downloading some software from Github a

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

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

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)