sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | clustalw 2.1+lgpl-6 (armel) Sun, 17 Nov 2019 13:45:57 +0000 | +==============================================================================+ Package: clustalw Version: 2.1+lgpl-6 Source Version: 2.1+lgpl-6 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-01d80a19-241f-4a48-9052-4f988bbb797e' with '<>' I: NOTICE: Log filtering will replace 'build/clustalw-V2G0GD/resolver-NMWIDx' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [139 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 2019-11-17-0816.02.pdiff [2730 B] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-11-17-0816.02.pdiff [2730 B] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-11-17-0816.02.pdiff [6469 B] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-11-17-0816.02.pdiff [6469 B] Get:6 http://debian.oregonstate.edu/debian unstable/main armel Packages [7932 kB] Fetched 8136 kB in 2s (4294 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: 'clustalw' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/clustalw.git Please use: git clone https://salsa.debian.org/med-team/clustalw.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 373 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main clustalw 2.1+lgpl-6 (dsc) [2050 B] Get:2 http://debian.oregonstate.edu/debian unstable/main clustalw 2.1+lgpl-6 (tar) [351 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main clustalw 2.1+lgpl-6 (diff) [19.9 kB] Fetched 373 kB in 0s (8107 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/clustalw-V2G0GD/clustalw-2.1+lgpl' with '<>' I: NOTICE: Log filtering will replace 'build/clustalw-V2G0GD' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 11~), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel Filtered Build-Depends: debhelper (>= 11~), 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 [404 B] Get:5 copy:/<>/apt_archive ./ Packages [491 B] Fetched 1852 B in 0s (92.1 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 cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi 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:armel libc6-dev-armel-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel libgcc-9-dev-armel-cross libgcc1:armel libgcc1-armel-cross libglib2.0-0 libgomp1:armel libgomp1-armel-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libpipeline1 libsigsegv2 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 po-debconf sensible-utils ucf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican | wordlist whois vacation gcc-9-locales cpp-doc dh-make binutils-multiarch gcc-9-doc libstdc++6-9-dbg-armel-cross libgcc1-dbg-armel-cross libgomp1-dbg-armel-cross libitm1-dbg-armel-cross libatomic1-dbg-armel-cross libasan5-dbg-armel-cross liblsan0-dbg-armel-cross libtsan0-dbg-armel-cross libubsan1-dbg-armel-cross libquadmath0-dbg-armel-cross 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 manpages-dev:armel libstdc++-9-doc:armel libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:armel libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgpm2 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 cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi 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:armel libc6-dev-armel-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel libgcc-9-dev-armel-cross libgcc1:armel libgcc1-armel-cross libglib2.0-0 libgomp1:armel libgomp1-armel-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libpipeline1 libsigsegv2 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 po-debconf sbuild-build-depends-main-dummy:armel sensible-utils ucf 0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 61.8 MB of archives. After this operation, 244 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [912 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 1.22.4-3 [916 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.0-1 [1307 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 armel gcc-9-base armel 9.2.1-19 [194 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.37-6 [253 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.37-6 [119 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.37-6 [67.2 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabi amd64 2.33.1-2 [2721 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi-base amd64 9.2.1-19cross1 [194 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-arm-linux-gnueabi amd64 9.2.1-19cross1 [6812 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabi amd64 4:9.2.1-3.1 [16.7 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.2.1-19cross1 [190 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armel-cross all 2.29-1cross7 [1139 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-armel-cross all 1:9.2.1-19cross1 [39.0 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armel-cross all 9.2.1-19cross1 [74.8 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armel-cross all 9.2.1-19cross1 [8944 B] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armel-cross all 9.2.1-19cross1 [340 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armel-cross all 9.2.1-19cross1 [377 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armel-cross all 9.2.1-19cross1 [110 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-armel-cross all 9.2.1-19cross1 [644 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi amd64 9.2.1-19cross1 [7157 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1464 B] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armel-cross all 5.2.9-2cross7 [1312 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armel-cross all 2.29-1cross7 [2155 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-armel-cross all 9.2.1-19cross1 [1709 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-arm-linux-gnueabi amd64 9.2.1-19cross1 [7390 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1180 B] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b4 [710 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1+b1 [344 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.29-1 [67.4 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armel all 12.8 [6640 B] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-11 [547 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 12.7.1 [173 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.67-1 [104 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.6.2-1 [23.6 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.6.2-1 [14.6 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-2 [145 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.62.2-3 [1318 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20191019-1 [102 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.7.1 [997 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main armel libgcc1 armel 1:9.2.1-19 [38.9 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main armel libc6 armel 2.29-3 [2348 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main armel libasan5 armel 9.2.1-19 [347 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main armel libatomic1 armel 9.2.1-19 [9092 B] Get:79 http://debian.oregonstate.edu/debian unstable/main armel linux-libc-dev armel 5.3.9-2 [986 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main armel libc6-dev armel 2.29-3 [2195 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main armel libgomp1 armel 9.2.1-19 [77.1 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main armel libstdc++6 armel 9.2.1-19 [415 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main armel libubsan1 armel 9.2.1-19 [111 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main armel libgcc-9-dev armel 9.2.1-19 [643 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main armel libstdc++-9-dev armel 9.2.1-19 [1739 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 61.8 MB in 1s (70.6 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 14998 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.9.0-1_amd64.deb ... Unpacking man-db (2.9.0-1) ... 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Unpacking libglib2.0-0:amd64 (2.62.2-3) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../67-libcroco3_0.6.13-1_amd64.deb ... Unpacking libcroco3:amd64 (0.6.13-1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../68-libncurses6_6.1+20191019-1_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20191019-1) ... Selecting previously unselected package gettext. Preparing to unpack .../69-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../70-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../71-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../72-debhelper_12.7.1_all.deb ... Unpacking debhelper (12.7.1) ... Selecting previously unselected package libgcc1:armel. Preparing to unpack .../73-libgcc1_1%3a9.2.1-19_armel.deb ... Unpacking libgcc1:armel (1:9.2.1-19) ... Selecting previously unselected package libc6:armel. Preparing to unpack .../74-libc6_2.29-3_armel.deb ... Unpacking libc6:armel (2.29-3) ... Selecting previously unselected package libasan5:armel. Preparing to unpack .../75-libasan5_9.2.1-19_armel.deb ... Unpacking libasan5:armel (9.2.1-19) ... Selecting previously unselected package libatomic1:armel. Preparing to unpack .../76-libatomic1_9.2.1-19_armel.deb ... Unpacking libatomic1:armel (9.2.1-19) ... Selecting previously unselected package linux-libc-dev:armel. Preparing to unpack .../77-linux-libc-dev_5.3.9-2_armel.deb ... Unpacking linux-libc-dev:armel (5.3.9-2) ... Selecting previously unselected package libc6-dev:armel. Preparing to unpack .../78-libc6-dev_2.29-3_armel.deb ... Unpacking libc6-dev:armel (2.29-3) ... Selecting previously unselected package libgomp1:armel. Preparing to unpack .../79-libgomp1_9.2.1-19_armel.deb ... Unpacking libgomp1:armel (9.2.1-19) ... Selecting previously unselected package libstdc++6:armel. Preparing to unpack .../80-libstdc++6_9.2.1-19_armel.deb ... Unpacking libstdc++6:armel (9.2.1-19) ... Selecting previously unselected package libubsan1:armel. Preparing to unpack .../81-libubsan1_9.2.1-19_armel.deb ... Unpacking libubsan1:armel (9.2.1-19) ... Selecting previously unselected package libgcc-9-dev:armel. Preparing to unpack .../82-libgcc-9-dev_9.2.1-19_armel.deb ... Unpacking libgcc-9-dev:armel (9.2.1-19) ... Selecting previously unselected