Case sensitive file names issue

[courcelm]

The following test fails on Ubuntu 16.04.4 LTS and with release https://github.com/GfellerLab/MixMHCp/archive/v2.1.tar.gz

./MixMHCp -i test/test.txt -o test/out -m 3 && rm -rf test/out

Processing input files...
Running MixMHCp...
Generating logos with ggseqlogo...
Registered S3 methods overwritten by 'ggplot2':
method from
[.quosures rlang
c.quosures rlang
print.quosures rlang
Error in file(filename, "r", encoding = encoding) :
cannot open the connection
Calls: source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
cannot open file '/home/biodocker/bin/MixMHCp-2.1/lib/R/ggseqlogo.R': No such file or directory
Execution halted
Generating HTML tables document...
Done

R look for .R file but files are named .r

Suggest to upper case the file extension to fix the issue.

[msolleder]

We tested MixMHCp on Ubuntu 18.04 with ./MixMHCp -i test/test.txt -o test/out -m 3 and had no issues.

From what we understand from your error given above, line 26 in "calling-ggseqlogoMOD.r" caused the issue. Our original code is source(paste(pathLib, 'R/ggseqlogo.r', sep = '')), however it seems that this was changed in your code into source(paste(pathLib, 'R/ggseqlogo.R', sep = '')) and thereby not finding the files in "MixMHCp-2.1/lib/R/".

[courcelm]

@msolleder I just reviewed code in https://github.com/GfellerLab/MixMHCp/archive/v2.1.tar.gz. There is different case for the extension of the files and the one found in calling-ggseqlogoMOD.r . Your master branch doesn't have this issue.