Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/a/altree/altree_1.3.1-10_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/altree-1.3.1-10a5xw58zm/altree_1.3.1-10_all.buildinfo Get source package info: altree=1.3.1-10 Source URL: http://snapshot.notset.fr/mr/package/altree/1.3.1-10/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.2-1 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.47 bash=5.0-6 bash-completion=1:2.10-1 binutils=2.34-8 binutils-common=2.34-8 binutils-x86-64-linux-gnu=2.34-8 bsdmainutils=12.1.2 bsdutils=1:2.35.2-4 build-essential=12.8 bzip2=1.0.8-3 coreutils=8.30-3+b1 cpp=4:9.2.1-3.1 cpp-9=9.3.0-14 dash=0.5.10.2-7 debconf=1.5.74 debhelper=13.1 debianutils=4.11 dh-autoreconf=19 dh-strip-nondeterminism=1.8.1-1 diffutils=1:3.7-3 dpkg=1.19.7 dpkg-dev=1.19.7 dwz=0.13-5 fig2dev=1:3.2.7b-4 file=1:5.38-5 findutils=4.7.0-1 fontconfig-config=2.13.1-4.2 fonts-lmodern=2.004.5-6 fonts-urw-base35=20170801.1-3 g++=4:9.2.1-3.1 g++-9=9.3.0-14 gawk=1:5.0.1+dfsg-1 gcc=4:9.2.1-3.1 gcc-10-base=10.1.0-4 gcc-9=9.3.0-14 gcc-9-base=9.3.0-14 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 ghostscript=9.52~dfsg-1 grep=3.4-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.57 intltool-debian=0.35.0+20060710.5 latex-make=2.4.0-1 libacl1=2.2.53-8 libapache-pom-java=18-1 libarchive-zip-perl=1.68-1 libasan5=9.3.0-14 libatomic1=10.1.0-4 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3 libaudit1=1:2.8.5-3+b1 libavahi-client3=0.8-3 libavahi-common-data=0.8-3 libavahi-common3=0.8-3 libbinutils=2.34-8 libblas-dev=3.9.0-2 libblas3=3.9.0-2 libblkid1=2.35.2-4 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-3 libc-bin=2.30-8 libc-dev-bin=2.30-8 libc6=2.30-8 libc6-dev=2.30-8 libcairo2=1.16.0-4 libcap-ng0=0.7.9-2.2 libcc1-0=10.1.0-4 libcom-err2=1.45.6-1 libcommons-logging-java=1.2-2 libcommons-parent-java=43-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.16-1 libcrypt1=1:4.4.16-1 libctf-nobfd0=2.34-8 libctf0=2.34-8 libcups2=2.3.3-1 libdb5.3=5.3.28+dfsg1-0.6 libdbus-1-3=1.12.18-1 libdebconfclient0=0.252 libdebhelper-perl=13.1 libdpkg-perl=1.19.7 libelf1=0.176-1.1 libexpat1=2.2.9-1 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.8.1-1 libfontbox-java=1:1.8.16-2 libfontconfig1=2.13.1-4.2 libfreetype6=2.10.1-2 libgcc-9-dev=9.3.0-14 libgcc-s1=10.1.0-4 libgcrypt20=1.8.5-5 libgdbm-compat4=1.18.1-5 libgdbm6=1.18.1-5 libglib2.0-0=2.64.3-1 libgmp10=2:6.2.0+dfsg-6 libgnutls30=3.6.14-2 libgomp1=10.1.0-4 libgpg-error0=1.38-1 libgraphite2-3=1.3.14-1 libgs9=9.52~dfsg-1 libgs9-common=9.52~dfsg-1 libgsl-dev=2.6+dfsg-2 libgsl25=2.6+dfsg-2 libgslcblas0=2.6+dfsg-2 libgssapi-krb5-2=1.17-10 libharfbuzz0b=2.6.7-1 libhogweed5=3.5.1+really3.5.1-2 libice6=2:1.0.9-2 libicu67=67.1-2 libidn11=1.33-2.4 libidn2-0=2.3.0-1 libijs-0.35=0.35-15 libisl22=0.22.1-1 libitm1=10.1.0-4 libjbig0=2.1-3.1+b2 libjbig2dec0=0.18+20200417-1 libjpeg62-turbo=1:1.5.2-2+b1 libk5crypto3=1.17-10 libkeyutils1=1.6.1-2 libkpathsea6=2020.20200327.54578-4+b1 libkrb5-3=1.17-10 libkrb5support0=1.17-10 liblcms2-2=2.9-4+b1 liblsan0=10.1.0-4 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-5 libmagic1=1:5.38-5 libmath-tamuanova-perl=1.0.2-2+b8 libmount1=2.35.2-4 libmpc3=1.1.0-1 libmpdec2=2.4.2-3 libmpfr6=4.0.2-1 libncursesw6=6.2-1 libnetpbm10=2:10.0-15.3+b2 libnettle7=3.5.1+really3.5.1-2 libopenjp2-7=2.3.1-1 libp11-kit0=0.23.20-1 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libpcre2-8-0=10.34-7 libpcre3=2:8.39-13 libpdfbox-java=1:1.8.16-2 libperl5.30=5.30.3-4 libpipeline1=1.5.2-2 libpixman-1-0=0.36.0-1 libpng16-16=1.6.37-2 libptexenc1=2020.20200327.54578-4+b1 libpython3-stdlib=3.8.2-3 libpython3.8-minimal=3.8.3-1 libpython3.8-stdlib=3.8.3-1 libquadmath0=10.1.0-4 libreadline8=8.0-4 libseccomp2=2.4.3-1+b1 libselinux1=3.0-1+b3 libsigsegv2=2.12-2 libsm6=2:1.2.3-1 libsmartcols1=2.35.2-4 libsqlite3-0=3.32.3-1 libssl1.1=1.1.1g-1 libstdc++-9-dev=9.3.0-14 libstdc++6=10.1.0-4 libsub-override-perl=0.09-2 libsynctex2=2020.20200327.54578-4+b1 libsystemd0=245.6-1 libtamuanova-0.2=0.2-4+b2 libtasn1-6=4.16.0-2 libteckit0=2.5.8+ds2-5 libtest-deep-perl=1.130-1 libtexlua53=2020.20200327.54578-4+b1 libtexluajit2=2020.20200327.54578-4+b1 libtiff5=4.1.0+git191117-2 libtinfo6=6.2-1 libtool=2.4.6-14 libtsan0=10.1.0-4 libubsan1=10.1.0-4 libuchardet0=0.0.7-1 libudev1=245.6-1 libunistring2=0.9.10-4 libuuid1=2.35.2-4 libwebp6=0.6.1-2+b1 libx11-6=2:1.6.9-2+b1 libx11-data=2:1.6.9-2 libxau6=1:1.0.8-1+b2 libxaw7=2:1.0.13-1+b2 libxcb-render0=1.14-2 libxcb-shm0=1.14-2 libxcb1=1.14-2 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1+b2 libxi6=2:1.7.10-1 libxml2=2.9.10+dfsg-5+b1 libxmu6=2:1.1.2-2+b3 libxpm4=1:3.5.12-1 libxrender1=1:0.9.10-1 libxt6=1:1.1.5-1+b3 libzstd1=1.4.5+dfsg-2 libzzip-0-13=0.13.62-3.2 linux-libc-dev=5.6.14-2 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.3-3 man-db=2.9.2-1 mawk=1.3.4.20200120-2 mime-support=3.64 ncurses-base=6.2-1 ncurses-bin=6.2-1 netpbm=2:10.0-15.3+b2 patch=2.7.6-6 perl=5.30.3-4 perl-base=5.30.3-4 perl-modules-5.30=5.30.3-4 po-debconf=1.0.21 poppler-data=0.4.9-2 preview-latex-style=11.91-2 python3=3.8.2-3 python3-minimal=3.8.2-3 python3.8=3.8.3-1 python3.8-minimal=3.8.3-1 readline-common=8.0-4 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-3 t1utils=1.41-4 tar=1.30+dfsg-7 tex-common=6.15 texlive-base=2020.20200522-1 texlive-binaries=2020.20200327.54578-4+b1 texlive-fonts-recommended=2020.20200522-1 texlive-lang-french=2020.20200522-1 texlive-latex-base=2020.20200522-1 texlive-latex-extra=2020.20200522-1 texlive-latex-recommended=2020.20200522-1 texlive-pictures=2020.20200522-1 ucf=3.0043 util-linux=2.35.2-4 x11-common=1:7.7+20 xdg-utils=1.1.3-2 xz-utils=5.2.4-1+b1 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200622T144846Z/ 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 altree=1.3.1-10 && mkdir -p /build/altree-079pC6 && dpkg-source --no-check -x /*.dsc /build/altree-079pC6/altree-1.3.1 && chown -R builduser:builduser /build/altree-079pC6" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/altree-079pC6/altree-1.3.