RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '271737-455925', '/home/buildd/filecache-default/b53690015c42f71e7f3bd2c5466028f00456869d'] Unpacking chroot for build 271737-455925 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '271737-455925'] Mounting chroot for build 271737-455925 RUN: /usr/share/launchpad-buildd/slavebin/apply-ogre-model ['apply-ogre-model', '271737-455925', 'multiverse'] Attempting OGRE for multiverse in build-271737-455925 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '271737-455925'] Updating debian chroot for build 271737-455925 Get:1 http://ftpmaster.internal feisty Release.gpg [191B] Get:2 http://ftpmaster.internal feisty Release [34.8kB] Get:3 http://ftpmaster.internal feisty/main Packages [942kB] Get:4 http://ftpmaster.internal feisty/restricted Packages [2158B] Get:5 http://ftpmaster.internal feisty/universe Packages [3503kB] Get:6 http://ftpmaster.internal feisty/multiverse Packages [109kB] Fetched 4590kB in 4s (1073kB/s) Reading package lists... Reading package lists... Building dependency tree... The following packages will be upgraded: belocs-locales-bin debconf debconf-english debianutils e2fslibs e2fsprogs findutils grep libblkid1 libcomerr2 libdb4.3 libsepol1 libslang2 libss2 libuuid1 linux-libc-dev make perl perl-base perl-modules procps tar tzdata 23 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 0B/10.6MB of archives. After unpacking 295kB of additional disk space will be used. (Reading database ... 9410 files and directories currently installed.) Preparing to replace debianutils 2.16.2 (using .../debianutils_2.17.3_sparc.deb) ... Unpacking replacement debianutils ... Setting up debianutils (2.17.3) ... (Reading database ... 9410 files and directories currently installed.) Preparing to replace e2fslibs 1.39-1 (using .../e2fslibs_1.39+1.40-WIP-2006.10.02+dfsg-2_sparc.deb) ... Unpacking replacement e2fslibs ... Setting up e2fslibs (1.39+1.40-WIP-2006.10.02+dfsg-2) ... (Reading database ... 9410 files and directories currently installed.) Preparing to replace e2fsprogs 1.39-1 (using .../e2fsprogs_1.39+1.40-WIP-2006.10.02+dfsg-2_sparc.deb) ... Unpacking replacement e2fsprogs ... Setting up e2fsprogs (1.39+1.40-WIP-2006.10.02+dfsg-2) ... (Reading database ... 9410 files and directories currently installed.) Preparing to replace findutils 4.2.27-3 (using .../findutils_4.2.28-1_sparc.deb) ... Unpacking replacement findutils ... Setting up findutils (4.2.28-1) ... (Reading database ... 9410 files and directories currently installed.) Preparing to replace grep 2.5.1.ds2-5 (using .../grep_2.5.1.ds2-6_sparc.deb) ... Unpacking replacement grep ... Setting up grep (2.5.1.ds2-6) ... (Reading database ... 9410 files and directories currently installed.) Preparing to replace perl-modules 5.8.8-6build1 (using .../perl-modules_5.8.8-6.1_all.deb) ... Unpacking replacement perl-modules ... Preparing to replace perl 5.8.8-6build1 (using .../perl_5.8.8-6.1_sparc.deb) ... Unpacking replacement perl ... Preparing to replace perl-base 5.8.8-6build1 (using .../perl-base_5.8.8-6.1_sparc.deb) ... Unpacking replacement perl-base ... Setting up perl-base (5.8.8-6.1) ... (Reading database ... 9410 files and directories currently installed.) Preparing to replace tar 1.15.91-2 (using .../archives/tar_1.16-1_sparc.deb) ... Unpacking replacement tar ... Setting up tar (1.16-1) ... (Reading database ... 9408 files and directories currently installed.) Preparing to replace debconf-english 1.5.2ubuntu2 (using .../debconf-english_1.5.8_all.deb) ... Unpacking replacement debconf-english ... Preparing to replace debconf 1.5.2ubuntu2 (using .../archives/debconf_1.5.8_all.deb) ... Unpacking replacement debconf ... Preparing to replace libsepol1 1.12-1 (using .../libsepol1_1.14-1_sparc.deb) ... Unpacking replacement libsepol1 ... Setting up libsepol1 (1.14-1) ... (Reading database ... 9408 files and directories currently installed.) Preparing to replace libblkid1 1.39-1 (using .../libblkid1_1.39+1.40-WIP-2006.10.02+dfsg-2_sparc.deb) ... Unpacking replacement libblkid1 ... Setting up libblkid1 (1.39+1.40-WIP-2006.10.02+dfsg-2) ... (Reading database ... 9408 files and directories currently installed.) Preparing to replace libcomerr2 1.39-1 (using .../libcomerr2_1.39+1.40-WIP-2006.10.02+dfsg-2_sparc.deb) ... Unpacking replacement libcomerr2 ... Setting up libcomerr2 (1.39+1.40-WIP-2006.10.02+dfsg-2) ... (Reading database ... 9408 files and directories currently installed.) Preparing to replace libss2 1.39-1 (using .../libss2_1.39+1.40-WIP-2006.10.02+dfsg-2_sparc.deb) ... Unpacking replacement libss2 ... Setting up libss2 (1.39+1.40-WIP-2006.10.02+dfsg-2) ... (Reading database ... 9408 files and directories currently installed.) Preparing to replace libuuid1 1.39-1 (using .../libuuid1_1.39+1.40-WIP-2006.10.02+dfsg-2_sparc.deb) ... Unpacking replacement libuuid1 ... Setting up libuuid1 (1.39+1.40-WIP-2006.10.02+dfsg-2) ... (Reading database ... 9408 files and directories currently installed.) Preparing to replace belocs-locales-bin 2.4-1ubuntu6 (using .../belocs-locales-bin_2.4-2ubuntu1_sparc.deb) ... Unpacking replacement belocs-locales-bin ... Preparing to replace libdb4.3 4.3.29-5build1 (using .../libdb4.3_4.3.29-6_sparc.deb) ... Unpacking replacement libdb4.3 ... Preparing to replace libslang2 2.0.6-2 (using .../libslang2_2.0.6-4_sparc.deb) ... Unpacking replacement libslang2 ... Preparing to replace procps 1:3.2.7-2ubuntu3 (using .../procps_1%3a3.2.7-3ubuntu1_sparc.deb) ... Unpacking replacement procps ... Preparing to replace tzdata 2006m-1ubuntu1 (using .../tzdata_2006n-1ubuntu1_all.deb) ... Unpacking replacement tzdata ... Preparing to replace linux-libc-dev 2.6.19-4.4 (using .../linux-libc-dev_2.6.19-5.7_sparc.deb) ... Unpacking replacement linux-libc-dev ... Preparing to replace make 3.81-2 (using .../archives/make_3.81-3_sparc.deb) ... Unpacking replacement make ... Setting up belocs-locales-bin (2.4-2ubuntu1) ... Setting up libdb4.3 (4.3.29-6) ... Setting up libslang2 (2.0.6-4) ... Setting up procps (3.2.7-3ubuntu1) ... Installing new version of config file /etc/init.d/procps.sh ... Setting up tzdata (2006n-1ubuntu1) ... Current default timezone: 'UTC'. Local time is now: Mon Nov 13 13:38:17 UTC 2006. Universal Time is now: Mon Nov 13 13:38:17 UTC 2006. Run 'tzconfig' if you wish to change it. Setting up linux-libc-dev (2.6.19-5.7) ... Setting up make (3.81-3) ... Setting up debconf-english (1.5.8) ... Setting up perl-modules (5.8.8-6.1) ... Setting up debconf (1.5.8) ... Setting up perl (5.8.8-6.1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', '271737-455925', '-dautobuild', '--nolog', '--batch', '--archive=ubuntu', '--comp=multiverse', 'molphy_2.3b3-3.dsc'] Initiating build Automatic build of molphy_2.3b3-3 on sejong by sbuild/sparc 1.170.5 Build started at 20061113-1338 ****************************************************************************** molphy_2.3b3-3.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: cdbs (>= 0.4.23-1.1), patchutils (>= 0.2.25), debhelper (>= 5) Checking for already installed source dependencies... cdbs: missing patchutils: missing debhelper: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install cdbs patchutils debhelper Reading package lists... Building dependency tree... The following extra packages will be installed: file gettext gettext-base html2text intltool-debian libmagic1 po-debconf Suggested packages: devscripts doc-base dh-make cvs gettext-doc Recommended packages: autotools-dev curl wget lynx libmail-sendmail-perl libcompress-zlib-perl The following NEW packages will be installed: cdbs debhelper file gettext gettext-base html2text intltool-debian libmagic1 patchutils po-debconf 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 0B/2662kB of archives. After unpacking 11.5MB of additional disk space will be used. Selecting previously deselected package gettext-base. (Reading database ... 9411 files and directories currently installed.) Unpacking gettext-base (from .../gettext-base_0.15-2ubuntu2_sparc.deb) ... Selecting previously deselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_4.17-2ubuntu1_sparc.deb) ... Selecting previously deselected package file. Unpacking file (from .../file_4.17-2ubuntu1_sparc.deb) ... Selecting previously deselected package cdbs. Unpacking cdbs (from .../cdbs_0.4.46ubuntu6_all.deb) ... Selecting previously deselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-3_sparc.deb) ... Selecting previously deselected package gettext. Unpacking gettext (from .../gettext_0.15-2ubuntu2_sparc.deb) ... Selecting previously deselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously deselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.7_all.deb) ... Selecting previously deselected package debhelper. Unpacking debhelper (from .../debhelper_5.0.40ubuntu1_all.deb) ... Selecting previously deselected package patchutils. Unpacking patchutils (from .../patchutils_0.2.31-3_sparc.deb) ... Setting up gettext-base (0.15-2ubuntu2) ... Setting up libmagic1 (4.17-2ubuntu1) ... Setting up file (4.17-2ubuntu1) ... Setting up cdbs (0.4.46ubuntu6) ... Setting up html2text (1.3.2a-3) ... Setting up gettext (0.15-2ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.7) ... Setting up debhelper (5.0.40ubuntu1) ... Setting up patchutils (0.2.31-3) ... Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.5-0ubuntu2 make_3.81-3 dpkg-dev_1.13.22ubuntu7 gcc-4.1_4.1.1-18ubuntu2 g++-4.1_4.1.1-18ubuntu2 binutils_2.17.50.0.6-0ubuntu1 libstdc++6-4.1-dev_4.1.1-18ubuntu2 libstdc++6_4.1.1-18ubuntu2 ------------------------------------------------------------------------------ dpkg-source: extracting molphy in molphy-2.3b3 dpkg-source: unpacking molphy_2.3b3.orig.tar.gz dpkg-source: applying /home/buildd/build-271737-455925/molphy_2.3b3-3.diff.gz dpkg-buildpackage: source package is molphy dpkg-buildpackage: source version is 2.3b3-3 dpkg-buildpackage: host architecture sparc dpkg-buildpackage: source version without epoch 2.3b3-3 /usr/bin/fakeroot debian/rules clean sed \ -e "s/@cdbs@/, cdbs (>= 0.4.23-1.1), patchutils (>= 0.2.25), debhelper (>= 5)/g" \ -e "s/^Build-Depends\(\|-Indep\): ,/Build-Depends\1:/g" \ \ -e "s/^Cpu: .*/Architecture: /g" \ -e "/^System: /d" \ \ -e "s/\[cpu: \([^]]*\)\]/\[\`type-handling \\\\\`echo \1 | tr ' ' ','\\\\\` any\`\]/g" \ -e "s/\[system: \([^]]*\)\]/\[\`type-handling any \\\\\`echo \1 | tr ' ' ','\\\\\`\`\]/g" \ \ -e "s/\"/\\\\\"/g" \ -e "s/^/echo \"/g" \ -e "s/\\$/\\\\$/g" \ -e "s/$/\"/g" \ < debian/control.in | /bin/sh > debian/control dpkg-checkbuilddeps -B test -x debian/rules test "`id -u`" = 0 /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/build/buildd/molphy-2.3b3' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/build/buildd/molphy-2.3b3' if [ "reverse-patches" = "reverse-patches" ]; then rm -f debian/stamp-patched; fi patches: debian/patches/src.diff debian/patches/utl_Install.diff Patch debian/patches/utl_Install.diff is not applied. Patch debian/patches/src.diff is not applied. if [ "reverse-patches" != "reverse-patches" ]; then touch debian/stamp-patched; fi if [ "reverse-patches" != "reverse-patches" ] ; then \ /usr/bin/make -f debian/rules update-config ; \ fi for dir in debian/patches ; do \ rm -f $dir/*.log ; \ done dh_clean cd src; make -C . CFLAGS="-g -Wall -O2" CXXFLAGS="-g -Wall -O2" -k clean make[1]: Entering directory `/build/buildd/molphy-2.3b3/src' rm -f core *.o protml protst nucml nucst njdist totalml make[1]: Leaving directory `/build/buildd/molphy-2.3b3/src' rm -f debian/stamp-makefile-build cd src; make clean make[1]: Entering directory `/build/buildd/molphy-2.3b3/src' rm -f core *.o protml protst nucml nucst njdist totalml make[1]: Leaving directory `/build/buildd/molphy-2.3b3/src' debian/rules build sed \ -e "s/@cdbs@/, cdbs (>= 0.4.23-1.1), patchutils (>= 0.2.25), debhelper (>= 5)/g" \ -e "s/^Build-Depends\(\|-Indep\): ,/Build-Depends\1:/g" \ \ -e "s/^Cpu: .*/Architecture: /g" \ -e "/^System: /d" \ \ -e "s/\[cpu: \([^]]*\)\]/\[\`type-handling \\\\\`echo \1 | tr ' ' ','\\\\\` any\`\]/g" \ -e "s/\[system: \([^]]*\)\]/\[\`type-handling any \\\\\`echo \1 | tr ' ' ','\\\\\`\`\]/g" \ \ -e "s/\"/\\\\\"/g" \ -e "s/^/echo \"/g" \ -e "s/\\$/\\\\$/g" \ -e "s/$/\"/g" \ < debian/control.in | /bin/sh > debian/control dpkg-checkbuilddeps -B test -x debian/rules mkdir -p "." /usr/bin/make -f debian/rules reverse-config make[1]: Entering directory `/build/buildd/molphy-2.3b3' make[1]: Nothing to be done for `reverse-config'. make[1]: Leaving directory `/build/buildd/molphy-2.3b3' if [ "debian/stamp-patched" = "reverse-patches" ]; then rm -f debian/stamp-patched; fi patches: debian/patches/src.diff debian/patches/utl_Install.diff Trying patch debian/patches/src.diff at level 1 ... 0 ... success. Trying patch debian/patches/utl_Install.diff at level 1 ... 0 ... success. if [ "debian/stamp-patched" != "reverse-patches" ]; then touch debian/stamp-patched; fi if [ "debian/stamp-patched" != "reverse-patches" ] ; then \ /usr/bin/make -f debian/rules update-config ; \ fi make[1]: Entering directory `/build/buildd/molphy-2.3b3' make[1]: Nothing to be done for `update-config'. make[1]: Leaving directory `/build/buildd/molphy-2.3b3' cd src; make -C . CFLAGS="-g -Wall -O2" CXXFLAGS="-g -Wall -O2" make[1]: Entering directory `/build/buildd/molphy-2.3b3/src' gcc -g -Wall -O2 -c getseq.c getseq.c: In function 'prsequence': getseq.c:412: warning: array subscript has type 'char' gcc -g -Wall -O2 -c seqproc.c seqproc.c: In function 'radixsort': seqproc.c:115: warning: array subscript has type 'char' seqproc.c:119: warning: array subscript has type 'char' seqproc.c: In function 'prcondenceseq': seqproc.c:236: warning: implicit declaration of function 'fputid' seqproc.c:240: warning: implicit declaration of function 'int2acid' seqproc.c: In function 'convfreq': seqproc.c:68: warning: 'maxi' may be used uninitialized in this function gcc -g -Wall -O2 -c mltree.c mltree.c: In function 'getusertree': mltree.c:239: warning: unused variable 'xp' mltree.c: In function 'resulttree': mltree.c:1380: warning: implicit declaration of function 'fputid' mltree.c:1361: warning: unused variable 'reli' mltree.c: In function 'tabletree': mltree.c:1528: warning: unused variable 'z' mltree.c: In function 'outlklhd': mltree.c:1682: warning: implicit declaration of function 'header' mltree.c: In function 'putsortseq': mltree.c:1725: warning: implicit declaration of function 'int2acid' mltree.c: In function 'bootstrap': mltree.c:1450: warning: 'nsite' may be used uninitialized in this function mltree.c:1450: warning: 'nptrn' may be used uninitialized in this function mltree.c: In function 'slslength': mltree.c:888: warning: 'ni' may be used uninitialized in this function mltree.c: In function 'lslength': mltree.c:654: warning: 'maxi' may be used uninitialized in this function gcc -g -Wall -O2 -c altree.c altree.c: In function 'aproxlkl': altree.c:148: warning: implicit declaration of function 'prodpart' altree.c: In function 'aproxtree': altree.c:234: warning: type defaults to 'int' in declaration of 'num' altree.c:245: warning: implicit declaration of function 'pathing' altree.c:246: warning: implicit declaration of function 'slslength' altree.c:259: warning: implicit declaration of function 'initpartlkl' altree.c:264: warning: implicit declaration of function 'putctopology' altree.c:275: warning: implicit declaration of function 'strctree' altree.c: In function 'wedge': altree.c:358: warning: suggest parentheses around assignment used as truth value altree.c: In function 'inbranode': altree.c:515: warning: format '%s' expects type 'char *', but argument 3 has type 'int' altree.c: In function 'streeinit': altree.c:589: warning: format '%s' expects type 'char *', but argument 3 has type 'int' altree.c:645: warning: implicit declaration of function 'fputid' altree.c: In function 'wedge': altree.c:312: warning: 'istart' may be used uninitialized in this function altree.c: In function 'streeinit': altree.c:531: warning: 'np' may be used uninitialized in this function gcc -g -Wall -O2 -c qltree.c qltree.c: In function 'addotu': qltree.c:159: warning: implicit declaration of function 'prcurtree' qltree.c:160: warning: implicit declaration of function 'pathing' qltree.c:161: warning: implicit declaration of function 'lslength' qltree.c: At top level: qltree.c:180: warning: return type defaults to 'int' qltree.c: In function 'addotual': qltree.c:208: warning: implicit declaration of function 'initpartlkl' qltree.c:209: warning: implicit declaration of function 'aproxlkl' qltree.c:212: warning: implicit declaration of function 'fputctopology' qltree.c:221: warning: control reaches end of non-void function qltree.c: In function 'addotu': qltree.c:176: warning: control reaches end of non-void function qltree.c: In function 'tableaddtree': qltree.c:354: warning: 'tail' may be used uninitialized in this function qltree.c: In function 'roundtree': qltree.c:231: warning: 'yp' may be used uninitialized in this function qltree.c:230: warning: 'maxlkp' may be used uninitialized in this function gcc -g -Wall -O2 -c sltree.c sltree.c: In function 'sdml': sltree.c:220: warning: implicit declaration of function 'partelkl' sltree.c:226: warning: implicit declaration of function 'prodpart' sltree.c:227: warning: implicit declaration of function 'partilkl' sltree.c:236: warning: implicit declaration of function 'mlibranch' sltree.c:262: warning: implicit declaration of function 'mlebranch' sltree.c:330: warning: implicit declaration of function 'evallkl' sltree.c:207: warning: unused variable 'i' sltree.c: In function 'decomposition': sltree.c:373: warning: implicit declaration of function 'slslength' sltree.c:435: warning: implicit declaration of function 'initpartlkl' sltree.c:436: warning: implicit declaration of