[Bioc-devel] changes to igraph break many Bioconductor packages (in release and devel)

[Glyn Bradley]

Hi All

Is it acceptable to specify a particular version of igraph for our package to use, even as a temporary fix?

Failing that, does anyone know of any way I can get R to tell me which functions in our package (CausalR) call which igraph functions?

Thanks
Glyn

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Today's Topics:

   1. changes to igraph break many Bioconductor packages (in
      release and devel) (Dan Tenenbaum)


----------------------------------------------------------------------

Message: 1
Date: Sun, 19 Jul 2015 14:38:39 -0700 (PDT)
From: Dan Tenenbaum <dtenenba at fredhutch.org>
To: bioc-devel <bioc-devel at r-project.org>
Subject: [Bioc-devel] changes to igraph break many Bioconductor
        packages (in release and devel)
Message-ID:
        <622339655.4339608.1437341919035.JavaMail.root at fredhutch.org>
Content-Type: text/plain; charset=utf-8

Hello,

The igraph package (in CRAN) recently had a major API change. The changes are detailed in its NEWS file:
https://cran.r-project.org/web/packages/igraph/news.html

The changes cause many Bioconductor packages to break in both release and devel. If you are the maintainer of one of the following packages, please see our build report (release: http://bioconductor.org/checkResults/release/bioc-LATEST/ ; devel: http://bioconductor.org/checkResults/devel/bioc-LATEST/ ) for a report of the error and fix it right away in release (if your package is in release) and devel. You should increment the package version number as well in order to cause your changes to propagate.


BioNet
CausalR
facopy
FEM *
FGNet *
geNetClassifier
GenomicInteractions
GenoView
HTSanalyzeR
netbiov



* - these packages also need to be sure to import (in DESCRIPTION and NAMESPACE) the graph package.


If you have any questions, please send them to the bioc-devel mailing list.

Thanks,
Dan



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