I: using fakeroot in build. Current time: Mon May 25 08:16:13 CEST 2009 pbuilder-time-stamp: 1243232173 Building the build Environment -> extracting base tarball [/home/debomatic/incoming/karmic/karmic] -> creating local configuration -> copying local configuration -> Installing apt-lines -> mounting /proc filesystem -> mounting /dev/pts filesystem -> policy-rc.d already exists Obtaining the cached apt archive contents 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 and should Depends: debhelper (>= 5.0.37.2), r-base-dev (>= 2.9.0), python-all-dev (>= 2.3.5-10), python-numpy, texinfo, texi2html, texlive-base, texlive-latex-base, python-central (>= 0.5) grep: debian/control: No such file or directory /usr/bin/pkgsanitychecks: Error: not in source package directory dpkg-deb: building package `pbuilder-satisfydepends-dummy' in `/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Reading package lists... Building dependency tree... Reading state information... aptitude is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Selecting previously deselected package pbuilder-satisfydepends-dummy. (Reading database ... 10591 files and directories currently installed.) Unpacking pbuilder-satisfydepends-dummy (from .../pbuilder-satisfydepends-dummy.deb) ... dpkg: dependency problems prevent configuration of pbuilder-satisfydepends-dummy: pbuilder-satisfydepends-dummy depends on debhelper (>= 5.0.37.2); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on r-base-dev (>= 2.9.0); however: Package r-base-dev is not installed. pbuilder-satisfydepends-dummy depends on python-all-dev (>= 2.3.5-10); however: Package python-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python-numpy; however: Package python-numpy is not installed. pbuilder-satisfydepends-dummy depends on texinfo; however: Package texinfo is not installed. pbuilder-satisfydepends-dummy depends on texi2html; however: Package texi2html is not installed. pbuilder-satisfydepends-dummy depends on texlive-base; however: Package texlive-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on python-central (>= 0.5); however: Package python-central is not installed. dpkg: error processing pbuilder-satisfydepends-dummy (--install): dependency problems - leaving unconfigured Errors were encountered while processing: pbuilder-satisfydepends-dummy Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... The following NEW packages will be installed: bsdmainutils{a} debhelper{a} defoma{a} dpatch{a} ed{a} file{a} fontconfig{a} fontconfig-config{a} gettext{a} gettext-base{a} gfortran{a} gfortran-4.4{a} groff-base{a} html2text{a} intltool-debian{a} libblas-dev{a} libblas3gf{a} libbz2-dev{a} libcairo2{a} libcroco3{a} libdatrie1{a} libdirectfb-1.0-0{a} libexpat1{a} libfontconfig1{a} libfreetype6{a} libgfortran3{a} libglib2.0-0{a} libice6{a} libicu40{a} libjpeg62{a} libjpeg62-dev{a} libkpathsea4{a} liblapack-dev{a} liblapack3gf{a} libmagic1{a} libncurses5-dev{a} libnewt0.52{a} libpango1.0-0{a} libpango1.0-common{a} libpaper-utils{a} libpaper1{a} libpcre3{a} libpcre3-dev{a} libpcrecpp0{a} libpixman-1-0{a} libpng12-0{a} libpng12-dev{a} libpoppler4{a} libpopt0{a} libpython2.6{a} libreadline5-dev{a} libsm6{a} libsqlite3-0{a} libsysfs2{a} libthai-data{a} libthai0{a} libtiff4{a} libts-0.0-0{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render-util0{a} libxcb-render0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxss1{a} libxt6{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-all{a} python-all-dev{a} python-central{a} python-dev{a} python-numpy{a} python2.5{a} python2.5-dev{a} python2.5-minimal{a} python2.6{a} python2.6-dev{a} r-base-core{a} r-base-dev{a} tcl8.5{a} tex-common{a} texi2html{a} texinfo{a} texlive-base{a} texlive-base-bin{a} texlive-common{a} texlive-doc-base{a} texlive-latex-base{a} tk8.5{a} tsconf{a} ttf-dejavu{a} ttf-dejavu-core{a} ttf-dejavu-extra{a} ucf{a} unzip{a} whiptail{a} x11-common{a} zip{a} zlib1g-dev{a} The following partially installed packages will be configured: pbuilder-satisfydepends-dummy 0 packages upgraded, 110 newly installed, 0 to remove and 0 not upgraded. Need to get 14.5MB/87.5MB of archives. After unpacking 268MB will be used. Writing extended state information... Get:1 http://127.0.0.1 karmic/main zip 3.0-1ubuntu1 [333kB] Get:2 http://127.0.0.1 karmic/main unzip 5.52-12ubuntu1 [170kB] Get:3 http://127.0.0.1 karmic/main libpaper-utils 1.1.23+nmu1 [18.2kB] Get:4 http://127.0.0.1 karmic/main tcl8.5 8.5.7-1 [1582kB] Get:5 http://127.0.0.1 karmic/main tk8.5 8.5.7-1 [1160kB] Get:6 http://127.0.0.1 karmic/universe r-base-core 2.9.0-2 [10.9MB] Get:7 http://127.0.0.1 karmic/universe r-base-dev 2.9.0-2 [3226B] Get:8 http://127.0.0.1 karmic/main texi2html 1.78-1 [345kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 14.5MB in 28s (517kB/s) Selecting previously deselected package libmagic1. (Reading database ... 