sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | comet-ms 2019015+cleaned1-2 (armel) Wed, 20 May 2020 15:12:04 +0000 | +==============================================================================+ Package: comet-ms Version: 2019015+cleaned1-2 Source Version: 2019015+cleaned1-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: armel Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-a315fb6a-5141-4d44-8594-2ddc480a1d73' with '<>' I: NOTICE: Log filtering will replace 'build/comet-ms-ENuPCw/resolver-hFcUFM' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [146 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2020-05-20-0812.30.pdiff [8205 B] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2020-05-20-1411.44.pdiff [16.8 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2020-05-20-1411.44.pdiff [16.8 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-05-20-0812.30.pdiff [6186 B] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-05-20-1411.44.pdiff [21.1 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-05-20-1411.44.pdiff [21.1 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main armel Packages [7899 kB] Fetched 8154 kB in 2s (5053 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'comet-ms' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/comet-ms.git Please use: git clone https://salsa.debian.org/debichem-team/comet-ms.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1387 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main comet-ms 2019015+cleaned1-2 (dsc) [2080 B] Get:2 http://debian.oregonstate.edu/debian unstable/main comet-ms 2019015+cleaned1-2 (tar) [1378 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main comet-ms 2019015+cleaned1-2 (diff) [6492 B] Fetched 1387 kB in 0s (62.3 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/comet-ms-ENuPCw/comet-ms-2019015+cleaned1' with '<>' I: NOTICE: Log filtering will replace 'build/comet-ms-ENuPCw' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), dpkg-dev (>= 1.16.1~), libmstoolkit-dev (>= 82), libmstoolkit-dev (<< 83), docbook-to-man, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel Filtered Build-Depends: debhelper-compat (= 12), dpkg-dev (>= 1.16.1~), libmstoolkit-dev (>= 82), libmstoolkit-dev (<< 83), docbook-to-man, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [448 B] Get:5 copy:/<>/apt_archive ./ Packages [537 B] Fetched 1942 B in 0s (82.4 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabi bsdmainutils build-essential cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism docbook docbook-to-man dpkg-cross dwz file g++ g++-9 g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-10-base:armel gcc-10-cross-base gcc-9-arm-linux-gnueabi gcc-9-arm-linux-gnueabi-base gcc-9-base:armel gcc-9-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:armel libasan5-armel-cross libatomic1:armel libatomic1-armel-cross libbsd0 libc6:armel libc6-armel-cross libc6-dev libc6-dev:armel libc6-dev-armel-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:armel libcrypt1:armel libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1:armel libexpat1-dev:armel libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel libgcc-9-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libglib2.0-0 libgomp1:armel libgomp1-armel-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libmstoolkit-dev:armel libmstoolkit82:armel libosp5 libpipeline1 libsigsegv2 libsqlite3-0:armel libsqlite3-dev:armel libstdc++-9-dev libstdc++-9-dev:armel libstdc++-9-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db opensp po-debconf sensible-utils sgml-base sgml-data ucf xml-core zlib1g:armel zlib1g-dev:armel Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican | wordlist whois vacation gcc-9-locales cpp-doc dh-make docbook-defguide docbook-dsssl docbook-xml psgml binutils-multiarch g++-multilib g++-9-multilib gcc-9-doc manpages-dev flex bison gdb-arm-linux-gnueabi gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:armel libc-l10n:armel locales:armel glibc-doc manpages-dev:armel sqlite3-doc:armel libstdc++-9-doc libstdc++-9-doc:armel libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser doc-base libmail-box-perl sgml-base-doc perlsgml w3-recs libxml2-utils Recommended packages: curl | wget | lynx libidn2-0:armel libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabi bsdmainutils build-essential cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism docbook docbook-to-man dpkg-cross dwz file g++ g++-9 g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-10-base:armel gcc-10-cross-base gcc-9-arm-linux-gnueabi gcc-9-arm-linux-gnueabi-base gcc-9-base:armel gcc-9-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:armel libasan5-armel-cross libatomic1:armel libatomic1-armel-cross libbsd0 libc6:armel libc6-armel-cross libc6-dev libc6-dev:armel libc6-dev-armel-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:armel libcrypt1:armel libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1:armel libexpat1-dev:armel libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel libgcc-9-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libglib2.0-0 libgomp1:armel libgomp1-armel-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libmstoolkit-dev:armel libmstoolkit82:armel libosp5 libpipeline1 libsigsegv2 libsqlite3-0:armel libsqlite3-dev:armel libstdc++-9-dev libstdc++-9-dev:armel libstdc++-9-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db opensp po-debconf sbuild-build-depends-main-dummy:armel sensible-utils sgml-base sgml-data ucf xml-core zlib1g:armel zlib1g-dev:armel 0 upgraded, 109 newly installed, 0 to remove and 0 not upgraded. Need to get 81.4 MB of archives. After this operation, 328 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [960 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-5 [920 