function 'aproxlkl' sltree.c:471: warning: implicit declaration of function 'mlikelihood' sltree.c:472: warning: implicit declaration of function 'mlvalue' sltree.c:508: warning: implicit declaration of function 'putctopology' sltree.c: In function 'ystardecomp': sltree.c:626: warning: implicit declaration of function 'regupartlkl' sltree.c:767: warning: implicit declaration of function 'prtopology' sltree.c:572: warning: unused variable 'maxjbp' sltree.c:572: warning: unused variable 'maxibp' sltree.c: In function 'xstardecomp': sltree.c:815: warning: implicit declaration of function 'fmlength' sltree.c:1011: warning: too many arguments for format sltree.c:1016: warning: implicit declaration of function 'reroot' sltree.c:786: warning: unused variable 'maxjbp' sltree.c:786: warning: unused variable 'maxibp' sltree.c: In function 'decomposition': sltree.c:348: warning: 'yp' may be used uninitialized in this function sltree.c:346: warning: 'maxjbp' may be used uninitialized in this function sltree.c:346: warning: 'maxibp' may be used uninitialized in this function gcc -g -Wall -O2 -c njtree.c njtree.c: In function 'emledis': njtree.c:145: warning: implicit declaration of function 'tdiffmtrx' njtree.c: In function 'enjtree': njtree.c:360: warning: implicit declaration of function 'new_npvector' njtree.c:481: warning: implicit declaration of function 'reroot' njtree.c:485: warning: implicit declaration of function 'free_npvector' njtree.c:344: warning: 'otuj' may be used uninitialized in this function njtree.c:344: warning: 'otui' may be used uninitialized in this function gcc -g -Wall -O2 -c njmtree.c njmtree.c: In function 'initsubplkl': njmtree.c:20: warning: implicit declaration of function 'partelkl' njmtree.c:37: warning: implicit declaration of function 'prodpart' njmtree.c:38: warning: implicit declaration of function 'partilkl' njmtree.c: In function 'mlepartlen': njmtree.c:74: warning: implicit declaration of function 'copypart1' njmtree.c:75: warning: implicit declaration of function 'prodpart1' njmtree.c:92: warning: implicit declaration of function 'mlebranch' njmtree.c:102: warning: implicit declaration of function 'mlibranch' njmtree.c: In function 'njmtree': njmtree.c:233: warning: implicit declaration of function 'new_npvector' njmtree.c:352: warning: implicit declaration of function 'reroot' njmtree.c:357: warning: implicit declaration of function 'free_npvector' njmtree.c:218: warning: 'otuj' may be used uninitialized in this function njmtree.c:218: warning: 'otui' may be used uninitialized in this function gcc -g -Wall -O2 -c prtree.c gcc -g -Wall -O2 -c pstree.c pstree.c: In function 'pstree': pstree.c:106: warning: 'smax' may be used uninitialized in this function pstree.c:106: warning: 'xmax' may be used uninitialized in this function gcc -g -Wall -O2 -c matrixut.c matrixut.c: In function 'maerror': matrixut.c:22: warning: implicit declaration of function 'exit' matrixut.c:22: warning: incompatible implicit declaration of built-in function 'exit' matrixut.c: In function 'new_fvector': matrixut.c:36: warning: implicit declaration of function 'malloc' matrixut.c:36: warning: incompatible implicit declaration of built-in function 'malloc' matrixut.c: In function 'new_fmatrix': matrixut.c:50: warning: incompatible implicit declaration of built-in function 'malloc' matrixut.c: In function 'new_fcube': matrixut.c:68: warning: incompatible implicit declaration of built-in function 'malloc' matrixut.c: In function 'free_fvector': matrixut.c:87: warning: implicit declaration of function 'free' matrixut.c: In function 'new_dvector': matrixut.c:119: warning: incompatible implicit declaration of built-in function 'malloc' matrixut.c: In function 'new_dmatrix': matrixut.c:133: warning: incompatible implicit declaration of built-in function 'malloc' matrixut.c: In function 'new_dcube': matrixut.c:151: warning: incompatible implicit declaration of built-in function 'malloc' matrixut.c: In function 'new_cvector': matrixut.c:202: warning: incompatible implicit declaration of built-in function 'malloc' matrixut.c: In function 'new_cmatrix': matrixut.c:216: warning: incompatible implicit declaration of built-in function 'malloc' matrixut.c: In function 'new_ccube': matrixut.c:234: warning: incompatible implicit declaration of built-in function 'malloc' matrixut.c: In function 'new_ivector': matrixut.c:285: warning: incompatible implicit declaration of built-in function 'malloc' matrixut.c: In function 'new_imatrix': matrixut.c:299: warning: incompatible implicit declaration of built-in function 'malloc' matrixut.c: In function 'new_icube': matrixut.c:317: warning: incompatible implicit declaration of built-in function 'malloc' gcc -g -Wall -O2 -c mygetopt.c gcc -g -Wall -O2 -c protml.c protml.c:93: warning: return type defaults to 'int' protml.c: In function 'main': protml.c:137: warning: implicit declaration of function 'mygetopt' protml.c:276: warning: suggest parentheses around assignment used as truth value protml.c:280: warning: suggest parentheses around assignment used as truth value protml.c:285: warning: suggest parentheses around assignment used as truth value protml.c:304: warning: suggest parentheses around assignment used as truth value protml.c:100: warning: unused variable 'buf' protml.c:99: warning: unused variable 'cp' protml.c: In function 'prologue': protml.c:600: warning: implicit declaration of function 'getsize' protml.c:618: warning: implicit declaration of function 'getseqs' protml.c:620: warning: implicit declaration of function 'getseqi' protml.c:622: warning: implicit declaration of function 'getseq' protml.c:623: warning: implicit declaration of function 'prsequence' protml.c:624: warning: implicit declaration of function 'getfreqepm' protml.c:626: warning: implicit declaration of function 'radixsort' protml.c:629: warning: implicit declaration of function 'condenceseq' protml.c:630: warning: implicit declaration of function 'convseq' protml.c:631: warning: implicit declaration of function 'getnumsites' protml.c:633: warning: implicit declaration of function 'prcondenceseq' protml.c:635: warning: implicit declaration of function 'checkseq' protml.c:636: warning: implicit declaration of function 'convfreq' protml.c:641: warning: implicit declaration of function 'tranprobmat' protml.c:663: warning: implicit declaration of function 'prfreq' protml.c:667: warning: implicit declaration of function 'lddistance' protml.c:669: warning: implicit declaration of function 'distance' protml.c:671: warning: implicit declaration of function 'tridistance' protml.c:675: warning: implicit declaration of function 'putdistance' protml.c:588: warning: unused variable 'maxdis' protml.c:586: warning: unused variable 'k' protml.c:586: warning: unused variable 'j' protml.c:586: warning: unused variable 'i' protml.c: In function 'pml': protml.c:760: warning: implicit declaration of function 'getbuftree' protml.c:763: warning: implicit declaration of function 'changedistan' protml.c:765: warning: implicit declaration of function 'getproportion' protml.c:783: warning: implicit declaration of function 'new_tree' protml.c:784: warning: implicit declaration of function 'getnumtree' protml.c:785: warning: implicit declaration of function 'newinfotrees' protml.c:797: warning: implicit declaration of function 'getusertree' protml.c:799: warning: implicit declaration of function 'constructtree' protml.c:804: warning: implicit declaration of function 'prcurtree' protml.c:818: warning: implicit declaration of function 'slslength' protml.c:824: warning: implicit declaration of function 'initpartlkl' protml.c:825: warning: implicit declaration of function 'aproxlkl' protml.c:826: warning: implicit declaration of function 'praproxlkl' protml.c:827: warning: implicit declaration of function 'putctopology' protml.c:831: warning: implicit declaration of function 'mlikelihood' protml.c:833: warning: implicit declaration of function 'mlvalue' protml.c:837: warning: implicit declaration of function 'reliabranch' protml.c:838: warning: implicit declaration of function 'fputctopology' protml.c:841: warning: implicit declaration of function 'prtopology' protml.c:842: warning: implicit declaration of function 'strctree' protml.c:844: warning: implicit declaration of function 'resulttree' protml.c:845: warning: implicit declaration of function 'pstree' protml.c:846: warning: implicit declaration of function 'fputcphylogeny' protml.c:875: warning: implicit declaration of function 'outlklhd' protml.c:878: warning: implicit declaration of function 'bootstrap' protml.c:879: warning: implicit declaration of function 'tabletree' protml.c:880: warning: implicit declaration of function 'tableinfo' protml.c:915: warning: implicit declaration of function 'lslength' protml.c:924: warning: implicit declaration of function 'annealing' protml.c:963: warning: implicit declaration of function 