eprimer3

[Alex Brown]

Hi.

Thanks for the help. This appears to have worked to some extent, after I 
modified the Makefile. I had to change the line CC = gcc to CC = CC (I 
think that CC on Darwin is GCC). This appeared to do something, but I 
this time I got a load of error messages:

[xxxx:/primer3_0_9_test/src] me% make
cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -include 
/usr/include/sys/types.h -O2 -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 
primer3_main.c
primer3_main.c: In function `oligo_param':
primer3_main.c:1113: warning: passing arg 3 of `oligo_overlaps_interval' 
from incompatible pointer type
primer3_main.c:1147: warning: passing arg 3 of `oligo_overlaps_interval' 
from incompatible pointer type
primer3_main.c:1151: warning: passing arg 3 of `oligo_overlaps_interval' 
from incompatible pointer type
cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -include /usr/include/sys/types.h 
-O2   -c -o oligotm.o oligotm.c
primer3_release.h:3: warning: `pr_release' defined but not used
cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -include 
/usr/include/sys/types.h -O2 -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 
-o dpal_primer.o dpal.c
dpal.c: In function `_dpal_generic':
dpal.c:332: warning: `i0' might be used uninitialized in this function
dpal.c:332: warning: `j0' might be used uninitialized in this function
dpal.c:336: warning: `I' might be used uninitialized in this function
dpal.c:336: warning: `J' might be used uninitialized in this function
dpal.c:338: warning: `score' might be used uninitialized in this function
dpal.c: In function `_dpal_long_nopath_generic':
dpal.c:560: warning: `I' might be used uninitialized in this function
dpal.c:560: warning: `J' might be used uninitialized in this function
dpal.c: At top level:
primer3_release.h:3: warning: `pr_release' defined but not used
cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -include 
/usr/include/sys/types.h -O2 -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 
-o format_output.o format_output.c
cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -include 
/usr/include/sys/types.h -O2 -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 
-o boulder_input.o boulder_input.c
primer3_release.h:3: warning: `pr_release' defined but not used
cc -g -o primer3_core primer3_main.o oligotm.o dpal_primer.o 
format_output.o boulder_input.o '-static' -lm
/usr/bin/ld: can't locate file for: -lcrt0.o
make: *** [primer3_core] Error 1

According to the README file, the warnings about i0, j0, I, J and score 
being possibly used unset in dpal.c are normal and harmless. However, 
the 'make' is still failing, the primer3_core exectuable does not 
appear. The problem seems to be in the line '/usr/bin/ld: can't locate 
file for: -lcrt0.o'. Any ideas ??

Many thanks,

Alex Brown.