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.1-1 [1308 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 sgml-base all 1.30 [15.1 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main armel gcc-10-base armel 10.1.0-2 [197 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main armel gcc-9-base armel 9.3.0-13 [197 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-5 [262 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.38-5 [120 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.38-5 [67.9 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0040 [73.6 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.2-1 [775 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabi amd64 2.34-8 [2747 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.16-1 [104 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.30-8 [2631 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev amd64 9.3.0-13 [1701 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9 amd64 9.3.0-13 [10.7 MB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:9.2.1-3.1 [1644 B] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.8 [7640 B] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi-base amd64 9.3.0-8cross1 [197 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-arm-linux-gnueabi amd64 9.3.0-8cross1 [6816 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabi amd64 4:9.2.1-3.1 [16.7 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.3.0-8cross1 [192 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-cross-base all 10-20200418-1cross1 [192 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armel-cross all 2.30-2cross1 [1128 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-armel-cross all 10-20200418-1cross1 [38.3 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armel-cross all 10-20200418-1cross1 [84.1 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armel-cross all 10-20200418-1cross1 [8812 B] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armel-cross all 9.3.0-8cross1 [340 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armel-cross all 10-20200418-1cross1 [368 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armel-cross all 10-20200418-1cross1 [114 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-armel-cross all 9.3.0-8cross1 [644 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi amd64 9.3.0-8cross1 [7174 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1464 B] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armel-cross all 5.4.19-1cross1 [1155 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armel-cross all 2.30-2cross1 [2148 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-armel-cross all 9.3.0-8cross1 [1712 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-arm-linux-gnueabi amd64 9.3.0-8cross1 [7401 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1180 B] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-3 [8296 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.10+dfsg-5 [709 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2 [343 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armel all 12.8 [6640 B] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-14 [513 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 13.1 [187 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.8.0-1 [24.2 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.8.0-1 [14.8 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.64.2-1 [1343 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 13.1 [1012 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 sgml-data all 2.0.11 [179 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 docbook all 4.5-6 [129 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 libosp5 amd64 1.5.2-13+b1 [948 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 opensp amd64 1.5.2-13+b1 [449 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 docbook-to-man amd64 1:2.0.0-42+b1 [76.8 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main armel libgcc-s1 armel 10.1.0-2 [38.2 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main armel libcrypt1 armel 1:4.4.16-1 [101 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main armel libc6 armel 2.30-8 [2348 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main armel libasan5 armel 9.3.0-13 [347 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main armel libatomic1 armel 10.1.0-2 [9008 B] Get:94 http://debian.oregonstate.edu/debian unstable/main armel linux-libc-dev armel 5.6.7-1 [1080 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main armel libcrypt-dev armel 1:4.4.16-1 [120 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main armel libc6-dev armel 2.30-8 [2189 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main armel libexpat1 armel 2.2.9-1 [70.8 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main armel libexpat1-dev armel 2.2.9-1 [117 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main armel libgomp1 armel 10.1.0-2 [86.2 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main armel libstdc++6 armel 10.1.0-2 [408 kB] Get:101 http://debian.oregonstate.edu/debian unstable/main armel libubsan1 armel 10.1.0-2 [115 kB] Get:102 http://debian.oregonstate.edu/debian unstable/main armel libgcc-9-dev armel 9.3.0-13 [645 kB] Get:103 http://debian.oregonstate.edu/debian unstable/main armel libsqlite3-0 armel 3.31.1-5 [575 kB] Get:104 http://debian.oregonstate.edu/debian unstable/main armel zlib1g armel 1:1.2.11.dfsg-2 [84.7 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main armel libmstoolkit82 armel 82-6 [115 kB] Get:106 http://debian.oregonstate.edu/debian unstable/main armel zlib1g-dev armel 1:1.2.11.dfsg-2 [185 kB] Get:107 http://debian.oregonstate.edu/debian unstable/main armel libsqlite3-dev armel 3.31.1-5 [739 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main armel libmstoolkit-dev armel 82-6 [131 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main armel libstdc++-9-dev armel 9.3.0-13 [1745 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 81.4 MB in 1s (116 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 12637 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../002-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-5_amd64.