Issue with shiny graphing (running ./angsd-wrapper)

[carlos-sarabia]

Hi guys,

I am here to report a problem I had when running ./angsd-wrapper shiny graphing. After doing the whole tutorial (which is very helpful, thanks for that!), I tried to run shiny graphing and got this:

~/Desktop/programs/angsd-wrapper$ ./angsd-wrapper shiny graphing
angsd-wrapper running from /home/carlos/Desktop/programs/angsd-wrapper

Loading required package: methods
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: ‘Hmisc’

The following objects are masked from ‘package:base’:

    format.pval, units

Error: package or namespace load failed for ‘ape’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/carlos/Desktop/programs/angsd-wrapper/.RLibs/ape/libs/ape.so':
  libRlapack.so: cannot open shared object file: No such file or directory
Execution halted

However, this directory exists:

~/Desktop/programs/angsd-wrapper$ ls /home/carlos/Desktop/programs/angsd-wrapper/.RLibs/ape/libs
ape.so

Re-installing the 'ape' package in R did not change the output. I did it and it automatically installed where I have my R-3.4:

> install.packages('ape')
Installing package into ‘/home/carlos/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
...
* DONE (ape)

The downloaded source packages are in
	‘/tmp/RtmpgvgvS3/downloaded_packages’

I tried adding /home/carlos/R/x86_64-pc-linux-gnu-library/3.4 in my PATH variable of .bashrc and the result is still the same:

export PATH="/home/carlos/R/x86_64-pc-linux-gnu-library/3.4/:$PATH"
export LD_LIBRARY_PATH=/home/carlos/Desktop/programs/angsd-wrapper/.RLibs/ape/libs/ape.so:${LD_LIBRARY_PATH}

I saw a similar issue here: mojaveazure/angsd-wrapper#47 and I realized I had also installed anaconda in my PC. I tried to deactivate it (adding # to #export PATH="/home/carlos/miniconda3/condabin/:$PATH" in .bashrc), but I still had the same issue.

What could be wrong?

Best regards and thanks

[arundurvasula]

Hi Carlos,

Sorry you're having issues with this -- it seems pretty thorny. Are you able to load ape after installing it?