Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/b/bioperl/bioperl_1.7.8-1_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/bioperl-1.7.8-1_k30lbl2/bioperl_1.7.8-1_all.buildinfo Get source package info: bioperl=1.7.8-1 Source URL: http://snapshot.notset.fr/mr/package/bioperl/1.7.8-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=11.1 base-passwd=3.5.51 bash=5.1-3+b1 binutils=2.35.2-2 binutils-common=2.35.2-2 binutils-x86-64-linux-gnu=2.35.2-2 bsdextrautils=2.36.1-8 bsdutils=1:2.36.1-8 build-essential=12.9 bzip2=1.0.8-4 ca-certificates=20210119 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.77 debhelper=13.3.4 debianutils=4.11.2 dh-autoreconf=20 dh-strip-nondeterminism=1.12.0-1 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 fontconfig=2.13.1-4.2 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gettext=0.21-4 gettext-base=0.21-4 graphviz=2.42.2-5 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-4 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libace-perl=1.92-10 libacl1=2.2.53-10 libalgorithm-diff-perl=1.201-1 libalgorithm-munkres-perl=0.08-3 libann0=1.1.2+doc-7 libarchive-zip-perl=1.68-1 libarray-compare-perl=3.0.8-1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libb-hooks-op-check-perl=0.22-1+b3 libbinutils=2.35.2-2 libbio-asn1-entrezgene-perl=1.730-2 libbio-cluster-perl=1.7.3-5 libbio-db-ncbihelper-perl=1.7.6-4 libbio-perl-perl=1.7.7-2 libbio-samtools-perl=1.43-3+b1 libbio-variation-perl=1.7.5-2 libblkid1=2.36.1-8 libbrotli1=1.0.9-2+b2 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-4 libc-bin=2.31-13 libc-dev-bin=2.31-13 libc6=2.31-13 libc6-dev=2.31-13 libcache-cache-perl=1.08-2 libcairo2=1.16.0-5 libcap-ng0=0.7.9-2.2+b1 libcapture-tiny-perl=0.48-1 libcc1-0=10.2.1-6 libcdt5=2.42.2-5 libcgi-pm-perl=4.51-1 libcgraph6=2.42.2-5 libclass-data-inheritable-perl=0.08-3 libclass-inspector-perl=1.36-1 libclass-method-modifiers-perl=2.13-1 libclass-unload-perl=0.11-1 libclone-perl=0.45-1+b1 libcom-err2=1.46.2-2 libconvert-binary-c-perl=0.84-1 libconvert-binhex-perl=1.125-1 libcrypt-dev=1:4.4.18-5 libcrypt-rc4-perl=2.02-3 libcrypt1=1:4.4.18-5 libctf-nobfd0=2.35.2-2 libctf0=2.35.2-2 libdata-stag-perl=0.14-2 libdatrie1=0.2.13-1 libdb5.3=5.3.28+dfsg1-0.8 libdbd-mysql-perl=4.050-3+b1 libdbd-pg-perl=3.14.2-1+b1 libdbd-sqlite3-perl=1.66-1+b1 libdbi-perl=1.643-3+b1 libdebconfclient0=0.260 libdebhelper-perl=13.3.4 libdeflate0=1.7-1 libdevel-callchecker-perl=0.008-1+b2 libdevel-cycle-perl=1.12-1 libdevel-stacktrace-perl=2.0400-1 libdigest-perl-md5-perl=1.9-1.1 libdpkg-perl=1.20.9 libdynaloader-functions-perl=0.003-1.1 libelf1=0.183-3 libencode-locale-perl=1.05-1.1 liberror-perl=0.17029-1 libexception-class-perl=1.44-1 libexpat1=2.2.10-2 libexporter-tiny-perl=1.002002-1 libfcgi-perl=0.79+ds-2 libfcgi0ldbl=2.4.2-2 libffi7=3.3-6 libfile-listing-perl=6.14-1 libfile-slurp-tiny-perl=0.004-1 libfile-stripnondeterminism-perl=1.12.0-1 libfontconfig1=2.13.1-4.2 libfreetype6=2.10.4+dfsg-1 libfribidi0=1.0.8-2 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-6 libgd-perl=2.73-1+b1 libgd3=2.3.0-2 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libglib2.0-0=2.66.8-1 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.1-5 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgraph-perl=1:0.9716-2 libgraphite2-3=1.3.14-1 libgraphviz-perl=2.24-1 libgssapi-krb5-2=1.18.3-6 libgts-0.7-5=0.7.6+darcs121130-4+b1 libgvc6=2.42.2-5 libgvpr2=2.42.2-5 libharfbuzz0b=2.7.4-1 libheap-perl=0.80-3 libhogweed6=3.7.3-1 libhtml-parser-perl=3.76-1 libhtml-tableextract-perl=2.15-1.1 libhtml-tagset-perl=3.20-4 libhtml-tree-perl=5.07-2 libhttp-cookies-perl=6.10-1 libhttp-daemon-perl=6.12-1 libhttp-date-perl=6.05-1 libhttp-message-perl=6.29-1 libhttp-negotiate-perl=6.01-1 libice6=2:1.0.10-1 libicu67=67.1-7 libidn2-0=2.3.0-5 libimport-into-perl=1.002005-1 libio-html-perl=1.004-2 libio-pty-perl=1:1.15-2 libio-sessiondata-perl=1.03-1.1 libio-socket-ssl-perl=2.069-1 libio-string-perl=1.08-3.1 libio-stringy-perl=2.111-3 libipc-run-perl=20200505.0-1 libipc-sharelite-perl=0.17-4+b5 libisl23=0.23-1 libitm1=10.2.1-6 libjbig0=2.1-3.1+b2 libjcode-pm-perl=2.06-1+b1 libjpeg62-turbo=1:2.0.6-4 libk5crypto3=1.18.3-6 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-6 libkrb5support0=1.18.3-6 liblab-gamut1=2.42.2-5 libldap-2.4-2=2.4.57+dfsg-3 liblist-moreutils-perl=0.430-2 liblist-moreutils-xs-perl=0.430-2 liblsan0=10.2.1-6 libltdl7=2.4.6-15 liblwp-mediatypes-perl=6.04-1 liblwp-protocol-https-perl=6.10-1 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmailtools-perl=2.21-1 libmariadb3=1:10.5.12-1 libmath-derivative-perl=1.01-1.1 libmath-spline-perl=0.02-2 libmd0=1.0.3-3 libmime-tools-perl=5.509-1 libmodule-build-perl=0.423100-1 libmodule-runtime-perl=0.016-1 libmoo-perl=2.004004-1 libmount1=2.36.1-8 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnet-http-perl=6.20-1 libnet-smtp-ssl-perl=1.04-1 libnet-ssleay-perl=1.88-3+b1 libnettle8=3.7.3-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libole-storage-lite-perl=0.20-1 libossp-uuid-perl=1.6.2-1.5+b9 libossp-uuid16=1.6.2-1.5+b9 libp11-kit0=0.23.22-1 libpadwalker-perl=2.5-1+b1 libpam-modules=1.4.0-9 libpam-modules-bin=1.4.0-9 libpam-runtime=1.4.0-9 libpam0g=1.4.0-9 libpango-1.0-0=1.46.2-3 libpangocairo-1.0-0=1.46.2-3 libpangoft2-1.0-0=1.46.2-3 libparams-classify-perl=0.015-1+b3 libparse-recdescent-perl=1.967015+dfsg-2 libpath-class-perl=0.37-1 libpathplan4=2.42.2-5 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-5 libperlio-eol-perl=0.17-1+b3 libpipeline1=1.5.3-1 libpixman-1-0=0.40.0-1 libpng16-16=1.6.37-3 libpostscript-perl=0.06-3.1 libpq5=13.4-1 libquadmath0=10.2.1-6 librole-tiny-perl=2.002004-1 libsasl2-2=2.1.27+dfsg-2.1 libsasl2-modules-db=2.1.27+dfsg-2.1 libseccomp2=2.5.1-1 libselinux1=3.1-3 libset-object-perl=1.41-1 libset-scalar-perl=1.29-2 libsigsegv2=2.13-1 libsm6=2:1.2.3-1 libsmartcols1=2.36.1-8 libsoap-lite-perl=1.27-1 libsort-naturally-perl=1.03-2 libspreadsheet-parseexcel-perl=0.6500-1.1 libspreadsheet-writeexcel-perl=2.40-1.1 libsqlite3-0=3.34.1-3 libssl1.1=1.1.1k-1 libstatistics-descriptive-perl=3.0800-1 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libstrictures-perl=2.000006-1 libsub-override-perl=0.09-2 libsub-quote-perl=2.006006-1 libsub-uplevel-perl=0.2800-1.1 libsvg-graph-perl=0.02-3 libsvg-perl=2.85-1 libsystemd0=247.3-6 libtask-weaken-perl=1.06-1 libtasn1-6=4.16.0-2 libtest-deep-perl=1.130-1 libtest-differences-perl=0.67-1 libtest-exception-perl=0.43-1 libtest-memory-cycle-perl=1.06-1 libtest-most-perl=0.37-1 libtest-pod-perl=1.52-1 libtest-requiresinternet-perl=0.05-3 libtest-warn-perl=0.36-1 libtest-weaken-perl=3.022000-1.1 libtext-diff-perl=1.45-1 libthai-data=0.1.28-4 libthai0=0.1.28-4 libtiff5=4.2.0-1 libtimedate-perl=2.3300-2 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtree-dagnode-perl=1.32-1 libtry-tiny-perl=0.30-1 libtsan0=10.2.1-6 libtype-tiny-perl=1.012002-1 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.3-6 libunicode-map-perl=0.112-12+b3 libunistring2=0.9.10-4 liburi-perl=5.08-1 libuuid1=2.36.1-8 libwebp6=0.6.1-2.1 libwww-perl=6.53-1 libwww-robotrules-perl=6.02-1 libx11-6=2:1.7.2-1 libx11-data=2:1.7.2-1 libxau6=1:1.0.9-1 libxaw7=2:1.0.13-1.1 libxcb-render0=1.14-3 libxcb-shm0=1.14-3 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1.1 libxml-dom-perl=1.46-1 libxml-dom-xpath-perl=0.14-3 libxml-filter-buffertext-perl=1.01-6 libxml-libxml-perl=2.0134+dfsg-2+b1 libxml-namespacesupport-perl=1.12-1.1 libxml-parser-perl=2.46-2 libxml-perl=0.08-3.1 libxml-regexp-perl=0.04-1.1 libxml-sax-base-perl=1.09-1.1 libxml-sax-expatxs-perl=1.33-2+b7 libxml-sax-perl=1.02+dfsg-1 libxml-sax-writer-perl=0.57-1.1 libxml-simple-perl=2.25-1 libxml-twig-perl=1:3.52-1 libxml-writer-perl=0.900-1 