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../004-libpipeline1_1.5.2-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.2-2) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.9.1-1_amd64.deb ... Unpacking man-db (2.9.1-1) ... 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Setting up libsigsegv2:amd64 (2.12-2) ... Setting up cpp-9-arm-linux-gnueabi (9.3.0-8cross1) ... Setting up autopoint (0.19.8.1-10) ... Setting up gcc-9-cross-base (9.3.0-8cross1) ... Setting up gcc-10-cross-base (10-20200418-1cross1) ... Setting up libc6-armel-cross (2.30-2cross1) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libcrypt-dev:amd64 (1:4.4.16-1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libc6-dev:amd64 (2.30-8) ... Setting up sgml-base (1.30) ... Setting up libc6-dev-armel-cross (2.30-2cross1) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.10+dfsg-5) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up gcc-9-base:armel (9.3.0-13) ... Setting up libfile-stripnondeterminism-perl (1.8.0-1) ... Setting up libgomp1-armel-cross (10-20200418-1cross1) ... Setting up libstdc++-9-dev:amd64 (9.3.0-13) ... Setting up libtool (2.4.6-14) ... Setting up libgcc-s1-armel-cross (10-20200418-1cross1) ... Setting up m4 (1.4.18-4) ... Setting up opensp (1.5.2-13+b1) ... Setting up libstdc++6-armel-cross (10-20200418-1cross1) ... Setting up libatomic1-armel-cross (10-20200418-1cross1) ... Setting up libasan5-armel-cross (9.3.0-8cross1) ... Setting up cpp-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up libubsan1-armel-cross (10-20200418-1cross1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:amd64 (0.6.13-1) ... Setting up ucf (3.0040) ... Setting up g++-9 (9.3.0-13) ... Setting up libgcc-9-dev-armel-cross (9.3.0-8cross1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.8.0-1) ... Setting up g++ (4:9.2.1-3.1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up xml-core (0.18+nmu1) ... Setting up build-essential (12.8) ... Setting up automake (1:1.16.2-1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10) ... Setting up libstdc++-9-dev-armel-cross (9.3.0-8cross1) ... Setting up gcc-9-arm-linux-gnueabi (9.3.0-8cross1) ... Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up g++-9-arm-linux-gnueabi (9.3.0-8cross1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxml-libxml-perl (2.0134+dfsg-2) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up gcc-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up po-debconf (1.0.21) ... Setting up g++-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-armel (12.8) ... Setting up libcrypt1:armel (1:4.4.16-1) ... Setting up libgcc-s1:armel (10.1.0-2) ... Setting up libc6:armel (2.30-8) ... Setting up libcrypt-dev:armel (1:4.4.16-1) ... Setting up libc6-dev:armel (2.30-8) ... Setting up libstdc++6:armel (10.1.0-2) ... Setting up libexpat1:armel (2.2.9-1) ... Setting up libsqlite3-0:armel (3.31.1-5) ... Setting up debhelper (13.1) ... Setting up zlib1g:armel (1:1.2.11.dfsg-2) ... Setting up libgomp1:armel (10.1.0-2) ... Setting up dh-autoreconf (19) ... Setting up libasan5:armel (9.3.0-13) ... Setting up libexpat1-dev:armel (2.2.9-1) ... Setting up libsqlite3-dev:armel (3.31.1-5) ... Setting up libatomic1:armel (10.1.0-2) ... Setting up libubsan1:armel (10.1.0-2) ... Setting up zlib1g-dev:armel (1:1.2.11.dfsg-2) ... Setting up libmstoolkit82:armel (82-6) ... Setting up libgcc-9-dev:armel (9.3.0-13) ... Setting up libmstoolkit-dev:armel (82-6) ... Setting up libstdc++-9-dev:armel (9.3.0-13) ... Processing triggers for libc-bin (2.30-8) ... Processing triggers for sgml-base (1.30) ... Setting up sgml-data (2.0.11) ... Processing triggers for sgml-base (1.30) ... Setting up docbook (4.5-6) ... Processing triggers for sgml-base (1.30) ... Setting up docbook-to-man (1:2.0.0-42+b1) ... Setting up sbuild-build-depends-main-dummy:armel (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armel included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-6-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) amd64 (x86_64) Toolchain package versions: binutils_2.34-8 dpkg-dev_1.19.7 g++-9_9.3.0-13 gcc-9_9.3.0-13 libc6-dev_2.30-8 libstdc++-9-dev_9.3.0-13 libstdc++-9-dev-armel-cross_9.3.0-8cross1 libstdc++6_10.1.0-2 libstdc++6-armel-cross_10-20200418-1cross1 linux-libc-dev_5.6.7-1 Package versions: adduser_3.118 apt_2.1.4 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-8 binutils-arm-linux-gnueabi_2.34-8 binutils-common_2.34-8 binutils-x86-64-linux-gnu_2.34-8 bsdmainutils_11.1.2+b1 bsdutils_1:2.35.1-5 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-8_8.4.0-4 cpp-9_9.3.0-13 cpp-9-arm-linux-gnueabi_9.3.0-8cross1 cpp-arm-linux-gnueabi_4:9.2.1-3.1 cross-config_2.6.15-3 crossbuild-essential-armel_12.8 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.1 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.8.0-1 diffutils_1:3.7-3 docbook_4.5-6 docbook-to-man_1:2.0.0-42+b1 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.1-5 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.3.0-13 g++-9-arm-linux-gnueabi_9.3.0-8cross1 g++-arm-linux-gnueabi_4:9.2.1-3.1 gcc_4:9.2.1-3.1 gcc-10-base_10.1.0-2 gcc-10-cross-base_10-20200418-1cross1 gcc-8-base_8.4.0-4 gcc-9_9.3.0-13 gcc-9-arm-linux-gnueabi_9.3.0-8cross1 gcc-9-arm-linux-gnueabi-base_9.3.0-8cross1 gcc-9-base_9.3.0-13 gcc-9-cross-base_9.3.0-8cross1 gcc-arm-linux-gnueabi_4:9.2.1-3.1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg5.0_1.8.4 