File not found error on program installation.

Question

[M.O.L.S]

x86_64-apple-darwin13.4.0-clang -c  -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -O3 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe from_samtools.c
clang-4.0: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument]
clang-4.0: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument]
In file included from from_samtools.c:1:
./from_samtools.h:7:10: fatal error: 'htslib/khash_str2int.h' file not found
#include <htslib/khash_str2int.h>
         ^~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [Makefile:61: from_samtools.o] Error 1

Can anyone help with this error message? I am having trouble downloading some software from Github and when i type make it comes up with this error. I have htslib installed and that file khash_... is in there because i can see it.

Any ideas?

[Pierre Lindenbaum]

downloading some software from Github a

"some software" ? what are you trying to install ?

[Pierre Lindenbaum]

is it https://github.com/ANGSD/angsd ?? show us all the command lines you typed from the section "Installation"

[M.O.L.S]

Yes, this was the software I wanted to download.

[M.O.L.S]

All of these commands didn't work to install the angsd, (they only worked to download it):

enter code here
 wget http://popgen.dk/software/download/angsd/angsd0.930.tar.gz
 tar xf angsd0.930.tar.gz
 cd htslib;make;cd ..
 cd angsd
 make HTSSRC=../htslib
 cd ..

I also tried...

git clone https://github.com/samtools/htslib.git
git clone https://github.com/ANGSD/angsd.git 
cd htslib;make;cd ../angsd ;
make HTSSRC=../htslib

... which gave the errors originally posted in the question.

I also tried....

changing the directory of the make HTSSRC by specifying where it was.

make HTSSRC=../Software/htslib
make HTSSRC=../samtools/htslib1.9/htslib

still didn't work.

Make HTSSRC=../htsdir

... and this didnt work either.

I think this is because the clang 4.0 compiler is the first to be on the scene in recognising something needs to be compiled. The clang++ compiler and the g++ compiler aren't called on for some reason when I execute these commands in the Terminal. The compilers don't use the -W command which might be the most important command to perform linking of sorts. ?!

The only commands that were successful were: compiling the program inside of a bash chunk, in an RMarkdown file, created inside RStudio.

A new R Markdown file was placed inside the angsd_folder folder from github.

 ```{bash}
pwd 
```

output: / The / path / to / Downloads / angsd_folder

```{bash}
ls
```

output : A list of the header files and c files.

```{bash}
make 
```

A brand new c++ compiler called c++ , compiled the files into functional angsd executable file.

```{bash}
 ./angsd
 ```

output : angsd version: 0.931 (htslib: 1.9) build(Oct 27 2989 00:00:07)