Dear all,
I am really sorry to ask for 3rd time in a day. But I am stuck at popbam compilation. I have run the commands for compilation
make
make clean
No error occured with these commands. But when I type the command starting with popbam, error appears
popbam: command not found
I have also tried
sudo make install
But I get error
g++ -o popbam popbam.o pop_utils.o pop_sample.o pop_tree.o pop_snp.o pop_nucdiv.o pop_ld.o pop_sfs.o pop_diverge.o pop_haplo.o getopt_pp.o gamma.o bam_aux.o bam.o bam_index.o faidx.o kstring.o bgzf.o sam_header.o bam_import.o razf.o sam.o bam_pileup.o -lz -lm
/usr/bin/ld: bam_index.o: in function `ks_combsort_off':
bam_index.c:(.text+0x970): undefined reference to `__ks_insertsort_off'
/usr/bin/ld: bam_index.o: in function `ks_introsort_off':
bam_index.c:(.text+0xd5a): undefined reference to `__ks_insertsort_off'
/usr/bin/ld: bgzf.o: in function `deflate_block':
bgzf.c:(.text+0x1552): undefined reference to `packInt16'
/usr/bin/ld: bgzf.c:(.text+0x15ba): undefined reference to `packInt32'
/usr/bin/ld: bgzf.c:(.text+0x15e1): undefined reference to `packInt32'
/usr/bin/ld: bgzf.o: in function `check_header':
bgzf.c:(.text+0x1860): undefined reference to `unpackInt16'
/usr/bin/ld: bgzf.c:(.text+0x18a7): undefined reference to `unpackInt16'
/usr/bin/ld: bgzf.o: in function `bgzf_read_block':
bgzf.c:(.text+0x1d20): undefined reference to `unpackInt16'
collect2: error: ld returned 1 exit status
make: *** [Makefile:43: popbam] Error 1
Please help me in resolving the issue. I shall be very thankful to you.
search the web for
bash PATH command not found
when you executed make, make install and make clean and it run's okay, then the compiled binary in general would be in the compiled directory it self or within bin folder of compiled directory. Check if the compiled binary is present in directory where you have compiled. If it's there check if it is executable. If it is executable, then execute it either by running
./popbam
or move it to your shell path.