libxml-xpath-perl=1.44-1 libxml-xpathengine-perl=0.14-1 libxml2=2.9.10+dfsg-6.7 libxmu6=2:1.1.2-2+b3 libxpm4=1:3.5.12-1 libxrender1=1:0.9.10-1 libxt6=1:1.2.0-1 libyaml-perl=1.30-1 libzstd1=1.4.8+dfsg-2.1 linux-libc-dev=5.10.46-4 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mariadb-common=1:10.5.12-1 mawk=1.3.4.20200120-2 mysql-common=5.8+1.0.7 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 netbase=6.3 openssl=1.1.1k-1 patch=2.7.6-7 perl=5.32.1-5 perl-base=5.32.1-5 perl-modules-5.32=5.32.1-5 perl-openssl-defaults=5 po-debconf=1.0.21+nmu1 rename=1.13-1 sed=4.7-1 sensible-utils=0.0.14 sysvinit-utils=2.96-7 tar=1.34+dfsg-1 ucf=3.0043 util-linux=2.36.1-8 x11-common=1:7.7+22 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210818T025459Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210818T025459Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210815T082041Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d bioperl=1.7.8-1 && mkdir -p /build/bioperl-0WLrhs && dpkg-source --no-check -x /*.dsc /build/bioperl-0WLrhs/bioperl-1.7.8 && chown -R builduser:builduser /build/bioperl-0WLrhs" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bioperl-0WLrhs/bioperl-1.7.8 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1629032163" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/bioperl-0WLrhs /tmp/bioperl-1.7.8-1_k30lbl2 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210815T082041Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.Pyln9JFF9M as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.Pyln9JFF9M Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-8). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210815T082041Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210815T082041Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (699 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4668 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-13) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210818T025459Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210818T025459Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210815T082041Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.Pyln9JFF9M Get:1 http://snapshot.notset.fr/archive/debian/20210818T025459Z bookworm InRelease [94.4 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210815T082041Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210818T025459Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210818T025459Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210818T025459Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210818T025459Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210818T025459Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210818T025459Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210818T025459Z bookworm/main Sources [11.5 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210818T025459Z bookworm/main amd64 Packages [11.2 MB] Fetched 22.8 MB in 19s (1180 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.Pyln9JFF9M I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d bioperl=1.7.8-1 && mkdir -p /build/bioperl-0WLrhs && dpkg-source --no-check -x /*.dsc /build/bioperl-0WLrhs/bioperl-1.7.8 && chown -R builduser:builduser /build/bioperl-0WLrhs"' exec /tmp/mmdebstrap.Pyln9JFF9M Reading package lists... NOTICE: 'bioperl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bioperl.git Please use: git clone https://salsa.debian.org/med-team/bioperl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 7543 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210818T025459Z bookworm/main bioperl 1.7.8-1 (dsc) [3170 B] Get:2 http://snapshot.notset.fr/archive/debian/20210818T025459Z bookworm/main bioperl 1.7.8-1 (tar) [7528 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210818T025459Z bookworm/main bioperl 1.7.8-1 (diff) [11.9 kB] Fetched 7543 kB in 6s (1275 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'bioperl_1.7.8-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting bioperl in /build/bioperl-0WLrhs/bioperl-1.7.8 dpkg-source: info: unpacking bioperl_1.7.8.orig.tar.gz dpkg-source: info: unpacking bioperl_1.7.8-1.debian.tar.xz I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bioperl-0WLrhs/bioperl-1.7.8 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1629032163" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.Pyln9JFF9M dpkg-buildpackage: info: source package bioperl dpkg-buildpackage: info: source version 1.7.8-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/bioperl-0WLrhs/bioperl-1.7.8' dh_clean build-stamp install-stamp bioperl.conf biodatabases.pod \ biodesign.pod bioperl.pod bioscripts.pod make[1]: Leaving directory '/build/bioperl-0WLrhs/bioperl-1.7.8' debian/rules binary-indep dh binary-indep dh_update_autotools_config -i dh_autoreconf -i debian/rules override_dh_auto_configure make[1]: Entering directory '/build/bioperl-0WLrhs/bioperl-1.7.8' dh_auto_configure -- perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -ffile-prefix-map=/build/bioperl-0WLrhs/bioperl-1.7.8=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/bioperl-0WLrhs/bioperl-1.7.8=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro" Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for BioPerl Writing MYMETA.yml and MYMETA.json make[1]: Leaving directory '/build/bioperl-0WLrhs/bioperl-1.7.8' dh_auto_build -i make -j10 make[1]: Entering directory '/build/bioperl-0WLrhs/bioperl-1.7.8' cp lib/Bio/Annotation/OntologyTerm.pm blib/lib/Bio/Annotation/OntologyTerm.pm cp lib/Bio/AlignIO/clustalw.pm blib/lib/Bio/AlignIO/clustalw.pm cp lib/Bio/AlignIO/proda.pm blib/lib/Bio/AlignIO/proda.pm cp lib/Bio/AnnotatableI.pm blib/lib/Bio/AnnotatableI.pm cp lib/Bio/AlignIO/msf.pm blib/lib/Bio/AlignIO/msf.pm cp lib/Bio/AlignIO.pm blib/lib/Bio/AlignIO.pm cp lib/Bio/AlignIO/bl2seq.pm blib/lib/Bio/AlignIO/bl2seq.pm cp lib/Bio/AnalysisResultI.pm blib/lib/Bio/AnalysisResultI.pm cp lib/Bio/AnalysisParserI.pm blib/lib/Bio/AnalysisParserI.pm cp lib/Bio/AlignIO/po.pm blib/lib/Bio/AlignIO/po.pm cp lib/Bio/AlignIO/maf.pm blib/lib/Bio/AlignIO/maf.pm cp lib/Bio/Annotation/AnnotationFactory.pm blib/lib/Bio/Annotation/AnnotationFactory.pm cp lib/Bio/AlignIO/prodom.pm blib/lib/Bio/AlignIO/prodom.pm cp lib/Bio/AlignIO/mase.pm blib/lib/Bio/AlignIO/mase.pm cp lib/Bio/AlignIO/mega.pm blib/lib/Bio/AlignIO/mega.pm cp lib/Bio/AlignIO/xmfa.pm blib/lib/Bio/AlignIO/xmfa.pm cp lib/Bio/Align/Utilities.pm blib/lib/Bio/Align/Utilities.pm cp lib/Bio/Annotation/Comment.pm blib/lib/Bio/Annotation/Comment.pm cp lib/Bio/AnalysisI.pm blib/lib/Bio/AnalysisI.pm cp lib/Bio/AlignIO/psi.pm blib/lib/Bio/AlignIO/psi.pm cp lib/Bio/Align/DNAStatistics.pm blib/lib/Bio/Align/DNAStatistics.pm cp lib/Bio/Annotation/Relation.pm blib/lib/Bio/Annotation/Relation.pm cp lib/Bio/Annotation/DBLink.pm blib/lib/Bio/Annotation/DBLink.pm cp lib/Bio/Annotation/Collection.pm blib/lib/Bio/Annotation/Collection.pm cp lib/Bio/Align/AlignI.pm blib/lib/Bio/Align/AlignI.pm cp lib/Bio/Align/PairwiseStatistics.pm blib/lib/Bio/Align/PairwiseStatistics.pm cp lib/Bio/Align/StatisticsI.pm blib/lib/Bio/Align/StatisticsI.pm cp lib/Bio/AlignIO/largemultifasta.pm blib/lib/Bio/AlignIO/largemultifasta.pm cp lib/Bio/AlignIO/nexus.pm blib/lib/Bio/AlignIO/nexus.pm cp lib/Bio/AlignIO/emboss.pm blib/lib/Bio/AlignIO/emboss.pm cp lib/Bio/Annotation/Reference.pm blib/lib/Bio/Annotation/Reference.pm cp lib/Bio/AlignIO/metafasta.pm blib/lib/Bio/AlignIO/metafasta.pm cp lib/Bio/AlignIO/meme.pm blib/lib/Bio/AlignIO/meme.pm cp lib/Bio/AlignIO/arp.pm blib/lib/Bio/AlignIO/arp.pm cp lib/Bio/AlignIO/pfam.pm blib/lib/Bio/AlignIO/pfam.pm cp lib/Bio/AlignIO/fasta.pm blib/lib/Bio/AlignIO/fasta.pm cp lib/Bio/AlignIO/phylip.pm