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

+Trying to yum install: EMBOSS


+Trying to build from spec: EMBOSS

make[1]: Entering directory `/usr/src/biopackages'
make[1]: `SPECS/EMBOSS.spec' is up to date.
make[1]: Leaving directory `/usr/src/biopackages'
+Calling parse_req on primer3.

+Cound not yum install: primer3


+Trying to build from spec: primer3

make[1]: Entering directory `/usr/src/biopackages'
cat SPECS/primer3.spec.in | /usr/bin/perl bin/in2spec.pl > SPECS/primer3.spec
make[1]: Leaving directory `/usr/src/biopackages'
+Calling parse_req on gcc.

+Trying to yum install: gcc


+make SPECS/primer3.spec SPECS/primer3.built

make[1]: Entering directory `/usr/src/biopackages'
make[1]: `SPECS/primer3.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/primer3.built
(/usr/bin/rpmbuild -ba SPECS/primer3.spec 2>&1 >> SPECS/primer3.built && \
perl -e '($f,$e,$d,$c,$b,$a)=localtime();print "#rpmbuild end ".join(":",$a+1900,$b,$c,$d,$e,$f),"\n"' >> SPECS/primer3.built) || rm -rf SPECS/primer3.built
+ umask 022
+ cd /usr/src/biopackages/BUILD
+ cd /usr/src/biopackages/BUILD
+ rm -rf primer3_1.0.0
+ /usr/bin/gzip -dc /usr/src/biopackages/SOURCES/primer3_1.0.0.tar.gz
+ tar -xf -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd primer3_1.0.0
++ /usr/bin/id -u
+ '[' 776 = 0 ']'
++ /usr/bin/id -u
+ '[' 776 = 0 ']'
+ /bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ perl -pi -e 's[/usr/local/bin][/usr/bin]g' test/dpal_gen.pl
+ perl -pi -e 's[/usr/local/bin][/usr/bin]g' test/long_seq_tm_test.pl
+ perl -pi -e 's[/usr/bin/perl5][/usr/bin/perl]g' test/dpal_gen.pl
+ perl -pi -e 's[/usr/bin/perl5][/usr/bin/perl]g' test/long_seq_tm_test.pl
+ perl -pi -e 's[/usr/bin/perl][/usr/bin/perl]g' test/dpal_gen.pl
+ perl -pi -e 's[/usr/bin/perl][/usr/bin/perl]g' test/long_seq_tm_test.pl
+ echo 'Patch #0 (primer3.patch):'
+ patch -p1 -s
+ exit 0
+ umask 022
+ cd /usr/src/biopackages/BUILD
+ cd primer3_1.0.0
+ export CC=gcc
+ CC=gcc
+ export 'CFLAGS=-O2 -g -march=i386 -mcpu=i686'
+ CFLAGS=-O2 -g -march=i386 -mcpu=i686
+ export LDLIBS=-lm
+ LDLIBS=-lm
+ cd src
+ make primer3_core
primer3_release.h:3: warning: `pr_release' defined but not used
primer3_release.h:3: warning: `pr_release' defined but not used
primer3_release.h:3: warning: `pr_release' defined but not used
primer3_release.h:3: warning: `pr_release' defined but not used
+ make ntdpal
primer3_release.h:3: warning: `pr_release' defined but not used
+ exit 0
+ umask 022
+ cd /usr/src/biopackages/BUILD
+ cd primer3_1.0.0
+ rm -rf /usr/src/biopackages/tmp/primer3-root
+ install -m 755 -d /usr/src/biopackages/tmp/primer3-root/usr/bin
+ install -m 755 -d /usr/src/biopackages/tmp/primer3-root/usr/share/primer3-1.0.0
+ install -m 755 src/primer3_core /usr/src/biopackages/tmp/primer3-root/usr/bin
+ ln -s /usr/bin/primer3_core /usr/src/biopackages/tmp/primer3-root/usr/bin/primer3
+ install -m 755 src/ntdpal /usr/src/biopackages/tmp/primer3-root/usr/bin
+ cp -pR test /usr/src/biopackages/tmp/primer3-root/usr/share/primer3-1.0.0
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/brp-strip
+ /usr/lib/rpm/brp-strip-static-archive
+ /usr/lib/rpm/brp-strip-comment-note
+ umask 022
+ cd /usr/src/biopackages/BUILD
+ cd primer3_1.0.0
+ DOCDIR=/usr/src/biopackages/tmp/primer3-root/usr/share/doc/primer3-1.0.0
+ export DOCDIR
+ rm -rf /usr/src/biopackages/tmp/primer3-root/usr/share/doc/primer3-1.0.0
+ /bin/mkdir -p /usr/src/biopackages/tmp/primer3-root/usr/share/doc/primer3-1.0.0
+ cp -pr Copyright README example /usr/src/biopackages/tmp/primer3-root/usr/share/doc/primer3-1.0.0
+ cp -pr src/release_notes /usr/src/biopackages/tmp/primer3-root/usr/share/doc/primer3-1.0.0
+ exit 0
+ umask 022
+ cd /usr/src/biopackages/BUILD
+ cd primer3_1.0.0
+ rm -rf /usr/src/biopackages/tmp/primer3-root
+ exit 0
make[1]: Leaving directory `/usr/src/biopackages'

+sudo rpm -Uvh  --oldpackage RPMS/i386/primer3*-1.0.0-1.3.bp.fc2.i386.rpm

Preparing...                ##################################################
primer3                     ##################################################
+Calling parse_req on gd.

+Cound not yum install: gd


+Trying to build from spec: gd

make[1]: Entering directory `/usr/src/biopackages'
cat SPECS/gd.spec.in | /usr/bin/perl bin/in2spec.pl > SPECS/gd.spec
make[1]: Leaving directory `/usr/src/biopackages'
+Calling parse_req on freetype-devel.

+Trying to yum install: freetype-devel

+Calling parse_req on libjpeg-devel.

+Trying to yum install: libjpeg-devel

+Calling parse_req on libpng-devel.

+Trying to yum install: libpng-devel

+Calling parse_req on zlib-devel.

+Trying to yum install: zlib-devel

+Calling parse_req on gd.

+Cound not yum install: gd

+Calling parse_req on perl.

+Trying to yum install: perl

+Calling parse_req on gd.

+Cound not yum install: gd


+make SPECS/gd.spec SPECS/gd.built

make[1]: Entering directory `/usr/src/biopackages'
make[1]: `SPECS/gd.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/gd.built
(/usr/bin/rpmbuild -ba SPECS/gd.spec 2>&1 >> SPECS/gd.built && \
perl -e '($f,$e,$d,$c,$b,$a)=localtime();print "#rpmbuild end ".join(":",$a+1900,$b,$c,$d,$e,$f),"\n"' >> SPECS/gd.built) || rm -rf SPECS/gd.built
+ umask 022
+ cd /usr/src/biopackages/BUILD
+ cd /usr/src/biopackages/BUILD
+ rm -rf gd-2.0.28
+ /usr/bin/gzip -dc /usr/src/biopackages/SOURCES/gd-2.0.28.tar.gz
+ tar -xf -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd gd-2.0.28
++ /usr/bin/id -u
+ '[' 776 = 0 ']'
++ /usr/bin/id -u
+ '[' 776 = 0 ']'
+ /bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ exit 0
+ umask 022
+ cd /usr/src/biopackages/BUILD
+ cd gd-2.0.28
+ CFLAGS=-O2 -g -march=i386 -mcpu=i686
+ export CFLAGS
+ CXXFLAGS=-O2 -g -march=i386 -mcpu=i686
+ export CXXFLAGS
+ FFLAGS=-O2 -g -march=i386 -mcpu=i686
+ export FFLAGS
+ ./configure --host=i686-redhat-linux-gnu --build=i686-redhat-linux-gnu --target=i386-redhat-linux --program-prefix= --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/usr/com --mandir=/usr/share/man --infodir=/usr/share/info --disable-rpath
+ make
+ exit 0
+ umask 022
+ cd /usr/src/biopackages/BUILD
+ cd gd-2.0.28
+ '[' /usr/src/biopackages/tmp/gd-root '!=' / ']'
+ rm -fr /usr/src/biopackages/tmp/gd-root