package libstdc++-9-dev:armel. Preparing to unpack .../83-libstdc++-9-dev_9.2.1-19_armel.deb ... Unpacking libstdc++-9-dev:armel (9.2.1-19) ... Selecting previously unselected package sbuild-build-depends-main-dummy:armel. Preparing to unpack .../84-sbuild-build-depends-main-dummy_0.invalid.0_armel.deb ... Unpacking sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000001-1) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up libfile-which-perl (1.23-1) ... Setting up binutils-arm-linux-gnueabi (2.33.1-2) ... Setting up libmagic-mgc (1:5.37-6) ... Setting up libarchive-zip-perl (1.67-1) ... Setting up libglib2.0-0:amd64 (2.62.2-3) ... No schema files found: doing nothing. Setting up libdebhelper-perl (12.7.1) ... Setting up libmagic1:amd64 (1:5.37-6) ... Setting up linux-libc-dev:armel (5.3.9-2) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.37-6) ... Setting up libyaml-perl (1.29-1) ... Setting up libicu63:amd64 (63.2-2) ... Setting up linux-libc-dev-armel-cross (5.2.9-2cross7) ... Setting up gcc-9-arm-linux-gnueabi-base:amd64 (9.2.1-19cross1) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up autotools-dev (20180224.1) ... Setting up cross-config (2.6.15-3) ... Setting up libncurses6:amd64 (6.1+20191019-1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up cpp-9-arm-linux-gnueabi (9.2.1-19cross1) ... Setting up autopoint (0.19.8.1-9) ... Setting up gcc-9-cross-base (9.2.1-19cross1) ... Setting up libc6-armel-cross (2.29-1cross7) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libc6-dev-armel-cross (2.29-1cross7) ... 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 (2.9.4+dfsg1-7+b4) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up gcc-9-base:armel (9.2.1-19) ... Setting up libfile-stripnondeterminism-perl (1.6.2-1) ... Setting up libgomp1-armel-cross (9.2.1-19cross1) ... Setting up libtool (2.4.6-11) ... Setting up m4 (1.4.18-4) ... Setting up libatomic1-armel-cross (9.2.1-19cross1) ... Setting up libgcc1-armel-cross (1:9.2.1-19cross1) ... Setting up libasan5-armel-cross (9.2.1-19cross1) ... Setting up cpp-arm-linux-gnueabi (4:9.2.1-3.1) ... 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 (3.0038+nmu1) ... Setting up autoconf (2.69-11) ... Setting up dh-strip-nondeterminism (1.6.2-1) ... Setting up dwz (0.13-2) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libstdc++6-armel-cross (9.2.1-19cross1) ... Setting up man-db (2.9.0-1) ... 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 intltool-debian (0.35.0+20060710.5) ... Setting up libubsan1-armel-cross (9.2.1-19cross1) ... Setting up libgcc-9-dev-armel-cross (9.2.1-19cross1) ... Setting up libxml-libxml-perl (2.0134+dfsg-1+b1) ... 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 po-debconf (1.0.21) ... Setting up libstdc++-9-dev-armel-cross (9.2.1-19cross1) ... Setting up gcc-9-arm-linux-gnueabi (9.2.1-19cross1) ... Setting up g++-9-arm-linux-gnueabi (9.2.1-19cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up gcc-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up g++-arm-linux-gnueabi (4:9.2.1-3.1) ... 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 libgcc1:armel (1:9.2.1-19) ... Setting up libc6:armel (2.29-3) ... Setting up libc6-dev:armel (2.29-3) ... Setting up libstdc++6:armel (9.2.1-19) ... Setting up debhelper (12.7.1) ... Setting up libgomp1:armel (9.2.1-19) ... Setting up dh-autoreconf (19) ... Setting up libasan5:armel (9.2.1-19) ... Setting up libatomic1:armel (9.2.1-19) ... Setting up libubsan1:armel (9.2.1-19) ... Setting up libgcc-9-dev:armel (9.2.1-19) ... Setting up libstdc++-9-dev:armel (9.2.1-19) ... Setting up sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Processing triggers for libc-bin (2.29-3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armel included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 #1 SMP Debian 4.9.144-3.1 (2019-02-19) amd64 (x86_64) Toolchain package versions: binutils_2.33.1-2 dpkg-dev_1.19.7 g++-8_8.3.0-24 g++-9_9.2.1-19 gcc-8_8.3.0-24 gcc-9_9.2.1-19 libc6-dev_2.29-3 libstdc++-8-dev_8.3.0-24 libstdc++-9-dev_9.2.1-19 libstdc++-9-dev-armel-cross_9.2.1-19cross1 libstdc++6_9.2.1-19 libstdc++6-armel-cross_9.2.1-19cross1 linux-libc-dev_5.3.9-2 Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.46 bash_5.0-5 binutils_2.33.1-2 binutils-arm-linux-gnueabi_2.33.1-2 binutils-common_2.33.1-2 binutils-x86-64-linux-gnu_2.33.1-2 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-8_8.3.0-24 cpp-9_9.2.1-19 cpp-9-arm-linux-gnueabi_9.2.1-19cross1 cpp-arm-linux-gnueabi_4:9.2.1-3.1 cross-config_2.6.15-3 crossbuild-essential-armel_12.8 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.1 debian-archive-keyring_2019.1 debianutils_4.9 dh-autoreconf_19 dh-strip-nondeterminism_1.6.2-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.13-2 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-8_8.3.0-24 g++-9_9.2.1-19 g++-9-arm-linux-gnueabi_9.2.1-19cross1 g++-arm-linux-gnueabi_4:9.2.1-3.1 gcc_4:9.2.1-3.1 gcc-8_8.3.0-24 gcc-8-base_8.3.0-24 gcc-9_9.2.1-19 gcc-9-arm-linux-gnueabi_9.2.1-19cross1 gcc-9-arm-linux-gnueabi-base_9.2.1-19cross1 gcc-9-base_9.2.1-19 gcc-9-cross-base_9.2.1-19cross1 gcc-arm-linux-gnueabi_4:9.2.1-3.1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.17-3 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3+b1 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-19 libasan5-armel-cross_9.2.1-19cross1 libatomic1_9.2.1-19 libatomic1-armel-cross_9.2.1-19cross1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2 libbinutils_2.33.1-2 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-3 libc-dev-bin_2.29-3 libc6_2.29-3 libc6-armel-cross_2.29-1cross7 libc6-dev_2.29-3 libc6-dev-armel-cross_2.29-1cross7 libcap-ng0_0.7.9-2.1+b1 libcc1-0_9.2.1-19 libcom-err2_1.45.4-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000001-1 libcroco3_0.6.13-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.1 libdebian-dpkgcross-perl_2.6.15-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.6.2-1 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-24 libgcc-9-dev_9.2.1-19 libgcc-9-dev-armel-cross_9.2.1-19cross1 libgcc1_1:9.2.1-19 libgcc1-armel-cross_1:9.2.1-19cross1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.10-5 libgomp1_9.2.1-19 libgomp1-armel-cross_9.2.1-19cross1 libgpg-error0_1.36-7 libhogweed4_3.5.1+really3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libio-string-perl_1.08-3 libisl19_0.20-2 libisl21_0.21-2 libitm1_9.2.1-19 liblocale-gettext-perl_1.07-4 liblsan0_9.2.1-19 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-24 libncurses6_6.1+20191019-1 libncursesw6_6.1+20191019-1 libnettle6_3.5.1+really3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libp11-kit0_0.23.18.1-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.32-5+b1 libpcre3_2:8.39-12+b1 libperl5.28_5.28.1-6 libperl5.30_5.30.0-9 libpipeline1_1.5.1-2 libquadmath0_9.2.1-19 libseccomp2_2.4.2-2 libselinux1_2.9-3+b1 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2+b2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libss2_1.45.4-1 libstdc++-8-dev_8.3.0-24 libstdc++-9-dev_9.2.1-19 libstdc++-9-dev-armel-cross_9.2.1-19cross1 libstdc++6_9.2.1-19 libstdc++6-armel-cross_9.2.1-19cross1 libsub-override-perl_0.09-2 libsystemd0_243-7 libtasn1-6_4.14-3 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libtsan0_9.2.1-19 libubsan1_9.2.1-19 libubsan1-armel-cross_9.2.1-19cross1 libuchardet0_0.0.6-3 libudev1_243-7 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml-libxml-perl_2.0134+dfsg-1+b1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.02+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7+b4 libyaml-perl_1.29-1 libzstd1_1.4.4+dfsg-1 linux-libc-dev_5.3.9-2 linux-libc-dev-armel-cross_5.2.9-2cross7 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-1 mawk_1.3.3-17+b3 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 passwd_1:4.7-2 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.0-9 po-debconf_1.0.21 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.96-1 tar_1.30+dfsg-6+b1 tzdata_2019c-3 ucf_3.0038+nmu1 util-linux_2.34-0.1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-1+b1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: clustalw Binary: clustalw Architecture: any Version: 2.1+lgpl-6 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Homepage: http://www.clustal.org/clustal2/ Standards-Version: 4.1.5 Vcs-Browser: https://salsa.debian.org/med-team/clustalw Vcs-Git: https://salsa.debian.org/med-team/clustalw.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~) Package-List: clustalw deb science optional arch=any Checksums-Sha1: f29784f68585544baa77cbeca6392e533d4cf433 350761 clustalw_2.1+lgpl.orig.tar.gz caa96d12fe4806f93574ecfd5f8428a1058f8cc2 19920 clustalw_2.1+lgpl-6.debian.tar.xz Checksums-Sha256: e052059b87abfd8c9e695c280bfba86a65899138c82abccd5b00478a80f49486 350761 clustalw_2.1+lgpl.orig.tar.gz 733ee21257189705234d10a61cf9db72028bcae49e0fe959f363464165032403 19920 clustalw_2.1+lgpl-6.debian.tar.xz Files: 144df8440a0ae083d5167616c8ceeb41 350761 clustalw_2.1+lgpl.orig.tar.gz 29fbeb5aa513189a9141eaf0f9b09c5b 19920 clustalw_2.1+lgpl-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- 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15:12:38 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./clustalw_2.1+lgpl-6.dsc dpkg-source: info: extracting clustalw in /<> dpkg-source: info: unpacking clustalw_2.1+lgpl.orig.tar.gz dpkg-source: info: unpacking clustalw_2.1+lgpl-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling.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-01d80a19-241f-4a48-9052-4f988bbb797e 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 clustalw dpkg-buildpackage: info: source version 2.1+lgpl-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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 dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a configure.ac:79: installing './compile' src/Makefile.am:21: warning: source file './pairwise/FullPairwiseAlign.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least a source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, automake: this behaviour will change in future Automake versions: they will automake: unconditionally cause object files to be placed in the same subdirectory automake: of the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. src/Makefile.am:21: warning: source file './pairwise/FastPairwiseAlign.