Error in running script [closed]

Posted by SWEngineer on Programmers See other posts from Programmers or by SWEngineer
Published on 2012-10-23T10:39:34Z Indexed on 2012/10/23 11:18 UTC
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I'm trying to run heathusf_v1.1.0.tar.gz found here

I installed tcsh to make build_heathusf work. But, when I run ./build_heathusf, I get the following (I'm running that on a Fedora Linux system from Terminal):

$ ./build_heathusf

Compiling programs to build a library of image processing functions.
convexpolyscan.c: In function ‘cdelete’:
convexpolyscan.c:346:5: warning: incompatible implicit declaration of built-in function ‘bcopy’ [enabled by default]
myalloc.c: In function ‘mycalloc’:
myalloc.c:68:16: error: invalid storage class for function ‘store_link’
myalloc.c: In function ‘mymalloc’:
myalloc.c:101:16: error: invalid storage class for function ‘store_link’
myalloc.c: In function ‘myfree’:
myalloc.c:129:27: error: invalid storage class for function ‘find_link’
myalloc.c:131:12: warning: assignment makes pointer from integer without a cast [enabled by default]
myalloc.c: At top level:
myalloc.c:150:13: warning: conflicting types for ‘store_link’ [enabled by default]
myalloc.c:150:13: error: static declaration of ‘store_link’ follows non-static declaration
myalloc.c:91:4: note: previous implicit declaration of ‘store_link’ was here
myalloc.c:164:24: error: conflicting types for ‘find_link’
myalloc.c:131:14: note: previous implicit declaration of ‘find_link’ was here

Building the mammogram resizing program.
gcc -O2 -I. -I../common mkimage.o -o mkimage -L../common -lmammo -lm
../common/libmammo.a(aggregate.o): In function `aggregate':
aggregate.c:(.text+0x7fa): undefined reference to `mycalloc'
aggregate.c:(.text+0x81c): undefined reference to `mycalloc'
aggregate.c:(.text+0x868): undefined reference to `mycalloc'
../common/libmammo.a(aggregate.o): In function `aggregate_median':
aggregate.c:(.text+0xbc5): undefined reference to `mymalloc'
aggregate.c:(.text+0xbfb): undefined reference to `mycalloc'
aggregate.c:(.text+0xc3c): undefined reference to `mycalloc'
../common/libmammo.a(aggregate.o): In function `aggregate':
aggregate.c:(.text+0x9b5): undefined reference to `myfree'
../common/libmammo.a(aggregate.o): In function `aggregate_median':
aggregate.c:(.text+0xd85): undefined reference to `myfree'
../common/libmammo.a(optical_density.o): In function `linear_optical_density':
optical_density.c:(.text+0x29e): undefined reference to `mymalloc'
optical_density.c:(.text+0x342): undefined reference to `mycalloc'
optical_density.c:(.text+0x383): undefined reference to `mycalloc'
../common/libmammo.a(optical_density.o): In function `log10_optical_density':
optical_density.c:(.text+0x693): undefined reference to `mymalloc'
optical_density.c:(.text+0x74f): undefined reference to `mycalloc'
optical_density.c:(.text+0x790): undefined reference to `mycalloc'
../common/libmammo.a(optical_density.o): In function `map_with_ushort_lut':
optical_density.c:(.text+0xb2e): undefined reference to `mymalloc'
optical_density.c:(.text+0xb87): undefined reference to `mycalloc'
optical_density.c:(.text+0xbc6): undefined reference to `mycalloc'
../common/libmammo.a(optical_density.o): In function `linear_optical_density':
optical_density.c:(.text+0x4d9): undefined reference to `myfree'
../common/libmammo.a(optical_density.o): In function `log10_optical_density':
optical_density.c:(.text+0x8f1): undefined reference to `myfree'
../common/libmammo.a(optical_density.o): In function `map_with_ushort_lut':
optical_density.c:(.text+0xd0d): undefined reference to `myfree'
../common/libmammo.a(virtual_image.o): In function `deallocate_cached_image':
virtual_image.c:(.text+0x3dc6): undefined reference to `myfree'
virtual_image.c:(.text+0x3dd7): undefined reference to `myfree'
../common/libmammo.a(virtual_image.o):virtual_image.c:(.text+0x3de5): more undefined references to `myfree' follow
../common/libmammo.a(virtual_image.o): In function `allocate_cached_image':
virtual_image.c:(.text+0x4233): undefined reference to `mycalloc'
virtual_image.c:(.text+0x4253): undefined reference to `mymalloc'
virtual_image.c:(.text+0x4275): undefined reference to `mycalloc'
virtual_image.c:(.text+0x42e7): undefined reference to `mycalloc'
virtual_image.c:(.text+0x44f9): undefined reference to `mycalloc'
virtual_image.c:(.text+0x47a9): undefined reference to `mycalloc'
virtual_image.c:(.text+0x4a45): undefined reference to `mycalloc'
virtual_image.c:(.text+0x4af4): undefined reference to `myfree'
collect2: error: ld returned 1 exit status
make: *** [mkimage] Error 1