'new_njtree' protml.c:964: warning: implicit declaration of function 'enjtree' protml.c:965: warning: implicit declaration of function 'pathing' protml.c:970: warning: implicit declaration of function 'free_njtree' protml.c:982: warning: implicit declaration of function 'new_atree' protml.c:988: warning: implicit declaration of function 'atreeinit' protml.c:993: warning: implicit declaration of function 'streeinit' protml.c:995: warning: implicit declaration of function 'newinfoaltrees' protml.c:1029: warning: implicit declaration of function 'autoconstruction' protml.c:1031: warning: implicit declaration of function 'wedge' protml.c:1034: warning: implicit declaration of function 'tablealtree' protml.c:1047: warning: implicit declaration of function 'new_stree' protml.c:1112: warning: implicit declaration of function 'xstardecomp' protml.c:1117: warning: implicit declaration of function 'fmlength' protml.c:1158: warning: implicit declaration of function 'qlrsearch' protml.c:1198: warning: implicit declaration of function 'newinfoqltrees' protml.c:1206: warning: implicit declaration of function 'initturn' protml.c:1208: warning: implicit declaration of function 'randturn' protml.c:1209: warning: implicit declaration of function 'qtreeinit' protml.c:1215: warning: implicit declaration of function 'convertdistan' protml.c:1217: warning: implicit declaration of function 'roundtree' protml.c:1232: warning: implicit declaration of function 'reroot' protml.c:1238: warning: implicit declaration of function 'newinfoaddtree' protml.c:1268: warning: implicit declaration of function 'tableaddtree' protml.c:752: warning: 'cltree' may be used uninitialized in this function protml.c:751: warning: 'topaddtree' may be used uninitialized in this function protml.c: In function 'main': protml.c:97: warning: 'num' may be used uninitialized in this function gcc -g -Wall -O2 -c protproc.c gcc -g -Wall -O2 -c dyhfjtt.c gcc -g -Wall -O2 -c mtrev24.c gcc -g -Wall -O2 -c tranprb.c tranprb.c: In function 'getrsr': tranprb.c:837: warning: implicit declaration of function 'mtrev' tranprb.c:839: warning: implicit declaration of function 'dyhfjtt' tranprb.c: In function 'tranprobmat': tranprb.c:921: warning: unused variable 'zero' tranprb.c:920: warning: unused variable 'k' tranprb.c: In function 'luinverse': tranprb.c:653: warning: 'maxi' may be used uninitialized in this function tranprb.c: In function 'hqr2': tranprb.c:119: warning: 'z' may be used uninitialized in this function tranprb.c:119: warning: 'x' may be used uninitialized in this function tranprb.c:119: warning: 's' may be used uninitialized in this function tranprb.c:119: warning: 'r' may be used uninitialized in this function tranprb.c:119: warning: 'q' may be used uninitialized in this function tranprb.c:119: warning: 'p' may be used uninitialized in this function tranprb.c:118: warning: 'l' may be used uninitialized in this function gcc -g -Wall -O2 -c distan.c distan.c: In function 'distan': distan.c:90: warning: implicit declaration of function 'tdiffmtrx' distan.c: In function 'distance': distan.c:206: warning: array subscript has type 'char' distan.c: In function 'tdistan': distan.c:552: warning: implicit declaration of function 'tprobmtrx' distan.c: In function 'tridistance': distan.c:848: warning: 'maxj3' may be used uninitialized in this function distan.c:848: warning: 'maxj2' may be used uninitialized in this function distan.c:848: warning: 'maxj' may be used uninitialized in this function distan.c: In function 'determinant': distan.c:334: warning: 'maxi' may be used uninitialized in this function gcc -g -Wall -O2 -c mlklhd.c mlklhd.c: In function 'partilkl': mlklhd.c:195: warning: implicit declaration of function 'tprobmtrx' mlklhd.c: In function 'partelkl': mlklhd.c:256: warning: implicit declaration of function 'tprobmtrxt' mlklhd.c: In function 'mlibranch': mlklhd.c:493: warning: implicit declaration of function 'tdiffmtrx' mlklhd.c: In function 'reliabranch': mlklhd.c:1813: warning: implicit declaration of function 'prtopology' mlklhd.c:1841: warning: implicit declaration of function 'pathing' mlklhd.c:1842: warning: implicit declaration of function 'slslength' mlklhd.c:1869: warning: implicit declaration of function 'putctopology' mlklhd.c: In function 'annealing': mlklhd.c:1941: warning: format '%7.3f' expects type 'double', but argument 2 has type 'int' mlklhd.c:1941: warning: too many arguments for format mlklhd.c: In function 'qlrsearch': mlklhd.c:1975: warning: unused variable 'muldiff' mlklhd.c:1974: warning: unused variable 'forder' mlklhd.c:1974: warning: unused variable 'j' mlklhd.c: In function 'mlebranch2': mlklhd.c:767: warning: 'distold' may be used uninitialized in this function mlklhd.c:766: warning: 'lkld2' may be used uninitialized in this function mlklhd.c:766: warning: 'lkld1' may be used uninitialized in this function mlklhd.c: In function 'mlibranch': mlklhd.c:461: warning: 'distold' may be used uninitialized in this function mlklhd.c:460: warning: 'lkld2' may be used uninitialized in this function mlklhd.c:460: warning: 'lkld1' may be used uninitialized in this function mlklhd.c: In function 'mlebranch': mlklhd.c:623: warning: 'lkld2' may be used uninitialized in this function mlklhd.c:623: warning: 'lkld1' may be used uninitialized in this function mlklhd.c: In function 'reliabranch': mlklhd.c:1667: warning: 'ncp' may be used uninitialized in this function mlklhd.c:1666: warning: 'minrel' may be used uninitialized in this function mlklhd.c:1666: warning: 'lklhd2' may be used uninitialized in this function mlklhd.c:1666: warning: 'lklhd1' may be used uninitialized in this function mlklhd.c: In function 'qlrsearch': mlklhd.c:1975: warning: 'minrel' may be used uninitialized in this function mlklhd.c:1975: warning: 'lklhd2' may be used uninitialized in this function mlklhd.c:1975: warning: 'lklhd1' may be used uninitialized in this function mlklhd.c:1976: warning: 'ncp' may be used uninitialized in this function gcc -g -Wall -O2 -o protml getseq.o seqproc.o mltree.o altree.o qltree.o sltree.o njtree.o njmtree.o prtree.o pstree.o matrixut.o mygetopt.o protml.o protproc.o dyhfjtt.o mtrev24.o tranprb.o distan.o mlklhd.o -lm -lc gcc -g -Wall -O2 -c protst.c protst.c:53: warning: return type defaults to 'int' protst.c: In function 'main': protst.c:69: warning: implicit declaration of function 'mygetopt' protst.c:74: warning: suggest parentheses around assignment used as truth value protst.c: In function 'prologue': protst.c:186: warning: implicit declaration of function 'getsize' protst.c:197: warning: implicit declaration of function 'getseqs' protst.c:199: warning: implicit declaration of function 'getseqi' protst.c:201: warning: implicit declaration of function 'getseq' protst.c:203: warning: implicit declaration of function 'getfreqepm' protst.c:205: warning: implicit declaration of function 'radixsort' protst.c:208: warning: implicit declaration of function 'condenceseq' protst.c:209: warning: implicit declaration of function 'convseq' protst.c:213: warning: implicit declaration of function 'seqinsdel' protst.c:215: warning: implicit declaration of function 'seqdiff' protst.c:218: warning: implicit declaration of function 'seqfreq' protst.c:221: warning: implicit declaration of function 'seqtran' protst.c:224: warning: implicit declaration of function 'prsequence' protst.c:228: warning: implicit declaration of function 'prcondenceseq' protst.c: At top level: protst.c:49: warning: 'pml' declared 'static' but never defined gcc -g -Wall -O2 -c seqstat.c seqstat.c: In function 'seqdiff': seqstat.c:118: warning: unused variable 'z' seqstat.c: In function 'seqfreq': seqstat.c:238: warning: array subscript has type 'char' seqstat.c: In function 'seqtran': seqstat.c:423: warning: array subscript has type 'char' seqstat.c:423: warning: array subscript has type 'char' seqstat.c:424: warning: array subscript has type 'char' seqstat.c:424: warning: array subscript has type 'char' seqstat.c:406: warning: unused variable 'jj' seqstat.c:406: warning: unused variable 'ii' gcc -g -Wall -O2 -o protst getseq.o seqproc.o matrixut.o mygetopt.o protst.o seqstat.o protproc.o -lm -lc gcc -g -Wall -O2 -DNUC -c Nucml.c Nucml.c:93: warning: return type defaults to 'int' Nucml.c: In function 'main': Nucml.c:137: warning: implicit declaration of function 'mygetopt' Nucml.c:182: warning: suggest parentheses around assignment used as truth value Nucml.c:186: warning: suggest parentheses around assignment used as truth value Nucml.c:190: warning: suggest parentheses around assignment used as truth value Nucml.c:198: warning: suggest parentheses around assignment used as truth value Nucml.c:200: warning: suggest parentheses around assignment used as truth value Nucml.c:276: warning: suggest parentheses around assignment used as truth value Nucml.c:280: warning: suggest parentheses around assignment used as truth