blib/lib/Bio/AlignIO/phylip.pm cp lib/Bio/AlignIO/selex.pm blib/lib/Bio/AlignIO/selex.pm cp lib/Bio/AlignIO/Handler/GenericAlignHandler.pm blib/lib/Bio/AlignIO/Handler/GenericAlignHandler.pm cp lib/Bio/Align/ProteinStatistics.pm blib/lib/Bio/Align/ProteinStatistics.pm cp lib/Bio/DB/IndexedBase.pm blib/lib/Bio/DB/IndexedBase.pm cp lib/Bio/DB/Failover.pm blib/lib/Bio/DB/Failover.pm cp lib/Bio/DB/GFF/Util/Rearrange.pm blib/lib/Bio/DB/GFF/Util/Rearrange.pm cp lib/Bio/CodonUsage/Table.pm blib/lib/Bio/CodonUsage/Table.pm cp lib/Bio/DB/FileCache.pm blib/lib/Bio/DB/FileCache.pm cp lib/Bio/DB/Qual.pm blib/lib/Bio/DB/Qual.pm cp lib/Bio/Annotation/TypeManager.pm blib/lib/Bio/Annotation/TypeManager.pm cp lib/Bio/CodonUsage/IO.pm blib/lib/Bio/CodonUsage/IO.pm cp lib/Bio/DB/Taxonomy/list.pm blib/lib/Bio/DB/Taxonomy/list.pm cp lib/Bio/DB/Taxonomy/greengenes.pm blib/lib/Bio/DB/Taxonomy/greengenes.pm cp lib/Bio/Annotation/Target.pm blib/lib/Bio/Annotation/Target.pm cp lib/Bio/DB/Fasta.pm blib/lib/Bio/DB/Fasta.pm cp lib/Bio/DB/Flat/BinarySearch.pm blib/lib/Bio/DB/Flat/BinarySearch.pm cp lib/Bio/DB/InMemoryCache.pm blib/lib/Bio/DB/InMemoryCache.pm cp lib/Bio/DB/LocationI.pm blib/lib/Bio/DB/LocationI.pm cp lib/Bio/DB/Taxonomy.pm blib/lib/Bio/DB/Taxonomy.pm cp lib/Bio/Annotation/TagTree.pm blib/lib/Bio/Annotation/TagTree.pm cp lib/Bio/Annotation/SimpleValue.pm blib/lib/Bio/Annotation/SimpleValue.pm cp lib/Bio/DB/QueryI.pm blib/lib/Bio/DB/QueryI.pm cp lib/Bio/DB/RandomAccessI.pm blib/lib/Bio/DB/RandomAccessI.pm cp lib/Bio/DB/Registry.pm blib/lib/Bio/DB/Registry.pm cp lib/Bio/DB/Flat/BDB/swiss.pm blib/lib/Bio/DB/Flat/BDB/swiss.pm cp lib/Bio/DB/SeqI.pm blib/lib/Bio/DB/SeqI.pm cp lib/Bio/DB/GFF/Util/Binning.pm blib/lib/Bio/DB/GFF/Util/Binning.pm cp lib/Bio/DB/Flat.pm blib/lib/Bio/DB/Flat.pm cp lib/Bio/DB/DBFetch.pm blib/lib/Bio/DB/DBFetch.pm cp lib/Bio/DB/Taxonomy/silva.pm blib/lib/Bio/DB/Taxonomy/silva.pm cp lib/Bio/DB/Flat/BDB.pm blib/lib/Bio/DB/Flat/BDB.pm cp lib/Bio/Annotation/StructuredValue.pm blib/lib/Bio/Annotation/StructuredValue.pm cp lib/Bio/DB/Flat/BDB/genbank.pm blib/lib/Bio/DB/Flat/BDB/genbank.pm cp lib/Bio/DB/Flat/BDB/embl.pm blib/lib/Bio/DB/Flat/BDB/embl.pm cp lib/Bio/DB/Taxonomy/flatfile.pm blib/lib/Bio/DB/Taxonomy/flatfile.pm cp lib/Bio/DB/ReferenceI.pm blib/lib/Bio/DB/ReferenceI.pm cp lib/Bio/AnnotationI.pm blib/lib/Bio/AnnotationI.pm cp lib/Bio/DB/UpdateableSeqI.pm blib/lib/Bio/DB/UpdateableSeqI.pm cp lib/Bio/DB/Query/WebQuery.pm blib/lib/Bio/DB/Query/WebQuery.pm cp lib/Bio/AnnotationCollectionI.pm blib/lib/Bio/AnnotationCollectionI.pm cp lib/Bio/Annotation/Tree.pm blib/lib/Bio/Annotation/Tree.pm cp lib/Bio/DB/Flat/BDB/fasta.pm blib/lib/Bio/DB/Flat/BDB/fasta.pm cp lib/Bio/DB/GenericWebAgent.pm blib/lib/Bio/DB/GenericWebAgent.pm cp lib/Bio/Index/Fasta.pm blib/lib/Bio/Index/Fasta.pm cp lib/Bio/Index/Blast.pm blib/lib/Bio/Index/Blast.pm cp lib/Bio/HandlerBaseI.pm blib/lib/Bio/HandlerBaseI.pm cp lib/Bio/Factory/ApplicationFactoryI.pm blib/lib/Bio/Factory/ApplicationFactoryI.pm cp lib/Bio/Factory/LocationFactoryI.pm blib/lib/Bio/Factory/LocationFactoryI.pm cp lib/Bio/Event/EventHandlerI.pm blib/lib/Bio/Event/EventHandlerI.pm cp lib/Bio/Event/EventGeneratorI.pm blib/lib/Bio/Event/EventGeneratorI.pm cp lib/Bio/Factory/SequenceFactoryI.pm blib/lib/Bio/Factory/SequenceFactoryI.pm cp lib/Bio/Factory/FTLocationFactory.pm blib/lib/Bio/Factory/FTLocationFactory.pm cp lib/Bio/Factory/AnalysisI.pm blib/lib/Bio/Factory/AnalysisI.pm cp lib/Bio/DBLinkContainerI.pm blib/lib/Bio/DBLinkContainerI.pm cp lib/Bio/LocatableSeq.pm blib/lib/Bio/LocatableSeq.pm cp lib/Bio/Index/AbstractSeq.pm blib/lib/Bio/Index/AbstractSeq.pm cp lib/Bio/IdentifiableI.pm blib/lib/Bio/IdentifiableI.pm cp lib/Bio/Index/Swissprot.pm blib/lib/Bio/Index/Swissprot.pm cp lib/Bio/DescribableI.pm blib/lib/Bio/DescribableI.pm cp lib/Bio/Factory/SequenceProcessorI.pm blib/lib/Bio/Factory/SequenceProcessorI.pm cp lib/Bio/Factory/ObjectBuilderI.pm blib/lib/Bio/Factory/ObjectBuilderI.pm cp lib/Bio/Factory/ObjectFactory.pm blib/lib/Bio/Factory/ObjectFactory.pm cp lib/Bio/Index/BlastTable.pm blib/lib/Bio/Index/BlastTable.pm cp lib/Bio/Index/Qual.pm blib/lib/Bio/Index/Qual.pm cp lib/Bio/Index/GenBank.pm blib/lib/Bio/Index/GenBank.pm cp lib/Bio/Index/EMBL.pm blib/lib/Bio/Index/EMBL.pm cp lib/Bio/IdCollectionI.pm blib/lib/Bio/IdCollectionI.pm cp lib/Bio/DB/WebDBSeqI.pm blib/lib/Bio/DB/WebDBSeqI.pm cp lib/Bio/Factory/ObjectFactoryI.pm blib/lib/Bio/Factory/ObjectFactoryI.pm cp lib/Bio/Factory/TreeFactoryI.pm blib/lib/Bio/Factory/TreeFactoryI.pm cp lib/Bio/Index/SwissPfam.pm blib/lib/Bio/Index/SwissPfam.pm cp lib/Bio/Das/FeatureTypeI.pm blib/lib/Bio/Das/FeatureTypeI.pm cp lib/Bio/FeatureHolderI.pm blib/lib/Bio/FeatureHolderI.pm cp lib/Bio/Index/Fastq.pm blib/lib/Bio/Index/Fastq.pm cp lib/Bio/Das/SegmentI.pm blib/lib/Bio/Das/SegmentI.pm cp lib/Bio/Factory/DriverFactory.pm blib/lib/Bio/Factory/DriverFactory.pm cp lib/Bio/Factory/SeqAnalysisParserFactory.pm blib/lib/Bio/Factory/SeqAnalysisParserFactory.pm cp lib/Bio/Index/Abstract.pm blib/lib/Bio/Index/Abstract.pm cp lib/Bio/Factory/SequenceStreamI.pm blib/lib/Bio/Factory/SequenceStreamI.pm cp lib/Bio/Factory/SeqAnalysisParserFactoryI.pm blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm cp lib/Bio/DasI.pm blib/lib/Bio/DasI.pm cp lib/Bio/Location/WidestCoordPolicy.pm blib/lib/Bio/Location/WidestCoordPolicy.pm cp lib/Bio/Matrix/PSM/InstanceSiteI.pm blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm cp lib/Bio/Matrix/PSM/IO/mast.pm blib/lib/Bio/Matrix/PSM/IO/mast.pm cp lib/Bio/Matrix/PSM/PsmI.pm blib/lib/Bio/Matrix/PSM/PsmI.pm cp lib/Bio/Ontology/DocumentRegistry.pm blib/lib/Bio/Ontology/DocumentRegistry.pm cp lib/Bio/LocationI.pm blib/lib/Bio/LocationI.pm cp lib/Bio/Matrix/PSM/IO/psiblast.pm blib/lib/Bio/Matrix/PSM/IO/psiblast.pm cp lib/Bio/Matrix/PSM/Psm.pm blib/lib/Bio/Matrix/PSM/Psm.pm cp lib/Bio/Location/AvWithinCoordPolicy.pm blib/lib/Bio/Location/AvWithinCoordPolicy.pm cp lib/Bio/Matrix/PSM/SiteMatrix.pm blib/lib/Bio/Matrix/PSM/SiteMatrix.pm cp lib/Bio/Location/Simple.pm blib/lib/Bio/Location/Simple.pm cp lib/Bio/Matrix/PhylipDist.pm blib/lib/Bio/Matrix/PhylipDist.pm cp lib/Bio/Matrix/PSM/IO/masta.pm blib/lib/Bio/Matrix/PSM/IO/masta.pm cp lib/Bio/Location/Atomic.pm blib/lib/Bio/Location/Atomic.pm cp lib/Bio/Matrix/PSM/IO.pm blib/lib/Bio/Matrix/PSM/IO.pm cp lib/Bio/Matrix/IO/mlagan.pm blib/lib/Bio/Matrix/IO/mlagan.pm cp lib/Bio/Matrix/PSM/PsmHeader.pm blib/lib/Bio/Matrix/PSM/PsmHeader.pm cp lib/Bio/Matrix/PSM/ProtPsm.pm blib/lib/Bio/Matrix/PSM/ProtPsm.pm cp lib/Bio/Matrix/Generic.pm blib/lib/Bio/Matrix/Generic.pm cp lib/Bio/Matrix/Scoring.pm blib/lib/Bio/Matrix/Scoring.pm cp lib/Bio/Matrix/PSM/SiteMatrixI.pm blib/lib/Bio/Matrix/PSM/SiteMatrixI.pm cp lib/Bio/Location/NarrowestCoordPolicy.pm blib/lib/Bio/Location/NarrowestCoordPolicy.pm cp lib/Bio/Location/CoordinatePolicyI.pm blib/lib/Bio/Location/CoordinatePolicyI.pm cp lib/Bio/Matrix/IO/scoring.pm blib/lib/Bio/Matrix/IO/scoring.pm cp lib/Bio/Matrix/PSM/InstanceSite.pm blib/lib/Bio/Matrix/PSM/InstanceSite.pm cp lib/Bio/Location/SplitLocationI.pm blib/lib/Bio/Location/SplitLocationI.pm cp lib/Bio/Matrix/MatrixI.pm blib/lib/Bio/Matrix/MatrixI.pm cp lib/Bio/Matrix/PSM/IO/meme.pm blib/lib/Bio/Matrix/PSM/IO/meme.pm cp lib/Bio/Location/FuzzyLocationI.pm blib/lib/Bio/Location/FuzzyLocationI.pm cp lib/Bio/Matrix/PSM/IO/transfac.pm blib/lib/Bio/Matrix/PSM/IO/transfac.pm cp lib/Bio/Matrix/IO.pm blib/lib/Bio/Matrix/IO.pm cp lib/Bio/Location/Fuzzy.pm blib/lib/Bio/Location/Fuzzy.pm cp lib/Bio/Matrix/Mlagan.pm blib/lib/Bio/Matrix/Mlagan.pm cp lib/Bio/Matrix/IO/phylip.pm blib/lib/Bio/Matrix/IO/phylip.pm cp lib/Bio/Matrix/PSM/ProtMatrix.pm