10591 files and directories currently installed.) Unpacking libmagic1 (from .../libmagic1_5.03-1ubuntu1_amd64.deb) ... Selecting previously deselected package file. 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Setting up gettext-base (0.17-6ubuntu2) ... Setting up gettext (0.17-6ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16) ... Setting up groff-base (1.18.1.1-22build1) ... Setting up bsdmainutils (6.1.10ubuntu4) ... Setting up man-db (2.5.5-1build1) ... Building database of manual pages ... Setting up debhelper (7.2.8ubuntu1) ... Setting up zip (3.0-1ubuntu1) ... Setting up unzip (5.52-12ubuntu1) ... Setting up ucf (3.0018) ... Setting up libpaper1 (1.1.23+nmu1) ... Creating config file /etc/papersize with new version Setting up libpaper-utils (1.1.23+nmu1) ... Setting up libgfortran3 (4.4.0-3ubuntu5) ... Setting up libblas3gf (1.2-2) ... Setting up libsysfs2 (2.1.0-5) ... Setting up tsconf (1.0-7) ... Setting up libts-0.0-0 (1.0-7) ... Setting up libdirectfb-1.0-0 (1.0.1-11ubuntu1) ... Setting up libexpat1 (2.0.1-4) ... Setting up libfreetype6 (2.3.9-4.1) ... Setting up libnewt0.52 (0.52.10-1ubuntu1) ... Setting up libpopt0 (1.14-4) ... Setting up whiptail (0.52.10-1ubuntu1) ... Setting up defoma (0.11.10-0.2ubuntu1) ... Setting up ttf-dejavu-core (2.29-2) ... Setting up ttf-dejavu-extra (2.29-2) ... Setting up ttf-dejavu (2.29-2) ... Setting up fontconfig-config (2.6.0-1ubuntu12) ... Setting up libfontconfig1 (2.6.0-1ubuntu12) ... Setting up libpixman-1-0 (0.14.0-1) ... Setting up libpng12-0 (1.2.35-1) ... Setting up libxau6 (1:1.0.4-2) ... Setting up libxdmcp6 (1:1.0.2-3) ... Setting up libxcb1 (1.2-1ubuntu1) ... Setting up libx11-data (2:1.2.1-1) ... Setting up libx11-6 (2:1.2.1-1) ... Setting up libxcb-render0 (1.2-1ubuntu1) ... Setting up libxcb-render-util0 (0.3.4-1) ... Setting up libxrender1 (1:0.9.4-2) ... Setting up libcairo2 (1.8.6-1ubuntu2) ... Setting up libice6 (2:1.0.5-1) ... Setting up libjpeg62 (6b-14build1) ... Setting up liblapack3gf (3.2.1-1) ... Setting up fontconfig (2.6.0-1ubuntu12) ... Updating font configuration of fontconfig... Cleaning up category cid.. Cleaning up category truetype.. Cleaning up category type1.. Updating category type1.. Updating category truetype.. Updating category cid.. Updating fontconfig cache for /usr/share/fonts/truetype/ttf-dejavu Cleaning up old fontconfig caches... done. Regenerating fonts cache... done. Setting up libpango1.0-common (1.24.2-1ubuntu1) ... Cleaning up font configuration of pango... Updating font configuration of pango... Cleaning up category xfont.. Updating category xfont.. *** You don't have any defomized font packages. *** So we are trying to force to generate pangox.aliases... Setting up libdatrie1 (0.2.2-1) ... Setting up libthai-data (0.1.11-3) ... Setting up libthai0 (0.1.11-3) ... Setting up libxft2 (2.1.13-3ubuntu1) ... Setting up libpango1.0-0 (1.24.2-1ubuntu1) ... Setting up libsm6 (2:1.1.0-2) ... Setting up libtiff4 (3.8.2-11) ... Setting up libxext6 (2:1.0.99.1-0ubuntu3) ... Setting up libxss1 (1:1.1.3-1) ... Setting up libxt6 (1:1.0.5-3ubuntu1) ... Setting up tcl8.5 (8.5.7-1) ... Setting up tk8.5 (8.5.7-1) ... Setting up r-base-core (2.9.0-2) ... Setting R_PAPERSIZE_USER default to 'a4' Creating config file /etc/R/Renviron with new version warning: Configuration file texmf.cnf not found! Searched these directories: /usr/share/texmf/web2c:/usr/share/texmf-texlive/web2c:/usr/local/share/texmf/web2c Trying to proceed... texhash: Done. Setting up gfortran-4.4 (4.4.0-3ubuntu5) ... Setting up gfortran (4:4.4.0-3ubuntu1) ... Setting up libblas-dev (1.2-2) ... Setting up liblapack-dev (3.2.1-1) ... Setting up libncurses5-dev (5.7+20090502-1ubuntu1) ... Setting up libreadline5-dev (5.2-4) ... Setting up libjpeg62-dev (6b-14build1) ... Setting up libpcrecpp0 (7.8-2ubuntu1) ... Setting up libpcre3-dev (7.8-2ubuntu1) ... Setting up zlib1g-dev (1:1.2.3.3.dfsg-13ubuntu1) ... Setting up libpng12-dev (1.2.35-1) ... Setting up libbz2-dev (1.0.5-1ubuntu1) ... Setting up dpatch (2.0.31) ... Setting up r-base-dev (2.9.0-2) ... Setting up mime-support (3.44-1) ... 