value Nucml.c:285: warning: suggest parentheses around assignment used as truth value Nucml.c:304: warning: suggest parentheses around assignment used as truth value Nucml.c:414: warning: embedded '\0' in format In file included from Nucml.c:572: optimtpm.c: In function 'abfunc': optimtpm.c:13: warning: implicit declaration of function 'tranprobmat' optimtpm.c:14: warning: implicit declaration of function 'fmlength' optimtpm.c:16: warning: implicit declaration of function 'initpartlkl' optimtpm.c:17: warning: implicit declaration of function 'mlikelihood' optimtpm.c: In function 'optimtpm': optimtpm.c:105: warning: unused variable 'buf' optimtpm.c:104: warning: unused variable 'i' In file included from Nucml.c:573: abratio.c: In function 'mlstar': abratio.c:40: warning: implicit declaration of function 'tdiffmtrx' abratio.c:75: warning: implicit declaration of function 'tprobmtrx' abratio.c:11: warning: unused variable 'prod' abratio.c:10: warning: unused variable 'loop' abratio.c: In function 'abratio': abratio.c:102: warning: unused variable 'ab' Nucml.c: In function 'prologue': Nucml.c:600: warning: implicit declaration of function 'getsize' Nucml.c:618: warning: implicit declaration of function 'getseqs' Nucml.c:620: warning: implicit declaration of function 'getseqi' Nucml.c:622: warning: implicit declaration of function 'getseq' Nucml.c:623: warning: implicit declaration of function 'prsequence' Nucml.c:624: warning: implicit declaration of function 'getfreqepm' Nucml.c:626: warning: implicit declaration of function 'radixsort' Nucml.c:629: warning: implicit declaration of function 'condenceseq' Nucml.c:630: warning: implicit declaration of function 'convseq' Nucml.c:631: warning: implicit declaration of function 'getnumsites' Nucml.c:633: warning: implicit declaration of function 'prcondenceseq' Nucml.c:635: warning: implicit declaration of function 'checkseq' Nucml.c:636: warning: implicit declaration of function 'convfreq' Nucml.c:663: warning: implicit declaration of function 'prfreq' Nucml.c:667: warning: implicit declaration of function 'lddistance' Nucml.c:669: warning: implicit declaration of function 'distance' Nucml.c:671: warning: implicit declaration of function 'tridistance' Nucml.c:675: warning: implicit declaration of function 'putdistance' Nucml.c:588: warning: unused variable 'maxdis' Nucml.c:586: warning: unused variable 'k' Nucml.c:586: warning: unused variable 'j' Nucml.c:586: warning: unused variable 'i' Nucml.c: In function 'pml': Nucml.c:760: warning: implicit declaration of function 'getbuftree' Nucml.c:763: warning: implicit declaration of function 'changedistan' Nucml.c:765: warning: implicit declaration of function 'getproportion' Nucml.c:783: warning: implicit declaration of function 'new_tree' Nucml.c:784: warning: implicit declaration of function 'getnumtree' Nucml.c:785: warning: implicit declaration of function 'newinfotrees' Nucml.c:797: warning: implicit declaration of function 'getusertree' Nucml.c:799: warning: implicit declaration of function 'constructtree' Nucml.c:804: warning: implicit declaration of function 'prcurtree' Nucml.c:818: warning: implicit declaration of function 'slslength' Nucml.c:825: warning: implicit declaration of function 'aproxlkl' Nucml.c:826: warning: implicit declaration of function 'praproxlkl' Nucml.c:827: warning: implicit declaration of function 'putctopology' Nucml.c:833: warning: implicit declaration of function 'mlvalue' Nucml.c:837: warning: implicit declaration of function 'reliabranch' Nucml.c:838: warning: implicit declaration of function 'fputctopology' Nucml.c:841: warning: implicit declaration of function 'prtopology' Nucml.c:842: warning: implicit declaration of function 'strctree' Nucml.c:844: warning: implicit declaration of function 'resulttree' Nucml.c:845: warning: implicit declaration of function 'pstree' Nucml.c:846: warning: implicit declaration of function 'fputcphylogeny' Nucml.c:875: warning: implicit declaration of function 'outlklhd' Nucml.c:878: warning: implicit declaration of function 'bootstrap' Nucml.c:879: warning: implicit declaration of function 'tabletree' Nucml.c:880: warning: implicit declaration of function 'tableinfo' Nucml.c:915: warning: implicit declaration of function 'lslength' Nucml.c:924: warning: implicit declaration of function 'annealing' Nucml.c:963: warning: implicit declaration of function 'new_njtree' Nucml.c:964: warning: implicit declaration of function 'enjtree' Nucml.c:965: warning: implicit declaration of function 'pathing' Nucml.c:970: warning: implicit declaration of function 'free_njtree' Nucml.c:982: warning: implicit declaration of function 'new_atree' Nucml.c:988: warning: implicit declaration of function 'atreeinit' Nucml.c:993: warning: implicit declaration of function 'streeinit' Nucml.c:995: warning: implicit declaration of function 'newinfoaltrees' Nucml.c:1029: warning: implicit declaration of function 'autoconstruction' Nucml.c:1031: warning: implicit declaration of function 'wedge' Nucml.c:1034: warning: implicit declaration of function 'tablealtree' Nucml.c:1047: warning: implicit declaration of function 'new_stree' Nucml.c:1112: warning: implicit declaration of function 'xstardecomp' Nucml.c:1158: warning: implicit declaration of function 'qlrsearch' Nucml.c:1198: warning: implicit declaration of function 'newinfoqltrees' Nucml.c:1206: warning: implicit declaration of function 'initturn' Nucml.c:1208: warning: implicit declaration of function 'randturn' Nucml.c:1209: warning: implicit declaration of function 'qtreeinit' Nucml.c:1215: warning: implicit declaration of function 'convertdistan' Nucml.c:1217: warning: implicit declaration of function 'roundtree' Nucml.c:1232: warning: implicit declaration of function 'reroot' Nucml.c:1238: warning: implicit declaration of function 'newinfoaddtree' Nucml.c:1268: warning: implicit declaration of function 'tableaddtree' Nucml.c:752: warning: 'cltree' may be used uninitialized in this function Nucml.c:751: warning: 'topaddtree' may be used uninitialized in this function Nucml.c: In function 'main': Nucml.c:97: warning: 'num' may be used uninitialized in this function gcc -g -Wall -O2 -DNUC -c nucproc.c gcc -g -Wall -O2 -DNUC -c Ntranprb.c Ntranprb.c: In function 'tranprobmat': Ntranprb.c:921: warning: unused variable 'zero' Ntranprb.c:920: warning: unused variable 'k' Ntranprb.c: In function 'luinverse': Ntranprb.c:653: warning: 'maxi' may be used uninitialized in this function Ntranprb.c: In function 'hqr2': Ntranprb.c:119: warning: 'z' may be used uninitialized in this function Ntranprb.c:119: warning: 'x' may be used uninitialized in this function Ntranprb.c:119: warning: 's' may be used uninitialized in this function Ntranprb.c:119: warning: 'r' may be used uninitialized in this function Ntranprb.c:119: warning: 'q' may be used uninitialized in this function Ntranprb.c:119: warning: 'p' may be used uninitialized in this function Ntranprb.c:118: warning: 'l' may be used uninitialized in this function gcc -g -Wall -O2 -DNUC -c Ndistan.c Ndistan.c: In function 'distan': Ndistan.c:90: warning: implicit declaration of function 'tdiffmtrx' Ndistan.c: In function 'distance': Ndistan.c:206: warning: array subscript has type 'char' Ndistan.c: In function 'tdistan': Ndistan.c:552: warning: implicit declaration of function 'tprobmtrx' Ndistan.c: In function 'tridistance': Ndistan.c:848: warning: 'maxj3' may be used uninitialized in this function Ndistan.c:848: warning: 'maxj2' may be used uninitialized in this function Ndistan.c:848: warning: 'maxj' may be used uninitialized in this function Ndistan.c: In function 'determinant': Ndistan.c:334: warning: 'maxi' may be used uninitialized in this function gcc -g -Wall -O2 -DNUC -c Nmlklhd.c Nmlklhd.c: In function 'partilkl': Nmlklhd.c:195: warning: implicit declaration of function 'tprobmtrx' Nmlklhd.c:193: warning: unused variable 'cpb2' Nmlklhd.c:190: warning: unused variable 'sum' Nmlklhd.c:189: warning: unused variable 'i' Nmlklhd.c: In function 'partelkl': Nmlklhd.c:256: warning: implicit declaration of function 'tprobmtrxt' Nmlklhd.c: In function 'mlibranch': Nmlklhd.c:493: warning: implicit declaration of function 'tdiffmtrx' Nmlklhd.c:460: warning: unused variable 'prod2' Nmlklhd.c:459: warning: unused variable 'j' Nmlklhd.c: In function 'mlebranch': Nmlklhd.c:623: warning: unused variable 'prod' Nmlklhd.c:622: warning: unused variable 'j' Nmlklhd.c: In function 'mlebranch2': Nmlklhd.c:766: warning: unused variable 'prod' Nmlklhd.c:765: warning: unused variable 'i' Nmlklhd.c: In function 'ribranch': Nmlklhd.c:1021: warning: unused variable 'j' Nmlklhd.c: In function 'reliabranch': Nmlklhd.c:1813: warning: implicit declaration of function 'prtopology' Nmlklhd.c:1841: warning: implicit declaration of function 'pathing' Nmlklhd.c:1842: warning: implicit declaration of function 'slslength' Nmlklhd.c:1869: warning: implicit