make: *** [all-recur] Error 1 when installing DWGSIM

[phoebee-h]

Hello everyone, and hello to Nils, My name is Phoebe. Everything seemed to work fine until I got this information. I had the complete package including samtools in its subdirectory. I have no idea what is going on.

make[1]: Leaving directory /home/phoebe/DWGSIM/samtools' make[1]: Entering directory/home/phoebe/DWGSIM' make[2]: Entering directory /home/phoebe/DWGSIM/samtools' make[2]: Nothing to be done forlib'. make[2]: Leaving directory /home/phoebe/DWGSIM/samtools' make[2]: Entering directory/home/phoebe/DWGSIM' make[2]: Nothing to be done for lib'. make[2]: Leaving directory/home/phoebe/DWGSIM' gcc -c -g -Wall -O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.11\" -I. src/dwgsim.c -o src/dwgsim.o src/dwgsim.c: In function ‘dwgsim_core’: src/dwgsim.c:868: error: ‘unsignedf’ undeclared (first use in this function) src/dwgsim.c:868: error: (Each undeclared identifier is reported only once src/dwgsim.c:868: error: for each function it appears in.) src/dwgsim.c:868: error: expected ‘)’ before ‘long’ src/dwgsim.c:868: error: expected ‘)’ before ‘ii’ src/dwgsim.c:902: error: expected ‘)’ before ‘long’ src/dwgsim.c:902: error: expected ‘)’ before ‘ii’ make[1]: [src/dwgsim.o] Error 1 make[1]: Leaving directory `/home/phoebe/DWGSIM' make: [all-recur] Error 1

Thank you.

[nh13]

Can you print look at line 868 in your source code and print that here? I have neither heard of a unsignedf (the f before), nor does google reveal anything.

[phoebee-h]

Here is the original source code in src/dwgsim.c, line 868 and 902, respectively: (unsignedf long long)ii, j+1); (unsignedf long long)ii);

As you mentioned, I then deleted the "f", making the source code like this: (unsigned long long)ii, j+1); (unsigned long long)ii); Then, no such an error message I've got. But, still some problems showed up as below:

make[1]: Leaving directory /home/phoebe/DWGSIM/samtools' make[1]: Entering directory/home/phoebe/DWGSIM' make[2]: Entering directory /home/phoebe/DWGSIM/samtools' make[2]: Nothing to be done forlib'. make[2]: Leaving directory /home/phoebe/DWGSIM/samtools' make[2]: Entering directory/home/phoebe/DWGSIM' make[2]: Nothing to be done for lib'. make[2]: Leaving directory/home/phoebe/DWGSIM' gcc -c -g -Wall -O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.11\" -I. src/dwgsim.c -o src/dwgsim.o gcc -g -Wall -O3 -o dwgsim src/dwgsim_opt.o src/mut.o src/contigs.o src/regions_bed.o src/mut_txt.o src/mut_bed.o src/mut_vcf.o src/mut_input.o src/dwgsim .o -lm -lz -lpthread gcc -c -g -Wall -O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.11\" -I. src/dwgsim_eval.c -o src/dwgsim_eval.o make[1]: No rule to make target samtools/knetfile.o', needed bydwgsim_eval'. Stop. make[1]: Leaving directory `/home/phoebe/DWGSIM' make: [all-recur] Error 1

[kma]

Hi,

try make clean && make

Best

[phoebee-h]

Thank you kma, But it still doesn't work. I'll keep figuring this out. Thanks again!

[phoebee-h]

Hi, Not sure if it's the problem of samtools' version. I can finally make it work.

I've already had samtools 1.3.1 installed in another directory. I've made symbolic link but it did not work, which showed the same result as in SEQanswers (gprakhar has asked before). http://seqanswers.com/forums/showthread.php?t=22578 Also, renaming the directory to "samtools" is necessary so I did that. Still not working.

Finally, I downloaded the "samtools @ 28391e5" that Nils provided and put it under the directory of DWGSIM with renaming. It finally works!

Though it might sound stupid for doing all this, I'm new in the bioinformatics field. Just hope others encountering the similar problems can benefit. Thanks!

[nh13]

@phoebee-h the version of samtools we use has not been updated in a while, and I am loathe to do it as the new stuff isn't really needed. I believe git clone --recursive should clone both dwgsim as well as samtools. Thanks for posting back!