libapt-pkg6.0_2.1.4 libarchive-zip-perl_1.68-1 libasan5_9.3.0-13 libasan5-armel-cross_9.3.0-8cross1 libatomic1_10.1.0-2 libatomic1-armel-cross_10-20200418-1cross1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3+b1 libbinutils_2.34-8 libblkid1_2.35.1-5 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-8 libc-dev-bin_2.30-8 libc6_2.30-8 libc6-armel-cross_2.30-2cross1 libc6-dev_2.30-8 libc6-dev-armel-cross_2.30-2cross1 libcap-ng0_0.7.9-2.1+b2 libcc1-0_10.1.0-2 libcom-err2_1.45.6-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000003-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-8 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+------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: comet-ms Binary: comet-ms Architecture: any Version: 2019015+cleaned1-2 Maintainer: The Debichem Group Uploaders: Filippo Rusconi Homepage: http://comet-ms.sourceforge.net Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/debichem-team/comet-ms Vcs-Git: https://salsa.debian.org/debichem-team/comet-ms.git Build-Depends: debhelper-compat (= 12), dpkg-dev (>= 1.16.1~), libmstoolkit-dev (>= 82), libmstoolkit-dev (<< 83), docbook-to-man Package-List: comet-ms deb science optional arch=any Checksums-Sha1: e8ce6f80224671a82f5c9123546c621fba5df7d0 1378100 comet-ms_2019015+cleaned1.orig.tar.gz 4513d9a698013c60060514fbfac5860449f95c41 6492 comet-ms_2019015+cleaned1-2.debian.tar.xz Checksums-Sha256: 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dpkg-source: info: applying cometsearch-makefile-to-handle-lib-debian-way-of-doing-things.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.armel DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-a315fb6a-5141-4d44-8594-2ddc480a1d73 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarmel -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package comet-ms dpkg-buildpackage: info: source version 2019015+cleaned1-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Filippo Rusconi dpkg-architecture: warning: specified GNU system type arm-linux-gnueabi does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armel fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -f debian/comet-ms.1 make[1]: Leaving directory '/<>' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/comet-ms.substvars debian/files rm -fr -- debian/comet-ms/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' docbook-to-man debian/comet-ms.sgml > debian/comet-ms.1 make make[2]: Entering directory '/<>' cd CometSearch ; make make[3]: Entering directory '/<>/CometSearch' g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit Threading.cpp -c g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometInterfaces.cpp -c g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometSearch.cpp -c In file included from CometSearch.cpp:19: ThreadPool.h: In instantiation of ‘ThreadManager::ThreadManager(ThreadPool*) [with T = SearchThreadData*]’: ThreadPool.h:69:10: required from ‘ThreadPool::ThreadPool(ThreadPool::ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadPool::ThreadProc = void (*)(SearchThreadData*)]’ CometSearch.cpp:138:66: required from here ThreadPool.h:257:13: warning: cast between incompatible function types from ‘uint32_t (*)(void*)’ {aka ‘unsigned int (*)(void*)’} to ‘ThreadProc’ {aka ‘void* (*)(void*)’} [-Wcast-function-type] 257 | reinterpret_cast(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometPreprocess.cpp -c In file included from CometPreprocess.h:21, from CometPreprocess.cpp:19: ThreadPool.h: In instantiation of ‘ThreadManager::ThreadManager(ThreadPool*) [with T = PreprocessThreadData*]’: ThreadPool.h:69:10: required from ‘ThreadPool::ThreadPool(ThreadPool::ThreadProc, int, int, int) [with T = PreprocessThreadData*; ThreadPool::ThreadProc = void (*)(PreprocessThreadData*)]’ CometPreprocess.cpp:74:65: required from here ThreadPool.h:257:13: warning: cast between incompatible function types from ‘uint32_t (*)(void*)’ {aka ‘unsigned int (*)(void*)’} to ‘ThreadProc’ {aka ‘void* (*)(void*)’} [-Wcast-function-type] 257 | reinterpret_cast(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometPostAnalysis.cpp -c In file included from CometPostAnalysis.cpp:19: ThreadPool.h: In instantiation of ‘ThreadManager::ThreadManager(ThreadPool*) [with T = PostAnalysisThreadData*]’: ThreadPool.h:69:10: required from ‘ThreadPool::ThreadPool(ThreadPool::ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadPool::ThreadProc = void (*)(PostAnalysisThreadData*)]’ CometPostAnalysis.cpp:46:38: required from here ThreadPool.h:257:13: warning: cast between incompatible function types from ‘uint32_t (*)(void*)’ {aka ‘unsigned int (*)(void*)’} to ‘ThreadProc’ {aka ‘void* (*)(void*)’} [-Wcast-function-type] 257 | reinterpret_cast(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometMassSpecUtils.cpp -c g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWriteOut.cpp -c CometWriteOut.cpp: In static member function ‘static bool CometWriteOut::PrintResults(int, bool, FILE*)’: CometWriteOut.cpp:124:32: warning: ‘%.5d’ directive writing between 5 and 11 bytes into a region of size between 0 and 1022 [-Wformat-overflow=] 124 | sprintf(szOutput, "%s/%s.%.5d.%.5d.%d.out", | ^~~~ CometWriteOut.cpp:124:14: note: ‘sprintf’ output between 20 and 1064 bytes into a destination of size 1024 124 | sprintf(szOutput, "%s/%s.%.5d.%.5d.%d.out", | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 125 | g_staticParams.inputFile.szBaseName, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 126 | pStr, | ~~~~~ 127 | pQuery->_spectrumInfoInternal.iScanNumber, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 128 | pQuery->_spectrumInfoInternal.iScanNumber, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 129 | pQuery->_spectrumInfoInternal.iChargeState); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometWriteOut.cpp:115:35: warning: ‘%s’ directive writing up to 511 bytes into a region of size between 506 and 1017 [-Wformat-overflow=] 115 | sprintf(szOutput, "%s_decoy/%s.