[Bioc-devel] check warning of QUALIFIER package

[Hervé Pagès]

Hi Mike,

On 10/22/2014 10:54 AM, Mike wrote:
> Hi,
>
> I am not able to find the cause of the following warning message
>
> Warning: no function found corresponding to methods exports from ‘flowWorkspace’ for: ‘sampleNames<-’
>
>
> First of all,  replacement method 'sampleNames<-' does not seem to be
> used by `QUALIFIER` anywhere.
> Secondly, adding 'importFrom(Biobase,"sampleNames<-")' to NAMESPACE file
> does not resolve the issue.

Adding this to the NAMESPACE file in flowWorkspace should solve the
problem. Note that a bunch of other imports are missing from that
file:

   read.ncdfFlowSet
   flowFrame  (the function)
   flowSet    (the function)
   nodes
   ncdfFlowList
   varMetadata
   phenoData<-
   etc...

See the "no visible global function definition" notes in the online
CHECK report for flowWorkspace for the complete list.

Same problem with the NAMESPACE file in QUALIFIER. Missing imports:

   sampleNames
   pData
   getData
   setcolorder
   rbindlist
   getSample
   getNodes
   parameters
   getGate
   data.table
   exprs
   rename
   standard.theme
   load_gs
   trellis.par.get
   current.panel.limits
   panel.polygon
   panel.segments
   etc...

See the "no visible global function definition" notes in the online
CHECK report for QUALIFIER for the complete list.

Looks like both NAMESPACE files were generated by roxygen2 (4.0.2) so
something must have gone wrong when that tool was used.

HTH,
H.

>
> Any suggestion?
>
> Mike
>
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>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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