declaration of function 'putctopology' Nmlklhd.c: In function 'annealing': Nmlklhd.c:1941: warning: format '%7.3f' expects type 'double', but argument 2 has type 'int' Nmlklhd.c:1941: warning: too many arguments for format Nmlklhd.c: In function 'qlrsearch': Nmlklhd.c:1975: warning: unused variable 'muldiff' Nmlklhd.c:1974: warning: unused variable 'forder' Nmlklhd.c:1974: warning: unused variable 'j' Nmlklhd.c: In function 'mlebranch2': Nmlklhd.c:767: warning: 'distold' may be used uninitialized in this function Nmlklhd.c:766: warning: 'lkld2' may be used uninitialized in this function Nmlklhd.c:766: warning: 'lkld1' may be used uninitialized in this function Nmlklhd.c: In function 'mlibranch': Nmlklhd.c:461: warning: 'distold' may be used uninitialized in this function Nmlklhd.c:460: warning: 'lkld2' may be used uninitialized in this function Nmlklhd.c:460: warning: 'lkld1' may be used uninitialized in this function Nmlklhd.c: In function 'mlebranch': Nmlklhd.c:623: warning: 'lkld2' may be used uninitialized in this function Nmlklhd.c:623: warning: 'lkld1' may be used uninitialized in this function Nmlklhd.c: In function 'reliabranch': Nmlklhd.c:1667: warning: 'ncp' may be used uninitialized in this function Nmlklhd.c:1666: warning: 'minrel' may be used uninitialized in this function Nmlklhd.c:1666: warning: 'lklhd2' may be used uninitialized in this function Nmlklhd.c:1666: warning: 'lklhd1' may be used uninitialized in this function Nmlklhd.c: In function 'qlrsearch': Nmlklhd.c:1976: warning: 'ncp' may be used uninitialized in this function Nmlklhd.c:1975: warning: 'minrel' may be used uninitialized in this function Nmlklhd.c:1975: warning: 'lklhd2' may be used uninitialized in this function Nmlklhd.c:1975: warning: 'lklhd1' may be used uninitialized in this function gcc -g -Wall -O2 -DNUC -o nucml getseq.o seqproc.o mltree.o altree.o qltree.o sltree.o njtree.o njmtree.o prtree.o pstree.o matrixut.o mygetopt.o Nucml.o nucproc.o Ntranprb.o Ndistan.o Nmlklhd.o -lm -lc gcc -g -Wall -O2 -DNUC -c Nucst.c Nucst.c:53: warning: return type defaults to 'int' Nucst.c: In function 'main': Nucst.c:69: warning: implicit declaration of function 'mygetopt' Nucst.c:74: warning: suggest parentheses around assignment used as truth value Nucst.c: In function 'prologue': Nucst.c:186: warning: implicit declaration of function 'getsize' Nucst.c:197: warning: implicit declaration of function 'getseqs' Nucst.c:199: warning: implicit declaration of function 'getseqi' Nucst.c:201: warning: implicit declaration of function 'getseq' Nucst.c:203: warning: implicit declaration of function 'getfreqepm' Nucst.c:205: warning: implicit declaration of function 'radixsort' Nucst.c:208: warning: implicit declaration of function 'condenceseq' Nucst.c:209: warning: implicit declaration of function 'convseq' Nucst.c:213: warning: implicit declaration of function 'seqinsdel' Nucst.c:215: warning: implicit declaration of function 'seqdiff' Nucst.c:218: warning: implicit declaration of function 'seqfreq' Nucst.c:221: warning: implicit declaration of function 'seqtran' Nucst.c:224: warning: implicit declaration of function 'prsequence' Nucst.c:228: warning: implicit declaration of function 'prcondenceseq' Nucst.c: At top level: Nucst.c:49: warning: 'pml' declared 'static' but never defined gcc -g -Wall -O2 -DNUC -c Nseqstat.c Nseqstat.c: In function 'seqfreq': Nseqstat.c:238: warning: array subscript has type 'char' Nseqstat.c: In function 'seqtran': Nseqstat.c:423: warning: array subscript has type 'char' Nseqstat.c:423: warning: array subscript has type 'char' Nseqstat.c:424: warning: array subscript has type 'char' Nseqstat.c:424: warning: array subscript has type 'char' Nseqstat.c:406: warning: unused variable 'jj' Nseqstat.c:406: warning: unused variable 'ii' gcc -g -Wall -O2 -DNUC -o nucst getseq.o seqproc.o matrixut.o mygetopt.o Nucst.o Nseqstat.o nucproc.o -lm -lc gcc -g -Wall -O2 -c distproc.c distproc.c: In function 'lslength': distproc.c:493: warning: 'maxi' may be used uninitialized in this function gcc -g -Wall -O2 -DNJ -c Dpstree.c Dpstree.c: In function 'pstree': Dpstree.c:107: warning: unused variable 'rel' Dpstree.c:106: warning: 'smax' may be used uninitialized in this function Dpstree.c:106: warning: 'xmax' may be used uninitialized in this function gcc -g -Wall -O2 -DNJ -c Njdist.c Njdist.c:69: warning: return type defaults to 'int' Njdist.c: In function 'main': Njdist.c:86: warning: implicit declaration of function 'mygetopt' Njdist.c:93: warning: suggest parentheses around assignment used as truth value Njdist.c:100: warning: suggest parentheses around assignment used as truth value Njdist.c:167: warning: implicit declaration of function 'fputcphylogeny' Njdist.c:178: warning: implicit declaration of function 'header' Njdist.c:179: warning: implicit declaration of function 'fputctopology' Njdist.c:194: warning: implicit declaration of function 'pstree' Njdist.c: In function 'prologue': Njdist.c:213: warning: implicit declaration of function 'getsize' Njdist.c:223: warning: implicit declaration of function 'getdatas' Njdist.c:225: warning: implicit declaration of function 'getdata' Njdist.c: In function 'distmethod': Njdist.c:238: warning: implicit declaration of function 'prdistanmat' Njdist.c:240: warning: implicit declaration of function 'changedistan' Njdist.c:241: warning: implicit declaration of function 'newtree' Njdist.c:248: warning: implicit declaration of function 'getproportion' Njdist.c:249: warning: implicit declaration of function 'distantree' Njdist.c:251: warning: implicit declaration of function 'prtopology' Njdist.c:252: warning: implicit declaration of function 'pathing' Njdist.c:254: warning: implicit declaration of function 'lslength' Njdist.c:255: warning: implicit declaration of function 'resulttree' Njdist.c:258: warning: implicit declaration of function 'copylengths' Njdist.c: In function 'main': Njdist.c:75: warning: 'tplgyfname' may be used uninitialized in this function Njdist.c:75: warning: 'treefname' may be used uninitialized in this function gcc -g -Wall -O2 -c njproc.c njproc.c: In function 'distantree': njproc.c:29: warning: implicit declaration of function 'new_npvector' njproc.c:164: warning: implicit declaration of function 'reroot' njproc.c:171: warning: implicit declaration of function 'free_npvector' njproc.c:19: warning: 'sij' may be used uninitialized in this function njproc.c:18: warning: 'otuj' may be used uninitialized in this function njproc.c:18: warning: 'otui' may be used uninitialized in this function gcc -g -Wall -O2 -o njdist distproc.o Dpstree.o matrixut.o mygetopt.o Njdist.o njproc.o -lm -lc gcc -g -Wall -O2 -c totalml.c totalml.c: In function 'getsize': totalml.c:95: warning: suggest parentheses around && within || totalml.c: In function 'getlnlklsite': totalml.c:157: warning: suggest parentheses around assignment used as truth value totalml.c: At top level: totalml.c:177: warning: return type defaults to 'int' totalml.c:440: warning: return type defaults to 'int' totalml.c: In function 'main': totalml.c:456: warning: implicit declaration of function 'mygetopt' totalml.c: In function 'prlnlklsite': totalml.c:190: warning: control reaches end of non-void function gcc -g -Wall -O2 -o totalml totalml.o matrixut.o mygetopt.o -lm -lc make[1]: Leaving directory `/build/buildd/molphy-2.3b3/src' touch debian/stamp-makefile-build DEB_MAKE_CHECK_TARGET unset, not running checks /usr/bin/fakeroot debian/rules binary-arch sed \ -e "s/@cdbs@/, cdbs (>= 0.4.23-1.1), patchutils (>= 0.2.25), debhelper (>= 5)/g" \ -e "s/^Build-Depends\(\|-Indep\): ,/Build-Depends\1:/g" \ \ -e "s/^Cpu: .*/Architecture: /g" \ -e "/^System: /d" \ \ -e "s/\[cpu: \([^]]*\)\]/\[\`type-handling \\\\\`echo \1 | tr ' ' ','\\\\\` any\`\]/g" \ -e "s/\[system: \([^]]*\)\]/\[\`type-handling any \\\\\`echo \1 | tr ' ' ','\\\\\`\`\]/g" \ \ -e "s/\"/\\\\\"/g" \ -e "s/^/echo \"/g" \ -e "s/\\$/\\\\$/g" \ -e "s/$/\"/g" \ < debian/control.in | /bin/sh > debian/control dpkg-checkbuilddeps -B test -x debian/rules test "`id -u`" = 0 dh_clean -k dh_installdirs -A mkdir -p "." DEB_MAKE_CHECK_TARGET unset, not running checks DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target dh_installdirs -pmolphy ### replace perl path from /usr/local/bin to /usr/bin which is ### in principle what utl/Install is doing # for utl in `ls utl/*.pl` ; do \ # sed 's?#!/usr/local/bin/perl?#!