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/MSFFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/FileReader.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/PIRFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/RSFFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/GDEFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/InFileStream.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/ClustalFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/PearsonFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/FileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './fileInput/EMBLFileParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/RootedClusterTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/UPGMAAlgorithm.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/Node.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/RootedGuideTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UPGMA/RootedTreeOutput.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/Tree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/ClusterTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/TreeInterface.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/UnRootedClusterTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/ClusterTreeOutput.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/RandomGenerator.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/NJTree.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './tree/AlignmentSteps.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './interface/InteractiveMenu.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './interface/CommandLineParser.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './substitutionMatrix/SubMatrix.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/Iteration.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/MSA.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/MyersMillerProfileAlign.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/ProfileStandard.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/ProfileWithSub.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/ProfileBase.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './multipleAlign/LowScoreSegProfile.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/OutputFile.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/UserParameters.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/Utility.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/InvalidCombination.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/DebugLog.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/ClustalWResources.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/VectorOutOfRange.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/SymMatrix.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './general/Stats.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './Help.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './alignment/Alignment.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './alignment/AlignmentOutput.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './alignment/ObjectiveScore.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './alignment/Sequence.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './Clustal.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled src/Makefile.am:21: warning: source file './main.cpp' is in a subdirectory, src/Makefile.am:21: but option 'subdir-objects' is disabled dh_auto_configure -a ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabi --libexecdir=\${prefix}/lib/arm-linux-gnueabi --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --host=arm-linux-gnueabi configure: WARNING: unrecognized options: --disable-maintainer-mode configure: loading site script /etc/dpkg-cross/cross-config.armel checking build system type... x86_64-pc-linux-gnu checking host system type... arm-unknown-linux-gnueabi checking target system type... arm-unknown-linux-gnueabi building for linux-gnueabi checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for arm-linux-gnueabi-strip... arm-linux-gnueabi-strip checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make sets $(MAKE)... (cached) yes checking for arm-linux-gnueabi-gcc... arm-linux-gnueabi-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... yes checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether arm-linux-gnueabi-gcc accepts -g... yes checking for arm-linux-gnueabi-gcc option to accept ISO C89... none needed checking whether arm-linux-gnueabi-gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of arm-linux-gnueabi-gcc... none checking for arm-linux-gnueabi-g++... arm-linux-gnueabi-g++ checking whether we are using the GNU C++ compiler... yes checking whether arm-linux-gnueabi-g++ accepts -g... yes checking dependency style of arm-linux-gnueabi-g++... none checking for arm-linux-gnueabi-ranlib... arm-linux-gnueabi-ranlib checking how to run the C++ preprocessor... arm-linux-gnueabi-g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for an ANSI C-conforming const... yes checking for size_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating m4/Makefile config.status: creating src/Makefile config.status: creating src/clustalw_version.h config.status: creating src/config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build -a make -j1 make[1]: Entering directory '/<>' Making all in m4 make[2]: Entering directory '/<>/m4' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/<>/m4' Making all in src make[2]: Entering directory '/<>/src' make all-recursive make[3]: Entering directory '/<>/src' make[4]: Entering directory '/<>/src' arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o FullPairwiseAlign.o `test -f './pairwise/FullPairwiseAlign.cpp' || echo './'`./pairwise/FullPairwiseAlign.cpp In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./pairwise/../alignment/Alignment.h:42, from ./pairwise/PairwiseAlignBase.h:10, from ./pairwise/FullPairwiseAlign.h:9, from ./pairwise/FullPairwiseAlign.cpp:9: ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o FastPairwiseAlign.o `test -f './pairwise/FastPairwiseAlign.cpp' || echo './'`./pairwise/FastPairwiseAlign.cpp In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./pairwise/../alignment/Alignment.h:42, from ./pairwise/PairwiseAlignBase.h:10, from ./pairwise/FastPairwiseAlign.h:9, from ./pairwise/FastPairwiseAlign.cpp:10: ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MSFFileParser.o `test -f './fileInput/MSFFileParser.cpp' || echo './'`./fileInput/MSFFileParser.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o FileReader.o `test -f './fileInput/FileReader.cpp' || echo './'`./fileInput/FileReader.cpp In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./fileInput/../alignment/Alignment.h:42, from ./fileInput/FileReader.h:12, from ./fileInput/FileReader.cpp:29: ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./fileInput/FileReader.cpp:29: ./fileInput/FileReader.h:42:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./fileInput/FileReader.h:11, from ./fileInput/FileReader.cpp:29: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./fileInput/FileReader.cpp: In member function ‘int clustalw::FileReader::readSeqs(clustalw::Alignment*, int, std::string*)’: ./fileInput/FileReader.cpp:155:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 155 | auto_ptr fileParser; // Means we dont need to delete it! | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./fileInput/FileReader.h:11, from ./fileInput/FileReader.cpp:29: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./fileInput/FileReader.cpp: At global scope: ./fileInput/FileReader.cpp:426:42: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 426 | void FileReader::checkInfile(int *nseqs, auto_ptr& fileParser) | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./fileInput/FileReader.h:11, from ./fileInput/FileReader.cpp:29: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PIRFileParser.o `test -f './fileInput/PIRFileParser.cpp' || echo './'`./fileInput/PIRFileParser.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RSFFileParser.o `test -f './fileInput/RSFFileParser.cpp' || echo './'`./fileInput/RSFFileParser.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GDEFileParser.o `test -f './fileInput/GDEFileParser.cpp' || echo './'`./fileInput/GDEFileParser.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o InFileStream.o `test -f './fileInput/InFileStream.cpp' || echo './'`./fileInput/InFileStream.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClustalFileParser.o `test -f './fileInput/ClustalFileParser.cpp' || echo './'`./fileInput/ClustalFileParser.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PearsonFileParser.o `test -f './fileInput/PearsonFileParser.cpp' || echo './'`./fileInput/PearsonFileParser.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o FileParser.o `test -f './fileInput/FileParser.cpp' || echo './'`./fileInput/FileParser.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o EMBLFileParser.o `test -f './fileInput/EMBLFileParser.cpp' || echo './'`./fileInput/EMBLFileParser.