%.5d.%.5d.%d.out", | ^~ CometWriteOut.cpp:115:14: note: ‘sprintf’ output between 26 and 1070 bytes into a destination of size 1024 115 | sprintf(szOutput, "%s_decoy/%s.%.5d.%.5d.%d.out", | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 116 | g_staticParams.inputFile.szBaseName, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 | pStr, | ~~~~~ 118 | pQuery->_spectrumInfoInternal.iScanNumber, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 119 | pQuery->_spectrumInfoInternal.iScanNumber, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 120 | pQuery->_spectrumInfoInternal.iChargeState); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometWriteOut.cpp:273:28: warning: ‘%+d’ directive writing between 2 and 11 bytes into a region of size 9 [-Wformat-overflow=] 273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates); | ^~~ CometWriteOut.cpp:273:26: note: directive argument in the range [1, 2147483647] 273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates); | ^~~~~~ CometWriteOut.cpp:273:14: note: ‘sprintf’ output between 4 and 13 bytes into a destination of size 10 273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometWriteOut.cpp:151:59: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 226 [-Wformat-overflow=] 151 | sprintf(szErrorMsg, " Error - cannot write to file %s.\n", szOutput); | ^~ ~~~~~~~~ CometWriteOut.cpp:151:14: note: ‘sprintf’ output between 33 and 1056 bytes into a destination of size 256 151 | sprintf(szErrorMsg, " Error - cannot write to file %s.\n", szOutput); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWriteSqt.cpp -c g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWritePepXML.cpp -c g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWritePercolator.cpp -c g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWriteTxt.cpp -c g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometSearchManager.cpp -c CometSearchManager.cpp: In static member function ‘static bool CometSearchManager::WriteIndexedDatabase()’: CometSearchManager.cpp:2756:28: warning: ‘.idx’ directive writing 4 bytes into a region of size between 1 and 512 [-Wformat-overflow=] 2756 | sprintf(szIndexFile, "%s.idx", g_staticParams.databaseInfo.szDatabase); | ^~~~ CometSearchManager.cpp:2756:11: note: ‘sprintf’ output between 5 and 516 bytes into a destination of size 512 2756 | sprintf(szIndexFile, "%s.idx", g_staticParams.databaseInfo.szDatabase); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’: CometSearchManager.cpp:416:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError); | ^~ CometSearchManager.cpp:416:26: note: directive argument in the range [1, 2147483647] 416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError); | ^~~~~~~~~~~ CometSearchManager.cpp:416:14: note: ‘sprintf’ output between 9 and 18 bytes into a destination of size 16 416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1597:71: warning: ‘%s’ directive writing up to 511 bytes into a region of size 218 [-Wformat-overflow=] 1597 | sprintf(szErrorMsg, " Error - cannot read DIA window file \"%s\".\n", g_staticParams.szDIAWindowsFile); | ^~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1597:17: note: ‘sprintf’ output between 42 and 553 bytes into a destination of size 256 1597 | sprintf(szErrorMsg, " Error - cannot read DIA window file \"%s\".\n", g_staticParams.szDIAWindowsFile); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:223:73: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 987 [-Wformat-overflow=] 223 | sprintf(szErrorMsg, " Error - could not create directory \"%s\".\n", szDecoyDir); | ^~ ~~~~~~~~~~ CometSearchManager.cpp:223:20: note: ‘sprintf’ output between 41 and 1064 bytes into a destination of size 1024 223 | sprintf(szErrorMsg, " Error - could not create directory \"%s\".\n", szDecoyDir); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1700:76: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=] 1700 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoySQT); | ^~ ~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1700:23: note: ‘sprintf’ output between 41 and 1064 bytes into a destination of size 256 1700 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoySQT); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1675:67: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=] 1675 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputSQT); | ^~ ~~~~~~~~~~~ CometSearchManager.cpp:1675:20: note: ‘sprintf’ output between 35 and 1058 bytes into a destination of size 256 1675 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputSQT); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1763:76: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=] 1763 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyTxt); | ^~ ~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1763:23: note: ‘sprintf’ output between 41 and 1064 bytes into a destination of size 256 1763 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyTxt); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1737:67: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=] 1737 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputTxt); | ^~ ~~~~~~~~~~~ CometSearchManager.cpp:1737:20: note: ‘sprintf’ output between 35 and 1058 bytes into a destination of size 256 1737 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputTxt); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1826:76: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=] 1826 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyPepXML); | ^~ ~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1826:23: note: ‘sprintf’ output between 41 and 1064 bytes into a destination of size 