Building the breast segmentation program.
gcc -O2 -I. -I../common breastsegment.o segment.o -o breastsegment -L../common -lmammo -lm
breastsegment.o: In function `render_segmentation_sketch':
breastsegment.c:(.text+0x43): undefined reference to `mycalloc'
breastsegment.c:(.text+0x58): undefined reference to `mycalloc'
breastsegment.c:(.text+0x12f): undefined reference to `mycalloc'
breastsegment.c:(.text+0x1b9): undefined reference to `myfree'
breastsegment.c:(.text+0x1c6): undefined reference to `myfree'
breastsegment.c:(.text+0x1e1): undefined reference to `myfree'
segment.o: In function `find_center':
segment.c:(.text+0x53): undefined reference to `mycalloc'
segment.c:(.text+0x71): undefined reference to `mycalloc'
segment.c:(.text+0x387): undefined reference to `myfree'
segment.o: In function `bordercode':
segment.c:(.text+0x4ac): undefined reference to `mycalloc'
segment.c:(.text+0x546): undefined reference to `mycalloc'
segment.c:(.text+0x651): undefined reference to `mycalloc'
segment.c:(.text+0x691): undefined reference to `myfree'
segment.o: In function `estimate_tissue_image':
segment.c:(.text+0x10d4): undefined reference to `mycalloc'
segment.c:(.text+0x14da): undefined reference to `mycalloc'
segment.c:(.text+0x1698): undefined reference to `mycalloc'
segment.c:(.text+0x1834): undefined reference to `mycalloc'
segment.c:(.text+0x1850): undefined reference to `mycalloc'
segment.o:segment.c:(.text+0x186a): more undefined references to `mycalloc' follow
segment.o: In function `estimate_tissue_image':
segment.c:(.text+0x1bbc): undefined reference to `myfree'
segment.c:(.text+0x1c4a): undefined reference to `mycalloc'
segment.c:(.text+0x1c7c): undefined reference to `mycalloc'
segment.c:(.text+0x1d8e): undefined reference to `myfree'
segment.c:(.text+0x1d9b): undefined reference to `myfree'
segment.c:(.text+0x1da8): undefined reference to `myfree'
segment.c:(.text+0x1dba): undefined reference to `myfree'
segment.c:(.text+0x1dc9): undefined reference to `myfree'
segment.o:segment.c:(.text+0x1dd8): more undefined references to `myfree' follow
segment.o: In function `estimate_tissue_image':
segment.c:(.text+0x20bf): undefined reference to `mycalloc'
segment.o: In function `segment_breast':
segment.c:(.text+0x24cd): undefined reference to `mycalloc'
segment.o: In function `find_center':
segment.c:(.text+0x3a4): undefined reference to `myfree'
segment.o: In function `bordercode':
segment.c:(.text+0x6ac): undefined reference to `myfree'
../common/libmammo.a(aggregate.o): In function `aggregate':
aggregate.c:(.text+0x7fa): undefined reference to `mycalloc'
aggregate.c:(.text+0x81c): undefined reference to `mycalloc'
aggregate.c:(.text+0x868): undefined reference to `mycalloc'
../common/libmammo.a(aggregate.o): In function `aggregate_median':
aggregate.c:(.text+0xbc5): undefined reference to `mymalloc'
aggregate.c:(.text+0xbfb): undefined reference to `mycalloc'
aggregate.c:(.text+0xc3c): undefined reference to `mycalloc'
../common/libmammo.a(aggregate.o): In function `aggregate':
aggregate.c:(.text+0x9b5): undefined reference to `myfree'
../common/libmammo.a(aggregate.o): In function `aggregate_median':
aggregate.c:(.text+0xd85): undefined reference to `myfree'
../common/libmammo.a(cc_label.o): In function `cc_label':
cc_label.c:(.text+0x20c): undefined reference to `mycalloc'
cc_label.c:(.text+0x6c2): undefined reference to `mycalloc'
cc_label.c:(.text+0xbaa): undefined reference to `myfree'
../common/libmammo.a(cc_label.o): In function `cc_label_0bkgd':
cc_label.c:(.text+0xe17): undefined reference to `mycalloc'
