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'
+ CFLAGS='-O2 -g'
+ export LDLIBS=-lm
+ LDLIBS=-lm
+ cd src
+ make primer3_core
primer3_main.c: In function ‘boulder_print_oligos’:
primer3_main.c:2172: warning: comparisons like X<=Y<=Z do not have their mathematical meaning
primer3_main.c: In function ‘align’:
primer3_main.c:2344: warning: pointer targets in passing argument 1 of ‘dpal’ differ in signedness
primer3_main.c:2344: warning: pointer targets in passing argument 2 of ‘dpal’ differ in signedness
primer3_main.c: In function ‘choose_pair’:
primer3_main.c:1350: warning: ‘n_int’ may be used uninitialized in this function
primer3_release.h:3: warning: ‘pr_release’ defined but not used
primer3_release.h:3: warning: ‘pr_release’ defined but not used
dpal.c: In function ‘dpal_set_ambiguity_code_matrix’:
dpal.c:156: warning: pointer targets in initialization differ in signedness
dpal.c:157: warning: pointer targets in initialization differ in signedness
dpal.c:161: warning: pointer targets in assignment differ in signedness
dpal.c:167: warning: pointer targets in assignment differ in signedness
dpal.c: In function ‘dpal’:
dpal.c:241: warning: passing argument 2 of ‘illegal_char’ from incompatible pointer type
dpal.c:242: warning: passing argument 2 of ‘illegal_char’ from incompatible pointer type
dpal.c:245: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
dpal.c:246: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
dpal.c: In function ‘_dpal_generic’:
dpal.c:542: warning: pointer targets in passing argument 1 of ‘print_align’ differ in signedness
dpal.c:542: warning: pointer targets in passing argument 2 of ‘print_align’ differ in signedness
dpal.c: At top level:
primer3_release.h:3: warning: ‘pr_release’ defined but not used
format_output.c: In function ‘print_summary’:
format_output.c:128: warning: passing argument 4 of ‘print_pair_array’ from incompatible pointer type
format_output.c:129: warning: passing argument 4 of ‘print_pair_array’ from incompatible pointer type
format_output.c:131: warning: passing argument 4 of ‘print_pair_array’ from incompatible pointer type
format_output.c: In function ‘print_oligo_summary’:
format_output.c:653: warning: passing argument 4 of ‘print_pair_array’ from incompatible pointer type
format_output.c:654: warning: passing argument 4 of ‘print_pair_array’ from incompatible pointer type
format_output.c:656: warning: passing argument 4 of ‘print_pair_array’ from incompatible pointer type
primer3_release.h:3: warning: ‘pr_release’ defined but not used
+ make ntdpal
ntdpal_main.c: In function ‘main’:
ntdpal_main.c:133: warning: pointer targets in passing argument 1 of ‘dpal’ differ in signedness
ntdpal_main.c:133: warning: pointer targets in passing argument 2 of ‘dpal’ differ in signedness
dpal.c: In function ‘dpal_set_ambiguity_code_matrix’:
dpal.c:156: warning: pointer targets in initialization differ in signedness
dpal.c:157: warning: pointer targets in initialization differ in signedness
dpal.c:161: warning: pointer targets in assignment differ in signedness
dpal.c:167: warning: pointer targets in assignment differ in signedness
dpal.c: In function ‘dpal’:
dpal.c:241: warning: passing argument 2 of ‘illegal_char’ from incompatible pointer type
dpal.c:242: warning: passing argument 2 of ‘illegal_char’ from incompatible pointer type
dpal.c:245: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
dpal.c:246: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
dpal.c: In function ‘_dpal_generic’:
dpal.c:542: warning: pointer targets in passing argument 1 of ‘print_align’ differ in signedness
dpal.c:542: warning: pointer targets in passing argument 2 of ‘print_align’ differ in signedness
dpal.c: At top level:
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/x86_64/primer3*-1.0.0-1.3.bp.fc5.x86_64.rpm

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

+Trying to yum install: gd

+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