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Creating config file /etc/texmf/texmf.d/05TeXMF.cnf with new version Creating config file /etc/texmf/texmf.d/15Plain.cnf with new version Creating config file /etc/texmf/texmf.d/45TeXinputs.cnf with new version Creating config file /etc/texmf/texmf.d/55Fonts.cnf with new version Creating config file /etc/texmf/texmf.d/65BibTeX.cnf with new version Creating config file /etc/texmf/texmf.d/75DviPS.cnf with new version Creating config file /etc/texmf/texmf.d/85Misc.cnf with new version Creating config file /etc/texmf/texmf.d/90TeXDoc.cnf with new version Creating config file /etc/texmf/texmf.d/95NonPath.cnf with new version Creating config file /etc/texmf/updmap.d/00updmap.cfg with new version Creating config file /etc/texmf/texmf.cnf with new version Running mktexlsr. This may take some time... done. Running updmap-sys. This may take some time... done. Building format(s) --all. This may take some time... done. Setting up texlive-common (2007.dfsg.2-4) ... Setting up texlive-doc-base (2007.dfsg.2-2) ... Running mktexlsr. This may take some time... done. Setting up ed (0.7-3ubuntu1) ... Setting up libkpathsea4 (2007.dfsg.2-6ubuntu1) ... Setting up libpoppler4 (0.10.6-1ubuntu1) ... Setting up libxmu6 (2:1.0.4-1build1) ... Setting up libxpm4 (1:3.5.7-1build1) ... Setting up libxaw7 (2:1.0.5-2) ... Setting up texlive-base-bin (2007.dfsg.2-6ubuntu1) ... Running mktexlsr. This may take some time... done. Building format(s) --all. This may take some time... done. Setting up texlive-base (2007.dfsg.2-4) ... Running mktexlsr. This may take some time... done. Building format(s) --all. 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. Setting up texlive-latex-base (2007.dfsg.2-4) ... 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. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Processing triggers for libc6 ... ldconfig deferred processing now taking place 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... pkgbinarymangler is already the newest version. pkg-create-dbgsym is already the newest version. 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 0B/117kB of archives. After this operation, 455kB of additional disk space will be used. Selecting previously deselected package fakeroot. (Reading database ... 22671 files and directories currently installed.) Unpacking fakeroot (from .../fakeroot_1.12.1ubuntu1_amd64.deb) ... Processing triggers for man-db ... Setting up fakeroot (1.12.1ubuntu1) ... Copying back the cached apt archive contents -> new cache content libpaper-utils_1.1.23+nmu1_amd64.deb added -> new cache content texi2html_1.78-1_all.deb added -> new cache content tcl8.5_8.5.7-1_amd64.deb added -> new cache content zip_3.0-1ubuntu1_amd64.deb added -> new cache content unzip_5.52-12ubuntu1_amd64.deb added -> new cache content tk8.5_8.5.7-1_amd64.deb added -> new cache content r-base-core_2.9.0-2_amd64.deb added -> new cache content r-base-dev_2.9.0-2_all.deb added Copying source file -> copying [/home/debomatic/incoming/rpy_1.0.3-7ubuntu1.dsc] -> copying [/home/debomatic/incoming/rpy_1.0.3.orig.tar.gz] -> copying [/home/debomatic/incoming/rpy_1.0.3-7ubuntu1.diff.gz] Extracting source gpg: new configuration file `/tmp/buildd/.gnupg/gpg.conf' created gpg: WARNING: options in `/tmp/buildd/.gnupg/gpg.conf' are not yet active during this run gpg: Signature made Mon May 25 06:14:55 2009 UTC using DSA key ID DCFC3FD0 gpg: Can't check signature: public key not found dpkg-source: extracting rpy in rpy-1.0.3 dpkg-source: info: unpacking rpy_1.0.3.orig.tar.gz dpkg-source: info: applying rpy_1.0.3-7ubuntu1.diff.gz -> Building the package dpkg-buildpackage: set CFLAGS to default value: -g -O2 dpkg-buildpackage: set CPPFLAGS to default value: dpkg-buildpackage: set LDFLAGS to default value: -Wl,-Bsymbolic-functions dpkg-buildpackage: set FFLAGS to default value: -g -O2 dpkg-buildpackage: set CXXFLAGS to default value: -g -O2 dpkg-buildpackage: source package rpy dpkg-buildpackage: source version 1.0.3-7ubuntu1 dpkg-buildpackage: source changed by Alessio Treglia dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh_testdir dh_testroot rm -f build-stamp configure-stamp [ ! -f Makefile ] || /usr/bin/make distclean (cd doc/ && make clean && rm -vf manual.pdf manual.info manual.dvi \ && rm -vfr manual_html manual_html.tgz) make[1]: Entering directory `/tmp/buildd/rpy-1.0.3/doc' rm -f rpy.cp rpy.cps rpy.fn rpy.fns rpy.ky rm -f rpy.kys rpy.log rpy.pg rpy.pgs rpy.tmp rm -f rpy.toc rpy.tp rpy.tps rpy.vr rpy.vrs rm -f rpy.aux make[1]: Leaving directory `/tmp/buildd/rpy-1.0.3/doc' for python in python2.5 python2.6; \ do $python setup.py clean; \ done RHOMES= [] DEBUG= False Setting RHOMES to ['/usr/lib64/R'] ### Using R verion 2.9.0 installed at /usr/lib64/R ### RHOME= /usr/lib64/R copying src/rpymodule.c -> src/rpymodule2090.c copying src/R_eval.c -> src/R_eval2090.c copying src/io.c -> src/io2090.c running clean RHOMES= [] DEBUG= False Setting RHOMES to ['/usr/lib64/R'] ### Using R verion 2.9.0 installed at /usr/lib64/R ### RHOME= /usr/lib64/R copying src/rpymodule.c -> src/rpymodule2090.c copying src/R_eval.c -> src/R_eval2090.c copying src/io.c -> src/io2090.c running clean rm -f `find . -name "*~"` rm -rf debian/tmp debian/files* core debian/substvars rm -f doc/html/function.html doc/html/packages.html rm -f doc/rpy.dvi doc/rpy.pdf doc/rpy_html.tgz rm -f config.cache config.status rm -rf build/* rm -rf rpy_version.pyc rpy_tools.pyc rm -rf doc/rpy_html/*.html doc/rpy.info dh_clean dpkg-source -b rpy-1.0.3 dpkg-source: info: using source format `1.0' dpkg-source: info: building rpy using existing rpy_1.0.3.orig.tar.gz dpkg-source: info: building rpy in rpy_1.0.3-7ubuntu1.diff.gz dpkg-source: warning: file rpy-1.0.3/debian/overrides has no final newline (either original or modified version) dpkg-source: info: building rpy in rpy_1.0.3-7ubuntu1.dsc debian/rules build dh_testdir touch configure-stamp dh_testdir for python in python2.5 python2.6; \ do CFLAGS="-O2 -Wall" $python setup.py build \ build_ext --include-dirs=/usr/share/R/include ; \ done RHOMES= [] DEBUG= False Setting RHOMES to ['/usr/lib64/R'] ### Using R verion 2.9.0 installed at /usr/lib64/R ### RHOME= /usr/lib64/R copying src/rpymodule.c -> src/rpymodule2090.c copying src/R_eval.c -> src/R_eval2090.c copying src/io.c -> src/io2090.c running build running build_py creating build creating build/lib.linux-x86_64-2.5 copying rpy.py -> build/lib.linux-x86_64-2.5 copying rpy_io.py -> build/lib.linux-x86_64-2.5 copying rpy_version.py -> build/lib.linux-x86_64-2.5 copying rpy_tools.py -> build/lib.linux-x86_64-2.5 copying rpy_options.py -> build/lib.linux-x86_64-2.5 copying rpy_wintools.py -> build/lib.linux-x86_64-2.5 running build_ext building '_rpy2090' extension creating build/temp.linux-x86_64-2.5 creating build/temp.linux-x86_64-2.5/src gcc -pthread -fno-strict-aliasing -DNDEBUG -O3 -Wall -O2 -Wall -fPIC -DWITH_NUMERIC=3 -DPY_ARRAY_TYPES_PREFIX=PyArray_ -DRPY_SHNAME=_rpy2090 -DINIT_RPY=init_rpy2090 -UPRE_2_2 -I/usr/lib64/R/include -Isrc -I/usr/share/R/include -I/usr/lib/python2.5/site-packages/numpy/core/include -I/usr/share/R/include -I/usr/include/python2.5 -c src/rpymodule2090.c -o build/temp.linux-x86_64-2.5/src/rpymodule2090.o -shared -llapack src/rpymodule2090.c:1565: warning: initialization from incompatible pointer type src/rpymodule2090.c:1568: warning: 'intargfunc' is deprecated src/rpymodule2090.c:1568: warning: initialization from incompatible pointer type src/rpymodule2090.c:1569: warning: 'intintargfunc' is deprecated src/rpymodule2090.c:1569: warning: initialization from incompatible pointer type src/rpymodule2090.c:1570: warning: initialization from incompatible pointer type gcc -pthread -fno-strict-aliasing -DNDEBUG -O3 -Wall -O2 -Wall -fPIC -DWITH_NUMERIC=3 -DPY_ARRAY_TYPES_PREFIX=PyArray_ -DRPY_SHNAME=_rpy2090 -DINIT_RPY=init_rpy2090 -UPRE_2_2 -I/usr/lib64/R/include -Isrc -I/usr/share/R/include -I/usr/lib/python2.5/site-packages/numpy/core/include -I/usr/share/R/include -I/usr/include/python2.5 -c src/R_eval2090.c -o