origdir = ../tarballs /home/sw/bin/buildPackage: line 17: .svn/deb-layout: No such file or directory Complete layout information: buildArea=/sw/debian-med/trunk/packages/rostlab/librostlab-blast/build-area origDir=/sw/debian-med/trunk/packages/rostlab/librostlab-blast/tarballs tagsDir=/sw/debian-med/trunk/packages/rostlab/librostlab-blast/tags tagsUrl=svn://svn.debian.org/svn/debian-med/trunk/packages/rostlab/librostlab-blast/tags trunkDir=/sw/debian-med/trunk/packages/rostlab/librostlab-blast/trunk trunkUrl=svn://svn.debian.org/svn/debian-med/trunk/packages/rostlab/librostlab-blast/trunk mergeWithUpstream mode detected, looking for /sw/debian-med/trunk/packages/rostlab/librostlab-blast/tarballs/librostlab-blast_1.0.1.orig.tar.gz I: mergeWithUpstream property set, looking for upstream source tarball... tar --no-same-owner --no-same-permissions --extract --gzip --file /sw/debian-med/trunk/packages/rostlab/librostlab-blast/tarballs/librostlab-blast-1.0.1.tar.gz <2 more arguments> mv /sw/debian-med/trunk/packages/rostlab/librostlab-blast/build-area/tmp-0.37405371021396/librostlab-blast-1.0.1 /sw/debian-med/trunk/packages/rostlab/librostlab-blast/build-area/librostlab-blast-1.0.1 mkdir -p /sw/debian-med/trunk/packages/rostlab/librostlab-blast/build-area/librostlab-blast-1.0.1/debian /sw/debian-med/trunk/packages/rostlab/librostlab-blast/build-area/librostlab-blast-1.0.1/debian/source cp --parents -laf debian/copyright debian/librostlab-blast0.install debian/rules debian/librostlab-blast0-dev.install debian/compat debian/librostlab-blast-doc.lintian-overrides <9 more arguments> rm -rf /sw/debian-med/trunk/packages/rostlab/librostlab-blast/build-area/tmp-0.37405371021396 chmod -R u+r+w+X,g+r-w+X,o+r-w+X -- /sw/debian-med/trunk/packages/rostlab/librostlab-blast/build-area/librostlab-blast-1.0.1 /bin/sh -c pdebuild --buildresult /sw/packages/build-area -- --basetgz /var/cache/pbuilder/base-sid-amd64.tgz --architecture amd64 --distribution sid W: /home/sw/.pbuilderrc does not exist dpkg-buildpackage: source package librostlab-blast dpkg-buildpackage: source version 1.0.1-2 dpkg-buildpackage: source changed by Laszlo Kajan dpkg-source --before-build librostlab-blast-1.0.1 fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel debian/rules override_dh_auto_clean make[1]: Entering directory `/sw/debian-med/trunk/packages/rostlab/librostlab-blast/build-area/librostlab-blast-1.0.1' dh_auto_clean --parallel rm -f lib/librostlab-blast.tag make[1]: Leaving directory `/sw/debian-med/trunk/packages/rostlab/librostlab-blast/build-area/librostlab-blast-1.0.1' dh_clean -O--parallel dpkg-source -b librostlab-blast-1.0.1 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building librostlab-blast using existing ./librostlab-blast_1.0.1.orig.tar.gz dpkg-source: info: building librostlab-blast in librostlab-blast_1.0.1-2.debian.tar.gz dpkg-source: info: building librostlab-blast in librostlab-blast_1.0.1-2.dsc dpkg-genchanges -S >../librostlab-blast_1.0.1-2_source.changes dpkg-genchanges: not including original source code in upload dpkg-source --after-build librostlab-blast-1.0.1 dpkg-buildpackage: binary and diff upload (original source NOT included) W: /home/sw/.pbuilderrc does not exist I: using fakeroot in build. I: Current time: Wed Mar 27 09:25:16 CET 2013 I: pbuilder-time-stamp: 1364372716 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/base-sid-amd64.tgz] I: creating local configuration I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /run/shm filesystem I: mounting /dev/pts filesystem I: policy-rc.d already exists I: Obtaining the cached apt archive contents I: Installing the build-deps -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 7.0.50~), autotools-dev, bison, doxygen, flex, graphviz, latex-xcolor, librostlab-dev, texlive-fonts-recommended, texlive-latex-extra dpkg-deb: building package `pbuilder-satisfydepends-dummy' in `/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 12010 files and directories currently installed.) Unpacking pbuilder-satisfydepends-dummy (from .../pbuilder-satisfydepends-dummy.deb) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 7.0.50~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on autotools-dev; however: Package autotools-dev is not installed. pbuilder-satisfydepends-dummy depends on bison; however: Package bison is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on flex; however: Package flex is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz is not installed. pbuilder-satisfydepends-dummy depends on latex-xcolor; however: Package latex-xcolor is not installed. pbuilder-satisfydepends-dummy depends on librostlab-dev; however: Package librostlab-dev is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... The following NEW packages will be installed: autotools-dev{a} bison{a} bsdmainutils{a} debhelper{a} doxygen{a} ed{a} file{a} flex{a} fontconfig{a} fontconfig-config{a} gettext{a} gettext-base{a} graphviz{a} groff-base{a} html2text{a} intltool-debian{a} latex-xcolor{a} libasprintf-dev{a} libasprintf0c2{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbison-dev{a} libcairo2{a} libcdt4{a} libcgraph5{a} libcroco3{a} libcups2{a} libcupsimage2{a} libdatrie1{a} libdbus-1-3{a} libexpat1{a} libffi5{a} libfontconfig1{a} libfreetype6{a} libgcrypt11{a} libgd2-noxpm{a} libgettextpo-dev{a} libgettextpo0{a} libglib2.0-0{a} libgnutls26{a} libgpg-error0{a} libgraph4{a} libgraphite3{a} libgs9{a} libgs9-common{a} libgssapi-krb5-2{a} libgvc5{a} libgvpr1{a} libice6{a} libidn11{a} libijs-0.35{a} libjasper1{a} libjbig0 libjbig2dec0{a} libjpeg8{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblcms1{a} liblcms2-2{a} libltdl7{a} libmagic1{a} libopenjpeg2{a} libp11-kit0{a} libpango1.0-0{a} libpaper-utils{a} libpaper1{a} libpathplan4{a} libpcre3{a} libpipeline1{a} libpixman-1-0{a} libpng12-0{a} libpoppler19{a} libptexenc1{a} librostlab3{a} librostlab3-dev{a} libsigsegv2{a} libsm6{a} libtasn1-3{a} libthai-data{a} libthai0{a} libtiff4{a} libunistring0{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxdot4{a} libxext6{a} libxft2{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6{a} luatex{a} m4{a} man-db{a} po-debconf{a} poppler-data{a} preview-latex-style{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-common{a} texlive-doc-base{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} ttf-dejavu-core{a} ttf-marvosym{a} x11-common{a} xdg-utils{a} 0 packages upgraded, 122 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/92.6 MB of archives. After unpacking 271 MB will be used. Writing extended state information... debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1:amd64. (Reading database ... 12010 files and directories currently installed.) Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.2-2_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.22.2-1_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.3-3_amd64.deb) ... Selecting previously unselected package libasprintf0c2:amd64. Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-10_amd64.deb) ... Selecting previously unselected package libgpg-error0:amd64. 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Setting up bison (2:2.5.dfsg-3) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up html2text (1.3.2a-15) ... Setting up libasprintf-dev:amd64 (0.18.1.1-10) ... Setting up libgettextpo-dev:amd64 (0.18.1.1-10) ... Setting up gettext (0.18.1.1-10) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120909) ... Setting up doxygen (1.8.1.2-2) ... Setting up ed (1.6-2) ... Setting up libcdt4 (2.26.3-14) ... Setting up libcgraph5 (2.26.3-14) ... Setting up libgraph4 (2.26.3-14) ... Setting up libpathplan4 (2.26.3-14) ... Setting up libxdot4 (2.26.3-14) ... Setting up libgvc5 (2.26.3-14) ... Setting up libgvpr1 (2.26.3-14) ... Setting up graphviz (2.26.3-14) ... Setting up libgraphite3 (1:2.3.1-0.2) ... Setting up libijs-0.35 (0.35-8) ... Setting up libjbig2dec0 (0.11+20120125-1) ... Setting up libgs9-common (9.05~dfsg-6.3) ... Setting up libgs9 (9.05~dfsg-6.3) ... Setting up libptexenc1 (2012.20120628-4) ... Setting up texlive-common (2012.20120611-5) ... Setting up texlive-binaries (2012.20120628-4) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Building format(s) --refresh. This may take some time... done. Setting up texlive-doc-base (2012.20120611-1) ... Setting up xdg-utils (1.1.0~rc1+git20111210-7) ... Setting up libpaper-utils (1.1.24+nmu2) ... Setting up librostlab3 (1.0.20-2) ... Setting up librostlab3-dev (1.0.20-2) ... Setting up preview-latex-style (11.87-1) ... Setting up ttf-marvosym (0.1+dfsg-2) ... Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Setting up texlive-base (2012.20120611-5) ... /usr/bin/tl-paper: setting paper size for dvips to a4. /usr/bin/tl-paper: setting paper size for dvipdfmx to a4. /usr/bin/tl-paper: setting paper size for xdvi to a4. /usr/bin/tl-paper: setting paper size for pdftex to a4. Running mktexlsr. This may take some time... done. Building format(s) --all. This may take some time... done. Processing triggers for tex-common ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up texlive-fonts-recommended (2012.20120611-5) ... Setting up texlive-pictures (2012.20120611-5) ... Setting up texlive-latex-base (2012.20120611-5) ... Running mktexlsr. This may take some time... done. Building format(s) --all --cnffile /etc/texmf/fmt.d/10texlive-latex-base.cnf. This may take some time... done. Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up texlive-latex-recommended (2012.20120611-5) ... Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Setting up latex-xcolor (2.11-1.1) ... Setting up texlive-latex-extra (2012.20120611-2) ... Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: fakeroot debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/109 kB of archives. After this operation, 325 kB of additional disk space will be used. Selecting previously unselected package fakeroot. (Reading database ... 28387 files and directories currently installed.) Unpacking fakeroot (from .../fakeroot_1.18.4-2_amd64.deb) ... Processing triggers for man-db ... Setting up fakeroot (1.18.4-2) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode I: Copying back the cached apt archive contents I: Copying source file I: copying [../librostlab-blast_1.0.1-2.dsc] I: copying [../librostlab-blast_1.0.1.orig.tar.gz] I: copying [../librostlab-blast_1.0.1-2.debian.tar.gz] I: Extracting source dpkg-source: warning: extracting unsigned source package (librostlab-blast_1.0.1-2.dsc) dpkg-source: info: extracting librostlab-blast in librostlab-blast-1.0.1 dpkg-source: info: unpacking librostlab-blast_1.0.1.orig.tar.gz dpkg-source: info: unpacking librostlab-blast_1.0.1-2.debian.tar.gz I: Building the package I: Running cd tmp/buildd/*/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin" dpkg-buildpackage -us -uc -rfakeroot dpkg-buildpackage: source package librostlab-blast dpkg-buildpackage: source version 1.0.1-2 dpkg-buildpackage: source changed by Laszlo Kajan dpkg-source --before-build librostlab-blast-1.0.1 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel debian/rules override_dh_auto_clean make[1]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1' dh_auto_clean --parallel rm -f lib/librostlab-blast.tag make[1]: Leaving directory `/tmp/buildd/librostlab-blast-1.0.1' dh_clean -O--parallel dpkg-source -b librostlab-blast-1.0.1 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building librostlab-blast using existing ./librostlab-blast_1.0.1.orig.tar.gz dpkg-source: info: building librostlab-blast in librostlab-blast_1.0.1-2.debian.tar.gz dpkg-source: info: building librostlab-blast in librostlab-blast_1.0.1-2.dsc debian/rules build dh build --parallel dh_testdir -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1' dh_auto_configure --parallel -- --enable-doxygen-dot --enable-doxygen-pdf configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... 