cc_label.c:(.text+0x12d7): undefined reference to `mycalloc'
cc_label.c:(.text+0x17e7): undefined reference to `myfree'
../common/libmammo.a(cc_label.o): In function `cc_relabel_by_intensity':
cc_label.c:(.text+0x18c5): undefined reference to `mycalloc'
../common/libmammo.a(cc_label.o): In function `cc_label_4connect':
cc_label.c:(.text+0x1cf0): undefined reference to `mycalloc'
cc_label.c:(.text+0x2195): undefined reference to `mycalloc'
cc_label.c:(.text+0x26a4): undefined reference to `myfree'
../common/libmammo.a(cc_label.o): In function `cc_relabel_by_intensity':
cc_label.c:(.text+0x1b06): undefined reference to `myfree'
../common/libmammo.a(convexpolyscan.o): In function `polyscan_coords':
convexpolyscan.c:(.text+0x6f0): undefined reference to `mycalloc'
convexpolyscan.c:(.text+0x75f): undefined reference to `mycalloc'
convexpolyscan.c:(.text+0x7ab): undefined reference to `myfree'
convexpolyscan.c:(.text+0x7b8): undefined reference to `myfree'
../common/libmammo.a(convexpolyscan.o): In function `polyscan_poly_cacheim':
convexpolyscan.c:(.text+0x805): undefined reference to `mycalloc'
convexpolyscan.c:(.text+0x894): undefined reference to `myfree'
../common/libmammo.a(mikesfileio.o): In function `read_segmentation_file':
mikesfileio.c:(.text+0x1e9): undefined reference to `mycalloc'
mikesfileio.c:(.text+0x205): undefined reference to `mycalloc'
../common/libmammo.a(optical_density.o): In function `linear_optical_density':
optical_density.c:(.text+0x29e): undefined reference to `mymalloc'
optical_density.c:(.text+0x342): undefined reference to `mycalloc'
optical_density.c:(.text+0x383): undefined reference to `mycalloc'
../common/libmammo.a(optical_density.o): In function `log10_optical_density':
optical_density.c:(.text+0x693): undefined reference to `mymalloc'
optical_density.c:(.text+0x74f): undefined reference to `mycalloc'
optical_density.c:(.text+0x790): undefined reference to `mycalloc'
../common/libmammo.a(optical_density.o): In function `map_with_ushort_lut':
optical_density.c:(.text+0xb2e): undefined reference to `mymalloc'
optical_density.c:(.text+0xb87): undefined reference to `mycalloc'
optical_density.c:(.text+0xbc6): undefined reference to `mycalloc'
../common/libmammo.a(optical_density.o): In function `linear_optical_density':
optical_density.c:(.text+0x4d9): undefined reference to `myfree'
../common/libmammo.a(optical_density.o): In function `log10_optical_density':
optical_density.c:(.text+0x8f1): undefined reference to `myfree'
../common/libmammo.a(optical_density.o): In function `map_with_ushort_lut':
optical_density.c:(.text+0xd0d): undefined reference to `myfree'
../common/libmammo.a(virtual_image.o): In function `deallocate_cached_image':
virtual_image.c:(.text+0x3dc6): undefined reference to `myfree'
virtual_image.c:(.text+0x3dd7): undefined reference to `myfree'
../common/libmammo.a(virtual_image.o):virtual_image.c:(.text+0x3de5): more undefined references to `myfree' follow
../common/libmammo.a(virtual_image.o): In function `allocate_cached_image':
virtual_image.c:(.text+0x4233): undefined reference to `mycalloc'
virtual_image.c:(.text+0x4253): undefined reference to `mymalloc'
virtual_image.c:(.text+0x4275): undefined reference to `mycalloc'
virtual_image.c:(.text+0x42e7): undefined reference to `mycalloc'
virtual_image.c:(.text+0x44f9): undefined reference to `mycalloc'
virtual_image.c:(.text+0x47a9): undefined reference to `mycalloc'
virtual_image.c:(.text+0x4a45): undefined reference to `mycalloc'
virtual_image.c:(.text+0x4af4): undefined reference to `myfree'
collect2: error: ld returned 1 exit status
make: *** [breastsegment] Error 1

