Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
cat SPECS/AmiGO.spec.in | /usr/bin/perl bin/in2spec.pl > SPECS/AmiGO.spec
echo 'spec=SPECS/AmiGO; spec=${spec#SPECS/}; perl bin/resolve_deps.pl --verbose --spec $spec' | /bin/bash
+Calling parse_req on AmiGO.

+Cound not yum install: AmiGO


RESOLVE_DEPS: BUILD COMPLETE!


RESOLVE_DEPS: MISSING REQS:
sudo rpm -e perl-Template-Toolkit-2.15-1.el4.rf postgresql-libs-7.4.16-1.RHEL4.1 docbook-dtds-1.0-25 perl-XML-LibXML-1.58-1 ncbi-ePCR-2.3.4-1.5.bp.centos4 libRmath-2.5.1-1.el4.rf perl-XML-LibXML-Common-0.13-7 rpm-build-4.3.3-22_nonptl genome-Hsa-17-1.1.bp.centos4 perl-GraphViz-2.02-1.2.el4.rf perl-IO-stringy-2.110-1.2.el4.rf netcdf-devel-3.5.1-1.1.bp.centos4 perl-Bio-PrimerDesigner-0.01-1.3.bp.centos4 libtiff-devel-3.6.1-12 perl-libxml-perl-0.07-30 blastGraphic-Hsa-0.01-1.4.bp.centos4 esound-0.2.35-2 perl-Win32-ODBC-1.0-1.2.bp.centos4 perl-HTML-Parser-3.35-6 php-4.3.9-3.22.5 R-affyio-1.4.1-1.5.bp.centos4 ImageMagick-perl-6.0.7.1-17 perl-Digest-SHA1-2.07-5 mod_perl-devel-2.0.1-1.3.bp.centos4 divx4linux-5.0.5-1.4.bp.centos4 sgml-common-0.6.3-17 perl-XML-XPath-1.13-2.2.el4.rf xorg-x11-xfs-6.8.2-1.EL.13.37.7 rrdtool-devel-1.2.23-1.el4.rf ncbi-2.2.8-1.3.bp.centos4 libvorbis-1.1.0-1 R-2.5.0-1.16.bp.centos4 ucsc-456-1.3.bp.centos4 fftw-2.1.5-4.2.el4.rf R-R.native-0.1.2-1.1.bp.centos4 perl-WeakRef-0.01-1.1.bp.centos4 ncbi-devel-2.2.8-1.3.bp.centos4 rpm-4.3.3-22_nonptl perl-GSSAPI-0.23-1.el4.rf libpng-1.2.7-3.el4 perl-SQL-Translator-0.07-1.4.bp.centos4 perl-Class-Data-Inheritable-0.06-1.el4.rf perl-Statistics-Descriptive-2.6-1.2.el4.rf tetex-2.0.2-22.EL4.7 audiofile-devel-0.2.6-1.el4.1 gdbm-devel-1.8.0-24 perl-Class-Trigger-0.10-1.2.el4.rf python-2.3.4-14.3 perl-Clone-0.22-1.el4.rf ucsc-blat-456-1.3.bp.centos4 perl-Class-AutoClass-0.09-1.2.bp.centos4 apr-util-0.9.4-21 shared-mime-info-0.15-10 divx4linux-devel-5.0.5-1.4.bp.centos4 perl-Cache-Cache-1.05-1.el4.rf xerces-c-devel-2.7.0-1.2.el4.rf R-devel-2.5.0-1.16.bp.centos4 libtool-libs-1.5.6-4.EL4.1.c4.4 tetex-dvips-2.0.2-22.EL4.7 dialog-1.0.20040731-3 gcc-objc-3.4.6-8 gcc-java-3.4.6-8 expat-devel-1.95.7-4 db4-devel-4.2.52-7.1 perl-Graph-0.20105-1.2.el4.rf GConf2-2.8.1-1 texinfo-4.7-5.el4.2 libf2c-3.4.6-8 gnome-vfs2-2.8.2-8.2 perl-XML-Parser-2.34-5 qt-3.3.3-10.RHEL4 httpd-suexec-2.0.52-32.2.ent.centos4 perl-Text-Iconv-1.4-1.2.el4.rf R-annotate-1.12.1-1.2.bp.centos4 perl-SVG-2.33-1.2.el4.rf clucene-core-devel-0.9.16a-1.7.bp.centos4 unzip-5.51-9.EL4.5 R-Bioconductor-Rdbi-1.4.0-1.4.bp.centos4 perl-Class-DBI-Plugin-Type-0.02-1.1.bp.centos4 perl-UNIVERSAL-moniker-0.08-1.1.bp.centos4 