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1592825529" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/altree-079pC6 /tmp/altree-1.3.1-10a5xw58zm bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20200622T144846Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.KyA7Avx6nX 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.KyA7Avx6nX Reading package lists... Building dependency tree... util-linux is already the newest version (2.35.2-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 393 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20200622T144846Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200622T144846Z unstable/main amd64 fakeroot amd64 1.24-1 [85.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (970 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 ... 4481 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.24-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.24-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.24-1_amd64.deb ... Unpacking fakeroot (1.24-1) ... Setting up libfakeroot:amd64 (1.24-1) ... Setting up fakeroot (1.24-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.30-8) ... 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200622T144846Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.KyA7Avx6nX Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20200622T144846Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 19s (1181 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.KyA7Avx6nX I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d altree=1.3.1-10 && mkdir -p /build/altree-079pC6 && dpkg-source --no-check -x /*.dsc /build/altree-079pC6/altree-1.3.1 && chown -R builduser:builduser /build/altree-079pC6"' exec /tmp/mmdebstrap.KyA7Avx6nX Reading package lists... NOTICE: 'altree' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/altree.git Please use: git clone https://salsa.debian.org/med-team/altree.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 520 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main altree 1.3.1-10 (dsc) [2299 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main altree 1.3.1-10 (tar) [509 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main altree 1.3.1-10 (diff) [8660 B] Fetched 520 kB in 1s (990 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'altree_1.3.1-10.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting altree in /build/altree-079pC6/altree-1.3.1 dpkg-source: info: unpacking altree_1.3.1.orig.tar.gz dpkg-source: info: unpacking altree_1.3.1-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying from-upstream-no-nested-functions.patch dpkg-source: info: applying no-quicksort.patch dpkg-source: info: applying blas.patch dpkg-source: info: applying figlatex.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/altree-079pC6/altree-1.3.1 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1592825529" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.KyA7Avx6nX dpkg-buildpackage: info: source package altree dpkg-buildpackage: info: source version 1.3.1-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/altree-079pC6/altree-1.3.1' /usr/bin/make -C Documentation distclean make[2]: Entering directory '/build/altree-079pC6/altree-1.3.1/Documentation' make[2]: Nothing to be done for 'distclean'. make[2]: Leaving directory '/build/altree-079pC6/altree-1.3.1/Documentation' dh_auto_clean make[1]: Leaving directory '/build/altree-079pC6/altree-1.3.1' dh_clean debian/rules binary-indep dh binary-indep dh_update_autotools_config -i dh_autoreconf -i dh_auto_configure -i perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -fdebug-prefix-map=/build/altree-079pC6/altree-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/altree-079pC6/altree-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro" Checking if your kit is complete... Looks good MakeMaker (v7.34) Warning (non-fatal): Target 'dynamic' depends on targets in skipped section 'dynamic_lib' Warning (non-fatal): Target 'static' depends on targets in skipped section 'static_lib' Generating a Unix-style Makefile Writing Makefile for ALTree::CUtils Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for ALTree::CUtils Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for altree Writing MYMETA.yml and MYMETA.json debian/rules override_dh_auto_build make[1]: Entering directory '/build/altree-079pC6/altree-1.3.1' /usr/bin/make -C Documentation pdf make[2]: Entering directory '/build/altree-079pC6/altree-1.3.1/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_SAVE make[3]: Entering directory '/build/altree-079pC6/altree-1.3.1/Documentation' make[3]: Nothing to be done for 'LU_WATCH_FILES_SAVE'. make[3]: Leaving directory '/build/altree-079pC6/altree-1.3.1/Documentation' ======> building