M3D package in Bioconductor 3.4
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@francescacairoli-11964
Last seen 5.7 years ago

Hello,

I'm trying to use the 'M3D' package. I've tried with the Bioconductor 3.2 release and everything works fine as in the M3D tutorial.

But when I tried with the release 3.4 I get the following message:

> source("https://bioconductor.org/biocLite.R")

Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help

> biocLite("M3D")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.1 (2016-06-21).

Installing package(s) ‘M3D’

Package which is only available in source form, and may need

compilation of C/C++/Fortran: ‘M3D’

These will not be installed.

I need to use the function 'readBedFiles' which is in the new version only. Do you have any idea on what's the problem and on how I can solve it?

Thank you very much for your time.

bioconductor methylation • 1.0k views
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@steve-lianoglou-2771
Last seen 2 days ago
United States

The rtracklayer package provides rather versatile methods to import a large number of file types used in genomics, bed files certainly being one of them.

If all you need is to import BED files, than try the import (or direct call to import.bed) function it provides to do that.

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@francescacairoli-11964
Last seen 5.7 years ago
No, I need to use the M3D package, but I cannot use the older versione because my bed files are not in the Encode format, so I need to use the newly created function to read bed bed files with format differenti from Encode, which is in the 3.4 release.
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Entering edit mode

I assume you are on Windows, as M3D is failing check on that OS. Since you didn't use the M3D tag for your question, it's possible that Tom Mayo, the maintainer for the package didn't see your question. You might consider emailing him directly and asking him to fix his package so it passes check on Windows. You can get his email at the M3D landing page.

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@dimitris-polychronopoulos-9192
Last seen 5.1 years ago
United Kingdom

You could also try the following to see if they work for you: