bwa compile failed at utils.c:29:10

lh3 / bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

GNU General Public License v3.0

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bwa compile failed at utils.c:29:10 #315

Open sagitaninta opened 3 years ago

sagitaninta commented 3 years ago

I am trying to install bwa at a Linux Cluster and the make command fail at this point

gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  utils.c -o utils.o
utils.c:29:10: fatal error: stdio.h: No such file or directory
 #include <stdio.h>
          ^~~~~~~~~
compilation terminated.
make: *** [Makefile:25: utils.o] Error 1

And when I seek the stdio.h within the bwa folder after git clone, it is absent also. Could you point me to a possible solution?

tomaskopsa commented 3 years ago

stdio.h is one of fundamental C/C++ header files, usually located at /usr/include/ directory. You either need to instal libc-dev or reinstall gcc compiler.