 05:27:53 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: adduser (= 3.118ubuntu5), apt (= 2.3.13), autoconf (= 2.71-2), automake (= 1:1.16.5-1.1), autopoint (= 0.21-4ubuntu3), autotools-dev (= 20180224.1+nmu1), base-files (= 12ubuntu2), base-passwd (= 3.5.52), bash (= 5.1-5ubuntu1), binutils (= 2.37-10ubuntu1), binutils-common (= 2.37-10ubuntu1), binutils-x86-64-linux-gnu (= 2.37-10ubuntu1), bsdextrautils (= 2.37.2-4ubuntu1), bsdutils (= 1:2.37.2-4ubuntu1), build-essential (= 12.9ubuntu2), bzip2 (= 1.0.8-5), coreutils (= 8.32-4ubuntu3), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.2.0-12ubuntu1), d-shlibs (= 0.104), dash (= 0.5.11+git20210903+057cd650a4ed-3), debconf (= 1.5.79), debhelper (= 13.5.2ubuntu1), debianutils (= 5.5-1ubuntu1), debugedit (= 1:5.0-3), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.12.1-1), diffutils (= 1:3.8-0ubuntu1), doxygen (= 1.9.1-2ubuntu1), dpkg (= 1.20.9ubuntu3), dpkg-dev (= 1.20.9ubuntu3), dwz (= 0.14-1build1), file (= 1:5.41-2), findutils (= 4.8.0-1ubuntu2), g++ (= 4:11.2.0-1ubuntu1), g++-11 (= 11.2.0-12ubuntu1), gcc (= 4:11.2.0-1ubuntu1), gcc-11 (= 11.2.0-12ubuntu1), gcc-11-base (= 11.2.0-12ubuntu1), gettext (= 0.21-4ubuntu3), gettext-base (= 0.21-4ubuntu3), gpgv (= 2.2.27-2ubuntu1), grep (= 3.7-1), groff-base (= 1.22.4-7), gzip (= 1.10-4ubuntu2), hostname (= 3.23ubuntu1), init-system-helpers (= 1.60build1), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-10ubuntu2), libapt-pkg6.0 (= 2.3.13), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.2.0-12ubuntu1), libatomic1 (= 11.2.0-12ubuntu1), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0-2ubuntu3), libaudit1 (= 1:3.0-2ubuntu3), libbinutils (= 2.37-10ubuntu1), libblkid1 (= 2.37.2-4ubuntu1), libbsd0 (= 0.11.3-1ubuntu3), libbz2-1.0 (= 1.0.8-5), libc-bin (= 2.34-0ubuntu3), libc-dev-bin (= 2.34-0ubuntu3), libc6 (= 2.34-0ubuntu3), libc6-dev (= 2.34-0ubuntu3), libcap-ng0 (= 0.7.9-2.2build2), libcap2 (= 1:2.44-1build2), libcc1-0 (= 11.2.0-12ubuntu1), libclang-cpp12 (= 1:12.0.1-17), libclang1-12 (= 1:12.0.1-17), libcom-err2 (= 1.46.4-1ubuntu1), libcrypt-dev (= 1:4.4.26-1), libcrypt1 (= 1:4.4.26-1), libctf-nobfd0 (= 2.37-10ubuntu1), libctf0 (= 2.37-10ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.8ubuntu2), libdebconfclient0 (= 0.256ubuntu4), libdebhelper-perl (= 13.5.2ubuntu1), libdpkg-perl (= 1.20.9ubuntu3), libdw1 (= 0.186-1), libedit2 (= 3.1-20210910-1), libelf1 (= 0.186-1), libffi8 (= 3.4.2-1ubuntu5), libfile-stripnondeterminism-perl (= 1.12.1-1), libgcc-11-dev (= 11.2.0-12ubuntu1), libgcc-s1 (= 11.2.0-12ubuntu1), libgcrypt20 (= 1.9.4-3ubuntu2), libgdbm-compat4 (= 1.22-1), libgdbm6 (= 1.22-1), libgmp10 (= 2:6.2.1+dfsg-1ubuntu3), libgnutls30 (= 3.7.2-2ubuntu1), libgomp1 (= 11.2.0-12ubuntu1), libgpg-error0 (= 1.42-3), libgssapi-krb5-2 (= 1.19.2-0ubuntu1), libhogweed6 (= 3.7.3-1build1), libicu67 (= 67.1-7ubuntu1), libidn2-0 (= 2.3.2-2), libisl23 (= 0.24-2), libitm1 (= 11.2.0-12ubuntu1), libk5crypto3 (= 1.19.2-0ubuntu1), libkeyutils1 (= 1.6.1-2ubuntu2), libkrb5-3 (= 1.19.2-0ubuntu1), libkrb5support0 (= 1.19.2-0ubuntu1), libllvm12 (= 1:12.0.1-17), liblsan0 (= 11.2.0-12ubuntu1), liblz4-1 (= 1.9.3-2build1), liblzma5 (= 5.2.5-2build1), libmagic-mgc (= 1:5.41-2), libmagic1 (= 1:5.41-2), libmd0 (= 1.0.4-1), libmount1 (= 2.37.2-4ubuntu1), libmpc3 (= 1.2.1-1), libmpfr6 (= 4.1.0-3build2), libnettle8 (= 3.7.3-1build1), libnsl-dev (= 1.3.0-2build1), libnsl2 (= 1.3.0-2build1), libp11-kit0 (= 0.24.0-6), libpam-modules (= 1.4.0-10ubuntu2), libpam-modules-bin (= 1.4.0-10ubuntu2), libpam-runtime (= 1.4.0-10ubuntu2), libpam0g (= 1.4.0-10ubuntu2), libpcre2-8-0 (= 10.39-3), libpcre3 (= 2:8.39-13build4), libperl5.32 (= 5.32.1-3ubuntu3), libpipeline1 (= 1.5.4-1), libquadmath0 (= 11.2.0-12ubuntu1), libseccomp2 (= 2.5.2-2ubuntu2), libselinux1 (= 3.3-1build1), libsemanage-common (= 3.3-1build1), libsemanage2 (= 3.3-1build1), libsepol2 (= 3.3-1), libsigsegv2 (= 2.13-1ubuntu2), libsmartcols1 (= 2.37.2-4ubuntu1), libssl-dev (= 3.0.0-1ubuntu2), libssl3 (= 3.0.0-1ubuntu2), libstdc++-11-dev (= 11.2.0-12ubuntu1), libstdc++6 (= 11.2.0-12ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 249.5-2ubuntu1), libtasn1-6 (= 4.18.0-4), libtinfo6 (= 6.3-1), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtool (= 2.4.6-15build1), libtsan0 (= 11.2.0-12ubuntu1), libubsan1 (= 11.2.0-12ubuntu1), libuchardet0 (= 0.0.7-1build1), libudev1 (= 249.5-2ubuntu1), libunistring2 (= 0.9.10-6), libuuid1 (= 2.37.2-4ubuntu1), libxapian30 (= 1.4.18-4), libxml2 (= 2.9.12+dfsg-5), libxxhash0 (= 0.8.0-2build1), libzstd1 (= 1.4.8+dfsg-3), linux-libc-dev (= 5.15.0-13.13), login (= 1:4.8.1-2ubuntu1), lsb-base (= 11.1.0ubuntu3), lto-disabled-list (= 17), m4 (= 1.4.18-5ubuntu1), make (= 4.3-4ubuntu2), man-db (= 2.9.4-2build1), mawk (= 1.3.4.20200120-2build1), ncurses-base (= 6.3-1), ncurses-bin (= 6.3-1), passwd (= 1:4.8.1-2ubuntu1), patch (= 2.7.6-7build1), perl (= 5.32.1-3ubuntu3), perl-base (= 5.32.1-3ubuntu3), perl-modules-5.32 (= 5.32.1-3ubuntu3), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu5), sed (= 4.8-1), sensible-utils (= 0.0.17), sysvinit-utils (= 2.96-7ubuntu2), tar (= 1.34+dfsg-1build2), ubuntu-keyring (= 2021.03.26), util-linux (= 2.37.2-4ubuntu1), xz-utils (= 5.2.5-2build1), zlib1g (= 1:1.2.11.dfsg-2ubuntu7), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu7) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1638914062" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libstatgen-dev_1.0.15-4_amd64.deb --------------------------------- new Debian package, version 2.0. size 122854 bytes: control archive=4277 bytes. 1060 bytes, 24 lines control 9504 bytes, 133 lines md5sums Package: libstatgen-dev Source: libstatgen Version: 1.0.15-4 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 753 Depends: libstatgen1 (= 1.0.15-4) Suggests: libstatgen-doc Section: libdevel Priority: optional Multi-Arch: same Homepage: https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen Description: development files for the libStatGen libStatGen is a library for statistical genetic programs. It includes some: A. General Operation Classes including: File/Stream I/O, String processing and Parameter Parsing. B. Statistical Genetic Specific Classes including: Handling Common file formats (Accessors to get/set values, Indexed access to BAM files) and some utility classes, including: 1. Cigar: interpretation and mapping between query and reference. 2. Pileup: structured access to data by individual reference position. . This package provides the development files for libstatgen. drwxr-xr-x root/root 0 2021-12-07 21:54 ./ drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/ drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/include/ drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/include/libStatGen/ -rw-r--r-- root/root 3681 2021-12-07 21:54 ./usr/include/libStatGen/BamIndex.h -rw-r--r-- root/root 2118 2021-12-07 21:54 ./usr/include/libStatGen/BamInterface.h -rw-r--r-- root/root 6819 2021-12-07 21:54 ./usr/include/libStatGen/BaseAsciiMap.h -rw-r--r-- root/root 2176 2021-12-07 21:54 ./usr/include/libStatGen/BaseComposition.h -rw-r--r-- root/root 2118 2021-12-07 21:54 ./usr/include/libStatGen/BaseCount.h -rw-r--r-- root/root 1008 2021-12-07 21:54 ./usr/include/libStatGen/BaseQualityHelper.h -rw-r--r-- root/root 1860 2021-12-07 21:54 ./usr/include/libStatGen/BaseUtilities.h -rw-r--r-- root/root 2251 2021-12-07 21:54 ./usr/include/libStatGen/BasicHash.h -rw-r--r-- root/root 5040 2021-12-07 21:54 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2021-12-07 21:54 ./usr/include/libStatGen/bgzf.h -rw-r--r-- root/root 3867 2021-12-07 21:54 ./usr/include/libStatGen/glfHandler.h -rw-r--r-- root/root 17860 2021-12-07 21:54 ./usr/include/libStatGen/khash.h -rw-r--r-- root/root 1777 2021-12-07 21:54 ./usr/include/libStatGen/knetfile.h drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/lib/ drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2021-12-07 21:54 ./usr/lib/x86_64-linux-gnu/libStatGen.so -> libStatGen.so.1 drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/share/ drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/share/doc/libstatgen-dev/ lrwxrwxrwx root/root 0 2021-12-07 21:54 ./usr/share/doc/libstatgen-dev/changelog.Debian.gz -> ../libstatgen1/changelog.Debian.gz -rw-r--r-- root/root 5551 2021-12-02 21:46 ./usr/share/doc/libstatgen-dev/copyright libstatgen-doc_1.0.15-4_all.deb ------------------------------- new Debian package, version 2.0. size 1171924 bytes: control archive=33035 bytes. 