[Bioc-devel] R CMD check problems

Luca De Sano l.desano at campus.unimib.it
Thu Feb 25 16:56:58 CET 2016 

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
>>>
>>>
>>>
>>
>

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