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

[Dan Tenenbaum]

----- Original Message -----
> From: "Glyn Bradley" <glyn.x.bradley at gsk.com>
> To: bioc-devel at r-project.org
> Sent: Wednesday, July 22, 2015 1:59:18 AM
> Subject: Re: [Bioc-devel] changes to igraph break many Bioconductor packages (in release and devel)
> 
> Hi All
> 
> Is it acceptable to specify a particular version of igraph for our
> package to use, even as a temporary fix?
> 

It's only possible to say "package(>= x.y.z)". So you can't depend on a specific version (and not one higher than that). Besides, there can only be one version of a package on the build system. 

> 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?

You could try using codetoolsBioC which is not available via biocLite() but is in svn at 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/codetoolsBioC

The function writeNamespaceImports() will attempt to generate the 'imports' section of a NAMESPACE file.

You could also just try building/checking your package against the latest igraph and see if there are any complaints. Though that might not catch every use of igraph...

Dan



> 
> Thanks
> Glyn
> 
> -----Original Message-----
> From: Bioc-devel [mailto:bioc-devel-bounces at r-project.org] On Behalf
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> Sent: 20 July 2015 11:00
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> Subject: Bioc-devel Digest, Vol 136, Issue 20
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>    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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