Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. cat SPECS/R.spec.in | /usr/bin/perl bin/in2spec.pl > SPECS/R.spec echo 'spec=SPECS/R; spec=${spec#SPECS/}; perl bin/resolve_deps.pl --verbose --spec $spec' | /bin/bash +Calling parse_req on R. +Cound not yum install: R +Trying to build from spec: R make[1]: Entering directory `/usr/src/biopackages' make[1]: `SPECS/R.spec' is up to date. make[1]: Leaving directory `/usr/src/biopackages' +Calling parse_req on gcc-c++. +Trying to yum install: gcc-c++ +Calling parse_req on gcc-objc. +Trying to yum install: gcc-objc +Calling parse_req on libpng-devel. +Trying to yum install: libpng-devel +Calling parse_req on libjpeg-devel. +Trying to yum install: libjpeg-devel +Calling parse_req on readline-devel. +Trying to yum install: readline-devel +Calling parse_req on libtermcap-devel. +Trying to yum install: libtermcap-devel +Calling parse_req on tetex-latex. +Trying to yum install: tetex-latex +Calling parse_req on tcl-devel. +Trying to yum install: tcl-devel +Calling parse_req on tk-devel. +Trying to yum install: tk-devel +Calling parse_req on R. +Cound not yum install: R +Calling parse_req on gcc-c++. +Trying to yum install: gcc-c++ +Previously yum installed +Calling parse_req on libpng-devel. +Trying to yum install: libpng-devel +Previously yum installed +Calling parse_req on libjpeg-devel. +Trying to yum install: libjpeg-devel +Previously yum installed +Calling parse_req on readline-devel. +Trying to yum install: readline-devel +Previously yum installed +Calling parse_req on libtermcap-devel. +Trying to yum install: libtermcap-devel +Previously yum installed +Calling parse_req on tetex-latex. +Trying to yum install: tetex-latex +Previously yum installed +Calling parse_req on texinfo. +Trying to yum install: texinfo +Calling parse_req on tcl-devel. +Trying to yum install: tcl-devel +Previously yum installed +Calling parse_req on tk-devel. +Trying to yum install: tk-devel +Previously yum installed +Calling parse_req on libRmath. +Trying to yum install: libRmath +make SPECS/R.spec SPECS/R.built make[1]: Entering directory `/usr/src/biopackages' make[1]: `SPECS/R.spec' is up to date. perl -e '($f,$e,$d,$c,$b,$a)=localtime();print "#rpmbuild begin ".join(":",$a+1900,$b,$c,$d,$e,$f),"\n"' > SPECS/R.built (/usr/bin/rpmbuild -ba SPECS/R.spec 2>&1 >> SPECS/R.built && \ perl -e '($f,$e,$d,$c,$b,$a)=localtime();print "#rpmbuild end ".join(":",$a+1900,$b,$c,$d,$e,$f),"\n"' >> SPECS/R.built) || rm -rf SPECS/R.built error: File /usr/src/biopackages/SOURCES/R-2.5.1.tar.gz: No such file or directory make[1]: Leaving directory `/usr/src/biopackages' RESOLVE_DEPS: BUILD COMPLETE! RESOLVE_DEPS: MISSING REQS: +tetex-latex +gcc-objc +libRmath +tcl-devel +readline-devel +libpng-devel +libjpeg-devel +libtermcap-devel +gcc-c++ +texinfo +tk-devel sudo rpm -e xmms-devel-1.2.10-25.fc5 perl-AppConfig-1.65-1.fc5.rf perl-Ima-DBI-0.35-1.fc5.rf php-devel-5.1.2-5 R-RColorBrewer-0.2.3-1.2.bp.fc5 perl-Path-Class-0.16-1.fc5.rf ant-trax-1.6.5-1jpp_7fc perl-Test-Deep-0.096-1.fc5.rf netcdf-devel-3.6.1-2.fc5 python-devel-2.4.2-3.2.1 scrollkeeper-0.3.14-5.2.1 perl-Convert-ASN1-0.19-1.2 gnu-crypto-2.1.0-1jpp_2fc libmng-1.0.9-3.2.1 gnome-keyring-0.4.9-1 gamin-0.1.7-1.2.1 perl-DBD-SQLite-1.13-1.fc5.rf perl-Carp-Assert-0.20-1.fc5.rf perl-Class-C3-XS-0.06-1.fc5 perl-ExtUtils-ParseXS-2.18-1.fc5.rf tetex-3.0-17 libid3tag-0.15.1b-3.fc5.rf ant-antlr-1.6.5-1jpp_7fc ant-apache-regexp-1.6.5-1jpp_7fc xml-commons-apis-1.3.02-0.b2.7jpp_7fc Rex-1.0-1.4.bp.fc5 perl-DateTime-Format-W3CDTF-0.04-1.fc5.rf perl-Graph-0.81-1.fc5.rf cdrecord-2.01.01.0.a03-3 perl-XML-RSS-Parser-4.0-1.2.fc5.rf perl-Text-CSV_XS-0.23-4.fc5 perl-Log-Log4perl-1.10-1.fc5 xvidcore-devel-1.1.2-1.fc5.rf ant-junit-1.6.5-1jpp_7fc perl-Digest-HMAC-1.01-14.2 perl-GD-2.35-1.fc5 esound-devel-0.2.36-2.2.1 netcdf-3.5.1-1.2.bp.fc5 perl-Tree-DAG_Node-1.05-3.fc5 perl-Config-IniFiles-2.39-4.fc5 libgomp-4.1.0-3 perl-Module-Loaded-0.01-1.fc5 rrdtool-1.2.23-3.fc5 curl-7.15.1-1.2.1 antlr-2.7.4-2jpp_6fc perl-RPM-Perlonly-1.0.1-1.2.fc5.rf avahi-0.6.9-3 perl-XML-LibXSLT-1.62-1.fc5.rf SDL-1.2.9-5.2.1 perl-Spiffy-0.30-5.fc5 perl-MailTools-1.77-1.fc5.rf gcc-4.1.0-3 gnome-mime-data-2.4.2-1.2.1 gcc-c++-4.1.0-3 faac-devel-1.25-2.fc5.rf jakarta-commons-discovery-0.3-1jpp_3fc perl-YAML-0.62-1.fc5.rf java-1.4.2-gcj-compat-devel-1.4.2.0-40jpp_83rh perl-Module-CoreList-2.11-1.fc5.rf perl-Authen-SASL-2.10-1.fc5.rf divx4linux-5.0.5-1.4.bp.fc5 perl-Time-modules-2003.1126-3.fc5 perl-Object-Signature-1.05-1.fc5.rf alsa-lib-1.0.11-3.rc2.2 perl-Tie-IxHash-1.21-5.fc5 tcl-8.4.12-4 perl-Class-Inspector-1.16-1.fc5.rf cups-libs-1.1.23-30.2 perl-Test-Tester-0.104-1.fc5.rf bsf-2.3.0-6jpp_3fc perl-Log-Dispatch-2.15-2.fc5 libgnomecanvas-2.14.0-1 jakarta-commons-el-1.0-4jpp_6fc perl-IPC-Run-0.80-1.fc5.rf bcel-5.1-1jpp_6fc perl-IO-String-1.08-1.2.fc5.rf junit-3.8.1-3jpp_7fc oro-2.0.8-1jpp_4fc faad2-devel-2.0-8.fc5.rf perl-HTTP-Server-Simple-0.27-1.fc5.rf perl-version-0.69-1.fc5 perl-Devel-CoreStack-1.3-1.2.fc5.rf mikmod-3.1.6-36.2.1 