"Holger Schwender" <holger.schw at="" gmx.de=""> writes: > Hi Seth, > > while following your suggestion and taking a look on the check > reports of siggenes 1.11.0 (for BioC 2.1) I found the following > note: > > checking R code for possible problems ... NOTE > filterALL: no visible binding for global variable 'ALL' > filterALL: no visible binding for global variable 'ALL' > . > . > . > make.tablecode: no visible global function definition for 'lookUp' > make.tablecode: no visible global function definition for 'getTDRows' > Thanks for mentioning that. This is yet another new R feature: R CMD check now runs some code checks from the codetools package. The results are currently reported using NOTE. > I think that has something to do with namespace, since all the > functions mentioned here (e.g., lookUp) are either from the annotate > or the the genefilter package which have both namespaces and are in > the suggests field of siggenes. Can I ignore this, since it is > "only" a note and not a warning or error? Or should I do something, > e.g. adding The messages about "no visible global function definition" are worth investigating. This can be an indication of a typo in a function name, a missing function definition, or a missing Depends listing. It can also be a false positive. One case where you will see false positives is if you Suggest a package and call require() to provide optional functionality. If you see these messages for function that you know will be made available by a call to require(), then you can ignore those messages. For siggenes, I think you have some of both going on. I think the message about variable ALL could be a real problem since you do not Depends or Suggests the ALL package. As you noted, lookUp is from annotate and you have annotate in Suggests and call require -- but you do not check the return value and that is really essential. I don't recognize getTDRows off the top of my head, but you should investigate similarly. Best, + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org