The following code is from the goProfiles package and works fine: require(goProfiles) data(prostateIds) welsh.MF <- basicProfile(welsh01EntrezIDs, onto = "MF",level = 2, orgPackage = "org.Hs.eg.db") singh.MF <- basicProfile(singh01EntrezIDs, onto = "MF",level = 2, orgPackage = "org.Hs.eg.db") welsh.singh.MF <- mergeProfilesLists(welsh.MF,singh.MF, profNames = c("Welsh", "Singh")) printProfiles(welsh.singh.MF, percentage = TRUE) But if I load the libraries: library(mouse4302.db) library(annaffy) library(annotate) library(GSEAlm) library(safe) and run the above code an error is produced: Error in function (classes, fdef, mtable) : unable to find an inherited method for function "toTable", for signature "environment" > sessionInfo() R version 2.7.0 (2008-04-22) x86_64-pc-linux-gnu locale: C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] org.Hs.eg.db_2.2.0 goProfiles_1.2.0 safe_2.2.0 [4] GO_2.2.0 SparseM_0.78 GSEAlm_1.0.0 [7] annotate_1.18.0 xtable_1.5-2 annaffy_1.12.1 [10] KEGG.db_2.2.0 GO.db_2.2.0 mouse4302.db_2.2.0 [13] AnnotationDbi_1.2.1 RSQLite_0.6-8 DBI_0.2-4 [16] Biobase_2.0.1 If I load only the libraries: library(mouse4302.db) library(annaffy) library(annotate) library(GSEAlm) or only the library library(safe) the above code works. Kind regards, Juerg UMASS Med School [[alternative HTML version deleted]]

Juerg -- Thanks for the report. Most packages use 'GO.db', but 'safe' Depends on 'GO'. The first time you run your code, the search path looks something like > search() [1] ".GlobalEnv" "package:goProfiles" "package:GO.db" [4] "package:AnnotationDbi" "package:RSQLite" "package:DBI" [7] "package:Biobase" "package:tools" "package:stats" [10] "package:graphics" "package:utils" "package:datasets" [13] "package:grDevices" "package:methods" "Autoloads" [16] "package:base" whereas after loading 'safe' you get > search() [1] ".GlobalEnv" "package:safe" "package:GO" [4] "package:SparseM" "package:annotate" "package:xtable" [7] "package:goProfiles" "package:GO.db" "package:AnnotationDbi" [10] "package:RSQLite" "package:DBI" "package:Biobase" [13] "package:tools" "package:stats" "package:graphics" [16] "package:utils" "package:datasets" "package:grDevices" [19] "package:methods" "Autoloads" "package:base" Note 'package:GO' in position 3. goProfiles tries to perform an operation (toTable) that works with objects from GO.db but not from GO. Unfortunately, goProfiles looks on the search path (implicitly) instead of asking for GO.db in particular. This means that after loading safe it finds the mapping in GO, and the error occurs. There are three different solutions. 1. You can work around this by issuing > detach('package:GO') after library(safe). This might cause problems if 'safe' really only works with GO, and not with GO.db 2. the 'safe' maintainer (cc'd) can update their package to use 'GO.db' instead of GO. This will have to be done before the next release anyway. 3. The 'goProfiiles' maintainer (also cc'd) can modify their package code to explicitly request the appropriate version of GO, e.g., library(annotate) getAnnMap("TERM", "GO.db") Thanks again for the report. Martin Straubhaar, Juerg wrote: > The following code is from the goProfiles package and works fine: > > require(goProfiles) > data(prostateIds) > welsh.MF <- basicProfile(welsh01EntrezIDs, onto = "MF",level = 2, orgPackage = "org.Hs.eg.db") > singh.MF <- basicProfile(singh01EntrezIDs, onto = "MF",level = 2, orgPackage = "org.Hs.eg.db") > welsh.singh.MF <- mergeProfilesLists(welsh.MF,singh.MF, profNames = c("Welsh", "Singh")) > printProfiles(welsh.singh.MF, percentage = TRUE) > > But if I load the libraries: > > library(mouse4302.db) > library(annaffy) > library(annotate) > library(GSEAlm) > library(safe) > > and run the above code an error is produced: > > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "toTable", for signature "environment" > >> sessionInfo() > R version 2.7.0 (2008-04-22) > x86_64-pc-linux-gnu > > locale: > C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] org.Hs.eg.db_2.2.0 goProfiles_1.2.0 safe_2.2.0 > [4] GO_2.2.0 SparseM_0.78 GSEAlm_1.0.0 > [7] annotate_1.18.0 xtable_1.5-2 annaffy_1.12.1 > [10] KEGG.db_2.2.0 GO.db_2.2.0 mouse4302.db_2.2.0 > [13] AnnotationDbi_1.2.1 RSQLite_0.6-8 DBI_0.2-4 > [16] Biobase_2.0.1 > > If I load only the libraries: > > library(mouse4302.db) > library(annaffy) > library(annotate) > library(GSEAlm) > > or only the library > > library(safe) > > the above code works. > > Kind regards, > Juerg > UMASS Med School > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793