/usr/bin/perl?' ${utl} > `pwd`/debian/`dh_listpackages`/usr/bin/`basename ${utl} .pl` ; \ # done ### But why not using the original script ?? cd utl; ./Install ../debian/molphy/usr/bin There is /usr/bin/perl. ali2mol.pl -> ../debian/molphy/usr/bin/ali2mol clus2mol.pl -> ../debian/molphy/usr/bin/clus2mol degene4.pl -> ../debian/molphy/usr/bin/degene4 degene4l.pl -> ../debian/molphy/usr/bin/degene4l disjoint.pl -> ../debian/molphy/usr/bin/disjoint dna2ami.pl -> ../debian/molphy/usr/bin/dna2ami eali2mol.pl -> ../debian/molphy/usr/bin/eali2mol egetcds.pl -> ../debian/molphy/usr/bin/egetcds getcds.pl -> ../debian/molphy/usr/bin/getcds ggetcds.pl -> ../debian/molphy/usr/bin/ggetcds inf2mol.pl -> ../debian/molphy/usr/bin/inf2mol infocode.pl -> ../debian/molphy/usr/bin/infocode infocode2.pl -> ../debian/molphy/usr/bin/infocode2 int2mol.pl -> ../debian/molphy/usr/bin/int2mol mc2mol.pl -> ../debian/molphy/usr/bin/mc2mol mega2mol.pl -> ../debian/molphy/usr/bin/mega2mol mol2inf.pl -> ../debian/molphy/usr/bin/mol2inf mol2int.pl -> ../debian/molphy/usr/bin/mol2int mol2mol.pl -> ../debian/molphy/usr/bin/mol2mol mol2phy.pl -> ../debian/molphy/usr/bin/mol2phy mol2seq.pl -> ../debian/molphy/usr/bin/mol2seq molcat.pl -> ../debian/molphy/usr/bin/molcat molcodon.pl -> ../debian/molphy/usr/bin/molcodon molcons.pl -> ../debian/molphy/usr/bin/molcons molcut.pl -> ../debian/molphy/usr/bin/molcut molinfo.pl -> ../debian/molphy/usr/bin/molinfo mollist.pl -> ../debian/molphy/usr/bin/mollist molmerge.pl -> ../debian/molphy/usr/bin/molmerge molrev.pl -> ../debian/molphy/usr/bin/molrev molsplit.pl -> ../debian/molphy/usr/bin/molsplit must2mol.pl -> ../debian/molphy/usr/bin/must2mol njt2tpl.pl -> ../debian/molphy/usr/bin/njt2tpl nuc2code.pl -> ../debian/molphy/usr/bin/nuc2code nuc2NUC.pl -> ../debian/molphy/usr/bin/nuc2NUC nuc2ptn.pl -> ../debian/molphy/usr/bin/nuc2ptn phy2mol.pl -> ../debian/molphy/usr/bin/phy2mol rmid3.pl -> ../debian/molphy/usr/bin/rmid3 rminsdel.pl -> ../debian/molphy/usr/bin/rminsdel rmleu.pl -> ../debian/molphy/usr/bin/rmleu rmsyno.pl -> ../debian/molphy/usr/bin/rmsyno seq2mol.pl -> ../debian/molphy/usr/bin/seq2mol seqwrap.pl -> ../debian/molphy/usr/bin/seqwrap dh_installdocs -pmolphy dh_installexamples -pmolphy dh_installman -pmolphy dh_installinfo -pmolphy dh_installmenu -pmolphy dh_installcron -pmolphy dh_installinit -pmolphy dh_installdebconf -pmolphy dh_installemacsen -pmolphy dh_installcatalogs -pmolphy dh_installpam -pmolphy dh_installlogrotate -pmolphy dh_installlogcheck -pmolphy dh_installmime -pmolphy dh_installchangelogs -pmolphy dh_installudev -pmolphy dh_install -pmolphy dh_link -pmolphy dh_strip -pmolphy dh_strip debug symbol extraction: all non-arch-all packages for this build platform sparc: molphy dh_strip debug symbol extraction: packages to act on: molphy dh_strip debug symbol extraction: ignored packages: pkgstriptranslations: processing control file: ./debian/molphy-dbgsym/DEBIAN/control, package molphy-dbgsym, directory ./debian/molphy-dbgsym pkgstriptranslations: molphy-dbgsym does not contain translations, skipping pkgstriptranslations: no translation files, not creating tarball pkgmaintainermangler: Maintainer field overridden to "Ubuntu MOTU Developers " warning, `/build/buildd/molphy-2.3b3/debian/molphy-dbgsym/DEBIAN/control' contains user-defined field `Original-Maintainer' warning, `/build/buildd/molphy-2.3b3/debian/molphy-dbgsym/DEBIAN/control' contains user-defined field `Tag' dpkg-deb: ignoring 2 warnings about the control file(s) tar: -: file name read contains nul character dpkg-deb: building package `molphy-dbgsym' in `../molphy-dbgsym_2.3b3-3_sparc.ddeb'. dh_compress -pmolphy dh_fixperms -pmolphy dh_makeshlibs -pmolphy dh_installdeb -pmolphy dh_perl -pmolphy dh_shlibdeps -pmolphy dh_gencontrol -pmolphy dh_md5sums -pmolphy dh_builddeb -pmolphy pkgstriptranslations: processing control file: ./debian/molphy/DEBIAN/control, package molphy, directory ./debian/molphy pkgstriptranslations: molphy does not contain translations, skipping pkgstriptranslations: no translation files, not creating tarball pkgmaintainermangler: Maintainer field overridden to "Ubuntu MOTU Developers " warning, `debian/molphy/DEBIAN/control' contains user-defined field `Original-Maintainer' warning, `debian/molphy/DEBIAN/control' contains user-defined field `Tag' dpkg-deb: ignoring 2 warnings about the control file(s) tar: -: file name read contains nul character dpkg-deb: building package `molphy' in `../molphy_2.3b3-3_sparc.deb'. dpkg-genchanges -B -mUbuntu/sparc Build Daemon dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: warning: unknown information field `Xb-Tag' in input data in package's section of control info file dpkg-genchanges: binary-only upload - not including any source code dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20061113-1339 Publishing debug debs. chroot-autobuild/build/buildd/molphy_2.3b3-3_sparc.deb: new debian package, version 2.0. size 256110 bytes: control archive= 3387 bytes. 1468 bytes, 30 lines control 5987 bytes, 91 lines md5sums Package: molphy Version: 2.3b3-3 Section: non-free/science Priority: optional Architecture: sparc Depends: libc6 (>= 2.5-0ubuntu1), perl Suggests: phylip Installed-Size: 836 Maintainer: Ubuntu MOTU Developers Original-Maintainer: Andreas Tille Description: [Biology] Program Package for MOLecular PHYlogenetics ProtML is a main program in MOLPHY for inferring evolutionary trees from PROTein (amino acid) sequences by using the Maximum Likelihood method. Other programs (C language) NucML: Maximum Likelihood Inference of Nucleic Acid Phylogeny ProtST: Basic Statistics of Protein Sequences NucST: Basic Statistics of Nucleic Acid Sequences NJdist: Neighbor Joining Phylogeny from Distance Matrix Utilities (Perl) mollist: get identifiers list molrev: reverse DNA sequences molcat: concatenate sequences molcut: get partial sequences molmerge: merge sequences nuc2ptn: DNA -> Amino acid rminsdel: remove INS/DEL sites molcodon: get specified codon sites molinfo: get varied sites mol2mol: MOLPHY format beautifer inl2mol: Interleaved -> MOLPHY mol2inl: MOLPHY -> Interleaved mol2phy: MOLPHY -> Sequential phy2mol: Sequential -> MOLPHY must2mol: MUST -> MOLPHY etc. . Homepage: http://www.ism.ac.jp/ismlib/softother.e.html Tag: suite::debian-med:bio, legacy::science, made-of::lang:c, made-of::lang:perl chroot-autobuild/build/buildd/molphy_2.3b3-3_sparc.deb: drwxr-xr-x root/root 0 2006-11-13 13:39:04 ./ drwxr-xr-x root/root 0 2006-11-13 13:39:03 ./usr/ drwxr-xr-x root/root 0 2006-11-13 13:39:09 ./usr/bin/ -rwxr-xr-x root/root 1808 2006-11-13 13:39:03 ./usr/bin/ali2mol -rwxr-xr-x root/root 1220 2006-11-13 13:39:03 ./usr/bin/clus2mol -rwxr-xr-x root/root 3135 2006-11-13 13:39:03 ./usr/bin/degene4 -rwxr-xr-x root/root 3122 2006-11-13 13:39:03 ./usr/bin/degene4l -rwxr-xr-x root/root 1535 2006-11-13 13:39:03 ./usr/bin/disjoint -rwxr-xr-x root/root 3175 2006-11-13 13:39:03 ./usr/bin/dna2ami -rwxr-xr-x root/root 1898 2006-11-13 13:39:03 ./usr/bin/eali2mol -rwxr-xr-x root/root 1580 2006-11-13 13:39:03 ./usr/bin/egetcds -rwxr-xr-x root/root 1398 2006-11-13 13:39:03 ./usr/bin/getcds -rwxr-xr-x root/root 1791 2006-11-13 13:39:03 ./usr/bin/ggetcds -rwxr-xr-x root/root 2066 2006-11-13 13:39:03 ./usr/bin/inf2mol -rwxr-xr-x root/root 5538 2006-11-13 13:39:03 ./usr/bin/infocode -rwxr-xr-x root/root 5064 2006-11-13 13:39:03 ./usr/bin/infocode2 -rwxr-xr-x root/root 1646 2006-11-13 13:39:03 ./usr/bin/int2mol -rwxr-xr-x root/root 1431 2006-11-13 13:39:03 ./usr/bin/mc2mol -rwxr-xr-x root/root 1240 2006-11-13 13:39:03 ./usr/bin/mega2mol -rwxr-xr-x root/root 1712 2006-11-13 13:39:03 ./usr/bin/mol2inf -rwxr-xr-x root/root 1466 2006-11-13 13:39:03 ./usr/bin/mol2int -rwxr-xr-x root/root 1490 2006-11-13 13:39:03 ./usr/bin/mol2mol -rwxr-xr-x root/root 1573 2006-11-13 13:39:03 ./usr/bin/mol2phy -rwxr-xr-x root/root 1762 2006-11-13 13:39:03 ./usr/bin/mol2seq -rwxr-xr-x root/root 1961 2006-11-13 13:39:03 ./usr/bin/molcat -rwxr-xr-x root/root 2435 2006-11-13 13:39:03 ./usr/bin/molcodon -rwxr-xr-x root/root 1869 2006-11-13 13:39:03 ./usr/bin/molcons -rwxr-xr-x root/root 2044 2006-11-13 13:39:03 ./usr/bin/molcut -rwxr-xr-x root/root 2506 2006-11-13 13:39:03 ./usr/bin/molinfo -rwxr-xr-x root/root 1416 2006-11-13 13:39:03 ./usr/bin/mollist -rwxr-xr-x root/root 2252 2006-11-13 13:39:03 ./usr/bin/molmerge -rwxr-xr-x root/root 1530 2006-11-13 13:39:03 ./usr/bin/molrev -rwxr-xr-x root/root 1575 2006-11-13 13:39:03 ./usr/bin/molsplit -rwxr-xr-x root/root 1468 2006-11-13 13:39:03 ./usr/bin/must2mol -rwxr-xr-x root/root 144 2006-11-13 13:39:03 ./usr/bin/njt2tpl -rwxr-xr-x root/root 1594 2006-11-13 13:39:03 ./usr/bin/nuc2code -rwxr-xr-x root/root 1561 2006-11-13 13:39:03 ./usr/bin/nuc2NUC -rwxr-xr-x root/root 4616 2006-11-13 13:39:03 ./usr/bin/nuc2ptn -rwxr-xr-x root/root 1498 2006-11-13 13:39:03 ./usr/bin/phy2mol -rwxr-xr-x root/root 2323 2006-11-13 13:39:03 ./usr/bin/rmid3 -rwxr-xr-x root/root 3262 2006-11-13 13:39:03 ./usr/bin/rminsdel -rwxr-xr-x root/root 3130 2006-11-13 13:39:03 ./usr/bin/rmleu -rwxr-xr-x root/root 4293 2006-11-13 13:39:03 ./usr/bin/rmsyno -rwxr-xr-x root/root 1686 2006-11-13 13:39:03 ./usr/bin/seq2mol -rwxr-xr-x root/root 321 2006-11-13 13:39:03 ./usr/bin/seqwrap -rwxr-xr-x root/root 160424 2006-11-13 13:39:09 ./usr/bin/protml -rwxr-xr-x root/root 27904 2006-11-13 13:39:09 ./usr/bin/protst -rwxr-xr-x root/root 152820 2006-11-13 