blib/lib/Bio/Matrix/PSM/ProtMatrix.pm cp lib/Bio/Location/Split.pm blib/lib/Bio/Location/Split.pm cp lib/Bio/Matrix/PSM/PsmHeaderI.pm blib/lib/Bio/Matrix/PSM/PsmHeaderI.pm cp lib/Bio/OntologyIO.pm blib/lib/Bio/OntologyIO.pm cp lib/Bio/Ontology/Term.pm blib/lib/Bio/Ontology/Term.pm cp lib/Bio/OntologyIO/simplehierarchy.pm blib/lib/Bio/OntologyIO/simplehierarchy.pm cp lib/Bio/Ontology/OBOEngine.pm blib/lib/Bio/Ontology/OBOEngine.pm cp lib/Bio/OntologyIO/goflat.pm blib/lib/Bio/OntologyIO/goflat.pm cp lib/Bio/OntologyIO/Handlers/InterProHandler.pm blib/lib/Bio/OntologyIO/Handlers/InterProHandler.pm cp lib/Bio/Ontology/PathI.pm blib/lib/Bio/Ontology/PathI.pm cp lib/Bio/Ontology/RelationshipFactory.pm blib/lib/Bio/Ontology/RelationshipFactory.pm cp lib/Bio/Range.pm blib/lib/Bio/Range.pm cp lib/Bio/Ontology/GOterm.pm blib/lib/Bio/Ontology/GOterm.pm cp lib/Bio/Ontology/TermI.pm blib/lib/Bio/Ontology/TermI.pm cp lib/Bio/Ontology/TermFactory.pm blib/lib/Bio/Ontology/TermFactory.pm cp lib/Bio/ParameterBaseI.pm blib/lib/Bio/ParameterBaseI.pm cp lib/Bio/PrimarySeq.pm blib/lib/Bio/PrimarySeq.pm cp lib/Bio/Ontology/Path.pm blib/lib/Bio/Ontology/Path.pm cp lib/Bio/Ontology/Ontology.pm blib/lib/Bio/Ontology/Ontology.pm cp lib/Bio/Root/Exception.pm blib/lib/Bio/Root/Exception.pm cp lib/Bio/OntologyIO/soflat.pm blib/lib/Bio/OntologyIO/soflat.pm cp lib/Bio/Ontology/OntologyI.pm blib/lib/Bio/Ontology/OntologyI.pm cp lib/Bio/PullParserI.pm blib/lib/Bio/PullParserI.pm cp lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm blib/lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm cp lib/Bio/Ontology/OntologyEngineI.pm blib/lib/Bio/Ontology/OntologyEngineI.pm cp lib/Bio/Ontology/RelationshipType.pm blib/lib/Bio/Ontology/RelationshipType.pm cp lib/Bio/Ontology/Relationship.pm blib/lib/Bio/Ontology/Relationship.pm cp lib/Bio/PrimarySeqI.pm blib/lib/Bio/PrimarySeqI.pm cp lib/Bio/OntologyIO/dagflat.pm blib/lib/Bio/OntologyIO/dagflat.pm cp lib/Bio/Ontology/SimpleOntologyEngine.pm blib/lib/Bio/Ontology/SimpleOntologyEngine.pm cp lib/Bio/Ontology/RelationshipI.pm blib/lib/Bio/Ontology/RelationshipI.pm cp lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm blib/lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm cp lib/Bio/OntologyIO/obo.pm blib/lib/Bio/OntologyIO/obo.pm cp lib/Bio/RangeI.pm blib/lib/Bio/RangeI.pm cp lib/Bio/Ontology/InterProTerm.pm blib/lib/Bio/Ontology/InterProTerm.pm cp lib/Bio/OntologyIO/InterProParser.pm blib/lib/Bio/OntologyIO/InterProParser.pm cp lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm cp lib/Bio/Ontology/OntologyStore.pm blib/lib/Bio/Ontology/OntologyStore.pm cp lib/Bio/Ontology/OBOterm.pm blib/lib/Bio/Ontology/OBOterm.pm cp lib/Bio/Search/HSP/HSPI.pm blib/lib/Bio/Search/HSP/HSPI.pm cp lib/Bio/Search/HSP/PSLHSP.pm blib/lib/Bio/Search/HSP/PSLHSP.pm cp lib/Bio/Search/Processor.pm blib/lib/Bio/Search/Processor.pm cp lib/Bio/Search/Hit/ModelHit.pm blib/lib/Bio/Search/Hit/ModelHit.pm cp lib/Bio/Root/TestObject.pm blib/lib/Bio/Root/TestObject.pm cp lib/Bio/Search/HSP/BlastPullHSP.pm blib/lib/Bio/Search/HSP/BlastPullHSP.pm cp lib/Bio/Root/Utilities.pm blib/lib/Bio/Root/Utilities.pm cp lib/Bio/Search/Hit/HitFactory.pm blib/lib/Bio/Search/Hit/HitFactory.pm cp lib/Bio/Root/RootI.pm blib/lib/Bio/Root/RootI.pm cp lib/Bio/Search/Hit/BlastPullHit.pm blib/lib/Bio/Search/Hit/BlastPullHit.pm cp lib/Bio/Search/HSP/FastaHSP.pm blib/lib/Bio/Search/HSP/FastaHSP.pm cp lib/Bio/Search/Hit/HitI.pm blib/lib/Bio/Search/Hit/HitI.pm cp lib/Bio/Search/HSP/PullHSPI.pm blib/lib/Bio/Search/HSP/PullHSPI.pm cp lib/Bio/Search/Iteration/GenericIteration.pm blib/lib/Bio/Search/Iteration/GenericIteration.pm cp lib/Bio/Search/HSP/GenericHSP.pm blib/lib/Bio/Search/HSP/GenericHSP.pm cp lib/Bio/Search/HSP/HSPFactory.pm blib/lib/Bio/Search/HSP/HSPFactory.pm cp lib/Bio/Root/Version.pm blib/lib/Bio/Root/Version.pm cp lib/Bio/Root/HTTPget.pm blib/lib/Bio/Root/HTTPget.pm cp lib/Bio/Search/Hit/PullHitI.pm blib/lib/Bio/Search/Hit/PullHitI.pm cp lib/Bio/Search/BlastUtils.pm blib/lib/Bio/Search/BlastUtils.pm cp lib/Bio/Search/BlastStatistics.pm blib/lib/Bio/Search/BlastStatistics.pm cp lib/Bio/Root/Storable.pm blib/lib/Bio/Root/Storable.pm cp lib/Bio/Root/IO.pm blib/lib/Bio/Root/IO.pm cp lib/Bio/Root/Root.pm blib/lib/Bio/Root/Root.pm cp lib/Bio/Search/HSP/PsiBlastHSP.pm blib/lib/Bio/Search/HSP/PsiBlastHSP.pm cp lib/Bio/Search/Hit/GenericHit.pm blib/lib/Bio/Search/Hit/GenericHit.pm cp lib/Bio/Search/Iteration/IterationI.pm blib/lib/Bio/Search/Iteration/IterationI.pm cp lib/Bio/Search/Hit/BlastHit.pm blib/lib/Bio/Search/Hit/BlastHit.pm cp lib/Bio/Search/HSP/ModelHSP.pm blib/lib/Bio/Search/HSP/ModelHSP.pm cp lib/Bio/Search/Hit/PsiBlastHit.pm blib/lib/Bio/Search/Hit/PsiBlastHit.pm cp lib/Bio/Search/HSP/WABAHSP.pm blib/lib/Bio/Search/HSP/WABAHSP.pm cp lib/Bio/Search/GenericStatistics.pm blib/lib/Bio/Search/GenericStatistics.pm cp lib/Bio/Search/HSP/BlastHSP.pm blib/lib/Bio/Search/HSP/BlastHSP.pm cp lib/Bio/Root/Test.pm blib/lib/Bio/Root/Test.pm cp lib/Bio/Search/Hit/Fasta.pm blib/lib/Bio/Search/Hit/Fasta.pm cp lib/Bio/Search/GenericDatabase.pm blib/lib/Bio/Search/GenericDatabase.pm cp lib/Bio/Search/DatabaseI.pm blib/lib/Bio/Search/DatabaseI.pm cp lib/Bio/SearchIO/EventHandlerI.pm blib/lib/Bio/SearchIO/EventHandlerI.pm cp lib/Bio/SearchIO/SearchWriterI.pm blib/lib/Bio/SearchIO/SearchWriterI.pm cp lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm blib/lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm cp lib/Bio/Search/StatisticsI.pm blib/lib/Bio/Search/StatisticsI.pm cp lib/Bio/SearchIO/Writer/TextResultWriter.pm blib/lib/Bio/SearchIO/Writer/TextResultWriter.pm cp lib/Bio/SearchIO/SearchResultEventBuilder.pm blib/lib/Bio/SearchIO/SearchResultEventBuilder.pm cp lib/Bio/Search/Result/INFERNALResult.pm blib/lib/Bio/Search/Result/INFERNALResult.pm cp lib/Bio/SearchIO/Writer/GbrowseGFF.pm blib/lib/Bio/SearchIO/Writer/GbrowseGFF.pm cp lib/Bio/Search/Result/PullResultI.pm blib/lib/Bio/Search/Result/PullResultI.pm cp lib/Bio/SearchIO/blast_pull.pm blib/lib/Bio/SearchIO/blast_pull.pm cp lib/Bio/SearchIO/blast.pm blib/lib/Bio/SearchIO/blast.pm cp lib/Bio/Search/Result/WABAResult.pm blib/lib/Bio/Search/Result/WABAResult.pm cp lib/Bio/SearchIO/FastHitEventBuilder.pm blib/lib/Bio/SearchIO/FastHitEventBuilder.pm cp lib/Bio/Search/Tiling/MapTileUtils.pm blib/lib/Bio/Search/Tiling/MapTileUtils.pm cp lib/Bio/Search/Result/CrossMatchResult.pm blib/lib/Bio/Search/Result/CrossMatchResult.pm cp lib/Bio/SearchIO/Writer/ResultTableWriter.pm blib/lib/Bio/SearchIO/Writer/ResultTableWriter.pm cp lib/Bio/SearchIO/cross_match.pm blib/lib/Bio/SearchIO/cross_match.pm cp lib/Bio/SearchIO/Writer/HSPTableWriter.pm blib/lib/Bio/SearchIO/Writer/HSPTableWriter.pm cp lib/Bio/Search/Tiling/TilingI.pm blib/lib/Bio/Search/Tiling/TilingI.pm cp lib/Bio/SearchIO/Writer/HitTableWriter.pm blib/lib/Bio/SearchIO/Writer/HitTableWriter.pm cp lib/Bio/SearchIO/Writer/HTMLResultWriter.pm blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm cp lib/Bio/Search/Tiling/MapTiling.pm blib/lib/Bio/Search/Tiling/MapTiling.pm cp lib/Bio/Search/Result/BlastResult.pm blib/lib/Bio/Search/Result/BlastResult.pm cp lib/Bio/SearchIO/erpin.pm blib/lib/Bio/SearchIO/erpin.pm cp lib/Bio/Search/Result/GenericResult.pm blib/lib/Bio/Search/Result/GenericResult.pm cp lib/Bio/SearchIO/axt.pm blib/lib/Bio/SearchIO/axt.pm cp lib/Bio/Search/Result/ResultI.pm blib/lib/Bio/Search/Result/ResultI.pm cp lib/Bio/SearchIO/blasttable.pm blib/lib/Bio/SearchIO/blasttable.pm cp lib/Bio/Search/Result/ResultFactory.pm blib/lib/Bio/Search/Result/ResultFactory.pm cp lib/Bio/SearchIO.pm blib/lib/Bio/SearchIO.pm cp lib/Bio/Search/Result/BlastPullResult.pm blib/lib/Bio/Search/Result/BlastPullResult.pm