genome-Sce-S228C-1.6.bp.centos4 clucene-core-0.9.16a-1.7.bp.centos4 libogg-1.1.2-1 apr-0.9.4-24.5.c4.2 perl-Lucene-0.02-1.5.bp.centos4 perl-Text-TabularDisplay-1.20-1.2.bp.centos4 SDL-devel-1.2.7-8 perl-Test-Base-0.52-1.el4.rf kernel-devel-2.6.9-42.EL chkfontpath-1.10.0-2 perl-Text-Shellwords-1.08-1.2.el4.rf perl-Math-Derivative-0.01-1.2.el4.rf xorg-x11-font-utils-6.8.2-1.EL.13.37.7 perl-Class-DBI-Pager-0.06-1.5.bp.centos4 perl-Text-RecordParser-0.08-1.3.bp.centos4 php-pear-4.3.9-3.22.5 primer3-1.0.0-1.3.bp.centos4 R-R.cache-0.1.4-1.2.bp.centos4 xerces-c-2.7.0-1.2.el4.rf esound-devel-0.2.35-2 rsync-2.6.9-1.el4.rf libvorbis-devel-1.1.0-1 perl-OLE-Storage_Lite-0.14-1.2.el4.rf libxml2-devel-2.6.16-10 alsa-lib-1.0.6-5.RHEL4 audit-libs-1.0.15-3.EL4 openssl-devel-0.9.7a-43.16 perl-Parse-RecDescent-1.94-1.el4.rf perl-Jcode-2.06-1.el4.rf perl-String-CRC32-1.4-1.el4.rf perl-Module-Build-0.2806-2.el4.rf perl-Class-DBI-Pg-0.08-1.7.bp.centos4 mysql-devel-4.1.20-2.RHEL4.1 autoconf-2.59-5 faac-1.25-2.el4.rf R-R.rsp-0.3.0-1.2.bp.centos4 biopackages-1.0.1-1.16 atk-1.8.0-2 perl-XML-DOM-XPath-0.13-1.el4.rf pkgconfig-0.15.0-3 perl-WWW-Mechanize-1.20-1.el4.rf perl-Log-Dispatch-2.11-1.7.bp.centos4 pam-devel-0.77-66.17 perl-File-HomeDir-0.62-1.el4.rf pcre-devel-4.5-3.2.RHEL4 perl-XML-NamespaceSupport-1.08-6 memcached-1.2.1-3.el4.rf R-R.oo-1.2.5-1.5.bp.centos4 t1lib-5.1.0-1.el4.rf gbrowse-1.62-1.3.bp.centos4 perl-SVG-Graph-0.01-1.3.bp.centos4 perl-XML-SAX-Writer-0.50-1.el4.rf perl-XML-Simple-2.16-1.el4.rf chado-schema-0.003-1.2.bp.centos4 libbonobo-2.8.0-2 perl-DBI-1.47-1.8.bp.centos4 urw-fonts-2.2-6.1 tetex-latex-2.0.2-22.EL4.7 perl-DBD-Pg-1.49-1.9.bp.centos4 perl-Apache-ParseFormData-0.09-1.6.bp.centos4 postgresql-server-7.4.16-1.RHEL4.1 libbonoboui-2.8.0.99cvs20040929-2 textpresso-1.0.0-1.10.bp.centos4 openldap-devel-2.2.13-7.4E ggv-2.8.0-1 pango-1.6.0-9 perl-Ima-DBI-0.34-1.2.el4.rf R-Bioconductor-Biobase-1.8.0-1.6.bp.centos4 perl-Spreadsheet-WriteExcel-2.17-1.el4.rf R-R.huge-0.1.2-1.2.bp.centos4 turnkey-1.3-1.22.bp.centos4 tcl-8.4.7-2 flex-2.5.4a-33 libmp4v2-1.5.0.1-3.el4.rf perl-Data-Stag-0.10-1.2.el4.rf perl-Unicode-Map-0.112-0.2.el4.rf perl-XML-SAX-0.12-7 gtk2-2.4.13-19 libevent-1.3b-1.el4.rf perl-XML-RegExp-0.03-1.2.el4.rf openjade-1.3.2-14 php-devel-4.3.9-3.22.5 perl-Module-Install-0.64-1.el4.rf qt-devel-3.3.3-10.RHEL4 automake14-1.4p6-12 e2fsprogs-devel-1.35-12.4.EL4 gnome-keyring-0.4.0-1 libgcc-3.4.6-3.1 perl-Class-MakeMethods-1.01-1.2.el4.rf perl-TimeDate-1.16-1.2.el4.rf lftp-3.5.10-1.el4.rf ImageMagick-6.0.7.1-17 curl-devel-7.12.1-11.el4 