Juerg and Martin Thanks for notifying the problem and for the suggestion. I will review the code, make the necessary changes, and as soon as it is done I will let you know Alex ---------------------------------------------------------------------- ------------------------------- Alex Sanchez Departament d'Estadistica. Universitat de Barcelona. asanchez at ub.edu Statistics and Bioinformatics Unit. Hospital de Vall d'Hebron. alesanch at ir.vhebron.net ---------------------------------------------------------------------- ------------------------------ Martin Morgan wrote: > Juerg -- > > Thanks for the report. > > Most packages use 'GO.db', but 'safe' Depends on 'GO'. The first time > you run your code, the search path looks something like > > > search() > [1] ".GlobalEnv" "package:goProfiles" "package:GO.db" > [4] "package:AnnotationDbi" "package:RSQLite" "package:DBI" > [7] "package:Biobase" "package:tools" "package:stats" > [10] "package:graphics" "package:utils" "package:datasets" > [13] "package:grDevices" "package:methods" "Autoloads" > [16] "package:base" > > whereas after loading 'safe' you get > > > search() > [1] ".GlobalEnv" "package:safe" "package:GO" > [4] "package:SparseM" "package:annotate" "package:xtable" > [7] "package:goProfiles" "package:GO.db" "package:AnnotationDbi" > [10] "package:RSQLite" "package:DBI" "package:Biobase" > [13] "package:tools" "package:stats" "package:graphics" > [16] "package:utils" "package:datasets" "package:grDevices" > [19] "package:methods" "Autoloads" "package:base" > > Note 'package:GO' in position 3. goProfiles tries to perform an > operation (toTable) that works with objects from GO.db but not from > GO. Unfortunately, goProfiles looks on the search path (implicitly) > instead of asking for GO.db in particular. This means that after > loading safe it finds the mapping in GO, and the error occurs. > > There are three different solutions. > > 1. You can work around this by issuing > > > detach('package:GO') > > after library(safe). This might cause problems if 'safe' really only > works with GO, and not with GO.db > > 2. the 'safe' maintainer (cc'd) can update their package to use > 'GO.db' instead of GO. This will have to be done before the next > release anyway. > > 3. The 'goProfiiles' maintainer (also cc'd) can modify their package > code to explicitly request the appropriate version of GO, e.g., > > library(annotate) > getAnnMap("TERM", "GO.db") > > Thanks again for the report. > > Martin > > Straubhaar, Juerg wrote: >> The following code is from the goProfiles package and works fine: >> >> require(goProfiles) >> data(prostateIds) >> welsh.MF <- basicProfile(welsh01EntrezIDs, onto = "MF",level = 2, >> orgPackage = "org.Hs.eg.db") >> singh.MF <- basicProfile(singh01EntrezIDs, onto = "MF",level = 2, >> orgPackage = "org.Hs.eg.db") >> welsh.singh.MF <- mergeProfilesLists(welsh.MF,singh.MF, profNames = >> c("Welsh", "Singh")) >> printProfiles(welsh.singh.MF, percentage = TRUE) >> >> But if I load the libraries: >> >> library(mouse4302.db) >> library(annaffy) >> library(annotate) >> library(GSEAlm) >> library(safe) >> >> and run the above code an error is produced: >> >> Error in function (classes, fdef, mtable) : unable to find an >> inherited method for function "toTable", for signature "environment" >> >>> sessionInfo() >> R version 2.7.0 (2008-04-22) x86_64-pc-linux-gnu >> locale: >> C >> >> attached base packages: >> [1] tools stats graphics grDevices utils datasets >> methods [8] base >> other attached packages: >> [1] org.Hs.eg.db_2.2.0 goProfiles_1.2.0 safe_2.2.0 [4] >> GO_2.2.0 SparseM_0.78 GSEAlm_1.0.0 [7] >> annotate_1.18.0 xtable_1.5-2 annaffy_1.12.1 [10] >> KEGG.db_2.2.0 GO.db_2.2.0 mouse4302.db_2.2.0 [13] >> AnnotationDbi_1.2.1 RSQLite_0.6-8 DBI_0.2-4 [16] >> Biobase_2.0.1 >> >> If I load only the libraries: >> >> library(mouse4302.db) >> library(annaffy) >> library(annotate) >> library(GSEAlm) >> >> or only the library >> >> library(safe) >> >> the above code works. >> >> Kind regards, >> Juerg >> UMASS Med School >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 > >