13:39:09 ./usr/bin/nucml -rwxr-xr-x root/root 26848 2006-11-13 13:39:09 ./usr/bin/nucst -rwxr-xr-x root/root 31512 2006-11-13 13:39:09 ./usr/bin/njdist -rwxr-xr-x root/root 15408 2006-11-13 13:39:09 ./usr/bin/totalml drwxr-xr-x root/root 0 2006-11-13 13:39:03 ./usr/share/ drwxr-xr-x root/root 0 2006-11-13 13:39:03 ./usr/share/doc/ drwxr-xr-x root/root 0 2006-11-13 13:39:09 ./usr/share/doc/molphy/ -rw-r--r-- root/root 533 2006-11-13 13:38:27 ./usr/share/doc/molphy/changelog.Debian.gz -rw-r--r-- root/root 1894 2006-11-13 13:38:27 ./usr/share/doc/molphy/README -rw-r--r-- root/root 2866 2006-11-13 13:38:27 ./usr/share/doc/molphy/README.Debian -rw-r--r-- root/root 767 2006-11-13 13:38:27 ./usr/share/doc/molphy/copyright drwxr-xr-x root/root 0 2006-11-13 13:39:03 ./usr/share/doc/molphy/examples/ drwxr-xr-x root/root 0 2006-11-13 13:39:09 ./usr/share/doc/molphy/examples/tests/ drwxr-xr-x root/root 0 2006-11-13 13:39:09 ./usr/share/doc/molphy/examples/tests/compare/ -rw-r--r-- root/root 694 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/README.compare -rw-r--r-- root/root 3611 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test15.dis -rw-r--r-- root/root 1673 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test5.ml.gz -rw-r--r-- root/root 952 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test15.nj -rw-r--r-- root/root 848 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test15.nj-2.2 -rw-r--r-- root/root 768 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test15.njo -rw-r--r-- root/root 1371 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test15.tpl -rw-r--r-- root/root 333 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test15.tree -rw-r--r-- root/root 301 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test4.dis -rw-r--r-- root/root 1545 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test4.ml -rw-r--r-- root/root 157 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test4.nj -rw-r--r-- root/root 189 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test4.nj-2.2 -rw-r--r-- root/root 1066 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test4.tpl -rw-r--r-- root/root 379 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test5.nj -rw-r--r-- root/root 1931 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test5.tpl -rw-r--r-- root/root 707 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test6.mlq -rw-r--r-- root/root 942 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test6.mls -rw-r--r-- root/root 744 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test6.mls-2.2 -rw-r--r-- root/root 1750 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test6.tpl -rw-r--r-- root/root 117 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test6.tplq -rw-r--r-- root/root 654 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test7.mlq -rw-r--r-- root/root 987 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test7.mls -rw-r--r-- root/root 949 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test7.mls-2.2 -rw-r--r-- root/root 134 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test7.tpl -rw-r--r-- root/root 1314 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test15.ml.gz -rw-r--r-- root/root 1416 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/compare/test6.ml.gz -rw-r--r-- root/root 1086 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/comparetests -rw-r--r-- root/root 2192 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/makefile -rw-r--r-- root/root 182 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/test15.cns -rw-r--r-- root/root 2349 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/test6.nuc.gz -rw-r--r-- root/root 333 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/test15.tree -rw-r--r-- root/root 407 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/test4.ptn -rw-r--r-- root/root 1856 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/test5.ptn -rw-r--r-- root/root 2989 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/test7.ptn -rw-r--r-- root/root 2142 2006-11-13 13:38:27 ./usr/share/doc/molphy/examples/tests/test15.ptn.gz -rw-r--r-- root/root 2255 2006-11-13 13:38:27 ./usr/share/doc/molphy/FORMAT.gz -rw-r--r-- root/root 10740 2006-11-13 13:38:27 ./usr/share/doc/molphy/PROTMLver1.DOC.gz drwxr-xr-x root/root 0 2006-11-13 13:39:03 ./usr/share/man/ drwxr-xr-x root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/ -rw-r--r-- root/root 837 2006-11-13 13:38:27 ./usr/share/man/man1/protml.1.gz -rw-r--r-- root/root 1104 2006-11-13 13:38:27 ./usr/share/man/man1/mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/seqwrap.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/seq2mol.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/rmsyno.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/rminsdel.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/phy2mol.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/nuc2ptn.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/nuc2NUC.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/int2mol.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 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root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/mol2inf.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/mega2mol.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/molcut.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/infocode.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/inf2mol.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/ggetcds.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/egetcds.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/protst.1.gz -> protml.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/dna2ami.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/getcds.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/degene4.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/clus2mol.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/ali2mol.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/totalml.1.gz -> protml.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/nucml.1.gz -> protml.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/nuc2code.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/mc2mol.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/molsplit.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/rmid3.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/nucst.1.gz -> protml.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/njdist.1.gz -> protml.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/molcat.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/infocode2.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/disjoint.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/eali2mol.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/rmleu.1.gz -> mollist.1.gz lrwxrwxrwx root/root 0 2006-11-13 13:39:09 ./usr/share/man/man1/degene4l.1.gz -> mollist.1.gz molphy_2.3b3-3_sparc.changes: Format: 1.7 Date: Sun, 10 Sep 2006 15:44:10 +0200 Source: molphy Binary: molphy Architecture: sparc Version: 2.3b3-3 Distribution: autobuild Urgency: low Maintainer: Ubuntu/sparc Build Daemon Changed-By: Andreas Tille Description: molphy - [Biology] Program Package for MOLecular PHYlogenetics Changes: molphy (2.3b3-3) unstable; urgency=low . * Standards-Version: 3.7.2 (no changes needed) * Switched to cdbs * Added DebTags Files: 3f760a45d1c7c40e99ca05690563ac7a 256110 non-free/science optional molphy_2.3b3-3_sparc.deb ****************************************************************************** Built successfully Purging chroot-autobuild/build/buildd/molphy-2.3b3 ------------------------------------------------------------------------------ /usr/bin/sudo dpkg --root=/home/buildd/build-271737-455925/chroot-autobuild --purge po-debconf patchutils intltool-debian libmagic1 gettext file cdbs html2text gettext-base debhelper (Reading database ... 10048 files and directories currently installed.) Removing patchutils ... Removing cdbs ... Removing debhelper ... Removing po-debconf ... Removing intltool-debian ... Removing gettext ... Removing file ... Purging configuration files for file ... Removing html2text ... Purging configuration files for html2text ... Removing gettext-base ... Removing libmagic1 ... Purging configuration files for libmagic1 ... ****************************************************************************** Finished at 20061113-1339 Build needed 00:00:46, 4380k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', '271737-455925'] Scanning for processes to kill in build 271737-455925... Scanning for processes to kill in build /home/buildd/build-271737-455925/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '271737-455925'] Unmounting chroot for build 271737-455925... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '271737-455925'] Removing build 271737-455925