buildPhylipLineage fails on Windows

[Kenneth Hoehn]

This appears to result from base::tempfile producing a file path with “\” and base::file.path appending strings with “/” on Windows. While using “/” on Windows seems to be okay, a mixture within the same string is not. One possible solution is to substitute “\” in makeTempDir with “/”, since “/” appears to work on Windows anyway. Another option would be to manually detect the OS and specify “\” in file.path on Windows, though this seems to defeat the purpose of file.path.

Example mixed temp file path below:

AppData\Local\Temp\Rtmpmexzqk\3138-phylip-temp-11d824967928/outfile

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[עמית קורנגוט]

It actually seems that the problem is that without the ‘.exe’ extension the file is not found. but with the extension it doesn’t match wither regex.

[Kenneth Hoehn]

That was definitely part of it. I think we may have just recently fixed this in the development version of alakazam, which you can try out using devtools::install_bitbucket(“kleinstein/alakazam”).