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedClusterTree.o `test -f './tree/UPGMA/RootedClusterTree.cpp' || echo './'`./tree/UPGMA/RootedClusterTree.cpp In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/../ClusterTree.h:20, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./tree/UPGMA/../ClusterTree.h:23, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: ./tree/UPGMA/../../general/OutputFile.h:26:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: ./tree/UPGMA/../ClusterTree.h:70:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 70 | auto_ptr quickDistMat; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/UPGMA/RootedClusterTree.cpp:9: ./tree/UPGMA/RootedClusterTree.h:22:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 22 | auto_ptr treeFromDistMatrix(RootedGuideTree* phyloTree, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/UPGMA/RootedClusterTree.cpp:11: ./tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 23 | auto_ptr generateTree(RootedGuideTree* phyTree, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/UPGMA/RootedClusterTree.cpp:11: ./tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 51 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./tree/UPGMA/RootedClusterTree.cpp:17:1: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 17 | auto_ptr RootedClusterTree::treeFromDistMatrix(RootedGuideTree* phyloTree,DistMatrix* distMat, Alignment *alignPtr, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./tree/UPGMA/RootedClusterTree.cpp: In member function ‘std::auto_ptr clustalw::RootedClusterTree::treeFromDistMatrix(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string&)’: ./tree/UPGMA/RootedClusterTree.cpp:21:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 21 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/UPGMA/../ClusterTree.h:16, from ./tree/UPGMA/RootedClusterTree.h:8, from ./tree/UPGMA/RootedClusterTree.cpp:9: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UPGMAAlgorithm.o `test -f './tree/UPGMA/UPGMAAlgorithm.cpp' || echo './'`./tree/UPGMA/UPGMAAlgorithm.cpp In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, from ./tree/UPGMA/UPGMAAlgorithm.h:8, from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: ./tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 23 | auto_ptr generateTree(RootedGuideTree* phyTree, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./tree/UPGMA/../../general/SquareMat.h:9, from ./tree/UPGMA/../../general/clustalw.h:43, from ./tree/UPGMA/UPGMAAlgorithm.h:6, from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: ./tree/UPGMA/UPGMAAlgorithm.h:51:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 51 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./tree/UPGMA/../../general/SquareMat.h:9, from ./tree/UPGMA/../../general/clustalw.h:43, from ./tree/UPGMA/UPGMAAlgorithm.h:6, from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./tree/UPGMA/UPGMAAlgorithm.cpp:27:1: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 27 | auto_ptr UPGMAAlgorithm::generateTree(RootedGuideTree* phyTree, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./tree/UPGMA/../../general/SquareMat.h:9, from ./tree/UPGMA/../../general/clustalw.h:43, from ./tree/UPGMA/UPGMAAlgorithm.h:6, from ./tree/UPGMA/UPGMAAlgorithm.cpp:4: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Node.o `test -f './tree/UPGMA/Node.cpp' || echo './'`./tree/UPGMA/Node.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedGuideTree.o `test -f './tree/UPGMA/RootedGuideTree.cpp' || echo './'`./tree/UPGMA/RootedGuideTree.cpp In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, from ./tree/UPGMA/RootedGuideTree.cpp:10: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RootedTreeOutput.o `test -f './tree/UPGMA/RootedTreeOutput.cpp' || echo './'`./tree/UPGMA/RootedTreeOutput.cpp In file included from ./tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/UPGMA/../../alignment/Alignment.h:42, from ./tree/UPGMA/RootedGuideTree.h:17, from ./tree/UPGMA/RootedTreeOutput.h:15, from ./tree/UPGMA/RootedTreeOutput.cpp:9: ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Tree.o `test -f './tree/Tree.cpp' || echo './'`./tree/Tree.cpp In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./tree/Tree.cpp:10: ./tree/Tree.h:26:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 26 | auto_ptr createSets(int firstSeq, int lastSeq); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./tree/../alignment/Alignment.h:38, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./tree/Tree.cpp:278:1: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 278 | auto_ptr Tree::createSets(int firstSeq, int lastSeq) | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./tree/../alignment/Alignment.h:38, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./tree/Tree.cpp: In member function ‘std::auto_ptr clustalw::Tree::createSets(int, int)’: ./tree/Tree.cpp:280:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 280 | auto_ptr progAlignSteps; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./tree/../alignment/Alignment.h:38, from ./tree/Tree.h:13, from ./tree/Tree.cpp:10: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClusterTree.o `test -f './tree/ClusterTree.cpp' || echo './'`./tree/ClusterTree.cpp In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/ClusterTree.h:20, from ./tree/ClusterTree.cpp:9: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./tree/ClusterTree.h:23, from ./tree/ClusterTree.cpp:9: ./tree/../general/OutputFile.h:26:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/ClusterTree.h:16, from ./tree/ClusterTree.cpp:9: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/ClusterTree.cpp:9: ./tree/ClusterTree.h:70:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 70 | auto_ptr quickDistMat; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/ClusterTree.h:16, from ./tree/ClusterTree.cpp:9: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o TreeInterface.o `test -f './tree/TreeInterface.cpp' || echo './'`./tree/TreeInterface.cpp In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/TreeInterface.h:19, from ./tree/TreeInterface.cpp:15: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:38:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 38 | auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:57:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 57 | auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:102:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 102 | auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:108:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 108 | auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:133:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 133 | auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:138:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 138 | auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:15: ./tree/TreeInterface.h:142:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 142 | auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/ClusterTree.h:23, from ./tree/UnRootedClusterTree.h:8, from ./tree/TreeInterface.cpp:17: ./tree/../general/OutputFile.h:26:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/UnRootedClusterTree.h:8, from ./tree/TreeInterface.cpp:17: ./tree/ClusterTree.h:70:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 70 | auto_ptr quickDistMat; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:18: ./tree/Tree.h:26:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 26 | auto_ptr createSets(int firstSeq, int lastSeq); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/TreeInterface.cpp:23: ./tree/UPGMA/RootedClusterTree.h:22:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 22 | auto_ptr treeFromDistMatrix(RootedGuideTree* phyloTree, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp:31:1: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 31 | auto_ptr | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp:103:1: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 103 | auto_ptr | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp:195:1: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 195 | auto_ptr | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: In member function ‘std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromDistMatNJ(std::vector*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string*, bool*)’: ./tree/TreeInterface.cpp:200:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 200 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./tree/TreeInterface.cpp:208:1: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 208 | auto_ptr | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: In member function ‘std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsUseOldGuideTreeNJ(clustalw::DistMatrix*, clustalw::Alignment*, std::string*, std::vector*, int, int, bool*)’: ./tree/TreeInterface.cpp:214:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 214 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./tree/TreeInterface.cpp:439:1: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 439 | auto_ptr | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: In member function ‘std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromTreeNJ(clustalw::Alignment*, clustalw::DistMatrix*, std::string*, std::vector*, int, int, bool*)’: ./tree/TreeInterface.cpp:445:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 445 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./tree/TreeInterface.cpp:485:1: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 485 | auto_ptr | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: In member function ‘std::auto_ptr clustalw::TreeInterface::getWeightsAndStepsFromDistMatUPGMA(std::vector*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string*, bool*)’: ./tree/TreeInterface.cpp:490:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 490 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: At global scope: ./tree/TreeInterface.cpp:503:1: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 503 | auto_ptr TreeInterface::generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, DistMatrix* distMat, Alignment *alignPtr, int seq1, int nSeqs, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./tree/TreeInterface.cpp: In member function ‘std::auto_ptr clustalw::TreeInterface::generateTreeFromDistMatUPGMA(clustalw::RootedGuideTree*, clustalw::DistMatrix*, clustalw::Alignment*, int, int, std::string*, bool*)’: ./tree/TreeInterface.cpp:506:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 506 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/TreeInterface.h:17, from ./tree/TreeInterface.