manual.pdf <====== Running: 'pdflatex' '--interaction' 'errorstopmode' '--jobname' 'manual' '\RequirePackage[extension=.pdf]{texdepends}\input{manual.tex}' Package texdepends Warning: graphicspath already redefined. Skipping it. on input line 34. Package texdepends Warning: Diverting empty macro 'Ginclude@eps' (texdepends) Probably a bug in texdepends.sty. Package texdepends Warning: Gin@getbase already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@pdf already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@pdf already redefined. Skipping it. on input line 87. Chapter 1. LaTeX Warning: Reference `fig:altree' on page 2 undefined on input line 121. Package texdepends Warning: No 'fig/overview.pdftex' file (texdepends) using 1 for graphic dimensions on input line 124. Package texdepends Warning: Figure 'fig/overview.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 124. LaTeX Warning: Reference `fig:nesting_algo' on page 2 undefined on input line 143. Package natbib Warning: Citation `Bardel05' on page 2 undefined on input line 143. Package natbib Warning: Citation `Ge03' on page 2 undefined on input line 146. Package natbib Warning: Citation `Becker04' on page 2 undefined on input line 146. Package texdepends Warning: No 'fig/altree-q.pdftex' file (texdepends) using 1 for graphic dimensions on input line 150. Package texdepends Warning: Figure 'fig/altree-q.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 150. LaTeX Warning: `h' float specifier changed to `ht'. Package natbib Warning: Citation `Bardel05' on page 4 undefined on input line 180. Package natbib Warning: Citation `Stephens01' on page 5 undefined on input line 197. Package natbib Warning: Citation `Stephens03' on page 5 undefined on input line 197. Package natbib Warning: Citation `Becker04' on page 5 undefined on input line 198. Package natbib Warning: Citation `Swofford02' on page 5 undefined on input line 199. Package natbib Warning: Citation `Felsenstein04' on page 5 undefined on input line 200. Package natbib Warning: Citation `YangPAML' on page 5 undefined on input line 200. Underfull \hbox (badness 1454) in paragraph at lines 196--201 []\T1/ptm/m/n/10.95 Currently, \T1/pcr/m/n/10.95 ALTree-convert \T1/ptm/m/n/10. Chapter 2. Package natbib Warning: Citation `Swofford02' on page 7 undefined on input line 278. Package natbib Warning: Citation `Felsenstein04' on page 7 undefined on input line 281. Underfull \hbox (badness 1142) in paragraph at lines 281--284 []\T1/pcr/m/n/10.95 phylip \T1/ptm/b/n/10.95 ?\T1/ptm/m/n/10.95 : freely avail- Package natbib Warning: Citation `YangPAML' on page 7 undefined on input line 284. Package natbib Warning: Citation `Guindon03' on page 7 undefined on input line 288. 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Overfull \hbox (8.63097pt too wide) in paragraph at lines 584--605 \T1/ptm/m/n/10.95 Examples: $[]$ $[]$ LaTeX Warning: Reference `description_etiquette' on page 14 undefined on input line 632. LaTeX Warning: Reference `description_etiquette' on page 14 undefined on input line 633. Package natbib Warning: Citation `Bardel05' on page 14 undefined on input line 634. LaTeX Warning: Reference `description_etiquette' on page 15 undefined on input line 649. LaTeX Warning: Reference `description_etiquette' on page 15 undefined on input line 649. Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --data-qual|-q Underfull \hbox (badness 1281) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 remove the out-group se-quence for the Underfull \hbox (badness 5681) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 ancestral se-quence (only use-ful with Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --tree-building-program|-p Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --s-site-characters Underfull \hbox (badness 1565) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 print the tree with the char-ac-ter state Overfull \hbox (2.0805pt too wide) in paragraph at lines 664--698 [] LaTeX Warning: Reference `help' on page 16 undefined on input line 701. 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LaTeX Warning: There were undefined references. /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_RESTORE make[3]: Entering directory '/build/altree-079pC6/altree-1.3.1/Documentation' ======> building fig/option_b.subfig.mk <====== make[3]: Leaving directory '/build/altree-079pC6/altree-1.3.1/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" manual.pdf_NEED_REBUILD make[3]: Entering directory '/build/altree-079pC6/altree-1.3.1/Documentation' *** Checking rebuild with rule 'latex' *** Checking rebuild with rule 'texdepends' ******************************************** *********** New build needed *************** ******************************************** New manual.aux file LU_rebuild_latex: new run needed (LaTeX message 'Rerun to get...') LU_rebuild_texdepends: new depends required ******************************************** /usr/bin/make LU_REC_LEVEL=2 manual.pdf make[4]: Entering directory '/build/altree-079pC6/altree-1.3.1/Documentation' ======> building manual.bbl <====== This is BibTeX, Version 0.99d (TeX Live 2020/Debian) The top-level auxiliary file: manual.aux The style file: plainnat.bst Database file #1: stage.bib Warning--empty year in YangPAML (There was 1 warning) ======> building fig/overview.pdftex <====== ======> building