Building the mass feature generation program.
gcc -O2 -I. -I../common afumfeature.o -o afumfeature -L../common -lmammo -lm
afumfeature.o: In function `afum_process':
afumfeature.c:(.text+0xd80): undefined reference to `mycalloc'
afumfeature.c:(.text+0xd9c): undefined reference to `mycalloc'
afumfeature.c:(.text+0xe80): undefined reference to `mycalloc'
afumfeature.c:(.text+0x11f8): undefined reference to `myfree'
afumfeature.c:(.text+0x1207): undefined reference to `myfree'
afumfeature.c:(.text+0x1214): undefined reference to `myfree'
../common/libmammo.a(aggregate.o): In function `aggregate':
aggregate.c:(.text+0x7fa): undefined reference to `mycalloc'
aggregate.c:(.text+0x81c): undefined reference to `mycalloc'
aggregate.c:(.text+0x868): undefined reference to `mycalloc'
../common/libmammo.a(aggregate.o): In function `aggregate_median':
aggregate.c:(.text+0xbc5): undefined reference to `mymalloc'
aggregate.c:(.text+0xbfb): undefined reference to `mycalloc'
aggregate.c:(.text+0xc3c): undefined reference to `mycalloc'
../common/libmammo.a(aggregate.o): In function `aggregate':
aggregate.c:(.text+0x9b5): undefined reference to `myfree'
../common/libmammo.a(aggregate.o): In function `aggregate_median':
aggregate.c:(.text+0xd85): undefined reference to `myfree'
../common/libmammo.a(convexpolyscan.o): In function `polyscan_coords':
convexpolyscan.c:(.text+0x6f0): undefined reference to `mycalloc'
convexpolyscan.c:(.text+0x75f): undefined reference to `mycalloc'
convexpolyscan.c:(.text+0x7ab): undefined reference to `myfree'
convexpolyscan.c:(.text+0x7b8): undefined reference to `myfree'
../common/libmammo.a(convexpolyscan.o): In function `polyscan_poly_cacheim':
convexpolyscan.c:(.text+0x805): undefined reference to `mycalloc'
convexpolyscan.c:(.text+0x894): undefined reference to `myfree'
../common/libmammo.a(mikesfileio.o): In function `read_segmentation_file':
mikesfileio.c:(.text+0x1e9): undefined reference to `mycalloc'
mikesfileio.c:(.text+0x205): undefined reference to `mycalloc'
../common/libmammo.a(optical_density.o): In function `linear_optical_density':
optical_density.c:(.text+0x29e): undefined reference to `mymalloc'
optical_density.c:(.text+0x342): undefined reference to `mycalloc'
optical_density.c:(.text+0x383): undefined reference to `mycalloc'
../common/libmammo.a(optical_density.o): In function `log10_optical_density':
optical_density.c:(.text+0x693): undefined reference to `mymalloc'
optical_density.c:(.text+0x74f): undefined reference to `mycalloc'
optical_density.c:(.text+0x790): undefined reference to `mycalloc'
../common/libmammo.a(optical_density.o): In function `map_with_ushort_lut':
optical_density.c:(.text+0xb2e): undefined reference to `mymalloc'
optical_density.c:(.text+0xb87): undefined reference to `mycalloc'
optical_density.c:(.text+0xbc6): undefined reference to `mycalloc'
../common/libmammo.a(optical_density.o): In function `linear_optical_density':
optical_density.c:(.text+0x4d9): undefined reference to `myfree'
../common/libmammo.a(optical_density.o): In function `log10_optical_density':
optical_density.c:(.text+0x8f1): undefined reference to `myfree'
../common/libmammo.a(optical_density.o): In function `map_with_ushort_lut':
optical_density.c:(.text+0xd0d): undefined reference to `myfree'
../common/libmammo.a(virtual_image.o): In function `deallocate_cached_image':
virtual_image.c:(.text+0x3dc6): undefined reference to `myfree'
virtual_image.c:(.text+0x3dd7): undefined reference to `myfree'
../common/libmammo.a(virtual_image.o):virtual_image.c:(.text+0x3de5): more undefined references to `myfree' follow
../common/libmammo.a(virtual_image.o): In function `allocate_cached_image':
virtual_image.c:(.text+0x4233): undefined reference to `mycalloc'
virtual_image.c:(.text+0x4253): undefined reference to `mymalloc'
virtual_image.c:(.text+0x4275): undefined reference to `mycalloc'
virtual_image.c:(.text+0x42e7): undefined reference to `mycalloc'
virtual_image.c:(.text+0x44f9): undefined reference to `mycalloc'
virtual_image.c:(.text+0x47a9): undefined reference to `mycalloc'
virtual_image.c:(.text+0x4a45): undefined reference to `mycalloc'
virtual_image.c:(.text+0x4af4): undefined reference to `myfree'
collect2: error: ld returned 1 exit status
make: *** [afumfeature] Error 1