dialog-1.0.20051107-1.2.1 libSM-devel-1.0.0-2.2 docbook-dtds-1.0-30 id3lib-devel-3.8.3-15.fc5 httpd-devel-2.2.0-5.1.2 perl-Test-Base-0.53-1.fc5.rf wsdl4j-1.5.1-1jpp_4fc perl-Object-Accessor-0.32-1.fc5.rf tomcat5-servlet-2.4-api-5.5.15-1jpp_6fc libX11-devel-1.0.0-3 perl-Feed-Find-0.06-1.2.fc5.rf perl-Heap-0.71-2.fc5 esound-0.2.36-2.2.1 perl-GDTextUtil-0.86-7.fc5 id3lib-3.8.3-15.fc5 perl-Log-Dispatch-FileRotate-1.16-1.fc5.rf ghostscript-8.15.1-7 perl-Class-Singleton-1.03-1.1.bp.fc5 byacc-1.9-29.2.1 perl-XML-LibXML-Common-0.13-8.2.1 tetex-fonts-3.0-17 xmms-1.2.10-25.fc5 startup-notification-0.8-3.2.1 R-Bioconductor-Biobase-1.8.0-1.8.bp.fc5 ant-jsch-1.6.5-1jpp_7fc perl-XML-Stream-1.22-5.fc5 perl-Digest-SHA1-2.11-1.2 libgfortran-4.1.0-3 a52dec-0.7.4-8.fc5.rf edb-1.0.5.007-1.fc5 libXtst-1.0.1-1.2 perl-DBIx-DBSchema-0.32-1.fc5.rf eclipse-platform-3.1.2-1jpp_13fc lcms-1.15-1.2.1 java-1.4.2-gcj-compat-javadoc-1.4.2.0-40jpp_83rh xml-commons-resolver-1.1-1jpp_8fc perl-XML-Feed-0.12-1.9.bp.fc5 hmmer-2.3.2-5.fc5 perl-Tree-Simple-VisitorFactory-0.10-2.fc5 curl-devel-7.15.1-1.2.1 perl-Text-Iconv-1.4-4.fc5 perl-Template-Toolkit-2.18-1.fc5 perl-GraphViz-2.02-2.fc5 ImageMagick-perl-6.2.5.4-4.2.1 jakarta-commons-logging-1.0.4-2jpp_10fc ant-jdepend-1.6.5-1jpp_7fc cups-1.1.23-30.2 ghostscript-fonts-5.50-13.1 libtermcap-devel-2.0.8-45 libwmf-0.2.8.4-4.2 gcc-objc-4.1.0-3 firefox-1.5.0.1-9 perl-XML-DOM-XPath-0.13-1.fc5.rf perl-XML-Twig-3.23-1 perl-Crypt-SSLeay-0.51-9.2.2 libXinerama-devel-1.0.1-1.2 perl-MP3-Info-1.22-1.fc5.rf perl-Statistics-Descriptive-2.6-1.2.fc5.rf perl-IPC-ShareLite-0.09-7.fc5 perl-Math-Spline-0.01-1.2.fc5.rf avahi-glib-0.6.9-3 jakarta-commons-daemon-1.0-2jpp_4fc perl-UNIVERSAL-require-0.11-1.fc5.rf ant-apache-oro-1.6.5-1jpp_7fc ant-commons-logging-1.6.5-1jpp_7fc gnome-menus-2.13.5-5.2 desktop-backgrounds-basic-2.0-31 perl-Data-Visitor-0.05-2.fc5 perl-Module-Load-0.10-1.2.fc5.rf rrdtool-devel-1.2.23-3.fc5 t1lib-devel-5.1.0-9.fc5 gnuplot-4.0.0-11 perl-Test-use-ok-0.02-3.fc5 x264-devel-0.0.0-0.3.20061214.fc5.rf tomcat5-jasper-5.5.15-1jpp_6fc gmp-4.1.4-6.2.1 mkisofs-2.01.01.0.a03-3 perl-WWW-Search-2.494-1.fc5.rf ucsc-456-1.3.bp.fc5 automake-1.9.6-2 libXpm-devel-3.5.4.2-2.2 cpp-4.1.0-3 jakarta-commons-launcher-0.9-3jpp_3fc glibc-devel-2.4-4 perl-Parse-Yapp-1.05-35.fc5 ant-1.6.5-1jpp_7fc intltool-0.34.2-1.1 nspr-4.6.1-2.2 apr-util-devel-1.2.2-4.2 perl-Mail-Sender-0.8.13-1.fc5.rf perl-DateTime-Format-Mail-0.30-3.fc5 cyrus-sasl-devel-2.1.21-10 libtool-1.5.22-2.2 ncbi-devel-2.2.8-1.3.bp.fc5 