cp lib/Bio/Search/SearchUtils.pm blib/lib/Bio/Search/SearchUtils.pm cp lib/Bio/Seq.pm blib/lib/Bio/Seq.pm cp lib/Bio/SearchIO/waba.pm blib/lib/Bio/SearchIO/waba.pm cp lib/Bio/Seq/RichSeq.pm blib/lib/Bio/Seq/RichSeq.pm cp lib/Bio/SeqFeature/Computation.pm blib/lib/Bio/SeqFeature/Computation.pm cp lib/Bio/Seq/LargeSeqI.pm blib/lib/Bio/Seq/LargeSeqI.pm cp lib/Bio/Seq/MetaI.pm blib/lib/Bio/Seq/MetaI.pm cp lib/Bio/Seq/PrimaryQual.pm blib/lib/Bio/Seq/PrimaryQual.pm cp lib/Bio/Seq/Meta.pm blib/lib/Bio/Seq/Meta.pm cp lib/Bio/SearchIO/rnamotif.pm blib/lib/Bio/SearchIO/rnamotif.pm cp lib/Bio/SearchIO/exonerate.pm blib/lib/Bio/SearchIO/exonerate.pm cp lib/Bio/Seq/SequenceTrace.pm blib/lib/Bio/Seq/SequenceTrace.pm cp lib/Bio/Seq/SeqBuilder.pm blib/lib/Bio/Seq/SeqBuilder.pm cp lib/Bio/Seq/Meta/Array.pm blib/lib/Bio/Seq/Meta/Array.pm cp lib/Bio/Seq/SeqFactory.pm blib/lib/Bio/Seq/SeqFactory.pm cp lib/Bio/Seq/QualI.pm blib/lib/Bio/Seq/QualI.pm cp lib/Bio/Seq/BaseSeqProcessor.pm blib/lib/Bio/Seq/BaseSeqProcessor.pm cp lib/Bio/Seq/SeqFastaSpeedFactory.pm blib/lib/Bio/Seq/SeqFastaSpeedFactory.pm cp lib/Bio/SearchIO/gmap_f9.pm blib/lib/Bio/SearchIO/gmap_f9.pm cp lib/Bio/Seq/EncodedSeq.pm blib/lib/Bio/Seq/EncodedSeq.pm cp lib/Bio/SeqFeature/Gene/Exon.pm blib/lib/Bio/SeqFeature/Gene/Exon.pm cp lib/Bio/Seq/SimulatedRead.pm blib/lib/Bio/Seq/SimulatedRead.pm cp lib/Bio/Seq/Quality.pm blib/lib/Bio/Seq/Quality.pm cp lib/Bio/Seq/LargePrimarySeq.pm blib/lib/Bio/Seq/LargePrimarySeq.pm cp lib/Bio/Seq/PrimedSeq.pm blib/lib/Bio/Seq/PrimedSeq.pm cp lib/Bio/SearchIO/megablast.pm blib/lib/Bio/SearchIO/megablast.pm cp lib/Bio/SearchIO/psl.pm blib/lib/Bio/SearchIO/psl.pm cp lib/Bio/SearchIO/sim4.pm blib/lib/Bio/SearchIO/sim4.pm cp lib/Bio/SearchIO/fasta.pm blib/lib/Bio/SearchIO/fasta.pm cp lib/Bio/SeqAnalysisParserI.pm blib/lib/Bio/SeqAnalysisParserI.pm cp lib/Bio/SeqFeature/Collection.pm blib/lib/Bio/SeqFeature/Collection.pm cp lib/Bio/Seq/LargeLocatableSeq.pm blib/lib/Bio/Seq/LargeLocatableSeq.pm cp lib/Bio/SeqFeature/Amplicon.pm blib/lib/Bio/SeqFeature/Amplicon.pm cp lib/Bio/SeqFeature/CollectionI.pm blib/lib/Bio/SeqFeature/CollectionI.pm cp lib/Bio/Seq/LargeSeq.pm blib/lib/Bio/Seq/LargeSeq.pm cp lib/Bio/SearchIO/wise.pm blib/lib/Bio/SearchIO/wise.pm cp lib/Bio/Seq/TraceI.pm blib/lib/Bio/Seq/TraceI.pm cp lib/Bio/Seq/RichSeqI.pm blib/lib/Bio/Seq/RichSeqI.pm cp lib/Bio/SeqFeature/AnnotationAdaptor.pm blib/lib/Bio/SeqFeature/AnnotationAdaptor.pm cp lib/Bio/SearchIO/infernal.pm blib/lib/Bio/SearchIO/infernal.pm cp lib/Bio/SeqFeature/FeaturePair.pm blib/lib/Bio/SeqFeature/FeaturePair.pm cp lib/Bio/SeqIO/asciitree.pm blib/lib/Bio/SeqIO/asciitree.pm cp lib/Bio/SeqFeature/Gene/Promoter.pm blib/lib/Bio/SeqFeature/Gene/Promoter.pm cp lib/Bio/SeqFeature/Gene/Intron.pm blib/lib/Bio/SeqFeature/Gene/Intron.pm cp lib/Bio/SeqFeature/Primer.pm blib/lib/Bio/SeqFeature/Primer.pm cp lib/Bio/SeqFeature/Generic.pm blib/lib/Bio/SeqFeature/Generic.pm cp lib/Bio/SeqFeature/Lite.pm blib/lib/Bio/SeqFeature/Lite.pm cp lib/Bio/SeqIO/MultiFile.pm blib/lib/Bio/SeqIO/MultiFile.pm cp lib/Bio/SeqFeature/Gene/ExonI.pm blib/lib/Bio/SeqFeature/Gene/ExonI.pm cp lib/Bio/SeqFeature/Similarity.pm blib/lib/Bio/SeqFeature/Similarity.pm cp lib/Bio/SeqFeature/Tools/Unflattener.pm blib/lib/Bio/SeqFeature/Tools/Unflattener.pm cp lib/Bio/SeqFeature/Tools/TypeMapper.pm blib/lib/Bio/SeqFeature/Tools/TypeMapper.pm cp lib/Bio/SeqFeature/Gene/NC_Feature.pm blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm cp lib/Bio/SeqFeature/Tools/IDHandler.pm blib/lib/Bio/SeqFeature/Tools/IDHandler.pm cp lib/Bio/SeqIO/embldriver.pm blib/lib/Bio/SeqIO/embldriver.pm cp lib/Bio/SeqFeature/TypedSeqFeatureI.pm blib/lib/Bio/SeqFeature/TypedSeqFeatureI.pm cp lib/Bio/SeqIO/fastq.pm blib/lib/Bio/SeqIO/fastq.pm cp lib/Bio/SeqFeature/SimilarityPair.pm blib/lib/Bio/SeqFeature/SimilarityPair.pm cp lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm blib/lib/Bio/SeqIO/Handler/GenericRichSeqHandler.pm cp lib/Bio/SeqFeature/PositionProxy.pm blib/lib/Bio/SeqFeature/PositionProxy.pm cp lib/Bio/SeqFeature/Tools/FeatureNamer.pm blib/lib/Bio/SeqFeature/Tools/FeatureNamer.pm cp lib/Bio/SeqIO/bsml_sax.pm blib/lib/Bio/SeqIO/bsml_sax.pm cp lib/Bio/SeqFeature/Gene/GeneStructure.pm blib/lib/Bio/SeqFeature/Gene/GeneStructure.pm cp lib/Bio/SeqIO/bsml.pm blib/lib/Bio/SeqIO/bsml.pm cp lib/Bio/SeqIO/embl.pm blib/lib/Bio/SeqIO/embl.pm cp lib/Bio/SeqIO/FTHelper.pm blib/lib/Bio/SeqIO/FTHelper.pm cp lib/Bio/SeqIO.pm blib/lib/Bio/SeqIO.pm cp lib/Bio/SeqFeatureI.pm blib/lib/Bio/SeqFeatureI.pm cp lib/Bio/SeqFeature/Gene/GeneStructureI.pm blib/lib/Bio/SeqFeature/Gene/GeneStructureI.pm cp lib/Bio/SeqFeature/Gene/UTR.pm blib/lib/Bio/SeqFeature/Gene/UTR.pm cp lib/Bio/SeqFeature/Gene/Poly_A_site.pm blib/lib/Bio/SeqFeature/Gene/Poly_A_site.pm cp lib/Bio/SeqFeature/Gene/TranscriptI.pm blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm cp lib/Bio/SeqIO/fasta.pm blib/lib/Bio/SeqIO/fasta.pm cp lib/Bio/SeqIO/ace.pm blib/lib/Bio/SeqIO/ace.pm cp lib/Bio/SeqI.pm blib/lib/Bio/SeqI.pm cp lib/Bio/SeqFeature/SubSeq.pm blib/lib/Bio/SeqFeature/SubSeq.pm cp lib/Bio/SeqFeature/Gene/Transcript.pm blib/lib/Bio/SeqFeature/Gene/Transcript.pm cp lib/Bio/Tools/AmpliconSearch.pm blib/lib/Bio/Tools/AmpliconSearch.pm cp lib/Bio/SeqIO/swissdriver.pm blib/lib/Bio/SeqIO/swissdriver.pm cp lib/Bio/SeqIO/scf.pm blib/lib/Bio/SeqIO/scf.pm cp lib/Bio/SeqIO/mbsout.pm blib/lib/Bio/SeqIO/mbsout.pm cp lib/Bio/SeqIO/tigrxml.pm blib/lib/Bio/SeqIO/tigrxml.pm cp lib/Bio/SeqIO/game/gameWriter.pm blib/lib/Bio/SeqIO/game/gameWriter.pm cp lib/Bio/SeqIO/table.pm blib/lib/Bio/SeqIO/table.pm cp lib/Bio/SeqIO/pir.pm blib/lib/Bio/SeqIO/pir.pm cp lib/Bio/SeqIO/swiss.pm blib/lib/Bio/SeqIO/swiss.pm cp lib/Bio/SeqIO/gbxml.pm blib/lib/Bio/SeqIO/gbxml.pm cp lib/Bio/SeqIO/metafasta.pm blib/lib/Bio/SeqIO/metafasta.pm cp lib/Bio/SeqIO/phd.pm blib/lib/Bio/SeqIO/phd.pm cp lib/Bio/SeqIO/genbank.pm blib/lib/Bio/SeqIO/genbank.pm cp lib/Bio/SeqIO/tab.pm blib/lib/Bio/SeqIO/tab.pm cp lib/Bio/SeqIO/locuslink.pm blib/lib/Bio/SeqIO/locuslink.pm cp lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm blib/lib/Bio/SeqIO/tinyseq/tinyseqHandler.pm cp lib/Bio/Tools/Blat.pm blib/lib/Bio/Tools/Blat.pm cp lib/Bio/SeqIO/tigr.pm blib/lib/Bio/SeqIO/tigr.pm cp lib/Bio/Tools/Alignment/Consed.pm blib/lib/Bio/Tools/Alignment/Consed.pm cp lib/Bio/SeqIO/gbdriver.pm blib/lib/Bio/SeqIO/gbdriver.pm cp lib/Bio/SeqIO/qual.pm blib/lib/Bio/SeqIO/qual.pm cp lib/Bio/SeqIO/kegg.pm blib/lib/Bio/SeqIO/kegg.pm cp lib/Bio/Tools/AnalysisResult.pm blib/lib/Bio/Tools/AnalysisResult.pm cp lib/Bio/SimpleAlign.pm blib/lib/Bio/SimpleAlign.pm cp lib/Bio/Taxon.pm blib/lib/Bio/Taxon.pm cp lib/Bio/SeqIO/game/featHandler.pm blib/lib/Bio/SeqIO/game/featHandler.pm cp lib/Bio/SeqIO/seqxml.pm blib/lib/Bio/SeqIO/seqxml.pm cp lib/Bio/SeqIO/game/gameHandler.pm blib/lib/Bio/SeqIO/game/gameHandler.pm cp lib/Bio/SeqIO/msout.pm blib/lib/Bio/SeqIO/msout.pm cp lib/Bio/SeqIO/gcg.pm blib/lib/Bio/SeqIO/gcg.pm cp lib/Bio/SeqIO/game.pm blib/lib/Bio/SeqIO/game.pm cp lib/Bio/SeqUtils.pm blib/lib/Bio/SeqUtils.pm cp lib/Bio/SimpleAnalysisI.pm blib/lib/Bio/SimpleAnalysisI.pm cp lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm blib/lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm cp lib/Bio/SeqIO/game/gameSubs.pm blib/lib/Bio/SeqIO/game/gameSubs.pm cp lib/Bio/Tools/Alignment/Trim.pm blib/lib/Bio/Tools/Alignment/Trim.pm cp lib/Bio/SeqIO/tinyseq.pm blib/lib/Bio/SeqIO/tinyseq.pm cp lib/Bio/Species.pm blib/lib/Bio/Species.pm cp lib/Bio/SeqIO/game/seqHandler.pm blib/lib/Bio/SeqIO/game/seqHandler.pm cp lib/Bio/SeqIO/largefasta.pm blib/lib/Bio/SeqIO/largefasta.pm cp lib/Bio/SeqIO/raw.pm blib/lib/Bio/SeqIO/raw.pm cp lib/Bio/Tools/Grail.pm