Building the mass detection program.
make: Nothing to be done for `all'.

Building the performance evaluation program.
gcc -O2 -I. -I../common DDSMeval.o polyscan.o -o DDSMeval -L../common -lmammo -lm
../common/libmammo.a(mikesfileio.o): In function `read_segmentation_file':
mikesfileio.c:(.text+0x1e9): undefined reference to `mycalloc'
mikesfileio.c:(.text+0x205): undefined reference to `mycalloc'
collect2: error: ld returned 1 exit status
make: *** [DDSMeval] Error 1

Building the template creation program.
gcc -O2 -I. -I../common mktemplate.o polyscan.o -o mktemplate -L../common -lmammo -lm

Building the drawimage program.
gcc -O2 -I. -I../common drawimage.o -o drawimage -L../common -lmammo -lm
../common/libmammo.a(mikesfileio.o): In function `read_segmentation_file':
mikesfileio.c:(.text+0x1e9): undefined reference to `mycalloc'
mikesfileio.c:(.text+0x205): undefined reference to `mycalloc'
collect2: error: ld returned 1 exit status
make: *** [drawimage] Error 1

Building the compression/decompression program jpeg.
gcc -O2 -DSYSV -DNOTRUNCATE -c lexer.c
lexer.c:41:1: error: initializer element is not constant
lexer.c:41:1: error: (near initialization for ‘yyin’)
lexer.c:41:1: error: initializer element is not constant
lexer.c:41:1: error: (near initialization for ‘yyout’)
lexer.c: In function ‘initparser’:
lexer.c:387:21: warning: incompatible implicit declaration of built-in function ‘strlen’ [enabled by default]
lexer.c: In function ‘MakeLink’:
lexer.c:443:16: warning: incompatible implicit declaration of built-in function ‘malloc’ [enabled by default]
lexer.c:447:7: warning: incompatible implicit declaration of built-in function ‘exit’ [enabled by default]
lexer.c:452:7: warning: incompatible implicit declaration of built-in function ‘exit’ [enabled by default]
lexer.c:455:34: warning: incompatible implicit declaration of built-in function ‘calloc’ [enabled by default]
lexer.c:458:7: warning: incompatible implicit declaration of built-in function ‘exit’ [enabled by default]
lexer.c:460:3: warning: incompatible implicit declaration of built-in function ‘strcpy’ [enabled by default]
lexer.c: In function ‘getstr’:
lexer.c:548:26: warning: incompatible implicit declaration of built-in function ‘malloc’ [enabled by default]
lexer.c:552:4: warning: incompatible implicit declaration of built-in function ‘exit’ [enabled by default]
lexer.c:557:21: warning: incompatible implicit declaration of built-in function ‘calloc’ [enabled by default]
lexer.c:557:28: warning: incompatible implicit declaration of built-in function ‘strlen’ [enabled by default]
lexer.c:561:7: warning: incompatible implicit declaration of built-in function ‘exit’ [enabled by default]
lexer.c: In function ‘parser’:
lexer.c:794:21: warning: incompatible implicit declaration of built-in function ‘calloc’ [enabled by default]
lexer.c:798:8: warning: incompatible implicit declaration of built-in function ‘exit’ [enabled by default]
lexer.c:1074:21: warning: incompatible implicit declaration of built-in function ‘calloc’ [enabled by default]
lexer.c:1078:8: warning: incompatible implicit declaration of built-in function ‘exit’ [enabled by default]
lexer.c:1116:21: warning: incompatible implicit declaration of built-in function ‘calloc’ [enabled by default]
lexer.c:1120:8: warning: incompatible implicit declaration of built-in function ‘exit’ [enabled by default]
lexer.c:1154:25: warning: incompatible implicit declaration of built-in function ‘calloc’ [enabled by default]
lexer.c:1158:5: warning: incompatible implicit declaration of built-in function ‘exit’ [enabled by default]
lexer.c:1190:5: warning: incompatible implicit declaration of built-in function ‘exit’ [enabled by default]
lexer.c:1247:25: warning: incompatible implicit declaration of built-in function ‘calloc’ [enabled by default]
lexer.c:1251:5: warning: incompatible implicit declaration of built-in function ‘exit’ [enabled by default]
lexer.c:1283:5: warning: incompatible implicit declaration of built-in function ‘exit’ [enabled by default]
lexer.c: In function ‘yylook’:
lexer.c:1867:9: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
lexer.c:1867:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
lexer.c:1877:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
lexer.c:1877:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
make: *** [lexer.o] Error 1

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