eprimer3 again

[Alex Brown]

Hi.

Thanks to David Mathog andPeter Slickers for their help in sorting out 
my last problem. I had to edit the Makefile to remove the line

LIBOPTS ='-static'

and then remove all reference to $(LIBOPTS), as well as changing the 
CC = CC (gcc in Darwin is cc). This new Makefile produced the executable 
primer3_core.

Howerver, on running the test program primer_test.pl in the ../test 
directory, I got the following errors :

[****:/primer3_0_9_test/test] me primer_test.pl


/primer3_0_9_test/test/primer_test.pl: testing ../src/primer3_core Tue 
Sep 10 16:49:41 BST 2002

Testing fatal errors
1,5d0
< PRIMER_SEQUENCE_ID=seq1
< 
SEQUENCE=ATGCTAGCTAGTCGATCGATGCTAGCTAGTCGATCTACTATCATCATGCTAGCATGGGGCATCTGTGGGATGCTGTCGTACTGATCGATGCTAGCTAGCTAGTCGATCGTAGCTATCATCATCTAGTCATCGTAGCTATCATCGTAGC
< PRIMER_MISPRIMING_LIBRARY=repeat_file
< PRIMER_ERROR=Cannot open mispriming library repeat_file
< =
Difference found between primer_global_err/repeat_lib_err.out and 
primer_global_err/repeat_lib_err.tmp

1d0
< ../src/primer3_core: Cannot open mispriming library repeat_file

Difference found between primer_global_err/repeat_lib_err.out2 and 
primer_global_err/repeat_lib_err.tmp2

1,6d0
< PRIMER_SEQUENCE_ID=seq1
< 
SEQUENCE=ATGCTAGCTAGTCGATCGATGCTAGCTAGTCGATCTACTATCATCATGCTAGCATGGGGCATCTGTGGGATGCTGTCGTACTGATCGATGCTAGCTAGCTAGTCGATCGTAGCTATCATCATCTAGTCATCGTAGCTATCATCGTAGC
< PRIMER_PICK_INTERNAL_OLIGO=1
< PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY=repeat_file
< PRIMER_ERROR=Cannot open internal oligo mishyb library repeat_file
< =
Difference found between primer_global_err/repeat_lib_int_err.out and 
primer_global_err/repeat_lib_int_err.tmp

1d0
< ../src/primer3_core: Cannot open internal oligo mishyb library 
repeat_file

Difference found between primer_global_err/repeat_lib_int_err.out2 and 
primer_global_err/repeat_lib_int_err.tmp2

FAILED

primer_boundary OK
primer_internal OK
primer_boundary_formated OK
primer_internal_formated OK
primer_start_codon OK
primer_boundary1 OK
primer_internal1 OK
primer_task OK
primer_task_formated OK
primer_boundary1_formated Cannot read primer_boundary1_formated_output 
at /Downloads/primer3_0_9_test/test/primer_test.pl line 80.

Somethng appears to be not quite right. I should point out that I had to 
edit the primer_test.pl file to change the first line to 
'#!/usr//bin/perl5.6.0 -w' to make it compatible with Darwin.

I then copied primer3_core to my EMBOSS bin directory, and tested it 
using the sequence file given in the EMBOSS manual. Without the -explain 
flag, the results were perfect, as shown in the manual. However, with 
the -explain flag set, I get the following error message:

Picks PCR primers and hybridization oligos
Output file [hsfau1.eprimer3]:
*** malloc[422]: error for object 0x1d7c80: Incorrect check sum for 
freed object - object was probably modified after beeing freed; break at 
szone_error
Bus error

Why is the test program failing, and why is the -explain flag causing 
these problems ? Are there some files missing from the installation ?

Hope someone can help.

Many thanks.

Alex Brown