glibc-devel-2.3.4-2.25 perl-GD-2.30-2.2.el4.rf libidn-devel-0.5.6-1 genome-Sce-ePCR-S228C-1.6.bp.centos4 perl-PlRPC-0.2018-1.2.el4.rf perl-bioperl-1.5-1.9.bp.centos4 R-affxparser-1.7.5-1.4.bp.centos4 python-devel-2.3.4-14.3 perl-XML-XQL-0.68-1.2.el4.rf perl-Digest-HMAC-1.01-13 libogg-devel-1.1.2-1 readline-devel-4.3-13 ucsc-cgi-456-1.3.bp.centos4 postgresql-devel-7.4.16-1.RHEL4.1 freetype-2.1.9-6.el4 libmng-1.0.8-1 perl-Mail-Sender-0.8.13-1.el4.rf cracklib-dicts-2.8.9-1.3 java-1.4.2-gcj-compat-1.4.2.0-27jpp rrdtool-1.2.23-1.el4.rf apt-0.5.15lorg3.2-1.el4.rf perl-Bio-Das-1.00-1.5.bp.centos4 perl-Net-Jabber-2.0-1.2.el4.rf netcdf-3.5.1-1.1.bp.centos4 perl-bioperl-db-0.01-1.3.bp.centos4 R-RSQLite-0.4.20-1.4.bp.centos4 perl-MIME-Lite-3.01-2.2.el4.rf gcc-3.4.6-8 perl-Class-Accessor-0.30-1.el4.rf python-elementtree-1.2.6-7.el4.rf faad2-2.5-2.el4.rf libobjc-3.4.6-8 perl-Parse-Yapp-1.05-32 firefox-1.5.0.5-0.el4.1.centos4 libstdc++-3.4.6-3.1 curl-7.12.1-11.el4 tetex-fonts-2.0.2-22.EL4.7 libglade2-2.4.0-5 postgresql-7.4.16-1.RHEL4.1 perl-rrdtool-1.2.23-1.el4.rf R-DBI-0.1.12-1.4.bp.centos4 swftools-0.8.1-1.el4.rf perl-Text-Reform-1.11-1.2.el4.rf perl-SOAP-Lite-0.69-1.el4.rf perl-YAML-0.62-1.el4.rf perl-XML-XPathEngine-0.05-1.el4.rf perl-Mail-Sendmail-0.79-1.2.el4.rf perl-Ace-1.89-1.2.bp.centos4 perl-Params-Validate-0.86-1.el4.rf perl-XML-Stream-1.22-1.2.el4.rf perl-Authen-SASL-2.10-1.el4.rf libgnomeui-2.8.0-1 mod_perl-2.0.1-1.3.bp.centos4 intltool-0.31.2-1 perl-Heap-0.71-1.2.el4.rf SDL-1.2.7-8 glibc-headers-2.3.4-2.25 libtool-1.5.6-4.EL4.1.c4.4 perl-XML-Filter-BufferText-1.01-1.2.el4.rf libmng-devel-1.0.8-1 ORBit2-2.12.0-3 perl-IPC-Run-0.80-1.el4.rf xorg-x11-libs-6.8.2-1.EL.13.37.7 tk-devel-8.4.7-2 psutils-1.17-23 openldap-2.2.13-7.4E genome-Hsa-blast-17-1.1.bp.centos4 faad2-devel-2.5-2.el4.rf blas-3.0-25.1 perl-Text-Autoformat-1.13-1.2.el4.rf mtr-0.72-1.el4.rf zlib-devel-1.2.1.2-1.2 bison-1.875c-2 VFlib2-2.25.6-25 libgnome-2.8.0-2 perl-IPC-ShareLite-0.09-2.2.el4.rf faac-devel-1.25-2.el4.rf perl-XML-Twig-3.13-6 genome-Hsa-nib-17-1.1.bp.centos4 perl-Tree-DAG_Node-1.05-1.2.el4.rf tcl-devel-8.4.7-2 libIDL-0.8.4-1.centos4 perl-BSD-Resource-1.28-1.el4.rf libart_lgpl-2.3.16-3 genome-Sce-nib-S228C-1.6.bp.centos4 perl-XML-DOM-1.44-1.el4.rf perl-Class-DBI-ConceptSearch-0.04-1.3.bp.centos4 libgcj-3.4.6-3 perl-Compress-Zlib-1.42-1.el4.rf perl-Log-Dispatch-FileRotate-1.16-1.el4.rf httpd-2.0.52-32.2.ent.centos4 perl-Spiffy-0.30-1.el4.rf nvidia-x11-drv-1.0.9755-1.nodist.rf graphviz-2.2-1.2.el4.rf gd-devel-2.0.28-5.4E netpbm-progs-10.25-2.EL4.3 fftw3-devel-3.1.1-1.3.bp.centos4 