build/temp.linux-x86_64-2.5/src/R_eval2090.o -shared -llapack /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:958: warning: '_import_array' defined but not used gcc -pthread -fno-strict-aliasing -DNDEBUG -O3 -Wall -O2 -Wall -fPIC -DWITH_NUMERIC=3 -DPY_ARRAY_TYPES_PREFIX=PyArray_ -DRPY_SHNAME=_rpy2090 -DINIT_RPY=init_rpy2090 -UPRE_2_2 -I/usr/lib64/R/include -Isrc -I/usr/share/R/include -I/usr/lib/python2.5/site-packages/numpy/core/include -I/usr/share/R/include -I/usr/include/python2.5 -c src/io2090.c -o build/temp.linux-x86_64-2.5/src/io2090.o -shared -llapack /usr/lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_api.h:958: warning: '_import_array' defined but not used gcc -pthread -fno-strict-aliasing -DNDEBUG -O3 -Wall -O2 -Wall -fPIC -DWITH_NUMERIC=3 -DPY_ARRAY_TYPES_PREFIX=PyArray_ -DRPY_SHNAME=_rpy2090 -DINIT_RPY=init_rpy2090 -UPRE_2_2 -I/usr/lib64/R/include -Isrc -I/usr/share/R/include -I/usr/lib/python2.5/site-packages/numpy/core/include -I/usr/share/R/include -I/usr/include/python2.5 -c src/setenv.c -o build/temp.linux-x86_64-2.5/src/setenv.o -shared -llapack gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -O2 -Wall build/temp.linux-x86_64-2.5/src/rpymodule2090.o build/temp.linux-x86_64-2.5/src/R_eval2090.o build/temp.linux-x86_64-2.5/src/io2090.o build/temp.linux-x86_64-2.5/src/setenv.o -L/usr/lib64/R/bin -L/usr/lib64/R/lib -Wl,-R/usr/lib64/R/bin -Wl,-R/usr/lib64/R/lib -lR -o build/lib.linux-x86_64-2.5/_rpy2090.so RHOMES= [] DEBUG= False Setting RHOMES to ['/usr/lib64/R'] ### Using R verion 2.9.0 installed at /usr/lib64/R ### RHOME= /usr/lib64/R copying src/rpymodule.c -> src/rpymodule2090.c copying src/R_eval.c -> src/R_eval2090.c copying src/io.c -> src/io2090.c running build running build_py creating build/lib.linux-x86_64-2.6 copying rpy.py -> build/lib.linux-x86_64-2.6 copying rpy_io.py -> build/lib.linux-x86_64-2.6 copying rpy_version.py -> build/lib.linux-x86_64-2.6 copying rpy_tools.py -> build/lib.linux-x86_64-2.6 copying rpy_options.py -> build/lib.linux-x86_64-2.6 copying rpy_wintools.py -> build/lib.linux-x86_64-2.6 running build_ext building '_rpy2090' extension creating build/temp.linux-x86_64-2.6 creating build/temp.linux-x86_64-2.6/src gcc -pthread -fno-strict-aliasing -DNDEBUG -O3 -Wall -O2 -Wall -fPIC -DWITH_NUMERIC=3 -DPY_ARRAY_TYPES_PREFIX=PyArray_ -DRPY_SHNAME=_rpy2090 -DINIT_RPY=init_rpy2090 -UPRE_2_2 -I/usr/lib64/R/include -Isrc -I/usr/share/R/include -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/share/R/include -I/usr/include/python2.6 -c src/rpymodule2090.c -o build/temp.linux-x86_64-2.6/src/rpymodule2090.o -shared -llapack src/rpymodule2090.c:1565: warning: initialization from incompatible pointer type src/rpymodule2090.c:1568: warning: 'intargfunc' is deprecated src/rpymodule2090.c:1568: warning: initialization from incompatible pointer type src/rpymodule2090.c:1569: warning: 'intintargfunc' is deprecated src/rpymodule2090.c:1569: warning: initialization from incompatible pointer type src/rpymodule2090.c:1570: warning: initialization from incompatible pointer type gcc -pthread -fno-strict-aliasing -DNDEBUG -O3 -Wall -O2 -Wall -fPIC -DWITH_NUMERIC=3 -DPY_ARRAY_TYPES_PREFIX=PyArray_ -DRPY_SHNAME=_rpy2090 -DINIT_RPY=init_rpy2090 -UPRE_2_2 -I/usr/lib64/R/include -Isrc -I/usr/share/R/include -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/share/R/include -I/usr/include/python2.6 -c src/R_eval2090.c -o build/temp.linux-x86_64-2.6/src/R_eval2090.o -shared -llapack /usr/lib/python2.6/dist-packages/numpy/core/include/numpy/__multiarray_api.h:958: warning: '_import_array' defined but not used gcc -pthread -fno-strict-aliasing -DNDEBUG -O3 -Wall -O2 -Wall -fPIC -DWITH_NUMERIC=3 -DPY_ARRAY_TYPES_PREFIX=PyArray_ -DRPY_SHNAME=_rpy2090 -DINIT_RPY=init_rpy2090 -UPRE_2_2 -I/usr/lib64/R/include -Isrc -I/usr/share/R/include -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/share/R/include -I/usr/include/python2.6 -c src/io2090.c -o build/temp.linux-x86_64-2.6/src/io2090.o -shared -llapack /usr/lib/python2.6/dist-packages/numpy/core/include/numpy/__multiarray_api.h:958: warning: '_import_array' defined but not used gcc -pthread -fno-strict-aliasing -DNDEBUG -O3 -Wall -O2 -Wall -fPIC -DWITH_NUMERIC=3 -DPY_ARRAY_TYPES_PREFIX=PyArray_ -DRPY_SHNAME=_rpy2090 -DINIT_RPY=init_rpy2090 -UPRE_2_2 -I/usr/lib64/R/include -Isrc -I/usr/share/R/include -I/usr/lib/python2.6/dist-packages/numpy/core/include -I/usr/share/R/include -I/usr/include/python2.6 -c src/setenv.c -o build/temp.linux-x86_64-2.6/src/setenv.o -shared -llapack gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -O2 -Wall build/temp.linux-x86_64-2.6/src/rpymodule2090.o build/temp.linux-x86_64-2.6/src/R_eval2090.o build/temp.linux-x86_64-2.6/src/io2090.o build/temp.linux-x86_64-2.6/src/setenv.o -L/usr/lib64/R/bin -L/usr/lib64/R/lib -Wl,-R/usr/lib64/R/bin -Wl,-R/usr/lib64/R/lib -lR -o build/lib.linux-x86_64-2.6/_rpy2090.so (cd doc && make all) make[1]: Entering directory `/tmp/buildd/rpy-1.0.3/doc' tex rpy.texi This is TeX, Version 3.141592 (Web2C 7.5.6) (./rpy.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, localization, formatting, and turning on texinfo input format.) (./defs.texi) (./rpy.tmp) (./rpy.tmp) [1] [2] [-1] Chapter 1 (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) Cross reference values unknown; you must run TeX again. (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) Chapter 2 [1] (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) [2] Chapter 3 [3] (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) [4] (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) [5] (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) [6] (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) [7] (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) [8] (./rpy.tmp) Chapter 4 [9] (./rpy.tmp) (./rpy.tmp) [10] (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) [11] (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) [12] (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) [13] (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) [14] (./rpy.tmp) (./rpy.tmp) [15] (./rpy.tmp) [16] Chapter 5 [17] (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) [18] Chapter 6 [19] Underfull \hbox (badness 10000) in paragraph at lines 1337--1342 []@textrm The rea-son for not do-ing @texttt 'class' in r.attributes(robj)[] @ textrm is that (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) [20] Chapter 7 [21] (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) [22] (./rpy.tmp) Chapter 8 [23] (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) (./rpy.tmp) [24] ) (see the transcript file for additional information) Output written on rpy.dvi (27 pages, 57184 bytes). Transcript written on rpy.log. tex rpy.texi This is TeX, Version 3.141592 (Web2C 7.5.6) (./rpy.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, localization, formatting, and turning on texinfo input format.) 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Transcript written on rpy.log. makeinfo rpy.texi makeinfo rpy.texi makeinfo --html rpy.texi makeinfo --html rpy.texi rm -rf rpy_html mv rpy rpy_html pdftex rpy.texi This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) %&-line parsing enabled. entering extended mode (./rpy.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, localization, formatting, and turning on texinfo input format.) (./rpy.aux) (./defs.texi) [1{/var/lib/tex mf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./rpy.toc) [-1] (./rpy.toc) (./rpy.toc) Chapter 1 Chapter 2 [1] [2] Chapter 3 [3] [4] [5] [6] [7] [8] Chapter 4 [9] [10] [11] [12] [13] [14] [15] [16] Chapter 5 [17] [18] Chapter 6 [19] Underfull \hbox (badness 10000) in paragraph at lines 1337--1342 []@textrm The rea-son for not do-ing @texttt 'class' in r.attributes(robj)[] @ textrm is that [20] Chapter 7 [21] [22] Chapter 8 [23] [24] ) (see the transcript file for additional information) Output written on rpy.pdf (27 pages, 156559 bytes). Transcript written on rpy.log. pdftex rpy.texi This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) %&-line parsing enabled. entering extended mode (./rpy.