256 1826 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyPepXML); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1800:67: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=] 1800 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPepXML); | ^~ ~~~~~~~~~~~~~~ CometSearchManager.cpp:1800:20: note: ‘sprintf’ output between 35 and 1058 bytes into a destination of size 256 1800 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPepXML); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1854:67: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=] 1854 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPercolator); | ^~ ~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1854:20: note: ‘sprintf’ output between 35 and 1058 bytes into a destination of size 256 1854 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPercolator); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1975:32: warning: ‘%s’ directive writing up to 255 bytes into a region of size 128 [-Wformat-overflow=] 1975 | sprintf(szOut, "%s", szStatusMsg); | ^~ ~~~~~~~~~~~ CometSearchManager.cpp:1975:23: note: ‘sprintf’ output between 1 and 256 bytes into a destination of size 128 1975 | sprintf(szOut, "%s", szStatusMsg); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometCheckForUpdates.cpp -c CometCheckForUpdates.cpp: In static member function ‘static void CometCheckForUpdates::SendAnalyticsHit()’: CometCheckForUpdates.cpp:161:11: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size between 895 and 898 [-Wformat-truncation=] 161 | "%s\r\n", host, (int)strlen(postData), postData); | ^~ ~~~~~~~~ CometCheckForUpdates.cpp:156:12: note: ‘snprintf’ output between 129 and 1155 bytes into a destination of size 1024 156 | snprintf(message, 1024, | ~~~~~~~~^~~~~~~~~~~~~~~ 157 | "POST /collect HTTP/1.1\r\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 | "Host: %s\r\n" | ~~~~~~~~~~~~~~ 159 | "Content-type: application/x-www-form-urlencoded\r\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 | "Content-length: %d\r\n\r\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 161 | "%s\r\n", host, (int)strlen(postData), postData); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ar rcs libcometsearch.a Threading.o CometInterfaces.o CometSearch.o CometPreprocess.o CometPostAnalysis.o CometMassSpecUtils.o CometWriteOut.o CometWriteSqt.o CometWritePepXML.o CometWritePercolator.o CometWriteTxt.o CometSearchManager.o CometCheckForUpdates.o make[3]: Leaving directory '/<>/CometSearch' g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch CometSearch/CometCheckForUpdates.cpp CometSearch/CometMassSpecUtils.cpp CometSearch/CometPreprocess.cpp CometSearch/CometSearchManager.cpp CometSearch/CometWritePepXML.cpp CometSearch/CometWriteSqt.cpp CometSearch/Threading.cpp CometSearch/CometInterfaces.cpp CometSearch/CometPostAnalysis.cpp CometSearch/CometSearch.cpp CometSearch/CometWriteOut.cpp CometSearch/CometWritePercolator.cpp CometSearch/CometWriteTxt.cpp Comet.cpp -c CometSearch/CometCheckForUpdates.cpp: In static member function ‘static void CometCheckForUpdates::SendAnalyticsHit()’: CometSearch/CometCheckForUpdates.cpp:146:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 146 | char *host = "www.google-analytics.com"; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometCheckForUpdates.cpp:161:11: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size between 895 and 898 [-Wformat-truncation=] 161 | "%s\r\n", host, (int)strlen(postData), postData); | ^~ ~~~~~~~~ CometSearch/CometCheckForUpdates.cpp:156:12: note: ‘snprintf’ output between 129 and 1155 bytes into a destination of size 1024 156 | snprintf(message, 1024, | ~~~~~~~~^~~~~~~~~~~~~~~ 157 | "POST /collect HTTP/1.1\r\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 | "Host: %s\r\n" | ~~~~~~~~~~~~~~ 159 | "Content-type: application/x-www-form-urlencoded\r\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 | "Content-length: %d\r\n\r\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 161 | "%s\r\n", host, (int)strlen(postData), postData); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from CometSearch/CometPreprocess.h:21, from CometSearch/CometPreprocess.cpp:19: CometSearch/ThreadPool.h: In instantiation of ‘ThreadManager::ThreadManager(ThreadPool*) [with T = PreprocessThreadData*]’: CometSearch/ThreadPool.h:69:10: required from ‘ThreadPool::ThreadPool(ThreadPool::ThreadProc, int, int, int) [with T = PreprocessThreadData*; ThreadPool::ThreadProc = void (*)(PreprocessThreadData*)]’ CometSearch/CometPreprocess.cpp:74:65: required from here CometSearch/ThreadPool.h:257:13: warning: cast between incompatible function types from ‘uint32_t (*)(void*)’ {aka ‘unsigned int (*)(void*)’} to ‘ThreadProc’ {aka ‘void* (*)(void*)’} [-Wcast-function-type] 257 | reinterpret_cast(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp: In static member function ‘static bool CometSearchManager::WriteIndexedDatabase()’: CometSearch/CometSearchManager.cpp:2756:28: warning: ‘.idx’ directive writing 4 bytes into a region of size between 1 and 512 [-Wformat-overflow=] 2756 | sprintf(szIndexFile, "%s.idx", g_staticParams.databaseInfo.szDatabase); | ^~~~ CometSearch/CometSearchManager.cpp:2756:11: note: ‘sprintf’ output between 5 and 516 bytes into a destination of size 512 2756 | sprintf(szIndexFile, "%s.idx", g_staticParams.databaseInfo.szDatabase); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’: CometSearch/CometSearchManager.cpp:416:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError); | ^~ CometSearch/CometSearchManager.cpp:416:26: note: directive argument in the range [1, 2147483647] 416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError); | ^~~~~~~~~~~ CometSearch/CometSearchManager.cpp:416:14: note: ‘sprintf’ output between 9 and 18 bytes into a destination of size 16 416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1597:71: warning: ‘%s’ directive writing up to 511 bytes into a region of size 218 [-Wformat-overflow=] 1597 | sprintf(szErrorMsg, " Error - cannot read DIA window file \"%s\".