gcc-g77-3.4.6-8 perl-AppConfig-1.64-1.el4.rf perl-Apache2-SOAP-0.72-1.2.bp.centos4 compat-libstdc++-296-2.96-132.7.2 netpbm-10.25-2.EL4.3 perl-Spreadsheet-ParseExcel-0.2603-1.2.bp.centos4 perl-Error-0.17008-1.el4.rf fftw-devel-2.1.5-4.2.el4.rf R-Biobase-1.14.0-1.4.bp.centos4 pam-0.77-66.21 perl-Tk-804.027-3.2.el4.rf lame-3.97-1.el4.rf xml-common-0.6.3-17 libgcj-devel-3.4.6-3 freetype-devel-2.1.9-6.el4 perl-XML-LibXSLT-1.62-1.el4.rf perl-Math-Spline-0.01-1.2.el4.rf perl-Net-XMPP-1.0-1.2.el4.rf krb5-libs-1.3.4-46 mx-2.0.5-3 perl-Data-Page-2.00-1.1.bp.centos4 ghostscript-fonts-5.50-13 perl-XML-Writer-0.602-1.el4.rf blastGraphic-0.01-1.4.bp.centos4 perl-Class-Base-0.03-1.2.bp.centos4 perl-FreezeThaw-0.43-1.2.el4.rf cpp-3.4.6-8 perl-MailTools-1.74-1.el4.rf R-genefilter-1.12.0-1.4.bp.centos4 fftw3-3.1.1-1.3.bp.centos4 genome-Sce-blast-S228C-1.6.bp.centos4 httpd-devel-2.0.52-28.ent.centos4 cups-libs-1.1.22-0.rc1.9.18 perl-HTML-Tagset-3.03-30 perl-Algorithm-Diff-1.1902-1.el4.rf cracklib-2.8.9-1.3 perl-Net-Daemon-0.39-1.el4.rf perl-XML-Checker-0.13-1.1.bp.centos4 R-R.utils-0.8.8-1.5.bp.centos4 automake-1.9.2-3 openssl-0.9.7a-43.16 scrollkeeper-0.3.14-3 gnome-mime-data-2.4.1-5 gcc-c++-3.4.6-8 libstdc++-devel-3.4.6-3.1 libungif-4.1.3-1.el4.2 libjpeg-devel-6b-33 perl-IPC-Shareable-0.60-1.2.el4.rf perl-PDF-Create-0.01-1.2.bp.centos4 libxslt-devel-1.1.11-1 rpm-python-4.3.3-22_nonptl initscripts-7.93.29.EL-1.centos4 perl-Time-HiRes-1.55-3 perl-libwww-perl-5.79-5 perl-Class-DBI-0.96-1.4.bp.centos4 perl-Sub-Uplevel-0.14-1.el4.rf libidn-0.5.6-1 fontconfig-devel-2.2.3-7.centos4 gamin-0.1.1-4.EL4 dkms-2.0.13-1.el4.rf perl-Test-Exception-0.24-1.el4.rf perl-IO-String-1.08-1.2.el4.rf apr-devel-0.9.4-24.5.c4.2 gnuplot-4.0.0-4 gd-progs-2.0.28-5.4E mysql-4.1.20-2.RHEL4.1 gd-2.0.28-5.4E perl-Apache-Session-1.81-1.el4.rf krb5-devel-1.3.4-46 alsa-lib-devel-1.0.6-5.RHEL4 ghostscript-7.07-33 perl-MLDBM-2.01-2.2.el4.rf libxml2-2.6.16-10 ttmkfdir-3.0.9-14.1.EL libf2c-3.4.6-3 xvidcore-devel-1.1.3-1.el4.rf libgnomecanvas-2.8.0-1 libgcc-3.4.6-8 cyrus-sasl-devel-2.1.19-5.EL4 xorg-x11-devel-6.8.2-1.EL.13.37 tk-8.4.7-2 audiofile-0.2.6-1.el4.1 libtermcap-devel-2.0.8-39 xvidcore-1.1.3-1.el4.rf genome-Sce-annotation-gene-S228C-1.6.bp.centos4 perl-Pod-POM-0.17-1.2.el4.rf R-RColorBrewer-0.2.3-1.2.bp.centos4 blastGraphic-Sce-0.01-1.4.bp.centos4 libpng-devel-1.2.7-3.el4 perl-Log-Log4perl-0.51-1.5.bp.centos4 apr-util-devel-0.9.4-21 perl-Text-Diff-0.35-1.2.el4.rf perl-URI-1.30-4 perl-Test-Differences-0.47-1.2.el4.rf glibc-kernheaders-2.4-9.1.98.EL
touch SPECS/AmiGO.rbuilt
rm SPECS/AmiGO.spec