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, localization, formatting, and turning on texinfo input format.) (./rpy.aux) (./defs.texi) [1{/var/lib/tex mf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./rpy.toc) [-1] (./rpy.toc) (./rpy.toc) Chapter 1 Chapter 2 [1] [2] Chapter 3 [3] [4] [5] [6] [7] [8] Chapter 4 [9] [10] [11] [12] [13] [14] [15] [16] Chapter 5 [17] [18] Chapter 6 [19] Underfull \hbox (badness 10000) in paragraph at lines 1337--1342 []@textrm The rea-son for not do-ing @texttt 'class' in r.attributes(robj)[] @ textrm is that [20] Chapter 7 [21] [22] Chapter 8 [23] [24] ) (see the transcript file for additional information) Output written on rpy.pdf (27 pages, 156559 bytes). Transcript written on rpy.log. tar -cvzf rpy_html.tgz rpy_html rpy_html/ rpy_html/Class-conversion.html rpy_html/R-objects-look-up.html rpy_html/Calling-R-objects.html rpy_html/Basic-conversion.html rpy_html/R-to-Python.html rpy_html/Proc-conversion.html rpy_html/Conversion-system.html rpy_html/Small-example.html rpy_html/Acknowledgements.html rpy_html/No-conversion.html rpy_html/R-exceptions.html rpy_html/Sequence-protocol.html rpy_html/R-boolean-objects.html rpy_html/Interface-description.html rpy_html/Robj-type.html rpy_html/Starting-up.html rpy_html/To-do.html rpy_html/Miscellaneous.html rpy_html/DataFrame-class.html rpy_html/Notes.html rpy_html/Installation.html rpy_html/Caveat-and-bugs.html rpy_html/Overview.html rpy_html/Modes.html rpy_html/Invocation.html rpy_html/Vector-conversion.html rpy_html/Enhanced-Robj.html rpy_html/Contact-info-and-contributing.html rpy_html/Input_002fOutput-functions.html rpy_html/index.html rpy_html/Methods-of-Robj-type.html rpy_html/Python-to-R.html rpy_html/Useful-examples.html make[1]: Leaving directory `/tmp/buildd/rpy-1.0.3/doc' touch build-stamp fakeroot debian/rules binary dh_testdir dh_testroot dh_clean -k dh_installdirs for python in python2.5 python2.6; \ do $python setup.py install --root=debian/python-rpy; \ done RHOMES= [] DEBUG= False Setting RHOMES to ['/usr/lib64/R'] ### Using R verion 2.9.0 installed at /usr/lib64/R ### RHOME= /usr/lib64/R copying src/rpymodule.c -> src/rpymodule2090.c copying src/R_eval.c -> src/R_eval2090.c copying src/io.c -> src/io2090.c running install running build running build_py running build_ext running install_lib creating debian/python-rpy/usr creating debian/python-rpy/usr/lib creating debian/python-rpy/usr/lib/python2.5 creating debian/python-rpy/usr/lib/python2.5/site-packages copying build/lib.linux-x86_64-2.5/_rpy2090.so -> debian/python-rpy/usr/lib/python2.5/site-packages copying build/lib.linux-x86_64-2.5/rpy_io.py -> debian/python-rpy/usr/lib/python2.5/site-packages copying build/lib.linux-x86_64-2.5/rpy_tools.py -> debian/python-rpy/usr/lib/python2.5/site-packages copying build/lib.linux-x86_64-2.5/rpy_wintools.py -> debian/python-rpy/usr/lib/python2.5/site-packages copying build/lib.linux-x86_64-2.5/rpy.py -> debian/python-rpy/usr/lib/python2.5/site-packages copying build/lib.linux-x86_64-2.5/rpy_options.py -> debian/python-rpy/usr/lib/python2.5/site-packages copying build/lib.linux-x86_64-2.5/rpy_version.py -> debian/python-rpy/usr/lib/python2.5/site-packages byte-compiling debian/python-rpy/usr/lib/python2.5/site-packages/rpy_io.py to rpy_io.pyc byte-compiling debian/python-rpy/usr/lib/python2.5/site-packages/rpy_tools.py to rpy_tools.pyc byte-compiling debian/python-rpy/usr/lib/python2.5/site-packages/rpy_wintools.py to rpy_wintools.pyc byte-compiling debian/python-rpy/usr/lib/python2.5/site-packages/rpy.py to rpy.pyc byte-compiling debian/python-rpy/usr/lib/python2.5/site-packages/rpy_options.py to rpy_options.pyc byte-compiling debian/python-rpy/usr/lib/python2.5/site-packages/rpy_version.py to rpy_version.pyc running install_egg_info Writing debian/python-rpy/usr/lib/python2.5/site-packages/rpy-1.0.3.egg-info RHOMES= [] DEBUG= False Setting RHOMES to ['/usr/lib64/R'] ### Using R verion 2.9.0 installed at /usr/lib64/R ### RHOME= /usr/lib64/R copying src/rpymodule.c -> src/rpymodule2090.c copying src/R_eval.c -> src/R_eval2090.c copying src/io.c -> src/io2090.c running install running build running build_py running build_ext running install_lib creating debian/python-rpy/usr/local creating debian/python-rpy/usr/local/lib creating debian/python-rpy/usr/local/lib/python2.6 creating debian/python-rpy/usr/local/lib/python2.6/dist-packages copying build/lib.linux-x86_64-2.6/_rpy2090.so -> debian/python-rpy/usr/local/lib/python2.6/dist-packages copying build/lib.linux-x86_64-2.6/rpy_io.py -> debian/python-rpy/usr/local/lib/python2.6/dist-packages copying build/lib.linux-x86_64-2.6/rpy_tools.py -> debian/python-rpy/usr/local/lib/python2.6/dist-packages copying build/lib.linux-x86_64-2.6/rpy_wintools.py -> debian/python-rpy/usr/local/lib/python2.6/dist-packages copying build/lib.linux-x86_64-2.6/rpy.py -> debian/python-rpy/usr/local/lib/python2.6/dist-packages copying build/lib.linux-x86_64-2.6/rpy_options.py -> debian/python-rpy/usr/local/lib/python2.6/dist-packages copying build/lib.linux-x86_64-2.6/rpy_version.py -> debian/python-rpy/usr/local/lib/python2.6/dist-packages byte-compiling debian/python-rpy/usr/local/lib/python2.6/dist-packages/rpy_io.py to rpy_io.pyc byte-compiling debian/python-rpy/usr/local/lib/python2.6/dist-packages/rpy_tools.py to rpy_tools.pyc byte-compiling debian/python-rpy/usr/local/lib/python2.6/dist-packages/rpy_wintools.py to rpy_wintools.pyc byte-compiling debian/python-rpy/usr/local/lib/python2.6/dist-packages/rpy.py to rpy.pyc byte-compiling debian/python-rpy/usr/local/lib/python2.6/dist-packages/rpy_options.py to rpy_options.pyc byte-compiling debian/python-rpy/usr/local/lib/python2.6/dist-packages/rpy_version.py to rpy_version.pyc running install_egg_info Writing debian/python-rpy/usr/local/lib/python2.6/dist-packages/rpy-1.0.3.egg-info install -d /tmp/buildd/rpy-1.0.3/debian/python-rpy/usr/share/lintian/overrides install -m 0644 debian/overrides /tmp/buildd/rpy-1.0.3/debian/python-rpy/usr/share/lintian/overrides/python-rpy dh_testdir -i dh_testroot -i dh_installdocs -i dh_installdocs -ppython-rpy-doc NEWS README TODO \ doc/rpy.pdf doc/rpy_html/ dh_installdirs -ppython-rpy-doc usr/share/info/ install -m 0644 doc/rpy.info \ /tmp/buildd/rpy-1.0.3/debian/python-rpy-doc/usr/share/info/rpy.info dh_installexamples -ppython-rpy-doc examples/* tests/ chmod -R 0644 debian/python-rpy-doc/usr/share/doc/python-rpy-doc/examples/ dh_installchangelogs -i dh_link -i dh_compress -i dh_fixperms -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i warning, `debian/python-rpy-doc/DEBIAN/control' contains user-defined field `Original-Maintainer' dpkg-deb: ignoring 1 warnings about the control file(s) dpkg-deb: building package `python-rpy-doc' in `../python-rpy-doc_1.0.3-7ubuntu1_all.deb'. dh_testdir -a dh_testroot -a dh_installdocs -a dh_installexamples -a dh_installchangelogs -a dh_strip -a dh_strip debug symbol extraction: all non-arch-all packages for this build platform amd64: python-rpy dh_strip debug symbol extraction: packages to act on: python-rpy dh_strip debug symbol extraction: ignored packages: dpkg-gencontrol: warning: unknown substitution variable ${python:Versions} warning, `/tmp/buildd/rpy-1.0.3/debian/python-rpy-dbgsym/DEBIAN/control' contains user-defined field `Original-Maintainer' dpkg-deb: ignoring 1 warnings about the control file(s) dpkg-deb: building package `python-rpy-dbgsym' in `../python-rpy-dbgsym_1.0.3-7ubuntu1_amd64.ddeb'. dh_link -a dh_compress -a dh_fixperms -a dh_pycentral -a renaming debian/python-rpy/usr/local/lib/python2.6/dist-packages to debian/python-rpy/usr/lib/python2.6/dist-packages diff debian/python-rpy/usr/lib/python2.6/dist-packages debian/python-rpy/usr/lib/python2.5/site-packages Differing files : ['_rpy2090.so'] dh_shlibdeps -a dpkg-shlibdeps: warning: dependency on libpthread.so.0 could be avoided if "debian/python-rpy/usr/lib/python2.6/dist-packages/_rpy2090.so debian/python-rpy/usr/lib/python2.5/site-packages/_rpy2090.so" were not uselessly linked against it (they use none of its symbols). dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a warning, `debian/python-rpy/DEBIAN/control' contains user-defined field `Original-Maintainer' warning, `debian/python-rpy/DEBIAN/control' contains user-defined field `Python-Version' dpkg-deb: ignoring 2 warnings about the control file(s) dpkg-deb: building package `python-rpy' in `../python-rpy_1.0.3-7ubuntu1_amd64.deb'. dpkg-genchanges >../rpy_1.0.3-7ubuntu1_amd64.changes dpkg-genchanges: not including original source code in upload dpkg-buildpackage: binary and diff upload (original source NOT included) Copying back the cached apt archive contents -> unmounting dev/pts filesystem -> unmounting proc filesystem -> cleaning the build env -> removing directory /home/debomatic/incoming/karmic/build/7773 and its subdirectories Current time: Mon May 25 08:18:45 CEST 2009 pbuilder-time-stamp: 1243232325