diffHiC error in mergePairs.
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Last seen 2.0 years ago


I was using the package diffHiC.

While using the mergePairs command I ran into a error which prevented R from opening .h5 files. The error I got was as follows

Error in H5Fopen(file, "H5FACCRDONLY", native = native) : HDF5. File accessibilty. Unable to open file.

Also the previous command prunePairs which also requires reading a .h5 file. It worked before but won't work now. Does anybody know what went wrong/ how I screwed it up ?


diffHiC rdhf5 • 186 views
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Aaron Lun ★ 27k
Last seen 2 hours ago
The city by the bay

You don't give a lot of information. So I won't give much of an answer.

The current release version of diffHic has not changed since the release in April, so it's nothing to do with a software update. The same is true of the current release version of rhdf5, which is responsible for reading and writing HDF5 files. The only other package involved is Rhdf5lib, which changed 17 days ago to fix some ZLIB-related path problems. This change should not be relevant, but I suppose you could try installing the old version (1.6.0) and see if it helps.

Other explanations are that the file doesn't exist, the file doesn't have the right permissions for reading, the file is corrupted, etc. If it was working before, and nothing relevant changed in the packages, then it seems that the problem lies with the files. See, for example, if running example(prunePairs) and example(mergePairs) works. If you're working on a shared file system, then https://github.com/grimbough/Rhdf5lib/issues/11 may be helpful.


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