fig/overview.pdftex_t <====== ======> building fig/altree-q.pdftex <====== ======> building fig/altree-q.pdftex_t <====== ======> building fig/option_b_1.fig <====== ======> building fig/option_b_2.fig <====== ======> building fig/create_file_paup.pdftex <====== ======> building fig/create_file_paup.pdftex_t <====== ======> building fig/create_file_phy.pdftex <====== ======> building fig/create_file_phy.pdftex_t <====== ======> building fig/association_paup.pdftex <====== ======> building fig/association_paup.pdftex_t <====== ======> building fig/localisation_paup.pdftex <====== ======> building fig/localisation_paup.pdftex_t <====== ======> building fig/association_phylip.pdftex <====== ======> building fig/association_phylip.pdftex_t <====== ======> building fig/association_paml.pdftex <====== ======> building fig/association_paml.pdftex_t <====== ======> building fig/localisation_paml.pdftex <====== ======> building fig/localisation_paml.pdftex_t <====== Previous compilation failed. Rerun needed /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_SAVE make[5]: Entering directory '/build/altree-079pC6/altree-1.3.1/Documentation' make[5]: Leaving directory '/build/altree-079pC6/altree-1.3.1/Documentation' ======> building manual.pdf <====== removed 'manual.pdf_NEED_REBUILD' removed 'manual.pdf.mk' Running: 'pdflatex' '--interaction' 'errorstopmode' '--jobname' 'manual' '\RequirePackage[extension=.pdf]{texdepends}\input{manual.tex}' Package texdepends Warning: graphicspath already redefined. Skipping it. on input line 34. Package texdepends Warning: Diverting empty macro 'Ginclude@eps' (texdepends) Probably a bug in texdepends.sty. Package texdepends Warning: Gin@getbase already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@pdf already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@pdf already redefined. Skipping it. on input line 87. Chapter 1. Package natbib Warning: Citation `Bardel05' on page 3 undefined on input line 143. Package natbib Warning: Citation `Ge03' on page 3 undefined on input line 146. Package natbib Warning: Citation `Becker04' on page 3 undefined on input line 146. LaTeX Warning: `h' float specifier changed to `ht'. Package natbib Warning: Citation `Bardel05' on page 4 undefined on input line 180. Package natbib Warning: Citation `Stephens01' on page 4 undefined on input line 197. Package natbib Warning: Citation `Stephens03' on page 4 undefined on input line 197. Package natbib Warning: Citation `Becker04' on page 4 undefined on input line 198. Package natbib Warning: Citation `Swofford02' on page 4 undefined on input line 199. Package natbib Warning: Citation `Felsenstein04' on page 4 undefined on input line 200. Package natbib Warning: Citation `YangPAML' on page 4 undefined on input line 200. Underfull \hbox (badness 1454) in paragraph at lines 196--201 []\T1/ptm/m/n/10.95 Currently, \T1/pcr/m/n/10.95 ALTree-convert \T1/ptm/m/n/10. Chapter 2. Package natbib Warning: Citation `Swofford02' on page 7 undefined on input line 278. Package natbib Warning: Citation `Felsenstein04' on page 7 undefined on input line 281. Underfull \hbox (badness 1142) in paragraph at lines 281--284 []\T1/pcr/m/n/10.95 phylip \T1/ptm/b/n/10.95 ?\T1/ptm/m/n/10.95 : freely avail- Package natbib Warning: Citation `YangPAML' on page 7 undefined on input line 284. Package natbib Warning: Citation `Guindon03' on page 7 undefined on input line 288. Underfull \hbox (badness 2486) in paragraph at lines 284--290 []\T1/pcr/m/n/10.95 paml \T1/ptm/b/n/10.95 ?\T1/ptm/m/n/10.95 : freely avail-ab Underfull \hbox (badness 10000) in paragraph at lines 314--315 Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 369--369 []|\T1/ptm/m/n/10.95 Output con-tain-ing the num-ber of Overfull \hbox (2.0805pt too wide) in paragraph at lines 355--370 [] Underfull \hbox (badness 10000) in paragraph at lines 396--397 Underfull \hbox (badness 10000) in paragraph at lines 400--401 Underfull \hbox (badness 10000) in paragraph at lines 416--417 Underfull \hbox (badness 1112) in paragraph at lines 505--507 []\T1/ptm/m/n/10.95 Other ex-am-ples may be found in the test di-rec-tory. Thes Chapter 4. Overfull \hbox (2.0805pt too wide) in paragraph at lines 537--553 [] Overfull \hbox (8.63097pt too wide) in paragraph at lines 584--605 \T1/ptm/m/n/10.95 Examples: $[]$ $[]$ Package natbib Warning: Citation `Bardel05' on page 14 undefined on input line 634. Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --data-qual|-q Underfull \hbox (badness 1281) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 remove the out-group se-quence for the Underfull \hbox (badness 5681) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 ancestral se-quence (only use-ful with Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --tree-building-program|-p Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --s-site-characters Underfull \hbox (badness 1565) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 print the tree with the char-ac-ter state Overfull \hbox (2.0805pt too wide) in paragraph at lines 664--698 [] Underfull \hbox (badness 10000) in paragraph at lines 735--738 Underfull \hbox (badness 1622) in paragraph at lines 747--755 \T1/ptm/m/n/10.95 Example of such files are given in the test di-rec-tory. Thes Package natbib Warning: Citation `Ge03' on page 19 undefined on input line 830. Package natbib Warning: Citation `Becker04' on page 19 undefined on input line 830. Package texdepends Warning: No 'fig/option_b_1.pdftex' file (texdepends) using 1 for graphic dimensions on input line 852. Package texdepends Warning: Figure 'fig/option_b_1.