1044 bytes, 23 lines control 137500 bytes, 1457 lines md5sums Package: libstatgen-doc Source: libstatgen Version: 1.0.15-4 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 22383 Recommends: libstatgen-dev (>= 1.0.15-4) Section: doc Priority: optional Multi-Arch: foreign Homepage: https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen Description: documentation files for the libStatGen libStatGen is a library for statistical genetic programs. It includes some: A. General Operation Classes including: File/Stream I/O, String processing and Parameter Parsing. B. Statistical Genetic Specific Classes including: Handling Common file formats (Accessors to get/set values, Indexed access to BAM files) and some utility classes, including: 1. Cigar: interpretation and mapping between query and reference. 2. Pileup: structured access to data by individual reference position. . This package provides the documentation files for libstatgen. drwxr-xr-x root/root 0 2021-12-07 21:54 ./ drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/ drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/share/ drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/share/doc-base/ -rw-r--r-- root/root 298 2021-11-30 20:29 ./usr/share/doc-base/libstatgen-doc.libstatgen-reference-manual drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/share/doc/libstatgen-dev/ drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/share/doc/libstatgen-dev/html/ -rw-r--r-- root/root 62830 2021-12-07 21:54 ./usr/share/doc/libstatgen-dev/html/BamIndexTest_8cpp_source.html -rw-r--r-- root/root 9080 2021-12-07 21:54 ./usr/share/doc/libstatgen-dev/html/BamIndexTest_8h_source.html -rw-r--r-- root/root 83848 2021-12-07 21:54 ./usr/share/doc/libstatgen-dev/html/BamIndex_8cpp_source.html -rw-r--r-- root/root 26047 2021-12-07 21:54 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processing and analyzing next generation sequencing and genotyping data library libStatGen is a library for statistical genetic programs. It includes some: A. General Operation Classes including: File/Stream I/O, String processing and Parameter Parsing. B. Statistical Genetic Specific Classes including: Handling Common file formats (Accessors to get/set values, Indexed access to BAM files) and some utility classes, including: 1. Cigar: interpretation and mapping between query and reference. 2. Pileup: structured access to data by individual reference position. . This package provides the shared library. drwxr-xr-x root/root 0 2021-12-07 21:54 ./ drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/ drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/lib/ drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 864240 2021-12-07 21:54 ./usr/lib/x86_64-linux-gnu/libStatGen.so.1 drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/share/ drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-12-07 21:54 ./usr/share/doc/libstatgen1/ -rw-r--r-- root/root 1052 2021-12-07 21:54 ./usr/share/doc/libstatgen1/changelog.Debian.gz -rw-r--r-- root/root 5551 2021-12-02 21:46 ./usr/share/doc/libstatgen1/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: n/a Build-Time: 239 Distribution: jammy-proposed Host Architecture: amd64 Install-Time: 47 Job: libstatgen_1.0.15-4.dsc Machine Architecture: amd64 Package: libstatgen Package-Time: 290 Source-Version: 1.0.15-4 Space: n/a Status: successful Version: 1.0.15-4 -------------------------------------------------------------------------------- Finished at 2021-12-08T05:27:54Z Build needed 00:04:50, no disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-22601457 Scanning for processes to kill in build PACKAGEBUILD-22601457