Hi Marc, I think there is something deeper going on in that the overloaded "get" generic function for the ProbeAnnDbBimap class does not work the way one would assume when called from a function inside a package. Unfortunately my understanding of intricacies of R packages, namespaces and generic functions does not help any further. The suggested getAnnMap() does not solve that, as changing the function (in the package) to getAnnotation <- function(gene, map, chip) { require(annotate) env <- getAnnMap(map, chip) show(env) return (get(gene, env=env)) } leads to the same result: > getAnnotation("1419728_at", "SYMBOL", "mouse430a2") Loading required package: annotate Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: org.Mm.eg.db Loading required package: DBI SYMBOL map for chip mouse430a2 (object of class "ProbeAnnDbBimap") Error in get(gene, env = env) : invalid 'envir' argument -------------------------------------------------------------------- Note the output of show(env), i.e. we are getting the correct map but the get() call still fails. At the same time doing the same on the command line works: ------------------------------------------------ > map <- getAnnMap("SYMBOL", "mouse430a2") > map SYMBOL map for chip mouse430a2 (object of class "ProbeAnnDbBimap") > get("1419728_at", map) [1] "Cxcl5" ------------------------------------------------ Antti On Mar 4, 2010, at 18:42 , Marc Carlson wrote: > Hi Antti, > > You didn't give a lot of detail, but this message probably means that > you did not load the Annotation package before calling (in the 3rd > case). You can put a call to require() in your function to make the > specific annotation package be loaded, but this is probably NOT the > best > way to handle that. It is probably a much better idea at this point > for > you to look at the getAnnMap() function from the annotate package. > > library(annotate) > ?getAnnMap > > As you read the manual page, you will see that getAnnMap is used to > return the map (what you are calling the envir) so that you can do > this > sort of thing in a more generic way. That is, you specify the package > name and the mapping you want, and getAnnMap will try to load any > needed > packages etc. to make sure that its there for you. > > Hope this helps, > > > Marc > > > > > On 03/04/2010 10:18 AM, Antti Honkela wrote: >> Hi all, >> >> I have a weird problem when I try to write a function in a package >> that would use annotation maps (e.g. mouse430a2SYMBOL) as an >> environment that the function works on its own breaks when moved into >> a package. >> >> The maps can usually be used as environments without problems and the >> following works fine: >>> library(mouse430a2.db) >>> get("1419728_at", env=mouse430a2SYMBOL) >> >> The same is true if I define an own function to access the map, and >> this runs without problems: >>> getAnnotation <- function(gene, env) { return (get(gene, env=env)) } >>> getAnnotation("1419728_at", env=mouse430a2SYMBOL) >> >> However, if I move the same function definition to an independent >> package, the same call results in an error: >>> getAnnotation("1419728_at", env=mouse430a2SYMBOL) >> Error in get(gene, env = env) : invalid 'envir' argument >> >> Any ideas how to fix or circumvent this? >> >> (Note that in the sessionInfo below, testpkg is a minimal package >> only >> containing the above function definition.) >> >> >> Best regards, >> >> Antti >> >> --------------------------------------------------------- >>> sessionInfo() >> R version 2.10.1 (2009-12-14) >> i386-apple-darwin9.8.0 >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] mouse430a2.db_2.3.5 org.Mm.eg.db_2.3.6 RSQLite_0.7-3 >> DBI_0.2-4 AnnotationDbi_1.8.1 Biobase_2.6.0 >> [7] testpkg_0.0-1 >> >> loaded via a namespace (and not attached): >> [1] affy_1.24.2 affyio_1.14.0 preprocessCore_1.8.0 >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Antti Honkela Antti.Honkela at tkk.fi - http://www.cis.hut.fi/ahonkela/

On Mar 4, 2010, at 19:51 , Hervé Pagès wrote: Hi Herv?, > I think you need to put a NAMESPACE to your package (you probably > already have one) and import the AnnotationDbi package. This is done > by putting AnnotationDbi in the Imports field of your DESCRIPTION > file and by adding the import(AnnotationDbi) directive to your > NAMESPACE file. Also you need to do the same for the methods > package (put it preferably first i.e. before AnnotationDbi). Thanks, that solved the problem! It might be useful if you could add a note of this to the AnnDbBimap- envirAPI help page as well. Antti -- Antti Honkela Antti.Honkela at tkk.fi - http://www.cis.hut.fi/ahonkela/