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 852. Package texdepends Warning: No 'fig/option_b_2.pdftex' file (texdepends) using 1 for graphic dimensions on input line 853. Package texdepends Warning: Figure 'fig/option_b_2.pdftex_t' needed (texdepends) Skipping it this time (the last one however) (texdepends) on input line 853. Package natbib Warning: Citation `Bardel05' on page 21 undefined on input line 921. Package natbib Warning: Citation `Bardel05' on page 21 undefined on input line 941. Chapter 6. Underfull \hbox (badness 5519) in paragraph at lines 968--971 []\T1/ptm/b/n/10.95 create_file \T1/ptm/m/n/10.95 which con-tains files and in- Underfull \hbox (badness 10000) in paragraph at lines 1024--1026 []\T1/ptm/m/n/10.95 the two \T1/pcr/m/n/10.95 FamHap \T1/ptm/m/n/10.95 out-put Underfull \hbox (badness 10000) in paragraph at lines 1125--1127 []\T1/ptm/m/n/10.95 a bash script con-tain-ing the three com-mand lines to run Package natbib Warning: Citation `Guindon03' on page 26 undefined on input line 1181. Underfull \hbox (badness 2662) in paragraph at lines 1188--1195 \T1/ptm/m/n/10.95 The files nec-es-sary for the phy-lo-ge-netic re-con-struc-ti Underfull \hbox (badness 10000) in paragraph at lines 1247--1249 []\T1/ptm/m/n/10.95 a bash script con-tain-ing the three com-mand lines to run Chapter 7. Underfull \hbox (badness 10000) in paragraph at lines 58--61 []\T1/ptm/m/n/10.95 Z Yang. 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(natbib) Rerun to get citations correct. /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_RESTORE make[5]: Entering directory '/build/altree-079pC6/altree-1.3.1/Documentation' make[5]: Leaving directory '/build/altree-079pC6/altree-1.3.1/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" manual.pdf_NEED_REBUILD make[5]: Entering directory '/build/altree-079pC6/altree-1.3.1/Documentation' *** Checking rebuild with rule 'latex' *** Checking rebuild with rule 'texdepends' ******************************************** *********** New build needed *************** ******************************************** New manual.aux file LU_rebuild_latex: new run needed (LaTeX message 'Rerun to get...') LU_rebuild_texdepends: new depends required ******************************************** /usr/bin/make LU_REC_LEVEL=3 manual.pdf make[6]: Entering directory '/build/altree-079pC6/altree-1.3.1/Documentation' ======> building manual.bbl <====== This is BibTeX, Version 0.99d (TeX Live 2020/Debian) The top-level auxiliary file: manual.aux The style file: plainnat.bst Database file #1: stage.bib Warning--empty year in YangPAML (There was 1 warning) ======> building fig/option_b_1.pdftex <====== ======> building fig/option_b_1.pdftex_t <====== ======> building fig/option_b_2.pdftex <====== ======> building fig/option_b_2.pdftex_t <====== Previous compilation failed. Rerun needed /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_SAVE make[7]: Entering directory '/build/altree-079pC6/altree-1.3.1/Documentation' make[7]: Leaving directory '/build/altree-079pC6/altree-1.3.1/Documentation' ======> building manual.pdf <====== removed 'manual.pdf_NEED_REBUILD' removed 'manual.pdf.mk' Running: 'pdflatex' '--interaction' 'errorstopmode' '--jobname' 'manual' '\RequirePackage[extension=.pdf]{texdepends}\input{manual.tex}' Package texdepends Warning: graphicspath already redefined. Skipping it. on input line 34. Package texdepends Warning: Diverting empty macro 'Ginclude@eps' (texdepends) Probably a bug in texdepends.sty. Package texdepends Warning: Gin@getbase already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@pdf already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@pdf already redefined. Skipping it. on input line 87. Chapter 1. LaTeX Warning: `h' float specifier changed to `ht'. Underfull \hbox (badness 1454) in paragraph at lines 196--201 []\T1/ptm/m/n/10.95 Currently, \T1/pcr/m/n/10.95 ALTree-convert \T1/ptm/m/n/10. Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 314--315 Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 369--369 []|\T1/ptm/m/n/10.95 Output con-tain-ing the num-ber of Overfull \hbox (2.0805pt too wide) in paragraph at lines 355--370 [] Underfull \hbox (badness 10000) in paragraph at lines 396--397 Underfull \hbox (badness 10000) in paragraph at lines 400--401 Underfull \hbox (badness 10000) in paragraph at lines 416--417 Underfull \hbox (badness 1112) in paragraph at lines 505--507 []\T1/ptm/m/n/10.95 Other ex-am-ples may be found in the test di-rec-tory. Thes Chapter 4. Overfull \hbox (2.0805pt too wide) in paragraph at lines 537--553 [] Overfull \hbox (8.63097pt too wide) in paragraph at lines 584--605 \T1/ptm/m/n/10.95 Examples: $[]$ $[]$ Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --data-qual|-q Underfull \hbox (badness 1281) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 remove the out-group se-quence for the Underfull \hbox (badness 5681) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 ancestral se-quence (only use-ful with Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --tree-building-program|-p Underfull \hbox (badness 10000) in paragraph at lines 697--697 []|\T1/pcr/m/n/10.95 --s-site-characters Underfull \hbox (badness 1565) in paragraph at lines 697--697 []|\T1/ptm/m/n/10.95 print the tree with the char-ac-ter state Overfull \hbox (2.0805pt too wide) in paragraph at lines 664--698 [] Underfull \hbox (badness 10000) in paragraph at lines 735--738 Underfull \hbox (badness 1622) in paragraph at lines 747--755 \T1/ptm/m/n/10.95 Example of such files are given in the test di-rec-tory. Thes Chapter 6. Underfull \hbox (badness 5519) in paragraph at lines 968--971 []\T1/ptm/b/n/10.95 create_file \T1/ptm/m/n/10.95 which con-tains files and in- Underfull \hbox (badness 10000) in paragraph at lines 1024--1026 []\T1/ptm/m/n/10.95 the two \T1/pcr/m/n/10.95 FamHap \T1/ptm/m/n/10.95 out-put Underfull \hbox (badness 10000) in paragraph at lines 1125--1127 []\T1/ptm/m/n/10.95 a bash script con-tain-ing the three com-mand lines to run Underfull \hbox (badness 2662) in paragraph at lines 1188--1195 \T1/ptm/m/n/10.95 The files nec-es-sary for the phy-lo-ge-netic re-con-struc-ti Underfull \hbox (badness 10000) in paragraph at lines 1247--1249 []\T1/ptm/m/n/10.95 a bash script con-tain-ing the three com-mand lines to run Chapter 7. Underfull \hbox (badness 10000) in paragraph at lines 58--61 []\T1/ptm/m/n/10.95 Z Yang. Phy-lo-ge-netic anal-y-sis by max-i-mum like-li-ho /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_RESTORE make[7]: Entering directory '/build/altree-079pC6/altree-1.3.1/Documentation' make[7]: Leaving directory '/build/altree-079pC6/altree-1.3.1/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" manual.pdf_NEED_REBUILD make[7]: Entering directory '/build/altree-079pC6/altree-1.3.1/Documentation' *** Checking rebuild with rule 'latex' *** Checking rebuild with rule 'texdepends' ******************************************** *********** New build needed *************** ******************************************** New manual.aux file LU_rebuild_latex: new run needed (LaTeX message 'Rerun to get...') ******************************************** /usr/bin/make LU_REC_LEVEL=4 manual.pdf make[8]: Entering directory '/build/altree-079pC6/altree-1.3.1/Documentation' ======> building manual.bbl <====== This is BibTeX, Version 0.99d (TeX Live 2020/Debian) The top-level auxiliary file: manual.aux The style file: plainnat.bst Database file #1: stage.bib Warning--empty year in YangPAML (There was 1 warning) Previous compilation failed. Rerun needed /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_SAVE make[9]: Entering directory '/build/altree-079pC6/altree-1.3.1/Documentation' make[9]: Leaving directory '/build/altree-079pC6/altree-1.3.1/Documentation' ======> building manual.pdf <====== removed 'manual.pdf_NEED_REBUILD' removed 'manual.pdf.mk' Running: 'pdflatex' '--interaction' 'errorstopmode' '--jobname' 'manual' '\RequirePackage[extension=.pdf]{texdepends}\input{manual.tex}' Package texdepends Warning: graphicspath already redefined. Skipping it. on input line 34. Package texdepends Warning: Diverting empty macro 'Ginclude@eps' (texdepends) Probably a bug in texdepends.sty. Package texdepends Warning: Gin@getbase already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Ginclude@pdf already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@eps already redefined. Skipping it. on input line 87. Package texdepends Warning: Gread@pdf already redefined. Skipping it. on input line 87. Chapter 1. LaTeX Warning: `h' float specifier changed to `ht'. Underfull \hbox (badness 1454) in paragraph at lines 196--201 []\T1/ptm/m/n/10.95 Currently, \T1/pcr/m/n/10.95 ALTree-convert \T1/ptm/m/n/10. Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 314--315 Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 369--369 []|\T1/ptm/m/n/10.95 Output con-tain-ing the num-ber of Overfull \hbox (2.0805pt too wide) in paragraph at lines 355--370 [] Underfull \hbox (badness 10000) in paragraph at lines 396--397 Underfull \hbox (badness 10000) in paragraph at lines 400--401 Underfull \hbox (badness 10000) in paragraph at lines 416--417 Underfull \hbox (badness 1112) in paragraph at lines 505--507 []\T1/ptm/m/n/10.95 Other ex-am-ples may be found in the test di-rec-tory. Thes Chapter 4. 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Underfull \hbox (badness 10000) in paragraph at lines 58--61 /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" LU_WATCH_FILES_RESTORE make[9]: Entering directory '/build/altree-079pC6/altree-1.3.1/Documentation' make[9]: Leaving directory '/build/altree-079pC6/altree-1.3.1/Documentation' /usr/bin/make LU_REC_MASTER="manual" LU_REC_FLAVOR="PDF" LU_REC_TARGET="manual.pdf" manual.pdf_NEED_REBUILD make[9]: Entering directory '/build/altree-079pC6/altree-1.3.1/Documentation' *** Checking rebuild with rule 'latex' *** Checking rebuild with rule 'texdepends' /usr/bin/make LU_REC_LEVEL=5 manual.pdf make[10]: Entering directory '/build/altree-079pC6/altree-1.3.1/Documentation' make[10]: 'manual.pdf' is up to date. make[10]: Leaving directory '/build/altree-079pC6/altree-1.3.1/Documentation' make[9]: Leaving directory '/build/altree-079pC6/altree-1.3.1/Documentation' make[8]: Leaving directory '/build/altree-079pC6/altree-1.3.1/Documentation' make[7]: Leaving directory '/build/altree-079pC6/altree-1.3.1/Documentation' make[6]: Leaving directory '/build/altree-079pC6/altree-1.3.1/Documentation' make[5]: Leaving directory '/build/altree-079pC6/altree-1.3.1/Documentation' make[4]: Leaving directory '/build/altree-079pC6/altree-1.3.1/Documentation' make[3]: Leaving directory '/build/altree-079pC6/altree-1.3.1/Documentation' make[2]: Leaving directory '/build/altree-079pC6/altree-1.3.1/Documentation' dh_auto_build make -j4 make[2]: Entering directory '/build/altree-079pC6/altree-1.3.1' make[3]: Entering directory '/build/altree-079pC6/altree-1.3.1/CUtils' make -C c_sources make[4]: Entering directory '/build/altree-079pC6/altree-1.3.1/CUtils/c_sources' x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/altree-079pC6/altree-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.30/CORE" chisq.c Running Mkbootstrap for CUtils () chmod 644 "CUtils.bs" "/usr/bin/perl" "/usr/share/perl/5.30.3/ExtUtils/xsubpp" -typemap '/usr/share/perl/5.30/ExtUtils/typemap' CUtils.xs > CUtils.xsc cp ALTree/SiteSensPerTree.pm blib/lib/ALTree/SiteSensPerTree.pm cp ALTree/SiteCollection.pm blib/lib/ALTree/SiteCollection.pm cp ALTree/SitePerForet.pm blib/lib/ALTree/SitePerForet.pm cp ALTree/Chi2.pm blib/lib/ALTree/Chi2.pm cp ALTree/Sens.pm blib/lib/ALTree/Sens.pm cp ALTree/Tree.pm blib/lib/ALTree/Tree.pm cp ALTree/SiteSensPerForet.pm blib/lib/ALTree/SiteSensPerForet.pm cp ALTree/Input.pm blib/lib/ALTree/Input.pm cp ALTree/Foret.pm blib/lib/ALTree/Foret.pm cp ALTree/Utils.pm blib/lib/ALTree/Utils.pm cp ALTree/Nanova.pm blib/lib/ALTree/Nanova.pm cp ALTree/Base.pm blib/lib/ALTree/Base.pm cp ALTree/Site.pm blib/lib/ALTree/Site.pm cp ALTree/Import.pm blib/lib/ALTree/Import.pm cp ALTree/Node.pm blib/lib/ALTree/Node.pm cp ALTree/to_rewrite.pm blib/lib/ALTree/to_rewrite.pm cp ALTree/SitePerTree.pm blib/lib/ALTree/SitePerTree.pm cp ALTree/SiteSens.pm blib/lib/ALTree/SiteSens.pm x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/altree-079pC6/altree-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.30/CORE" double_permutation.c cp lib/ALTree/CUtils.pm ../blib/lib/ALTree/CUtils.pm AutoSplitting ../blib/lib/ALTree/CUtils.pm (../blib/lib/auto/ALTree/CUtils) x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/altree-079pC6/altree-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.30/CORE" fisher.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/altree-079pC6/altree-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.30/CORE" mt19937ar.c Please specify prototyping behavior for CUtils.xs (see perlxs manual) mv CUtils.xsc CUtils.c "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 x86_64-linux-gnu-gcc -c -ggdb3 -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/altree-079pC6/altree-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"1.1\" -DXS_VERSION=\"1.1\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.30/CORE" CUtils.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/altree-079pC6/altree-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.30/CORE" myrand.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/altree-079pC6/altree-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.30/CORE" resampling.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/altree-079pC6/altree-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.30/CORE" rhyper.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/altree-079pC6/altree-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.30/CORE" stats.c x86_64-linux-gnu-gcc -c -Wall -I. -Ic_sources -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/altree-079pC6/altree-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.30/CORE" z.c In file included from CUtils.xs:5: ppport.h:237: warning: "PERL_UNUSED_DECL" redefined 237 | # define PERL_UNUSED_DECL | In file included from CUtils.xs:2: /usr/lib/x86_64-linux-gnu/perl/5.30/CORE/perl.h:328: note: this is the location of the previous definition 328 | # define PERL_UNUSED_DECL __attribute__unused__ | CUtils.xs: In function ‘XS_ALTree__CUtils_RHyper’: CUtils.xs:69:16: warning: implicit declaration of function ‘rhyper’ [-Wimplicit-function-declaration] 69 | RETVAL=rhyper(n1, n2, k); | ^~~~~~ z.c:12:13: warning: ‘sccsfid’ defined but not used [-Wunused-variable] 12 | static char sccsfid[] = "@(#) z.c 5.1 (|stat) 12/26/85"; | ^~~~~~~ ar cr libaltree-cutils.a chisq.o double_permutation.o fisher.o mt19937ar.o myrand.o resampling.o rhyper.o stats.o z.o : libaltree-cutils.a make[4]: Leaving directory '/build/altree-079pC6/altree-1.3.1/CUtils/c_sources' make[4]: Entering directory '/build/altree-079pC6/altree-1.3.1/CUtils/c_sources' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/altree-079pC6/altree-1.3.1/CUtils/c_sources' rm -f ../blib/arch/auto/ALTree/CUtils/CUtils.so x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/altree-079pC6/altree-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -shared -L/usr/local/lib -fstack-protector-strong CUtils.o -o ../blib/arch/auto/ALTree/CUtils/CUtils.so c_sources/libaltree-cutils.a \ -lm -lpthread -lgsl -lblas \ chmod 755 ../blib/arch/auto/ALTree/CUtils/CUtils.so Manifying 1 pod document make[3]: Leaving directory '/build/altree-079pC6/altree-1.3.1/CUtils' cp progs/altree blib/script/altree cp progs/altree-add-S blib/script/altree-add-S cp progs/altree-convert blib/script/altree-convert "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/altree "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/altree-add-S "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/altree-convert Manifying 3 pod documents make[2]: Leaving directory '/build/altree-079pC6/altree-1.3.1' make[1]: Leaving directory '/build/altree-079pC6/altree-1.3.1' dh_auto_test -i make -j4 test TEST_VERBOSE=1 make[1]: Entering directory '/build/altree-079pC6/altree-1.3.1' make[2]: Entering directory '/build/altree-079pC6/altree-1.3.1/CUtils' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 make[3]: Entering directory '/build/altree-079pC6/altree-1.3.1/CUtils/c_sources' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/altree-079pC6/altree-1.3.1/CUtils/c_sources' Manifying 1 pod document make[2]: Leaving directory '/build/altree-079pC6/altree-1.3.1/CUtils' make[2]: Entering directory '/build/altree-079pC6/altree-1.3.1/CUtils' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 make[3]: Entering directory '/build/altree-079pC6/altree-1.3.1/CUtils/c_sources' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/altree-079pC6/altree-1.3.1/CUtils/c_sources' make[3]: Entering directory '/build/altree-079pC6/altree-1.3.1/CUtils/c_sources' No tests defined for ALTree::CUtils extension. make[3]: Leaving directory '/build/altree-079pC6/altree-1.3.1/CUtils/c_sources' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, '../blib/lib', '../blib/arch')" t/*.t t/ALTree-CUtils.t ....... 1..1 ok 1 - use ALTree::CUtils; ok t/double_permutation.t .. 1..3 ok 1 - use ALTree::CUtils; ok 2 - undef when bad args ok 3 - double_permutation ok All tests successful. Files=2, Tests=4, 0 wallclock secs ( 0.02 usr 0.01 sys + 0.17 cusr 0.04 csys = 0.24 CPU) Result: PASS make[2]: Leaving directory '/build/altree-079pC6/altree-1.3.1/CUtils' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/ALTree.t .. 1..1 ok 1 - use ALTree::Import; ok All tests successful. Files=1, Tests=1, 0 wallclock secs ( 0.02 usr 0.01 sys + 0.12 cusr 0.02 csys = 0.17 CPU) Result: PASS make[1]: Leaving directory '/build/altree-079pC6/altree-1.3.1' create-stamp debian/debhelper-build-stamp dh_testroot -i dh_prep -i dh_auto_install -i make -j4 install DESTDIR=/build/altree-079pC6/altree-1.3.1/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/altree-079pC6/altree-1.3.1' make[2]: Entering directory '/build/altree-079pC6/altree-1.3.1/CUtils' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CUtils.bs ../blib/arch/auto/ALTree/CUtils/CUtils.bs 644 make[3]: Entering directory '/build/altree-079pC6/altree-1.3.1/CUtils/c_sources' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/altree-079pC6/altree-1.3.1/CUtils/c_sources' Manifying 1 pod document make[2]: Leaving directory '/build/altree-079pC6/altree-1.3.1/CUtils' Manifying 3 pod documents Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/auto/ALTree/CUtils/CUtils.so Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/auto/ALTree/CUtils/autosplit.ix Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/Input.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/Node.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/SitePerTree.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/Site.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/Foret.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/Nanova.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/Sens.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/CUtils.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/SiteSensPerForet.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/Utils.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/Import.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/to_rewrite.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/Chi2.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/SiteSens.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/Tree.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/SitePerForet.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/Base.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/SiteSensPerTree.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.30/ALTree/SiteCollection.pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/share/man/man1/altree-convert.1p Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/share/man/man1/altree-add-S.1p Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/share/man/man1/altree.1p Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/share/man/man3/ALTree::CUtils.3pm Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/bin/altree Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/bin/altree-add-S Installing /build/altree-079pC6/altree-1.3.1/debian/tmp/usr/bin/altree-convert make[1]: Leaving directory '/build/altree-079pC6/altree-1.3.1' dh_install -i dh_installdocs -i dh_installchangelogs -i dh_perl -i dh_link -i dh_strip_nondeterminism -i debian/rules override_dh_compress make[1]: Entering directory '/build/altree-079pC6/altree-1.3.1' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/altree-079pC6/altree-1.3.1' dh_fixperms -i dh_missing -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'altree-examples' in '../altree-examples_1.3.1-10_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../altree_1.3.1-10_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/altree-079pC6 /tmp/altree-1.3.1-10a5xw58zm I: cleaning package lists and apt cache... W: deleting files in /tmp: out.txt I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.KyA7Avx6nX... I: success in 479.9068 seconds md5: altree-examples_1.3.1-10_all.deb: OK sha1: altree-examples_1.3.1-10_all.deb: OK sha256: altree-examples_1.3.1-10_all.deb: OK Checksums: OK