\n", g_staticParams.szDIAWindowsFile); | ^~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1597:17: note: ‘sprintf’ output between 42 and 553 bytes into a destination of size 256 1597 | sprintf(szErrorMsg, " Error - cannot read DIA window file \"%s\".\n", g_staticParams.szDIAWindowsFile); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:223:73: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 987 [-Wformat-overflow=] 223 | sprintf(szErrorMsg, " Error - could not create directory \"%s\".\n", szDecoyDir); | ^~ ~~~~~~~~~~ CometSearch/CometSearchManager.cpp:223:20: note: ‘sprintf’ output between 41 and 1064 bytes into a destination of size 1024 223 | sprintf(szErrorMsg, " Error - could not create directory \"%s\".\n", szDecoyDir); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1700:76: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=] 1700 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoySQT); | ^~ ~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1700:23: note: ‘sprintf’ output between 41 and 1064 bytes into a destination of size 256 1700 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoySQT); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1675:67: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=] 1675 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputSQT); | ^~ ~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1675:20: note: ‘sprintf’ output between 35 and 1058 bytes into a destination of size 256 1675 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputSQT); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1763:76: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=] 1763 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyTxt); | ^~ ~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1763:23: note: ‘sprintf’ output between 41 and 1064 bytes into a destination of size 256 1763 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyTxt); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1737:67: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=] 1737 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputTxt); | ^~ ~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1737:20: note: ‘sprintf’ output between 35 and 1058 bytes into a destination of size 256 1737 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputTxt); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1826:76: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=] 1826 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyPepXML); | ^~ ~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1826:23: note: ‘sprintf’ output between 41 and 1064 bytes into a destination of size 256 1826 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyPepXML); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1800:67: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=] 1800 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPepXML); | ^~ ~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1800:20: note: ‘sprintf’ output between 35 and 1058 bytes into a destination of size 256 1800 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPepXML); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1854:67: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=] 1854 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPercolator); | ^~ ~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1854:20: note: ‘sprintf’ output between 35 and 1058 bytes into a destination of size 256 1854 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPercolator); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1975:32: warning: ‘%s’ directive writing up to 255 bytes into a region of size 128 [-Wformat-overflow=] 1975 | sprintf(szOut, "%s", szStatusMsg); | ^~ ~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1975:23: note: ‘sprintf’ output between 1 and 256 bytes into a destination of size 128 1975 | sprintf(szOut, "%s", szStatusMsg); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometWritePepXML.cpp: In static member function ‘static void CometWritePepXML::ReadInstrument(char*, char*)’: CometSearch/CometWritePepXML.cpp:910:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 910 | GetVal(szMsInstrumentElement, "\"msModel\" value", szModel); | ^~~~~~~~~~~~~~~~~~~ CometSearch/CometWritePepXML.cpp:911:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 911 | GetVal(szMsInstrumentElement, "\"msManufacturer\" value", szManufacturer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from CometSearch/CometPostAnalysis.cpp:19: CometSearch/ThreadPool.h: In instantiation of ‘ThreadManager::ThreadManager(ThreadPool*) [with T = PostAnalysisThreadData*]’: CometSearch/ThreadPool.h:69:10: required from ‘ThreadPool::ThreadPool(ThreadPool::ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadPool::ThreadProc = void (*)(PostAnalysisThreadData*)]’ CometSearch/CometPostAnalysis.cpp:46:38: required from here CometSearch/ThreadPool.h:257:13: warning: cast between incompatible function types from ‘uint32_t (*)(void*)’ {aka ‘unsigned int (*)(void*)’} to ‘ThreadProc’ {aka ‘void* (*)(void*)’} [-Wcast-function-type] 257 | reinterpret_cast(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from CometSearch/CometSearch.cpp:19: CometSearch/ThreadPool.h: In instantiation of ‘ThreadManager::ThreadManager(ThreadPool*) [with T = SearchThreadData*]’: CometSearch/ThreadPool.h:69:10: required from ‘ThreadPool::ThreadPool(ThreadPool::ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadPool::ThreadProc = void (*)(SearchThreadData*)]’ CometSearch/CometSearch.cpp:138:66: required from here CometSearch/ThreadPool.h:257:13: warning: cast between incompatible function types from ‘uint32_t (*)(void*)’ {aka ‘unsigned int (*)(void*)’} to ‘ThreadProc’ {aka ‘void* (*)(void*)’} [-Wcast-function-type] 257 | reinterpret_cast(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometWriteOut.cpp: In static member function ‘static bool CometWriteOut::PrintResults(int, bool, FILE*)’: CometSearch/CometWriteOut.cpp:124:32: warning: ‘%.5d’ directive writing between 5 and 11 bytes into a region of size between 0 and 1022 [-Wformat-overflow=] 124 | sprintf(szOutput, "%s/%s.