+ make prefix=/usr/src/biopackages/tmp/gd-root/usr exec_prefix=/usr/src/biopackages/tmp/gd-root/usr bindir=/usr/src/biopackages/tmp/gd-root/usr/bin sbindir=/usr/src/biopackages/tmp/gd-root/usr/sbin sysconfdir=/usr/src/biopackages/tmp/gd-root/etc datadir=/usr/src/biopackages/tmp/gd-root/usr/share includedir=/usr/src/biopackages/tmp/gd-root/usr/include libdir=/usr/src/biopackages/tmp/gd-root/usr/lib libexecdir=/usr/src/biopackages/tmp/gd-root/usr/libexec localstatedir=/usr/src/biopackages/tmp/gd-root/var sharedstatedir=/usr/src/biopackages/tmp/gd-root/usr/com mandir=/usr/src/biopackages/tmp/gd-root/usr/share/man infodir=/usr/src/biopackages/tmp/gd-root/usr/share/info install
libtool: install: warning: remember to run `libtool --finish /usr/lib'
libtool: install: warning: `./libgd.la' has not been installed in `/usr/lib'
libtool: install: warning: `./libgd.la' has not been installed in `/usr/lib'
libtool: install: warning: `./libgd.la' has not been installed in `/usr/lib'
libtool: install: warning: `./libgd.la' has not been installed in `/usr/lib'
libtool: install: warning: `./libgd.la' has not been installed in `/usr/lib'
libtool: install: warning: `./libgd.la' has not been installed in `/usr/lib'
libtool: install: warning: `./libgd.la' has not been installed in `/usr/lib'
libtool: install: warning: `./libgd.la' has not been installed in `/usr/lib'
+ rm -rf /usr/src/biopackages/tmp/gd-root//usr/lib/libgd.la
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/brp-strip
+ /usr/lib/rpm/brp-strip-static-archive
+ /usr/lib/rpm/brp-strip-comment-note
+ umask 022
+ cd /usr/src/biopackages/BUILD
+ cd gd-2.0.28
+ DOCDIR=/usr/src/biopackages/tmp/gd-root/usr/share/doc/gd-2.0.28
+ export DOCDIR
+ rm -rf /usr/src/biopackages/tmp/gd-root/usr/share/doc/gd-2.0.28
+ /bin/mkdir -p /usr/src/biopackages/tmp/gd-root/usr/share/doc/gd-2.0.28
+ cp -pr index.html /usr/src/biopackages/tmp/gd-root/usr/share/doc/gd-2.0.28
+ exit 0
+ umask 022
+ cd /usr/src/biopackages/BUILD
+ cd gd-2.0.28
+ '[' /usr/src/biopackages/tmp/gd-root '!=' / ']'
+ rm -fr /usr/src/biopackages/tmp/gd-root
+ exit 0
make[1]: Leaving directory `/usr/src/biopackages'

+sudo rpm -Uvh  --oldpackage RPMS/i386/gd*-2.0.28-1.2.bp.fc2.i386.rpm

Preparing...                ##################################################
gd                          ##################################################
gd-devel                    ##################################################
gd-progs                    ##################################################
+Calling parse_req on libpng.

+Trying to yum install: libpng

+Calling parse_req on EMBOSS-libs.

+Trying to yum install: EMBOSS-libs


+Trying to build from spec: EMBOSS-libs

make[1]: Entering directory `/usr/src/biopackages'
make[1]: Leaving directory `/usr/src/biopackages'
rm SPECS/EMBOSS.spec