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BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 3458764513820540925 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... 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GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for bison... bison -y checking for flex... flex checking lex output file root... lex.yy checking lex library... -lfl checking whether yytext is a pointer... yes checking rostlab/aux_functions.h usability... yes checking rostlab/aux_functions.h presence... yes checking for rostlab/aux_functions.h... yes checking rostlab/rostlab_stdexcept.h usability... yes checking rostlab/rostlab_stdexcept.h presence... yes checking for rostlab/rostlab_stdexcept.h... yes checking for doxygen... /usr/bin/doxygen checking for perl... /usr/bin/perl checking for dot... /usr/bin/dot checking for pdflatex... /usr/bin/pdflatex checking for makeindex... /usr/bin/makeindex checking for egrep... /bin/egrep configure: creating ./config.status config.status: creating Makefile config.status: creating lib/Makefile config.status: creating lib/Doxyfile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory `/tmp/buildd/librostlab-blast-1.0.1' debian/rules override_dh_auto_build make[1]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1' dh_auto_build --parallel make[2]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1' make all-recursive make[3]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1' Making all in lib make[4]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1/lib' mkdir -p rostlab /bin/bash ../ylwrap blast-parser-parser.ypp y.tab.c blast-parser-parser.cpp y.tab.h rostlab/blast-parser-parser.h y.output blast-parser-parser.output stack.hh rostlab/blast-parser-stack.h location.hh rostlab/blast-parser-location.h position.hh rostlab/blast-parser-position.h -- bison -y updating rostlab/blast-parser-parser.h updating rostlab/blast-parser-stack.h updating rostlab/blast-parser-location.h updating rostlab/blast-parser-position.h sed -i -e 's,\by.tab.h\b,rostlab/blast-parser-parser.h,g' blast-parser-parser.cpp sed -i -e 's,\bstack.hh\b,rostlab/blast-parser-stack.h,g;s,\blocation.hh\b,rostlab/blast-parser-location.h,g;' rostlab/blast-parser-parser.h sed -i -e 's,\bposition.hh\b,rostlab/blast-parser-position.h,g;' rostlab/blast-parser-location.h /bin/bash ../ylwrap blast-parser-scanner.lpp lex.yy.c blast-parser-scanner.cpp -- flex make all-am make[5]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1/lib' /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o librostlab_blast_la-blast-parser-driver.lo `test -f 'blast-parser-driver.cpp' || echo './'`blast-parser-driver.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c blast-parser-driver.cpp -fPIC -DPIC -o .libs/librostlab_blast_la-blast-parser-driver.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c blast-parser-driver.cpp -o librostlab_blast_la-blast-parser-driver.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o librostlab_blast_la-blast-parser-parser.lo `test -f 'blast-parser-parser.cpp' || echo './'`blast-parser-parser.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c blast-parser-parser.cpp -fPIC -DPIC -o .libs/librostlab_blast_la-blast-parser-parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c blast-parser-parser.cpp -o librostlab_blast_la-blast-parser-parser.o >/dev/null 2>&1 \ \ /bin/bash ../ylwrap `test -f 'blast-parser-scanner.lpp' || echo './'`blast-parser-scanner.lpp lex.yy.c librostlab_blast_la-blast-parser-scanner.cpp -- flex -Cfe /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o librostlab_blast_la-librostlab_blast_la-blast-parser-scanner.lo `test -f 'librostlab_blast_la-blast-parser-scanner.cpp' || echo './'`librostlab_blast_la-blast-parser-scanner.