admixr does not find qpDstat

[nicolo-tellini]

Dear @bodkan ,

I am running admixtools v.7.0.2 and admixr v.0.9.1 I am using the d function but I am getting the following error:

` sh: qpDstat: command not found Warning in system(paste(cmd, "-p", par_file, ">", log_file)) : error in running command BEGINNING OF OUTPUT FILE

END OF OUTPUT FILE

Error: The output file we got from ADMIXTOOLS is truncated. Please examine the full output above and check for errors. `

This is a bit confusing because qpDstat is already in my $PATH :

[ntellini@hulk AMH]$ which qpDstat

output

/home/tools/bin/qpDstat

my $PATH :

[ntellini@hulk AMH]$ echo $PATH | grep "/home/tools/bin"

[...]/home/tools/bin[...]

Am I missing something ?

thanks,

best regards,

nic

[nicolo-tellini]

Hi,

I have just read issue #33

I have not run : 'echo \"PATH=$PATH\" >> .Renviron' in the shell, yet.

I will try and, in case, close the issue.

Thanks,

nic

[nicolo-tellini]

Dear @bodkan,

I solved the problem following #33. I would also add, in the comment at #33, that for loading .Renviron is necessary running (in R)

readRenviron(path = ".Renviron")

assuming that .Renviron is in the wd(). This can be useful given that loading .Renviron is an uncommon task.

best regards,

nic

[bodkan]

Hello. Glad to hear you've arrived at a solution.

Just for completeness, normally you would use an ~/.Renviron file. I.e., put the file in your $HOME directory, not in your working directory. That way, R loads it automatically upon startup, setting up the path for each R session. No additional work is necessary.

Using ~/.Renviron (or, similarly, ~/.Rprofile) file is actually very common.

(That said, thank you for pointing out the existence of the readEnviron function. I've been using R for > 10 years and I wasn't aware of this function. :))