make failed on macOS fatal error: 'common.h' file not found

[crazyhottommy]

Hi,

I am installing wiggleTools, and failed on my macOS:

cd samtools; make
make[1]: Nothing to be done for `all'.
cd src; make -e
cc -g -Wall -O3 -std=gnu99 -I../samtools -I/inc -I -D_PBGZF_USE -c bigWiggleReader.c -o bigWiggleReader.o
In file included from bigWiggleReader.c:16:
./bigFileReader.h:24:10: fatal error: 'common.h' file not found
#include "common.h"
         ^
1 error generated.
make[1]: *** [bigWiggleReader.o] Error 1
make: *** [Wiggletools] Error 2

Any ideas why?

Thanks!

Ming

[dzerbino]

You seem to have forgotten to set the KENT_SRC and TABIX_SRC environment variables.

[crazyhottommy]

Thanks. After setting up the environment variables. I did make again. See errors:

1 warning generated.
cc -g -Wall -O3 -std=gnu99 -I../samtools -I/Users/mtang1/github_repos/WiggleTools/userApps/kent/src/inc -I/Users/mtang1/github_repos/WiggleTools/tabix -D_PBGZF_USE -c bigBedReader.c -o bigBedReader.o
cc -g -Wall -O3 -std=gnu99 -I../samtools -I/Users/mtang1/github_repos/WiggleTools/userApps/kent/src/inc -I/Users/mtang1/github_repos/WiggleTools/tabix -D_PBGZF_USE -c bamReader.c -o bamReader.o
bamReader.c:17:10: fatal error: 'faidx.h' file not found
#include "faidx.h"

[dzerbino]

Thats weird, it's normally in the samtools directory. Is the file missing?

[dzerbino]

No news...