blib/lib/Bio/Tools/Grail.pm cp lib/Bio/Tools/Glimmer.pm blib/lib/Bio/Tools/Glimmer.pm cp lib/Bio/Tools/MZEF.pm blib/lib/Bio/Tools/MZEF.pm cp lib/Bio/Tools/Phylo/Phylip/ProtDist.pm blib/lib/Bio/Tools/Phylo/Phylip/ProtDist.pm cp lib/Bio/Tools/Phylo/Molphy/Result.pm blib/lib/Bio/Tools/Phylo/Molphy/Result.pm cp lib/Bio/Tools/Match.pm blib/lib/Bio/Tools/Match.pm cp lib/Bio/Tools/EPCR.pm blib/lib/Bio/Tools/EPCR.pm cp lib/Bio/Tools/EMBOSS/Palindrome.pm blib/lib/Bio/Tools/EMBOSS/Palindrome.pm cp lib/Bio/Tools/Est2Genome.pm blib/lib/Bio/Tools/Est2Genome.pm cp lib/Bio/Tools/Prediction/Gene.pm blib/lib/Bio/Tools/Prediction/Gene.pm cp lib/Bio/Tools/GuessSeqFormat.pm blib/lib/Bio/Tools/GuessSeqFormat.pm cp lib/Bio/Tools/GFF.pm blib/lib/Bio/Tools/GFF.pm cp lib/Bio/Tools/Primer/Assessor/Base.pm blib/lib/Bio/Tools/Primer/Assessor/Base.pm cp lib/Bio/Tools/Geneid.pm blib/lib/Bio/Tools/Geneid.pm cp lib/Bio/Tools/Coil.pm blib/lib/Bio/Tools/Coil.pm cp lib/Bio/Tools/Genscan.pm blib/lib/Bio/Tools/Genscan.pm cp lib/Bio/Tools/OddCodes.pm blib/lib/Bio/Tools/OddCodes.pm cp lib/Bio/Tools/Lucy.pm blib/lib/Bio/Tools/Lucy.pm cp lib/Bio/Tools/Profile.pm blib/lib/Bio/Tools/Profile.pm cp lib/Bio/Tools/Pseudowise.pm blib/lib/Bio/Tools/Pseudowise.pm cp lib/Bio/Tools/IUPAC.pm blib/lib/Bio/Tools/IUPAC.pm cp lib/Bio/Tools/Fgenesh.pm blib/lib/Bio/Tools/Fgenesh.pm cp lib/Bio/Tools/Prediction/Exon.pm blib/lib/Bio/Tools/Prediction/Exon.pm cp lib/Bio/Tools/Genomewise.pm blib/lib/Bio/Tools/Genomewise.pm cp lib/Bio/Tools/Primer3.pm blib/lib/Bio/Tools/Primer3.pm cp lib/Bio/Tools/Genemark.pm blib/lib/Bio/Tools/Genemark.pm cp lib/Bio/Tools/Eponine.pm blib/lib/Bio/Tools/Eponine.pm cp lib/Bio/Tools/Promoterwise.pm blib/lib/Bio/Tools/Promoterwise.pm cp lib/Bio/Tools/Primer/Feature.pm blib/lib/Bio/Tools/Primer/Feature.pm cp lib/Bio/Tools/Prints.pm blib/lib/Bio/Tools/Prints.pm cp lib/Bio/Tools/ESTScan.pm blib/lib/Bio/Tools/ESTScan.pm cp lib/Bio/Tools/Primer/AssessorI.pm blib/lib/Bio/Tools/Primer/AssessorI.pm cp lib/Bio/Tools/ECnumber.pm blib/lib/Bio/Tools/ECnumber.pm cp lib/Bio/Tools/Primer/Pair.pm blib/lib/Bio/Tools/Primer/Pair.pm cp lib/Bio/Tools/PrositeScan.pm blib/lib/Bio/Tools/PrositeScan.pm cp lib/Bio/Tools/Genewise.pm blib/lib/Bio/Tools/Genewise.pm cp lib/Bio/Tools/CodonTable.pm blib/lib/Bio/Tools/CodonTable.pm cp lib/Bio/Tools/Phylo/Molphy.pm blib/lib/Bio/Tools/Phylo/Molphy.pm cp lib/Bio/Tools/Phylo/Gerp.pm blib/lib/Bio/Tools/Phylo/Gerp.pm cp lib/Bio/Tools/FootPrinter.pm blib/lib/Bio/Tools/FootPrinter.pm cp lib/Bio/Tools/RepeatMasker.pm blib/lib/Bio/Tools/RepeatMasker.pm cp lib/Bio/Tree/DistanceFactory.pm blib/lib/Bio/Tree/DistanceFactory.pm cp lib/Bio/Tools/Run/Phylo/PhyloBase.pm blib/lib/Bio/Tools/Run/Phylo/PhyloBase.pm cp lib/Bio/Tree/NodeI.pm blib/lib/Bio/Tree/NodeI.pm cp lib/Bio/Tools/Sim4/Results.pm blib/lib/Bio/Tools/Sim4/Results.pm cp lib/Bio/Tools/RandomDistFunctions.pm blib/lib/Bio/Tools/RandomDistFunctions.pm cp lib/Bio/Tree/AnnotatableNode.pm blib/lib/Bio/Tree/AnnotatableNode.pm cp lib/Bio/Tree/NodeNHX.pm blib/lib/Bio/Tree/NodeNHX.pm cp lib/Bio/Tools/Signalp/ExtendedSignalp.pm blib/lib/Bio/Tools/Signalp/ExtendedSignalp.pm cp lib/Bio/Tree/Compatible.pm blib/lib/Bio/Tree/Compatible.pm cp lib/Bio/Tree/RandomFactory.pm blib/lib/Bio/Tree/RandomFactory.pm cp lib/Bio/Tools/Run/ParametersI.pm blib/lib/Bio/Tools/Run/ParametersI.pm cp lib/Bio/Tools/pICalculator.pm blib/lib/Bio/Tools/pICalculator.pm cp lib/Bio/Tree/Node.pm blib/lib/Bio/Tree/Node.pm cp lib/Bio/Tools/Run/GenericParameters.pm blib/lib/Bio/Tools/Run/GenericParameters.pm cp lib/Bio/Tools/Tmhmm.pm blib/lib/Bio/Tools/Tmhmm.pm cp lib/Bio/Tools/ipcress.pm blib/lib/Bio/Tools/ipcress.pm cp lib/Bio/Tree/Tree.pm blib/lib/Bio/Tree/Tree.pm cp lib/Bio/Tools/Sim4/Exon.pm blib/lib/Bio/Tools/Sim4/Exon.pm cp lib/Bio/Tools/Run/Analysis.pm blib/lib/Bio/Tools/Run/Analysis.pm cp lib/Bio/Tools/Seg.pm blib/lib/Bio/Tools/Seg.pm cp lib/Bio/Tools/SeqWords.pm blib/lib/Bio/Tools/SeqWords.pm cp lib/Bio/Tools/Sigcleave.pm blib/lib/Bio/Tools/Sigcleave.pm cp lib/Bio/Tools/QRNA.pm blib/lib/Bio/Tools/QRNA.pm cp lib/Bio/Tools/Signalp.pm blib/lib/Bio/Tools/Signalp.pm cp lib/Bio/Tools/TandemRepeatsFinder.pm blib/lib/Bio/Tools/TandemRepeatsFinder.pm cp lib/Bio/Tools/tRNAscanSE.pm blib/lib/Bio/Tools/tRNAscanSE.pm cp lib/Bio/Tools/TargetP.pm blib/lib/Bio/Tools/TargetP.pm cp lib/Bio/Tools/Spidey/Exon.pm blib/lib/Bio/Tools/Spidey/Exon.pm cp lib/Bio/Tools/Run/WrapperBase.pm blib/lib/Bio/Tools/Run/WrapperBase.pm cp lib/Bio/Tools/Run/AnalysisFactory.pm blib/lib/Bio/Tools/Run/AnalysisFactory.pm cp lib/Bio/Tools/isPcr.pm blib/lib/Bio/Tools/isPcr.pm cp lib/Bio/Tools/Run/WrapperBase/CommandExts.pm blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm cp lib/Bio/Tools/Spidey/Results.pm blib/lib/Bio/Tools/Spidey/Results.pm cp lib/Bio/Tools/SeqPattern/Backtranslate.pm blib/lib/Bio/Tools/SeqPattern/Backtranslate.pm cp lib/Bio/Tree/Statistics.pm blib/lib/Bio/Tree/Statistics.pm cp lib/Bio/Tools/SeqPattern.pm blib/lib/Bio/Tools/SeqPattern.pm cp lib/Bio/Tools/SeqStats.pm blib/lib/Bio/Tools/SeqStats.pm cp lib/Bio/TreeIO/pag.pm blib/lib/Bio/TreeIO/pag.pm cp lib/Bio/TreeIO/lintree.pm blib/lib/Bio/TreeIO/lintree.pm cp lib/Bio/TreeIO/nhx.pm blib/lib/Bio/TreeIO/nhx.pm cp lib/Bio/TreeIO/NewickParser.pm blib/lib/Bio/TreeIO/NewickParser.pm cp lib/Bio/TreeIO.pm blib/lib/Bio/TreeIO.pm cp lib/Bio/Tree/TreeFunctionsI.pm blib/lib/Bio/Tree/TreeFunctionsI.pm cp lib/Bio/TreeIO/TreeEventBuilder.pm blib/lib/Bio/TreeIO/TreeEventBuilder.pm cp lib/Bio/Tree/TreeI.pm blib/lib/Bio/Tree/TreeI.pm cp lib/Bio/TreeIO/newick.pm blib/lib/Bio/TreeIO/newick.pm cp lib/Bio/TreeIO/nexus.pm blib/lib/Bio/TreeIO/nexus.pm cp lib/Bio/WebAgent.pm blib/lib/Bio/WebAgent.pm cp lib/Bio/TreeIO/tabtree.pm blib/lib/Bio/TreeIO/tabtree.pm cp lib/Bio/UpdateableSeqI.pm blib/lib/Bio/UpdateableSeqI.pm cp lib/BioPerl.pm blib/lib/BioPerl.pm cp lib/Bio/TreeIO/cluster.pm blib/lib/Bio/TreeIO/cluster.pm cp lib/Bio/TreeIO/phyloxml.pm blib/lib/Bio/TreeIO/phyloxml.pm cp bin/bp_aacomp blib/script/bp_aacomp cp bin/bp_bioflat_index blib/script/bp_bioflat_index cp bin/bp_biogetseq blib/script/bp_biogetseq cp bin/bp_dbsplit blib/script/bp_dbsplit "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_aacomp "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_bioflat_index cp bin/bp_extract_feature_seq blib/script/bp_extract_feature_seq "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_biogetseq "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_dbsplit "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_extract_feature_seq cp bin/bp_fastam9_to_table blib/script/bp_fastam9_to_table cp bin/bp_fetch blib/script/bp_fetch "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_fastam9_to_table cp bin/bp_filter_search blib/script/bp_filter_search "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_fetch cp bin/bp_find-blast-matches blib/script/bp_find-blast-matches "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_filter_search "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_find-blast-matches cp bin/bp_gccalc blib/script/bp_gccalc "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_gccalc cp bin/bp_genbank2gff3 blib/script/bp_genbank2gff3 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_genbank2gff3 cp bin/bp_index blib/script/bp_index cp bin/bp_local_taxonomydb_query blib/script/bp_local_taxonomydb_query "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_index cp bin/bp_mask_by_search blib/script/bp_mask_by_search "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_local_taxonomydb_query cp bin/bp_mrtrans blib/script/bp_mrtrans cp bin/bp_make_mrna_protein blib/script/bp_make_mrna_protein "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mask_by_search "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mrtrans "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_make_mrna_protein cp bin/bp_mutate blib/script/bp_mutate "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_mutate cp bin/bp_nexus2nh blib/script/bp_nexus2nh "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_nexus2nh cp bin/bp_nrdb blib/script/bp_nrdb "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_nrdb cp bin/bp_oligo_count blib/script/bp_oligo_count "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_oligo_count cp bin/bp_process_gadfly blib/script/bp_process_gadfly "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_process_gadfly cp bin/bp_process_sgd blib/script/bp_process_sgd "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_process_sgd cp bin/bp_revtrans-motif blib/script/bp_revtrans-motif cp bin/bp_search2alnblocks blib/script/bp_search2alnblocks "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_revtrans-motif "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2alnblocks cp bin/bp_search2gff blib/script/bp_search2gff "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2gff cp bin/bp_search2table blib/script/bp_search2table cp bin/bp_search2tribe blib/script/bp_search2tribe "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2table "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_search2tribe cp bin/bp_seq_length blib/script/bp_seq_length "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seq_length cp bin/bp_seqconvert blib/script/bp_seqconvert "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqconvert cp bin/bp_seqcut blib/script/bp_seqcut "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqcut cp bin/bp_seqpart blib/script/bp_seqpart cp bin/bp_seqret blib/script/bp_seqret cp bin/bp_seqretsplit blib/script/bp_seqretsplit "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqret "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqpart "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_seqretsplit cp bin/bp_split_seq blib/script/bp_split_seq "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_split_seq cp bin/bp_sreformat blib/script/bp_sreformat "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_sreformat cp bin/bp_taxid4species blib/script/bp_taxid4species cp bin/bp_taxonomy2tree blib/script/bp_taxonomy2tree "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_taxid4species cp bin/bp_translate_seq blib/script/bp_translate_seq "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_taxonomy2tree "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_translate_seq cp bin/bp_tree2pag blib/script/bp_tree2pag "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_tree2pag cp bin/bp_unflatten_seq blib/script/bp_unflatten_seq "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_unflatten_seq Manifying 40 pod documents Manifying 35 pod documents Manifying 33 pod documents Manifying 32 pod documents Manifying 34 pod documents Manifying 32 pod documents Manifying 32 pod documents Manifying 30 pod documents Manifying 27 pod documents Manifying 35 pod documents Manifying 29 pod documents Manifying 35 pod documents Manifying 36 pod documents Manifying 33 pod documents Manifying 33 pod documents Manifying 15 pod documents make[1]: Leaving directory '/build/bioperl-0WLrhs/bioperl-1.7.8' dh: command-omitted: The call to "dh_auto_test -i" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -i dh_auto_install -i make -j10 install DESTDIR=/build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/bioperl-0WLrhs/bioperl-1.7.8' Manifying 40 pod documents Manifying 35 pod documents Manifying 33 pod documents Manifying 32 pod documents Manifying 34 pod documents Manifying 32 pod documents Manifying 32 pod documents Manifying 30 pod documents Manifying 27 pod documents Manifying 35 pod documents Manifying 29 pod documents Manifying 35 pod documents Manifying 36 pod documents Manifying 33 pod documents Manifying 33 pod documents Manifying 15 pod documents Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/BioPerl.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnnotatableI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnalysisResultI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnalysisParserI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnalysisI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnnotationI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AnnotationCollectionI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/HandlerBaseI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DBLinkContainerI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/LocatableSeq.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/IdentifiableI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DescribableI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/IdCollectionI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/FeatureHolderI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DasI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/LocationI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/OntologyIO.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Range.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/ParameterBaseI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/PrimarySeq.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/PullParserI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/PrimarySeqI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/RangeI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SearchIO.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Seq.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqAnalysisParserI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqIO.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqFeatureI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SimpleAlign.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Taxon.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SeqUtils.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/SimpleAnalysisI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Species.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/TreeIO.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/WebAgent.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/UpdateableSeqI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/OntologyTerm.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/AnnotationFactory.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Comment.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Relation.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/DBLink.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Collection.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Reference.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/TypeManager.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Target.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/TagTree.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/SimpleValue.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/StructuredValue.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Annotation/Tree.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/clustalw.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/proda.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/msf.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/bl2seq.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/po.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/maf.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/prodom.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/mase.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/mega.