perl-FreezeThaw-0.43-4.fc5 lame-devel-3.97-1.fc5.rf faac-1.25-2.fc5.rf perl-URI-Fetch-0.08-1.1.bp.fc5 perl-Class-XPath-1.4-1.2.fc5.rf perl-IPC-Run3-0.036-1.fc5.rf perl-SVG-2.33-2.fc5 clucene-core-devel-0.9.16a-1.7.bp.fc5 libdca-0.0.2-4.fc5.rf perl-Cache-Memcached-1.18-1.1.bp.fc5 perl-XML-Elemental-2.0-1.fc5.rf libXext-devel-1.0.0-3.2 nautilus-cd-burner-2.14.0.1-1 mysql-5.0.18-2.1 qt-devel-3.3.5-13 dbus-python-0.61-3 gnome-vfs2-2.14.0-1 perl-File-Copy-Recursive-0.33-1.fc5.rf libxslt-1.1.15-1.2.1 qt-3.3.5-13 ffmpeg-0.4.9-0.7.20061215.fc5.rf ant-apache-bsf-1.6.5-1jpp_7fc xmms-libs-1.2.10-25.fc5 perl-LWP-Authen-Wsse-0.05-1.2.fc5.rf perl-MLDBM-2.01-4.fc5 zlib-devel-1.2.3-1.2.1 jpackage-utils-1.6.6-1jpp_2rh geronimo-specs-compat-1.0-0.M2.2jpp_7fc perl-Archive-Extract-0.22-1.fc5.rf jakarta-commons-beanutils-1.7.0-2jpp_6fc classpathx-jaf-1.0-2jpp_5fc glib-devel-1.2.10-18.2.2 perl-Algorithm-C3-0.07-1.fc5.rf perl-Pod-Simple-3.05-1.fc5.rf nss-3.11-4 perl-Tree-Simple-1.17-1.fc5.rf gnome-desktop-2.14.0-1 perl-HTTP-Body-0.9-1.fc5.rf lucene-1.4.3-1jpp_11fc ant-apache-bcel-1.6.5-1jpp_7fc xorg-x11-proto-devel-7.0-6 R-Bioconductor-Rdbi-1.4.0-1.4.bp.fc5 openjade-1.3.2-23.2 ncbi-2.2.8-1.3.bp.fc5 perl-Class-Data-Accessor-0.04001-1.fc5 perl-Params-Check-0.26-1.fc5.rf netpbm-10.31-4 evince-0.5.1-3 perl-Module-ScanDeps-0.74-1.fc5.rf R-R.native-0.1.2-1.1.bp.fc5 libtiff-devel-3.7.4-3.2.1 perl-enum-1.016-1.2.fc5.rf R-affyio-1.4.1-1.5.bp.fc5 perl-Locale-Maketext-Simple-0.18-1.fc5.rf libgcj-devel-4.1.0-3 libXft-devel-2.1.8.2-3.2 libvorbis-devel-1.1.2-1.2 binutils-2.16.91.0.6-4 perl-IPC-Cmd-0.36-1.fc5.rf libXi-devel-1.0.0-2.2 t1lib-5.1.0-9.fc5 perl-Cache-Cache-1.05-1.fc5.rf ant-apache-log4j-1.6.5-1jpp_7fc jzlib-1.0.5-2jpp_2fc libidn-0.6.2-1.1 perl-Module-Pluggable-Fast-0.18-1.2.fc5.rf perl-Set-Object-1.18-1.fc5.rf libjpeg-devel-6b-36.2.1 perl-Devel-Symdump-2.06-1.fc5.rf perl-File-Modified-0.07-4.fc5 perl-Test-Manifest-1.17-1.fc5.rf perl-Term-ProgressBar-2.09-2.fc5 jakarta-commons-modeler-1.1-4jpp_6fc xml-common-0.6.3-17.1 perl-UNIVERSAL-isa-0.06-1.fc5.rf lucene-demo-1.4.3-1jpp_11fc libXdmcp-devel-1.0.0-2.2 log4j-1.2.8-7jpp_8fc gail-1.8.11-1 perl-Test-LongString-0.11-1.fc5.rf perl-UNIVERSAL-can-1.12-1.fc5.rf mx4j-3.0.1-1jpp_9fc shared-mime-info-0.16.cvs20060212-3 perl-Apache-Session-1.81-1.fc5.rf xalan-j2-2.6.0-3jpp_9fc perl-Text-SimpleTable-0.03-2.fc5 libgnome-2.14.0-1 perl-Class-ErrorHandler-0.01-2.fc5 perl-Carp-Assert-More-1.12-2.fc5 perl-HTML-Tree-3.23-1.fc5 perl-Statistics-Distributions-1.02-1.2.fc5.rf