[Bioc-devel] R CMD check problems
Dan Tenenbaum
dtenenba at fredhutch.org
Thu Feb 25 17:20:53 CET 2016
Options:
1) Don't use roxygen2
2) after running document(), move the bnlearn imports to the top of the imports section of the NAMESPACE.
3) Report a bug to the roxygen2 authors.
I tried to put
#' @import bnlearn
before any other imports in tronco.R, but it still ended up after the Rgraphviz import in the generated NAMESPACE, which causes this problem.
Dan
----- Original Message -----
> From: "Luca De Sano" <l.desano at campus.unimib.it>
> To: "Vincent Carey" <stvjc at channing.harvard.edu>
> Cc: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Thursday, February 25, 2016 7:56:58 AM
> Subject: Re: [Bioc-devel] R CMD check problems
> The problem is that the NAMESPACE is regenerated every time I execute the
> document() command.
>
> At the moment, in the description file I've added bnlean
>
> Depends:
> R (>= 3.1),
> bnlearn,
> doParallel,
>
> to prevent this:
>
>> library(devtools)
>> document()
> Updating TRONCO documentation
> Loading TRONCO
> Loading required package: doParallel
> Loading required package: foreach
> foreach: simple, scalable parallel programming from Revolution Analytics
> Use Revolution R for scalability, fault tolerance and more.
> http://www.revolutionanalytics.com
> Loading required package: iterators
> Loading required package: parallel
> Warning messages:
> 1: .onLoad failed in loadNamespace() for 'bnlearn', details:
> call: setMethod("nodes", cl, function(object) .nodes(object))
> error: no existing definition for function ‘nodes’
> 2: .onLoad failed in loadNamespace() for 'bnlearn', details:
> call: setMethod("nodes", cl, function(object) .nodes(object))
> error: no existing definition for function ‘nodes’
> 3: .onLoad failed in loadNamespace() for 'bnlearn', details:
> call: setMethod("nodes", cl, function(object) .nodes(object))
> error: no existing definition for function ‘nodes’
> 4: .onLoad failed in loadNamespace() for 'bnlearn', details:
> call: setMethod("nodes", cl, function(object) .nodes(object))
> error: no existing definition for function ‘nodes’
>
> With this configuration I can build and check the package, but the warnings
> mentioned above still remain.
>
>
>
>
> --
> Luca De Sano
> tel: +393337177338
> email: l.desano at campus.unimib.it
> PEC: luca.desano at pec.it
>
> On 25 February 2016 at 16:23, Vincent Carey <stvjc at channing.harvard.edu>
> wrote:
>
>> 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
>>>>
>>>>
>>>>
>>>
>>
>
> [[alternative HTML version deleted]]
>
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