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/xmfa.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/psi.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/largemultifasta.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/nexus.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/emboss.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/metafasta.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/meme.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/arp.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/pfam.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/fasta.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/phylip.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/selex.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/AlignIO/Handler/GenericAlignHandler.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/Utilities.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/DNAStatistics.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/AlignI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/PairwiseStatistics.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/StatisticsI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Align/ProteinStatistics.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/IndexedBase.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Failover.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/FileCache.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Qual.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Fasta.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/InMemoryCache.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/LocationI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/QueryI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/RandomAccessI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Registry.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/SeqI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/DBFetch.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/ReferenceI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/UpdateableSeqI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GenericWebAgent.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/WebDBSeqI.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GFF/Util/Rearrange.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/GFF/Util/Binning.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/list.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/greengenes.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/silva.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Taxonomy/flatfile.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BinarySearch.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/swiss.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/genbank.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/embl.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Flat/BDB/fasta.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/DB/Query/WebQuery.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/CodonUsage/Table.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/CodonUsage/IO.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Fasta.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/Blast.pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/perl5/Bio/Index/AbstractSeq.pm Installing 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/build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::UpdateableSeqI.3pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/man/man3/Bio::WebAgent.3pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/share/man/man3/BioPerl.3pm Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqpart Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_seq_length Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqretsplit Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqcut Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_bioflat_index Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_biogetseq Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_extract_feature_seq Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_dbsplit Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_filter_search Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_fastam9_to_table Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_aacomp Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2gff Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_taxid4species Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_fetch Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_unflatten_seq Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_find-blast-matches Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_gccalc Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqret Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_local_taxonomydb_query Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_mrtrans Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_genbank2gff3 Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_mask_by_search Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_split_seq Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_tree2pag Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_nexus2nh Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_sreformat Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_make_mrna_protein Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_index Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_mutate Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_taxonomy2tree Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_nrdb Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_oligo_count Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_translate_seq Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_process_gadfly Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_revtrans-motif Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2alnblocks Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_process_sgd Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2table Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_search2tribe Installing /build/bioperl-0WLrhs/bioperl-1.7.8/debian/tmp/usr/bin/bp_seqconvert make[1]: Leaving directory '/build/bioperl-0WLrhs/bioperl-1.7.8' dh_install -i dh_installdocs -i debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/bioperl-0WLrhs/bioperl-1.7.8' dh_installchangelogs Changes make[1]: Leaving directory '/build/bioperl-0WLrhs/bioperl-1.7.8' debian/rules override_dh_installexamples make[1]: Entering directory '/build/bioperl-0WLrhs/bioperl-1.7.8' dh_installexamples examples/* for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done for pl in `grep -Rl '#![[:space:]]*/usr/local/bin/perl' debian/*/usr/*` ; do \ sed -i '1s?^#![[:space:]]*/usr/local/bin/[[:space:]]*perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/bioperl-0WLrhs/bioperl-1.7.8' dh_installman -i dh_perl -i dh_link -i dh_strip_nondeterminism -i dh_compress -i dh_fixperms -i dh_missing -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'bioperl' in '../bioperl_1.7.8-1_all.deb'. dpkg-deb: building package 'libbio-perl-perl' in '../libbio-perl-perl_1.7.8-1_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../bioperl_1.7.8-1_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/bioperl-0WLrhs /tmp/bioperl-1.7.8-1_k30lbl2 I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.Pyln9JFF9M... I: success in 434.0610 seconds md5: bioperl_1.7.8-1_all.deb: OK md5: libbio-perl-perl_1.7.8-1_all.deb: OK sha1: bioperl_1.7.8-1_all.deb: OK sha1: libbio-perl-perl_1.7.8-1_all.deb: OK sha256: bioperl_1.7.8-1_all.deb: OK sha256: libbio-perl-perl_1.7.8-1_all.deb: OK Checksums: OK