%.5d.%.5d.%d.out", | ^~~~ CometSearch/CometWriteOut.cpp:124:14: note: ‘sprintf’ output between 20 and 1064 bytes into a destination of size 1024 124 | sprintf(szOutput, "%s/%s.%.5d.%.5d.%d.out", | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 125 | g_staticParams.inputFile.szBaseName, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 126 | pStr, | ~~~~~ 127 | pQuery->_spectrumInfoInternal.iScanNumber, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 128 | pQuery->_spectrumInfoInternal.iScanNumber, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 129 | pQuery->_spectrumInfoInternal.iChargeState); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometWriteOut.cpp:115:35: warning: ‘%s’ directive writing up to 511 bytes into a region of size between 506 and 1017 [-Wformat-overflow=] 115 | sprintf(szOutput, "%s_decoy/%s.%.5d.%.5d.%d.out", | ^~ CometSearch/CometWriteOut.cpp:115:14: note: ‘sprintf’ output between 26 and 1070 bytes into a destination of size 1024 115 | sprintf(szOutput, "%s_decoy/%s.%.5d.%.5d.%d.out", | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 116 | g_staticParams.inputFile.szBaseName, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 | pStr, | ~~~~~ 118 | pQuery->_spectrumInfoInternal.iScanNumber, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 119 | pQuery->_spectrumInfoInternal.iScanNumber, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 120 | pQuery->_spectrumInfoInternal.iChargeState); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometWriteOut.cpp:273:28: warning: ‘%+d’ directive writing between 2 and 11 bytes into a region of size 9 [-Wformat-overflow=] 273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates); | ^~~ CometSearch/CometWriteOut.cpp:273:26: note: directive argument in the range [1, 2147483647] 273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates); | ^~~~~~ CometSearch/CometWriteOut.cpp:273:14: note: ‘sprintf’ output between 4 and 13 bytes into a destination of size 10 273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometWriteOut.cpp:151:59: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 226 [-Wformat-overflow=] 151 | sprintf(szErrorMsg, " Error - cannot write to file %s.\n", szOutput); | ^~ ~~~~~~~~ CometSearch/CometWriteOut.cpp:151:14: note: ‘sprintf’ output between 33 and 1056 bytes into a destination of size 256 151 | sprintf(szErrorMsg, " Error - cannot write to file %s.\n", szOutput); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd CometSearch ; make make[3]: Entering directory '/<>/CometSearch' ar rcs libcometsearch.a Threading.o CometInterfaces.o CometSearch.o CometPreprocess.o CometPostAnalysis.o CometMassSpecUtils.o CometWriteOut.o CometWriteSqt.o CometWritePepXML.o CometWritePercolator.o CometWriteTxt.o CometSearchManager.o CometCheckForUpdates.o make[3]: Leaving directory '/<>/CometSearch' g++ Comet.o CometSearch/CometCheckForUpdates.o CometSearch/CometMassSpecUtils.o CometSearch/CometPreprocess.o CometSearch/CometSearchManager.o CometSearch/CometWritePepXML.o CometSearch/CometWriteSqt.o CometSearch/Threading.o CometSearch/CometInterfaces.o CometSearch/CometPostAnalysis.o CometSearch/CometSearch.o CometSearch/CometWriteOut.o CometSearch/CometWritePercolator.o CometSearch/CometWriteTxt.o -o comet-ms -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -L/usr/lib -lmstoolkitlite -lm -lpthread /usr/bin/ld: skipping incompatible /usr/lib/libmstoolkitlite.so when searching for -lmstoolkitlite /usr/bin/ld: skipping incompatible /usr/lib/libmstoolkitlite.a when searching for -lmstoolkitlite /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib/libmstoolkitlite.so when searching for -lmstoolkitlite /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib/libmstoolkitlite.a when searching for -lmstoolkitlite /usr/bin/ld: skipping incompatible /usr/lib/../lib/libmstoolkitlite.so when searching for -lmstoolkitlite /usr/bin/ld: skipping incompatible /usr/lib/../lib/libmstoolkitlite.a when searching for -lmstoolkitlite /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/9/../../../libmstoolkitlite.so when searching for -lmstoolkitlite /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/9/../../../libmstoolkitlite.a when searching for -lmstoolkitlite /usr/bin/ld: skipping incompatible /usr/lib/libmstoolkitlite.so when searching for -lmstoolkitlite /usr/bin/ld: skipping incompatible /usr/lib/libmstoolkitlite.a when searching for -lmstoolkitlite /usr/bin/ld: cannot find -lmstoolkitlite collect2: error: ld returned 1 exit status make[2]: *** [Makefile:20: comet-ms] Error 1 make[2]: Leaving directory '/<>' make[1]: *** [debian/rules:21: override_dh_auto_build] Error 2 make[1]: Leaving directory '/<>' make: *** [debian/rules:12: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-05-20T15:13:43Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 74032 Build-Time: 71 Distribution: unstable Fail-Stage: build Foreign Architectures: armel Host Architecture: armel Install-Time: 19 Job: comet-ms_2019015+cleaned1-2 Machine Architecture: amd64 Package: comet-ms Package-Time: 99 Source-Version: 2019015+cleaned1-2 Space: 74032 Status: attempted Version: 2019015+cleaned1-2 -------------------------------------------------------------------------------- Finished at 2020-05-20T15:13:43Z Build needed 00:01:39, 74032k disk space