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UnRootedClusterTree.o `test -f './tree/UnRootedClusterTree.cpp' || echo './'`./tree/UnRootedClusterTree.cpp In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/ClusterTree.h:20, from ./tree/UnRootedClusterTree.h:8, from ./tree/UnRootedClusterTree.cpp:9: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./tree/ClusterTree.h:23, from ./tree/UnRootedClusterTree.h:8, from ./tree/UnRootedClusterTree.cpp:9: ./tree/../general/OutputFile.h:26:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/ClusterTree.h:16, from ./tree/UnRootedClusterTree.h:8, from ./tree/UnRootedClusterTree.cpp:9: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./tree/UnRootedClusterTree.h:8, from ./tree/UnRootedClusterTree.cpp:9: ./tree/ClusterTree.h:70:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 70 | auto_ptr quickDistMat; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./tree/ClusterTree.h:16, from ./tree/UnRootedClusterTree.h:8, from ./tree/UnRootedClusterTree.cpp:9: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClusterTreeOutput.o `test -f './tree/ClusterTreeOutput.cpp' || echo './'`./tree/ClusterTreeOutput.cpp In file included from ./tree/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./tree/../alignment/Alignment.h:42, from ./tree/ClusterTreeOutput.h:11, from ./tree/ClusterTreeOutput.cpp:9: ./tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RandomGenerator.o `test -f './tree/RandomGenerator.cpp' || echo './'`./tree/RandomGenerator.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o NJTree.o `test -f './tree/NJTree.cpp' || echo './'`./tree/NJTree.cpp In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from ./tree/NJTree.h:9, from ./tree/NJTree.cpp:10: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67, from ./tree/NJTree.h:9, from ./tree/NJTree.cpp:10: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In member function ‘virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 957 | _M_fill_insert(end(), __new_size - size(), __x); | ^~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o AlignmentSteps.o `test -f './tree/AlignmentSteps.cpp' || echo './'`./tree/AlignmentSteps.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o InteractiveMenu.o `test -f './interface/InteractiveMenu.cpp' || echo './'`./interface/InteractiveMenu.cpp In file included from ./interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./interface/../fileInput/../alignment/Alignment.h:42, from ./interface/../fileInput/FileReader.h:12, from ./interface/../Clustal.h:18, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./interface/../Clustal.h:18, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../fileInput/FileReader.h:42:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:68:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:69:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:75:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:76:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:77:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:78:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:79:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:80:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./interface/InteractiveMenu.cpp:23: ./interface/../alignment/AlignmentOutput.h:81:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/InteractiveMenu.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./interface/InteractiveMenu.cpp: In member function ‘void clustalw::InteractiveMenu::doSystem()’: ./interface/InteractiveMenu.cpp:1190:15: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 1190 | system(lin1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o CommandLineParser.o `test -f './interface/CommandLineParser.cpp' || echo './'`./interface/CommandLineParser.cpp In file included from ./interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./interface/../fileInput/../alignment/Alignment.h:42, from ./interface/../fileInput/FileReader.h:12, from ./interface/../Clustal.h:18, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./interface/../Clustal.h:18, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../fileInput/FileReader.h:42:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../alignment/AlignmentOutput.h:68:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../alignment/AlignmentOutput.h:69:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../alignment/AlignmentOutput.h:75:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../alignment/AlignmentOutput.h:76:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../alignment/AlignmentOutput.h:77:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../alignment/AlignmentOutput.h:78:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../alignment/AlignmentOutput.h:79:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../alignment/AlignmentOutput.h:80:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: ./interface/../alignment/AlignmentOutput.h:81:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./interface/../general/SquareMat.h:9, from ./interface/../general/clustalw.h:43, from ./interface/../Clustal.h:15, from ./interface/CommandLineParser.h:18, from ./interface/CommandLineParser.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SubMatrix.o `test -f './substitutionMatrix/SubMatrix.cpp' || echo './'`./substitutionMatrix/SubMatrix.cpp In file included from ./substitutionMatrix/SubMatrix.cpp:15: ./substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Iteration.o `test -f './multipleAlign/Iteration.cpp' || echo './'`./multipleAlign/Iteration.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:38:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 38 | auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:57:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 57 | auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:102:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 102 | auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:108:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 108 | auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:133:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 133 | auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:138:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 138 | auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./multipleAlign/Iteration.cpp:17: ./multipleAlign/../tree/TreeInterface.h:142:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 142 | auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./multipleAlign/../alignment/Alignment.h:38, from ./multipleAlign/Iteration.h:8, from ./multipleAlign/Iteration.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./multipleAlign/Iteration.cpp: In member function ‘bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)’: ./multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of ‘char* tmpnam(char*)’, declared with attribute warn_unused_result [-Wunused-result] 231 | tmpnam (buffer); | ~~~~~~~^~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MSA.o `test -f './multipleAlign/MSA.cpp' || echo './'`./multipleAlign/MSA.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileBase.h:14, from ./multipleAlign/MSA.h:10, from ./multipleAlign/MSA.cpp:16: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MyersMillerProfileAlign.o `test -f './multipleAlign/MyersMillerProfileAlign.cpp' || echo './'`./multipleAlign/MyersMillerProfileAlign.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileAlignAlgorithm.h:10, from ./multipleAlign/MyersMillerProfileAlign.h:10, from ./multipleAlign/MyersMillerProfileAlign.cpp:10: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileStandard.o `test -f './multipleAlign/ProfileStandard.cpp' || echo './'`./multipleAlign/ProfileStandard.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileStandard.h:9, from ./multipleAlign/ProfileStandard.cpp:9: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileWithSub.o `test -f './multipleAlign/ProfileWithSub.cpp' || echo './'`./multipleAlign/ProfileWithSub.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileWithSub.h:9, from ./multipleAlign/ProfileWithSub.cpp:9: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProfileBase.o `test -f './multipleAlign/ProfileBase.cpp' || echo './'`./multipleAlign/ProfileBase.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/ProfileBase.h:14, from ./multipleAlign/ProfileBase.cpp:9: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o LowScoreSegProfile.o `test -f './multipleAlign/LowScoreSegProfile.cpp' || echo './'`./multipleAlign/LowScoreSegProfile.cpp In file included from ./multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./multipleAlign/../alignment/Alignment.h:42, from ./multipleAlign/LowScoreSegProfile.h:13, from ./multipleAlign/LowScoreSegProfile.cpp:9: ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o OutputFile.o `test -f './general/OutputFile.cpp' || echo './'`./general/OutputFile.cpp In file included from ./general/OutputFile.cpp:9: ./general/OutputFile.h:26:14: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 26 | std::auto_ptr file; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./general/OutputFile.h:8, from ./general/OutputFile.cpp:9: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UserParameters.o `test -f './general/UserParameters.cpp' || echo './'`./general/UserParameters.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Utility.o `test -f './general/Utility.cpp' || echo './'`./general/Utility.cpp ./general/Utility.cpp: In member function ‘double clustalw::Utility::getReal(const char*, double, double, double)’: ./general/Utility.cpp:183:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 183 | fgets(line, MAXLINE, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ ./general/Utility.cpp: In member function ‘int clustalw::Utility::getInt(const char*, int, int, int)’: ./general/Utility.cpp:221:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 221 | fgets(line, MAXLINE, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62, from ./general/Utility.cpp:18: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62, from ./general/Utility.cpp:18: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62, from ./general/Utility.cpp:18: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In member function ‘double clustalw::Utility::median(std::vector)’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o InvalidCombination.o `test -f './general/InvalidCombination.cpp' || echo './'`./general/InvalidCombination.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o DebugLog.o `test -f './general/DebugLog.cpp' || echo './'`./general/DebugLog.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ClustalWResources.o `test -f './general/ClustalWResources.cpp' || echo './'`./general/ClustalWResources.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o VectorOutOfRange.o `test -f './general/VectorOutOfRange.cpp' || echo './'`./general/VectorOutOfRange.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SymMatrix.o `test -f './general/SymMatrix.cpp' || echo './'`./general/SymMatrix.