error compiling mdust

[epistatic]

Hi all,

I am installing RUM (http://cbil.upenn.edu/RUM/) to analyze RNA-Seq data. It has been recommended over TopHat by a collaborator. RUM requires mdust, bowtie, and blat. I ran into problems compiling mdust.

I am running OS X 10.6.5 with Xcode 3.2.4 installed. I am biologist converting to bioinformatics so I am most likely doing something simple wrong. Any suggestions are greatly appreciated.


gcc -O2 -Wall -I. -I- -D_REENTRANT -c mdust.c -o mdust.o
cc1: note: obsolete option -I- used, please use -iquote instead
mdust.c: In function ‘main’:
mdust.c:66: warning: implicit declaration of function ‘strlen’
mdust.c:66: warning: incompatible implicit declaration of built-in function ‘strlen’
gcc -O2 -Wall -I. -I- -D_REENTRANT -c dust.c -o dust.o
cc1: note: obsolete option -I- used, please use -iquote instead
gcc -O2 -Wall -I. -I- -D_REENTRANT -c fastafile.c -o fastafile.o
cc1: note: obsolete option -I- used, please use -iquote instead
fastafile.c:3:20: error: malloc.h: No such file or directory
fastafile.c: In function ‘myabort’:
fastafile.c:12: warning: implicit declaration of function ‘exit’
fastafile.c:12: warning: incompatible implicit declaration of built-in function ‘exit’
fastafile.c: In function ‘mymalloc’:
fastafile.c:17: warning: implicit declaration of function ‘malloc’
fastafile.c:17: warning: incompatible implicit declaration of built-in function ‘malloc’
fastafile.c: In function ‘myrealloc’:
fastafile.c:25: warning: implicit declaration of function ‘realloc’
fastafile.c:25: warning: assignment makes pointer from integer without a cast
fastafile.c: In function ‘freeFastaSeq’:
fastafile.c:40: warning: implicit declaration of function ‘free’
fastafile.c: In function ‘myfopen’:
fastafile.c:84: warning: incompatible implicit declaration of built-in function ‘exit’
fastafile.c: In function ‘putfasta’:
fastafile.c:174: warning: implicit declaration of function ‘strlen’
fastafile.c:174: warning: incompatible implicit declaration of built-in function ‘strlen’
make: *** [fastafile.o] Error 1

[dsidote]

From within the mdust directory, open fastafile.c with vi or nano and delete the line '#include <malloc.h>'. It should be line 3. Save the file and then try 'make' again.