[Bioc-devel] bnlearn method / generic definition (was Re: R CMD check problems)

[Morgan, Martin]

This reproduces the problem

> loadNamespace('graph')
<environment: namespace:graph>
> loadNamespace('bnlearn')
Error: .onLoad failed in loadNamespace() for 'bnlearn', details:
  call: setMethod("nodes", cl, function(object) .nodes(object))
  error: no existing definition for function 'nodes'


and it's because of the way bnlearn loads itself


  if ("graph" %!in% loadedNamespaces()) {

    setGeneric("nodes", function(object, ...) standardGeneric("nodes"))
    setGeneric("nodes<-", function(object, value) standardGeneric("nodes<-"))
    setGeneric("degree", function(object, Nodes, ...) standardGeneric("degree"))

  }#THEN

  # add the methods.
  for (cl in bnlearn.classes) {

    setMethod("nodes", cl, function(object) .nodes(object))
    setMethod("nodes<-", cl, function(object, value) .relabel(object, value))
    setMethod("degree", cl, function(object, Nodes) .degree(object, Nodes))

  }#FOR

graph is loaded but not attached, so the generic that it defines is not visible to bnlearn.

I'm ccing the bnlearn maintainer

________________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Vincent Carey <stvjc at channing.harvard.edu>
Sent: Thursday, February 25, 2016 10:23 AM
To: Luca De Sano; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] R CMD check problems

I am evidently not expert in this topic.  However I was able to get past
the warning/halt you identified by moving the importFrom(bnlearn,...)
statements to the top of the NAMESPACE.  I cannot see in the WRE manual how
the order of namespace imports/exports should be controlled.  Other minds
will be needed to set this straight.

On Thu, Feb 25, 2016 at 6:06 AM, Luca De Sano <l.desano at campus.unimib.it>
wrote:

> This is my sessionInfo(), I've the current stable release of bnlearn (3.9).
>
> > sessionInfo()
> R version 3.2.3 (2015-12-10)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 14.04.3 LTS
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=it_IT.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] TRONCO_2.4.0      bnlearn_3.9       doParallel_1.0.10 iterators_1.0.8
> [5] foreach_1.4.3     devtools_1.10.0
>
> loaded via a namespace (and not attached):
>  [1] igraph_1.0.1        graph_1.44.1        Rcpp_0.12.3
>  [4] magrittr_1.5        roxygen2_5.0.1      BiocGenerics_0.12.1
>  [7] munsell_0.4.3       xtable_1.8-2        colorspace_1.2-6
> [10] stringr_1.0.0       plyr_1.8.3          tools_3.2.3
> [13] grid_3.2.3          gtable_0.1.2        R.oo_1.20.0
> [16] withr_1.0.1         digest_0.6.9        gridExtra_2.0.0
> [19] RColorBrewer_1.1-2  Rgraphviz_2.10.0    reshape2_1.4.1
> [22] ggplot2_2.0.0       cgdsr_1.2.5         codetools_0.2-14
> [25] memoise_1.0.0       stringi_1.0-1       R.methodsS3_1.7.1
> [28] scales_0.3.0        stats4_3.2.3
>
>
> --
> Luca De Sano
> tel: +393337177338
> email: l.desano at campus.unimib.it
> PEC: luca.desano at pec.it
>
> On 25 February 2016 at 12:03, Vincent Carey <stvjc at channing.harvard.edu>
> wrote:
>
>> sessionInfo might help.  my guess is that you have an outofdate bnlearn
>> installed?
>>
>> On Thu, Feb 25, 2016 at 5:57 AM, Luca De Sano <l.desano at campus.unimib.it>
>> wrote:
>>
>>> Hi all,
>>> I'm working on a package named TRONCO (
>>> http://bioconductor.org/packages/devel/bioc/html/TRONCO.html ) which was
>>> released last year on bioconductor. Everytime I run R CMD check I get
>>> these
>>> two warnings:
>>>
>>> * checking whether the namespace can be loaded with stated dependencies
>>> ...
>>> WARNING
>>> Error: .onLoad failed in loadNamespace() for 'bnlearn', details:
>>>   call: setMethod("nodes", cl, function(object) .nodes(object))
>>>   error: no existing definition for function ‘nodes’
>>> Execution halted
>>>
>>> * checking whether the namespace can be unloaded cleanly ... WARNING
>>> Error: .onLoad failed in loadNamespace() for 'bnlearn', details:
>>>   call: setMethod("nodes", cl, function(object) .nodes(object))
>>>   error: no existing definition for function ‘nodes’
>>> Execution halted
>>>
>>> I've searched informations about these errors and I've only found some
>>> old
>>> posts on StackOverflow which suggested to change the order of the import.
>>> I've tried to do it with no result. At the moment I can't figure out what
>>> those warnings mean!
>>>
>>> Any suggestions?
>>>
>>> Warnings can be reproduced with the code listed below:
>>>
>>> git clone https://github.com/BIMIB-DISCo/TRONCO.git
>>> R CMD build TRONCO
>>> R CMD check TRONCO_2.3.0.tar.gz
>>>
>>> Thank you
>>>
>>> --
>>> Luca De Sano
>>> tel: +393337177338
>>> email: l.desano at campus.unimib.it
>>> PEC: luca.desano at pec.it
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>>
>

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