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Stats.o `test -f './general/Stats.cpp' || echo './'`./general/Stats.cpp In file included from ./general/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./general/../alignment/Alignment.h:42, from ./general/Stats.cpp:15: ./general/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./general/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from ./general/../alignment/Alignment.h:36, from ./general/Stats.cpp:15: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void clustalw::Stats::logInputSeqStats(clustalw::Alignment*)’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Help.o `test -f './Help.cpp' || echo './'`./Help.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Alignment.o `test -f './alignment/Alignment.cpp' || echo './'`./alignment/Alignment.cpp In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, from ./alignment/Alignment.h:42, from ./alignment/Alignment.cpp:25: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o AlignmentOutput.o `test -f './alignment/AlignmentOutput.cpp' || echo './'`./alignment/AlignmentOutput.cpp In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, from ./alignment/Alignment.h:42, from ./alignment/AlignmentOutput.h:24, from ./alignment/AlignmentOutput.cpp:27: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:68:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:69:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:75:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:76:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:77:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:78:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:79:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:80:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./alignment/AlignmentOutput.cpp:27: ./alignment/AlignmentOutput.h:81:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./alignment/AlignmentOutput.cpp:512:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 512 | bool AlignmentOutput::openExplicitFile(auto_ptr& outFile, string fileName) | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./alignment/AlignmentOutput.cpp:535:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 535 | string AlignmentOutput::openOutputFile(auto_ptr& outFile, string prompt, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from ./alignment/AlignmentOutput.h:20, from ./alignment/AlignmentOutput.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ObjectiveScore.o `test -f './alignment/ObjectiveScore.cpp' || echo './'`./alignment/ObjectiveScore.cpp In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, from ./alignment/ObjectiveScore.h:15, from ./alignment/ObjectiveScore.cpp:10: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Sequence.o `test -f './alignment/Sequence.cpp' || echo './'`./alignment/Sequence.cpp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Clustal.o `test -f './Clustal.cpp' || echo './'`./Clustal.cpp In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8, from ./fileInput/../alignment/Alignment.h:42, from ./fileInput/FileReader.h:12, from ./Clustal.h:18, from ./Clustal.cpp:27: ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./Clustal.h:18, from ./Clustal.cpp:27: ./fileInput/FileReader.h:42:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./alignment/AlignmentOutput.h:68:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./alignment/AlignmentOutput.h:69:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./alignment/AlignmentOutput.h:75:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./alignment/AlignmentOutput.h:76:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./alignment/AlignmentOutput.h:77:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./alignment/AlignmentOutput.h:78:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./alignment/AlignmentOutput.h:79:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./alignment/AlignmentOutput.h:80:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.h:20, from ./Clustal.cpp:27: ./alignment/AlignmentOutput.h:81:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:38:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 38 | auto_ptr getWeightsAndStepsFromDistMat(vector* seqWeights, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:57:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 57 | auto_ptr getWeightsAndStepsFromTree(Alignment* alignPtr, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:102:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 102 | auto_ptr getWeightsAndStepsFromDistMatNJ(vector* seqWeights, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:108:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 108 | auto_ptr getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:133:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 133 | auto_ptr getWeightsAndStepsFromTreeNJ(Alignment* alignPtr, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:138:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 138 | auto_ptr getWeightsAndStepsFromDistMatUPGMA(vector* seqWeights, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./Clustal.cpp:33: ./tree/TreeInterface.h:142:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 142 | auto_ptr generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./Clustal.cpp: In member function ‘void clustalw::Clustal::align(std::string*, bool)’: ./Clustal.cpp:162:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 162 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ./Clustal.cpp: In member function ‘void clustalw::Clustal::doAlignUseOldTree(std::string*)’: ./Clustal.cpp:837:5: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 837 | auto_ptr progSteps; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./general/SquareMat.h:9, from ./general/clustalw.h:43, from ./Clustal.h:15, from ./Clustal.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o `test -f './main.cpp' || echo './'`./main.cpp In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8, from ./alignment/Alignment.h:42, from ./main.cpp:10: ./alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 96 | void printInFormat(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ ./alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 97 | void printVectorToFile(vector& temp, char* name = "tempfile.out"); | ^~~~~~~~~~~~~~ In file included from ./main.cpp:16: ./fileInput/FileReader.h:42:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 42 | void checkInfile(int* nseqs, auto_ptr& fileParser); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./interface/../alignment/AlignmentOutput.h:68:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 68 | bool openExplicitFile(auto_ptr& outFile, string fileName); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./interface/../alignment/AlignmentOutput.h:69:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 69 | string openOutputFile(auto_ptr& outFile, string prompt, string path, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./interface/../alignment/AlignmentOutput.h:75:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 75 | auto_ptr clustalOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./interface/../alignment/AlignmentOutput.h:76:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 76 | auto_ptr gcgOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./interface/../alignment/AlignmentOutput.h:77:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 77 | auto_ptr nbrfOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./interface/../alignment/AlignmentOutput.h:78:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 78 | auto_ptr phylipOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./interface/../alignment/AlignmentOutput.h:79:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 79 | auto_ptr gdeOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./interface/../alignment/AlignmentOutput.h:80:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 80 | auto_ptr nexusOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ./interface/../Clustal.h:20, from ./interface/InteractiveMenu.h:15, from ./main.cpp:17: ./interface/../alignment/AlignmentOutput.h:81:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 81 | auto_ptr fastaOutFile; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from ./alignment/Alignment.h:38, from ./main.cpp:10: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ arm-linux-gnueabi-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o clustalw2 FullPairwiseAlign.o FastPairwiseAlign.o MSFFileParser.o FileReader.o PIRFileParser.o RSFFileParser.o GDEFileParser.o InFileStream.o ClustalFileParser.o PearsonFileParser.o FileParser.o EMBLFileParser.o RootedClusterTree.o UPGMAAlgorithm.o Node.o RootedGuideTree.o RootedTreeOutput.o Tree.o ClusterTree.o TreeInterface.o UnRootedClusterTree.o ClusterTreeOutput.o RandomGenerator.o NJTree.o AlignmentSteps.o InteractiveMenu.o CommandLineParser.o SubMatrix.o Iteration.o MSA.o MyersMillerProfileAlign.o ProfileStandard.o ProfileWithSub.o ProfileBase.o LowScoreSegProfile.o OutputFile.o UserParameters.o Utility.o InvalidCombination.o DebugLog.o ClustalWResources.o VectorOutOfRange.o SymMatrix.o Stats.o Help.o Alignment.o AlignmentOutput.o ObjectiveScore.o Sequence.o Clustal.o main.o /usr/lib/gcc-cross/arm-linux-gnueabi/9/../../../../arm-linux-gnueabi/bin/ld: Iteration.o: in function `clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)': ./src/./multipleAlign/Iteration.cpp:231: warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[4]: Leaving directory '/<>/src' make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>/src' make[2]: Entering directory '/<>' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a make -j1 install DESTDIR=/<>/clustalw-2.1\+lgpl/debian/clustalw AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>' Making install in m4 make[2]: Entering directory '/<>/m4' make[3]: Entering directory '/<>/m4' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Leaving directory '/<>/m4' make[2]: Leaving directory '/<>/m4' Making install in src make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/src' make[4]: Entering directory '/<>/src' /bin/mkdir -p '/<>/debian/clustalw/usr/bin' /usr/bin/install -c clustalw2 '/<>/debian/clustalw/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/src' make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>/src' make[2]: Entering directory '/<>' make[3]: Entering directory '/<>' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install # We have to ask upstream if it is important for them that the binary is named clustalw2 mv /<>/debian/clustalw/usr/bin/clustalw2 /<>/debian/clustalw/usr/bin/clustalw make[1]: Leaving directory '/<>' dh_installdocs -a debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs debian/CHANGELOG.upstream make[1]: Leaving directory '/<>' dh_installexamples -a dh_installman -a dh_installmenu -a dh_perl -a dh_perl: /usr/lib/arm-linux-gnueabi/perl/cross-config-5.30.0/Config.pm does not exist (missing build dependency on perl-xs-dev?) dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/clustalw/usr/bin/clustalw contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'clustalw' in '../clustalw_2.1+lgpl-6_armel.deb'. dpkg-deb: building package 'clustalw-dbgsym' in '../clustalw-dbgsym_2.1+lgpl-6_armel.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../clustalw_2.1+lgpl-6_armel.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2019-11-17T13:48:21Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ clustalw_2.1+lgpl-6_armel.changes: ---------------------------------- Format: 1.8 Date: Sat, 14 Jul 2018 17:09:36 +0200 Source: clustalw Binary: clustalw clustalw-dbgsym Built-For-Profiles: cross nocheck Architecture: armel Version: 2.1+lgpl-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: clustalw - global multiple nucleotide or peptide sequence alignment Changes: clustalw (2.1+lgpl-6) unstable; urgency=medium . * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.5 * d/rules: - drop now unneeded hack to remove aclocal dir - drop explicit mentioning of autotools_dev Checksums-Sha1: a21581e70943189aa1e60141712b9cc88f4852b1 4695808 clustalw-dbgsym_2.1+lgpl-6_armel.deb 1041373dd186178cfdf4f40f243406c9a4aef054 4667 clustalw_2.1+lgpl-6_armel.buildinfo 3f7ad455bded1046f0c68fa4fa2420aaa7bfce10 243392 clustalw_2.1+lgpl-6_armel.deb Checksums-Sha256: ccf237c978dc71b0ac624af57aa1afc4ec51171a8eb8c7eec4c4fe346d17da5c 4695808 clustalw-dbgsym_2.1+lgpl-6_armel.deb 1f2edef8f95938e896c96bd0c77518f27f648973102134d4be5f98dc10cb808b 4667 clustalw_2.1+lgpl-6_armel.buildinfo 9e3e5fe1d3722ce3e676f41e71616afc2d2dccea706ab4a162789e5b4b5c1dd5 243392 clustalw_2.1+lgpl-6_armel.deb Files: 2739d32164e704bb7ffff16bd6885071 4695808 debug optional clustalw-dbgsym_2.1+lgpl-6_armel.deb 6660b6c73798d58e054cf08a7638473d 4667 science optional clustalw_2.1+lgpl-6_armel.buildinfo 63f763ce719838f6106bb740312d3759 243392 science optional clustalw_2.1+lgpl-6_armel.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: clustalw Binary: clustalw Architecture: armel Version: 2.1+lgpl-6 Checksums-Md5: 2739d32164e704bb7ffff16bd6885071 4695808 clustalw-dbgsym_2.1+lgpl-6_armel.deb 63f763ce719838f6106bb740312d3759 243392 clustalw_2.1+lgpl-6_armel.deb Checksums-Sha1: a21581e70943189aa1e60141712b9cc88f4852b1 4695808 clustalw-dbgsym_2.1+lgpl-6_armel.deb 3f7ad455bded1046f0c68fa4fa2420aaa7bfce10 243392 clustalw_2.1+lgpl-6_armel.deb Checksums-Sha256: ccf237c978dc71b0ac624af57aa1afc4ec51171a8eb8c7eec4c4fe346d17da5c 4695808 clustalw-dbgsym_2.1+lgpl-6_armel.deb 9e3e5fe1d3722ce3e676f41e71616afc2d2dccea706ab4a162789e5b4b5c1dd5 243392 clustalw_2.1+lgpl-6_armel.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 17 Nov 2019 13:48:21 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.69-11), automake (= 1:1.16.1-4), autopoint (= 0.19.8.1-9), autotools-dev (= 20180224.1), base-files (= 11), base-passwd (= 3.5.46), bash (= 5.0-5), binutils (= 2.33.1-2), binutils-common (= 2.33.1-2), binutils-x86-64-linux-gnu (= 2.33.1-2), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.34-0.1), build-essential (= 12.8), bzip2 (= 1.0.8-2), coreutils (= 8.30-3+b1), cpp (= 4:9.2.1-3.1), cpp-8 (= 8.3.0-24), cpp-9 (= 9.2.1-19), dash (= 0.5.10.2-6), debconf (= 1.5.73), debhelper (= 12.7.1), debianutils (= 4.9), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.6.2-1), diffutils (= 1:3.7-3), dpkg (= 1.19.7), dpkg-dev (= 1.19.7), dwz (= 0.13-2), fdisk (= 2.34-0.1), file (= 1:5.37-6), findutils (= 4.7.0-1), g++ (= 4:9.2.1-3.1), g++-9 (= 9.2.1-19), gcc (= 4:9.2.1-3.1), gcc-8 (= 8.3.0-24), gcc-8-base (= 8.3.0-24), gcc-9 (= 9.2.1-19), gcc-9-base (= 9.2.1-19), gettext (= 0.19.8.1-9), gettext-base (= 0.19.8.1-9), grep (= 3.3-1), groff-base (= 1.22.4-3), gzip (= 1.9-3+b1), hostname (= 3.23), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-5), libarchive-zip-perl (= 1.67-1), libasan5 (= 9.2.1-19), libatomic1 (= 9.2.1-19), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-2), libaudit1 (= 1:2.8.5-2), libbinutils (= 2.33.1-2), libblkid1 (= 2.34-0.1), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-2), libc-bin (= 2.29-3), libc-dev-bin (= 2.29-3), libc6 (= 2.29-3), libc6-dev (= 2.29-3), libcap-ng0 (= 0.7.9-2.1+b1), libcc1-0 (= 9.2.1-19), libcroco3 (= 0.6.13-1), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.250), libdebhelper-perl (= 12.7.1), libdpkg-perl (= 1.19.7), libelf1 (= 0.176-1.1), libfdisk1 (= 2.34-0.1), libffi6 (= 3.2.1-9), libfile-stripnondeterminism-perl (= 1.6.2-1), libgcc-8-dev (= 8.3.0-24), libgcc-9-dev (= 9.2.1-19), libgcc1 (= 1:9.2.1-19), libgcrypt20 (= 1.8.5-3), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libglib2.0-0 (= 2.62.2-3), libgmp10 (= 2:6.1.2+dfsg-4), libgomp1 (= 9.2.1-19), libgpg-error0 (= 1.36-7), libicu63 (= 63.2-2), libisl21 (= 0.21-2), libitm1 (= 9.2.1-19), liblsan0 (= 9.2.1-19), liblz4-1 (= 1.9.2-2), liblzma5 (= 5.2.4-1+b1), libmagic-mgc (= 1:5.37-6), libmagic1 (= 1:5.37-6), libmount1 (= 2.34-0.1), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libmpx2 (= 8.3.0-24), libncurses6 (= 6.1+20191019-1), libncursesw6 (= 6.1+20191019-1), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpcre2-8-0 (= 10.32-5+b1), libpcre3 (= 2:8.39-12+b1), libperl5.30 (= 5.30.0-9), libpipeline1 (= 1.5.1-2), libquadmath0 (= 9.2.1-19), libseccomp2 (= 2.4.2-2), libselinux1 (= 2.9-3+b1), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.34-0.1), libstdc++-9-dev (= 9.2.1-19), libstdc++6 (= 9.2.1-19), libsub-override-perl (= 0.09-2), libsystemd0 (= 243-7), libtinfo6 (= 6.1+20191019-1), libtool (= 2.4.6-11), libtsan0 (= 9.2.1-19), libubsan1 (= 9.2.1-19), libuchardet0 (= 0.0.6-3), libudev1 (= 243-7), libunistring2 (= 0.9.10-2), libuuid1 (= 2.34-0.1), libxml2 (= 2.9.4+dfsg1-7+b4), linux-libc-dev (= 5.3.9-2), login (= 1:4.7-2), lsb-base (= 11.1.0), m4 (= 1.4.18-4), make (= 4.2.1-1.2), man-db (= 2.9.0-1), mawk (= 1.3.3-17+b3), ncurses-base (= 6.1+20191019-1), ncurses-bin (= 6.1+20191019-1), patch (= 2.7.6-6), perl (= 5.30.0-9), perl-base (= 5.30.0-9), perl-modules-5.30 (= 5.30.0-9), po-debconf (= 1.0.21), sed (= 4.7-1), sensible-utils (= 0.0.12), sysvinit-utils (= 2.96-1), tar (= 1.30+dfsg-6+b1), util-linux (= 2.34-0.1), xz-utils (= 5.2.4-1+b1), zlib1g (= 1:1.2.11.dfsg-1+b1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1531580976" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ clustalw-dbgsym_2.1+lgpl-6_armel.deb ------------------------------------ new Debian package, version 2.0. size 4695808 bytes: control archive=540 bytes. 381 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: clustalw-dbgsym Source: clustalw Version: 2.1+lgpl-6 Auto-Built-Package: debug-symbols Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 4725 Depends: clustalw (= 2.1+lgpl-6) Section: debug Priority: optional Description: debug symbols for clustalw Build-Ids: 75c5a6af655cb38f71ebbb696f5490b1a98ec134 drwxr-xr-x root/root 0 2018-07-14 15:09 ./ drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/ drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/lib/ drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/lib/debug/ drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/lib/debug/.build-id/75/ -rw-r--r-- root/root 4828088 2018-07-14 15:09 ./usr/lib/debug/.build-id/75/c5a6af655cb38f71ebbb696f5490b1a98ec134.debug drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/ drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/doc/ lrwxrwxrwx root/root 0 2018-07-14 15:09 ./usr/share/doc/clustalw-dbgsym -> clustalw clustalw_2.1+lgpl-6_armel.deb ----------------------------- new Debian package, version 2.0. size 243392 bytes: control archive=1472 bytes. 1094 bytes, 22 lines control 948 bytes, 13 lines md5sums 192 bytes, 7 lines * postinst #!/bin/sh 167 bytes, 5 lines * postrm #!/bin/sh Package: clustalw Version: 2.1+lgpl-6 Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 694 Depends: libc6 (>= 2.29), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2) Suggests: clustalx, seaview Enhances: bioperl-run, emboss, t-coffee Section: science Priority: optional Homepage: http://www.clustal.org/clustal2/ Description: global multiple nucleotide or peptide sequence alignment This program performs an alignment of multiple nucleotide or amino acid sequences. It recognizes the format of input sequences and whether the sequences are nucleic acid (DNA/RNA) or amino acid (proteins). The output format may be selected from in various formats for multiple alignments such as Phylip or FASTA. Clustal W is very well accepted. . The output of Clustal W can be edited manually but preferably with an alignment editor like SeaView or within its companion Clustal X. When building a model from your alignment, this can be applied for improved database searches. The Debian package hmmer creates such in form of an HMM. drwxr-xr-x root/root 0 2018-07-14 15:09 ./ drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/ drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/bin/ -rwxr-xr-x root/root 635004 2018-07-14 15:09 ./usr/bin/clustalw drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/ drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/clustalw/ -rw-r--r-- root/root 33751 2018-07-14 15:09 ./usr/share/clustalw/clustalw_help drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/doc/clustalw/ -rw-r--r-- root/root 715 2010-09-09 14:26 ./usr/share/doc/clustalw/README -rw-r--r-- root/root 821 2018-07-14 15:09 ./usr/share/doc/clustalw/README.Debian -rw-r--r-- root/root 5219 2018-07-14 15:09 ./usr/share/doc/clustalw/changelog.Debian.gz -rw-r--r-- root/root 3440 2018-07-14 15:09 ./usr/share/doc/clustalw/changelog.gz -rw-r--r-- root/root 2091 2018-07-14 15:09 ./usr/share/doc/clustalw/copyright drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/doc/clustalw/examples/ drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/doc/clustalw/examples/tests.clustalw/ -rw-r--r-- root/root 552 2018-07-14 15:09 ./usr/share/doc/clustalw/examples/tests.clustalw/Makefile -rw-r--r-- root/root 1007 2018-07-14 15:09 ./usr/share/doc/clustalw/examples/tests.clustalw/nuc.data -rw-r--r-- root/root 1013 2018-07-14 15:09 ./usr/share/doc/clustalw/examples/tests.clustalw/nuc2.data -rw-r--r-- root/root 157 2018-07-14 15:09 ./usr/share/doc/clustalw/examples/tests.clustalw/seq drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/man/ drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/man/man1/ -rw-r--r-- root/root 4184 2018-07-14 15:09 ./usr/share/man/man1/clustalw.1.gz drwxr-xr-x root/root 0 2018-07-14 15:09 ./usr/share/menu/ -rw-r--r-- root/root 193 2018-07-14 15:09 ./usr/share/menu/clustalw lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [531 B] Get:5 copy:/<>/apt_archive ./ Packages [616 B] Fetched 2110 B in 0s (99.8 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libdevel-callchecker-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libnamespace-clean-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libssl1.1 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common t1utils Suggested packages: libdata-dump-perl ca-certificates libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libdevel-lexalias-perl libdevel-stacktrace-perl libwww-perl binutils-multiarch libtext-template-perl readline-doc Recommended packages: gnupg libcgi-fast-perl libhttp-message-perl libasync-mergepoint-perl libsereal-perl libtest-fatal-perl libtest-refcount-perl libfreezethaw-perl libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl libauthen-sasl-perl libpackage-stash-xs-perl libunicode-utf8-perl libref-util-perl libtype-tiny-xs-perl libperlio-gzip-perl The following NEW packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libdevel-callchecker-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libnamespace-clean-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libssl1.1 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common sbuild-build-depends-lintian-dummy:armel t1utils 0 upgraded, 75 newly installed, 0 to remove and 0 not upgraded. Need to get 8876 kB of archives. After this operation, 25.1 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 8.0-3 [72.5 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline8 amd64 8.0-3 [160 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 netbase all 5.6 [19.4 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.62-1+b1 [33.6 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.3-7 [50.4 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.17-3 [524 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.30.1-1 [649 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.17-3 [881 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.36+b2 [71.3 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b2 [11.3 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-1 [12.6 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.008-1+b1 [15.9 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libparams-classify-perl amd64 0.015-1+b2 [25.6 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-implementation-perl all 0.09-1 [12.9 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libvariable-magic-perl amd64 0.62-1+b2 [46.0 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-endofscope-perl all 0.24-1 [18.6 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libberkeleydb-perl amd64 0.62-1+b1 [124 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-3+b4 [105 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libcgi-pm-perl all 4.44-1 [223 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.26-1 [13.5 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-accessor-perl all 0.51-1 [23.2 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-method-modifiers-perl all 2.13-1 [19.2 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-xsaccessor-perl amd64 1.19-3+b3 [38.4 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libclone-perl amd64 0.43-1 [14.9 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libdigest-hmac-perl all 1.03+dfsg-2 [10.6 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1d-2 [1540 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ssleay-perl amd64 1.88-1+b1 [321 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libio-socket-ssl-perl all 2.066-1 [210 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-smtp-ssl-perl all 1.04-1 [6184 B] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libmailtools-perl all 2.21-1 [95.5 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ip-perl all 1.26-2 [29.0 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-dns-perl all 1.20-1 [367 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-valid-perl all 1.202-1 [23.0 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002001-1 [36.9 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.25-4 [26.5 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libnumber-compare-perl all 0.03-1 [7642 B] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-glob-perl all 0.10-1 [8362 B] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libfuture-perl all 0.42-1 [82.6 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libstruct-dumb-perl all 0.09-1 [11.1 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-perl all 0.74-1 [268 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 liblinux-epoll-perl amd64 0.016-1+b2 [16.9 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-loop-epoll-perl all 0.20-1 [11.9 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libio-pty-perl amd64 1:1.08-1.1+b6 [33.6 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run-perl all 20180523.0-2 [101 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-compare-perl all 0.53-1 [68.9 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b5 [63.6 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libmldbm-perl all 2.05-2 [18.4 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.001004-1 [20.8 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.003006-1 [58.7 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libpackage-stash-perl all 0.38-1 [21.7 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-identify-perl amd64 0.14-1+b2 [12.0 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.108-1 [53.3 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.004004-1 [266 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.80+repack-2+b1 [34.8 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-2+b1 [91.4 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-3 [62.3 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.36.0 [1294 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 8876 kB in 0s (34.7 MB/s) Selecting previously unselected package readline-common. (Reading database ... 20891 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.0-3_all.deb ... Unpacking readline-common (8.0-3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../01-libreadline8_8.0-3_amd64.deb ... Unpacking libreadline8:amd64 (8.0-3) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_5.6_all.deb ... Unpacking netbase (5.6) ... Selecting previously unselected package diffstat. Preparing to unpack .../03-diffstat_1.62-1+b1_amd64.deb ... Unpacking diffstat (1.62-1+b1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../04-libassuan0_2.5.3-7_amd64.deb ... Unpacking libassuan0:amd64 (2.5.3-7) ... Selecting previously unselected package gpgconf. Preparing to unpack .../05-gpgconf_2.2.17-3_amd64.deb ... Unpacking gpgconf (2.2.17-3) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../06-libsqlite3-0_3.30.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.30.1-1) ... Selecting previously unselected package gpg. Preparing to unpack .../07-gpg_2.2.17-3_amd64.deb ... Unpacking gpg (2.2.17-3) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../08-libapt-pkg-perl_0.1.36+b2_amd64.deb ... Unpacking libapt-pkg-perl (0.1.36+b2) ... Selecting previously unselected package libb-hooks-op-check-perl. Preparing to unpack .../09-libb-hooks-op-check-perl_0.22-1+b2_amd64.deb ... Unpacking libb-hooks-op-check-perl (0.22-1+b2) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../10-libdynaloader-functions-perl_0.003-1_all.deb ... Unpacking libdynaloader-functions-perl (0.003-1) ... Selecting previously unselected package libdevel-callchecker-perl. Preparing to unpack .../11-libdevel-callchecker-perl_0.008-1+b1_amd64.deb ... Unpacking libdevel-callchecker-perl (0.008-1+b1) ... 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Setting up libpath-tiny-perl (0.108-1) ... Setting up librole-tiny-perl (2.001004-1) ... Setting up netbase (5.6) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006006-1) ... Setting up libclass-xsaccessor-perl (1.19-3+b3) ... Setting up libexporter-tiny-perl (1.002001-1) ... Setting up libclass-accessor-perl (0.51-1) ... Setting up libnet-ip-perl (1.26-2) ... Setting up readline-common (8.0-3) ... Setting up liburi-perl (1.76-1) ... Setting up libnet-ssleay-perl (1.88-1+b1) ... Setting up libfile-basedir-perl (0.08-1) ... Setting up liblist-moreutils-perl (0.416-1+b5) ... Setting up libreadline8:amd64 (8.0-3) ... Setting up libtype-tiny-perl (1.004004-1) ... Setting up libnet-dns-perl (1.20-1) ... Setting up libdevel-callchecker-perl (0.008-1+b1) ... Setting up libio-async-loop-epoll-perl (0.20-1) ... Setting up libhtml-parser-perl (3.72-3+b4) ... Setting up gpgconf (2.2.17-3) ... Setting up libio-socket-ssl-perl (2.066-1) ... 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I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 55836 Build-Time: 114 Distribution: unstable Foreign Architectures: armel Host Architecture: armel Install-Time: 17 Job: clustalw_2.1+lgpl-6 Lintian: pass Machine Architecture: amd64 Package: clustalw Package-Time: 144 Source-Version: 2.1+lgpl-6 Space: 55836 Status: successful Version: 2.1+lgpl-6 -------------------------------------------------------------------------------- Finished at 2019-11-17T13:48:21Z Build needed 00:02:24, 55836k disk space