seq2pathway is not platform-independent
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afrendeiro • 0
@afrendeiro-8809
Last seen 6.0 years ago
Austria

There are several cross-platform issues with seq2pathway.

This package calls a Python script in a Windows-specific manner (see here: https://github.com/Bioconductor-mirror/seq2pathway/blob/master/R/seq2pathway-internal.r#L750) and the way paths are built is also not platform-independent.

It is easy to fix this to run on Linux but I don't know how to do it in a way that is compatible with all platforms.

Perhaps the best option would be to call the revelant Python functions using a library which allows this interface in R instead of running the python script from the command line.

 

seq2pathway • 555 views
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The package maintainer has been notified about this problem; they have not yet updated their package and in the interim it has been marked as 'deprecated' in the devel branch. Superficially it seems that it would be straight-forward to implement the python code using GenomicRanges; calling python in a system independent way is also straight-forward.

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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 7 months ago
China/Guangzhou/Southern Medical Univer…

I discovered this issue too. Quite surprising, since Bioconductor emphasize runnable examples presented in both vignette and man files.  This package doesn't contain any runnable example. This should be pointed out in package review process.

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