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c librostlab_blast_la-blast-parser-scanner.cpp -fPIC -DPIC -o .libs/librostlab_blast_la-librostlab_blast_la-blast-parser-scanner.o libtool: compile: g++ 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(./blast-parser-driver_8h.tex [37 <./blast-parser-driver_8h__incl.pdf> ]) (./blast-parser-location_8h.tex Underfull \vbox (badness 4060) has occurred while \output is active [38] [39 <./blast-parser-location_8h__ incl.pdf> <./blast-parser-location_8h__dep__incl.pdf pdfTeX warning: /usr/bin/pdflatex (file ./blast-parser-location_8h__dep__incl.p df): PDF inclusion: multiple pdfs with page group included in a single page >]) (./blast-parser-parser_8h.tex Underfull \vbox (badness 4328) has occurred while \output is active [40 <./blas t-parser-parser_8h__incl.pdf>]) (./blast-parser-position_8h.tex [41 <./blast-parser-parser_8h__dep__in cl.pdf>] [42 <./blast-parser-position_8h__ incl.pdf> <./blast-parser-position_8h__dep__incl.pdf pdfTeX warning: /usr/bin/pdflatex (file ./blast-parser-position_8h__dep__incl.p df): PDF inclusion: multiple pdfs with page group included in a single page >]) (./blast-parser-stack_8h.tex [43 <./blast-parser-stack_8h__incl.p df>]) (./blast-result_8h.tex Underfull \vbox (badness 10000) has occurred while \output is active [44 <./bla st-parser-stack_8h__dep__incl.pdf>] [45 <./blast-result_8h__incl.pdf> <./blast -result_8h__dep__incl.pdf pdfTeX warning: /usr/bin/pdflatex (file ./blast-result_8h__dep__incl.pdf): PDF inclusion: multiple pdfs with page group included in a single page >]) No file refman.ind. [46] (./refman.aux) Package rerunfilecheck Warning: File `refman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Font Warning: Some font shapes were not available, defaults substituted. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information)pdfTeX warning (dest): name {blast\\unhbox\040\\voidb@x\040\\kern\040\\z@\040\\char\040`\\discretionary\040 {-}{}{}parser\\unhbox\040\\voidb@x\040\\kern\040\\z@\040\\char\040`\\discretion ary\040{-}{}{}driver_8h} has been referenced but does not exist, replaced by a fixed one {/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on refman.pdf (50 pages, 257662 bytes). Transcript written on refman.log. This is makeindex, version 2.15 [TeX Live 2012] (kpathsea + Thai support). 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(./namespaces.tex) [1] [2] Chapter 2. (./annotated.tex) [3] [4] Chapter 3. (./files.tex) [5] [6] Chapter 4. (./namespacerostlab.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1phv.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) LaTeX Font Warning: Font shape `OT1/pcr/bc/n' undefined (Font) using `OT1/pcr/m/n' instead on input line 32. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 32. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 32. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 32. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 32. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 48. 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(./blast-parser-driver_8h.tex [37 <./blast-parser-driver_8h__incl.pdf> ]) (./blast-parser-location_8h.tex Underfull \vbox (badness 4060) has occurred while \output is active [38] [39 <./blast-parser-location_8h__ incl.pdf> <./blast-parser-location_8h__dep__incl.pdf pdfTeX warning: /usr/bin/pdflatex (file ./blast-parser-location_8h__dep__incl.p df): PDF inclusion: multiple pdfs with page group included in a single page >]) (./blast-parser-parser_8h.tex Underfull \vbox (badness 4328) has occurred while \output is active [40 <./blas t-parser-parser_8h__incl.pdf>]) (./blast-parser-position_8h.tex [41 <./blast-parser-parser_8h__dep__in cl.pdf>] [42 <./blast-parser-position_8h__ incl.pdf> <./blast-parser-position_8h__dep__incl.pdf