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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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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