tetex-dvips-3.0-17 texinfo-4.8-9.2 jdepend-2.6-2jpp_4fc.1.1 perl-Net-Daemon-0.43-1.fc5.rf pam-devel-0.99.3.0-2 perl-Term-UI-0.14-1.fc5.rf gjdoc-0.7.7-3.1 perl-Package-Constants-0.01-1.fc5.rf automake14-1.4p6-12.1 perl-File-Slurp-9999.12-1.fc5.rf hicolor-icon-theme-0.9-2 perl-libxml-perl-0.08-1.2 libswt3-gtk2-3.1.2-1jpp_13fc libXau-devel-1.0.0-2.2 libidn-devel-0.6.2-1.1 ucsc-cgi-456-1.3.bp.fc5 perl-Jcode-2.06-1.fc5.rf perl-Text-Shellwords-1.08-1.2.fc5.rf perl-Test-MockObject-1.07-1.fc5.rf libmad-0.15.1b-4.fc5.rf audiofile-0.2.6-2.2.1 libXt-devel-1.0.0-2.2 nautilus-2.14.0-1 pcre-devel-6.3-1.2.1 perl-Class-Data-Inheritable-0.06-1.fc5.rf krb5-devel-1.4.3-4.1 db4-devel-4.3.29-2 glib-1.2.10-18.2.2 libvorbis-1.1.2-1.2 perl-ExtUtils-CBuilder-0.19-1.fc5.rf perl-Math-Derivative-0.01-2.fc5 perl-File-HomeDir-0.62-1.fc5.rf perl-Class-C3-0.18-1.fc5 ImageMagick-6.2.5.4-4.2.1 perl-Net-SSLeay-1.30-3.fc5 libICE-devel-1.0.0-2.2 perl-XML-Simple-2.14-2.2.fc5.rf jakarta-commons-pool-1.2-2jpp_4fc libgnomeui-2.14.0-1 perl-Class-WhiteHole-0.04-1.2.fc5.rf gcc-gfortran-4.1.0-3 libXrender-devel-0.9.0.2-3.2 perl-HTTP-Request-AsCGI-0.5-2.fc5 libbeagle-0.2.2-3 perl-GSSAPI-0.23-1.fc5.rf perl-Log-Message-0.01-2.2.fc5.rf R-R.utils-0.8.8-1.5.bp.fc5 imlib2-devel-1.3.0-3.fc5 perl-JSON-Any-1.08-1.6.bp.fc5 perl-Module-Build-0.2808-1.fc5.rf libsndfile-1.0.15-1.fc5 jessie-1.0.1-3 ldapjdk-4.17-1jpp_3fc.1.1 libXcursor-devel-1.1.5.2-2.2 gdk-pixbuf-0.22.0-22 perl-Sub-Uplevel-0.14-1.fc5.rf ffmpeg-devel-0.4.9-0.7.20061215.fc5.rf xvidcore-1.1.2-1.fc5.rf poppler-0.5.1-2 perl-XML-XQL-0.68-2.fc5.rf jsch-0.1.18-1jpp_7fc bison-2.1-1.2.1 perl-Inline-0.44-15.2 php-5.1.2-5 tomcat5-5.5.15-1jpp_6fc affyfile-2-1.10.bp.fc5 R-R.huge-0.1.2-1.2.bp.fc5 libRmath-2.5.0-3.fc5 fftw3-devel-3.1.1-1.3.bp.fc5 perl-Class-Base-0.03-2.fc5 perl-Text-TabularDisplay-1.22-3.fc5 jakarta-commons-fileupload-1.0-3jpp_5fc libstdc++-devel-4.1.0-3 perl-Lucene-0.02-1.5.bp.fc5 ant-javamail-1.6.5-1jpp_7fc perl-Net-XMPP-1.02-2.fc5 perl-XML-SAX-Writer-0.50-2.fc5 perl-PlRPC-0.2020-1.fc5.rf R-R.rsp-0.3.0-1.2.bp.fc5 gnome-icon-theme-2.14.1-1 perl-Class-MethodMaker-2.08-2 tomcat5-server-lib-5.5.15-1jpp_6fc audiofile-devel-0.2.6-2.2.1 jakarta-commons-dbcp-1.2.1-3jpp_3fc R-genefilter-1.12.0-1.5.bp.fc5 perl-Time-Piece-1.11-1.fc5.rf memcached-1.1.12-2.fc5.rf gsm-devel-1.0.12-3.fc5 libdaemon-0.10-3.1 tcl-devel-8.4.12-4 perl-Spreadsheet-WriteExcel-2.18-1.fc5.rf jakarta-commons-digester-1.7-2jpp_10fc libcroco-0.6.1-1 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