pdfTeX warning: /usr/bin/pdflatex (file ./blast-parser-position_8h__dep__incl.p df): PDF inclusion: multiple pdfs with page group included in a single page >]) (./blast-parser-stack_8h.tex [43 <./blast-parser-stack_8h__incl.p df>]) (./blast-result_8h.tex Underfull \vbox (badness 10000) has occurred while \output is active [44 <./bla st-parser-stack_8h__dep__incl.pdf>] [45 <./blast-result_8h__incl.pdf> <./blast -result_8h__dep__incl.pdf pdfTeX warning: /usr/bin/pdflatex (file ./blast-result_8h__dep__incl.pdf): PDF inclusion: multiple pdfs with page group included in a single page >]) (./refman.ind [46] [47] [48] [49] [50] [51]) (./refman.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information)pdfTeX warning (dest): name {blast\\unhbox\040\\voidb@x\040\\kern\040\\z@\040\\char\040`\\discretionary\040 {-}{}{}parser\\unhbox\040\\voidb@x\040\\kern\040\\z@\040\\char\040`\\discretion ary\040{-}{}{}driver_8h} has been referenced but does not exist, replaced by a fixed one {/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on refman.pdf (59 pages, 302084 bytes). Transcript written on refman.log. make[2]: Leaving directory `/tmp/buildd/librostlab-blast-1.0.1/lib' make[1]: Leaving directory `/tmp/buildd/librostlab-blast-1.0.1' dh_auto_test -O--parallel make[1]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1' Making check in lib make[2]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1/lib' make check-am make[3]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1/lib' make[3]: Nothing to be done for `check-am'. make[3]: Leaving directory `/tmp/buildd/librostlab-blast-1.0.1/lib' make[2]: Leaving directory `/tmp/buildd/librostlab-blast-1.0.1/lib' make[2]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1' make[2]: Nothing to be done for `check-am'. make[2]: Leaving directory `/tmp/buildd/librostlab-blast-1.0.1' make[1]: Leaving directory `/tmp/buildd/librostlab-blast-1.0.1' fakeroot debian/rules binary dh binary --parallel dh_testroot -O--parallel dh_prep -O--parallel dh_installdirs -O--parallel dh_auto_install -O--parallel make[1]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1' Making install in lib make[2]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1/lib' make install-am make[3]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1/lib' make[4]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1/lib' /bin/mkdir -p '/tmp/buildd/librostlab-blast-1.0.1/debian/tmp/usr/lib' /bin/bash ../libtool --mode=install /usr/bin/install -c librostlab-blast.la '/tmp/buildd/librostlab-blast-1.0.1/debian/tmp/usr/lib' libtool: install: /usr/bin/install -c .libs/librostlab-blast.so.0.0.0 /tmp/buildd/librostlab-blast-1.0.1/debian/tmp/usr/lib/librostlab-blast.so.0.0.0 libtool: install: (cd /tmp/buildd/librostlab-blast-1.0.1/debian/tmp/usr/lib && { ln -s -f librostlab-blast.so.0.0.0 librostlab-blast.so.0 || { rm -f librostlab-blast.so.0 && ln -s librostlab-blast.so.0.0.0 librostlab-blast.so.0; }; }) libtool: install: (cd /tmp/buildd/librostlab-blast-1.0.1/debian/tmp/usr/lib && { ln -s -f librostlab-blast.so.0.0.0 librostlab-blast.so || { rm -f librostlab-blast.so && ln -s librostlab-blast.so.0.0.0 librostlab-blast.so; }; }) libtool: install: /usr/bin/install -c .libs/librostlab-blast.lai /tmp/buildd/librostlab-blast-1.0.1/debian/tmp/usr/lib/librostlab-blast.la libtool: install: /usr/bin/install -c .libs/librostlab-blast.a /tmp/buildd/librostlab-blast-1.0.1/debian/tmp/usr/lib/librostlab-blast.a libtool: install: chmod 644 /tmp/buildd/librostlab-blast-1.0.1/debian/tmp/usr/lib/librostlab-blast.a libtool: install: ranlib /tmp/buildd/librostlab-blast-1.0.1/debian/tmp/usr/lib/librostlab-blast.a libtool: install: warning: remember to run `libtool --finish /usr/lib' /bin/mkdir -p '/tmp/buildd/librostlab-blast-1.0.1/debian/tmp/usr/include/rostlab' /usr/bin/install -c -m 644 rostlab/blast-parser-driver.h rostlab/blast-result.h '/tmp/buildd/librostlab-blast-1.0.1/debian/tmp/usr/include/rostlab' /bin/mkdir -p '/tmp/buildd/librostlab-blast-1.0.1/debian/tmp/usr/include/rostlab' /usr/bin/install -c -m 644 rostlab/blast-parser-location.h rostlab/blast-parser-parser.h rostlab/blast-parser-position.h rostlab/blast-parser-stack.h '/tmp/buildd/librostlab-blast-1.0.1/debian/tmp/usr/include/rostlab' make[4]: Leaving directory `/tmp/buildd/librostlab-blast-1.0.1/lib' make[3]: Leaving directory `/tmp/buildd/librostlab-blast-1.0.1/lib' make[2]: Leaving directory `/tmp/buildd/librostlab-blast-1.0.1/lib' make[2]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1' make[3]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1' make[3]: Nothing to be done for `install-exec-am'. /bin/mkdir -p '/tmp/buildd/librostlab-blast-1.0.1/debian/tmp/usr/share/doc/librostlab-blast/examples' /usr/bin/install -c -m 644 examples/converged.ali examples/parseblast.cpp '/tmp/buildd/librostlab-blast-1.0.1/debian/tmp/usr/share/doc/librostlab-blast/examples' make[3]: Leaving directory `/tmp/buildd/librostlab-blast-1.0.1' make[2]: Leaving directory `/tmp/buildd/librostlab-blast-1.0.1' make[1]: Leaving directory `/tmp/buildd/librostlab-blast-1.0.1' dh_install -O--parallel dh_installdocs -O--parallel dh_installchangelogs -O--parallel dh_installexamples -O--parallel dh_installman -O--parallel dh_installcatalogs -O--parallel dh_installcron -O--parallel dh_installdebconf -O--parallel dh_installemacsen -O--parallel dh_installifupdown -O--parallel dh_installinfo -O--parallel dh_installinit -O--parallel dh_installmenu -O--parallel dh_installmime -O--parallel dh_installmodules -O--parallel dh_installlogcheck -O--parallel dh_installlogrotate -O--parallel dh_installpam -O--parallel dh_installppp -O--parallel dh_installudev -O--parallel dh_installwm -O--parallel dh_installxfonts -O--parallel dh_installgsettings -O--parallel dh_bugfiles -O--parallel dh_ucf -O--parallel dh_lintian -O--parallel dh_gconf -O--parallel dh_icons -O--parallel dh_perl -O--parallel dh_usrlocal -O--parallel dh_link -O--parallel debian/rules override_dh_compress make[1]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1' dh_compress -Xlibrostlab-blast.tag make[1]: Leaving directory `/tmp/buildd/librostlab-blast-1.0.1' dh_fixperms -O--parallel debian/rules override_dh_strip make[1]: Entering directory `/tmp/buildd/librostlab-blast-1.0.1' dh_strip --dbg-package=librostlab-blast0-dbg make[1]: Leaving directory `/tmp/buildd/librostlab-blast-1.0.1' dh_makeshlibs -O--parallel dh_shlibdeps -O--parallel dh_installdeb -O--parallel dh_gencontrol -O--parallel dpkg-gencontrol: warning: Depends field of package librostlab-blast-doc: unknown substitution variable ${shlibs:Depends} dh_md5sums -O--parallel dh_builddeb -O--parallel dpkg-deb: building package `librostlab-blast0' in `../librostlab-blast0_1.0.1-2_amd64.deb'. dpkg-deb: building package `librostlab-blast0-dev' in `../librostlab-blast0-dev_1.0.1-2_amd64.deb'. dpkg-deb: building package `librostlab-blast-doc' in `../librostlab-blast-doc_1.0.1-2_all.deb'. dpkg-deb: building package `librostlab-blast0-dbg' in `../librostlab-blast0-dbg_1.0.1-2_amd64.deb'. dpkg-genchanges >../librostlab-blast_1.0.1-2_amd64.changes dpkg-genchanges: not including original source code in upload dpkg-source --after-build librostlab-blast-1.0.1 dpkg-buildpackage: binary and diff upload (original source NOT included) I: Copying back the cached apt archive contents I: unmounting dev/pts filesystem I: unmounting run/shm filesystem I: unmounting proc filesystem I: cleaning the build env I: removing directory /var/cache/pbuilder/build//2497 and its subdirectories I: Current time: Wed Mar 27 09:29:32 CET 2013 I: pbuilder-time-stamp: 1364372972 Could not read the .changes file: /sw/debian-med/trunk/packages/rostlab/librostlab-blast/build-area/. rm -rf /sw/debian-med/trunk/packages/rostlab/librostlab-blast/build-area/librostlab-blast-1.0.1