[BioC] Error when trying to build a package that needs to import GO.db, GOstats, ath1121501.db packages
Rich Savage
r.s.savage at warwick.ac.uk
Wed Oct 29 14:17:49 CET 2008
Hi all,
I am trying to build a small package that contains some specific functions to
perform GO annotation and have encountered an error when running 'R CMD check'
on the package I (try to) build. Specifically:
[1] "S4"
Length Class Mode
25369 GOTermsAnnDbBimap S4
TERM map for GO (object of class "GOTermsAnnDbBimap")
Error in eapply(GOTERM, function(x) { : argument must be an environment
Calls: WriteGoAnnotationToCsv -> AnnotateClusters -> unlist -> eapply
Execution halted
The relevant code in my package (that generates the above) is:
print(mode(GOTERM))
print(summary(GOTERM))
print(GOTERM)
print(is.environment(GOTERM))
goTermMaster <- unlist(eapply(GOTERM, function(x) {x at Term}));
These functions work fine when I just 'source' them and run them via a script.
The example in my package that 'check' is testing also runs fine when I
cut-and-paste it into R (having sourced the relevant functions). Then problem
only occurs with the package version.
My concern is that I might not be importing something properly into my package.
My NAMESPACE file looks like this:
export(WriteGoAnnotationToCsv)
export(WriteGoAnnotationToLatex)
import(GO.db)
import(GOstats)
import(ath1121501.db)
(both the exports are my own functions)
Finally, I've also noticed that when I use the above print statements in R on
GOTERM, I get different info. Compare:
CODE
----
print(mode(GOTERM))
print(summary(GOTERM))
print(GOTERM)
PACKAGE-BUILDING
----------------
[1] "S4"
Length Class Mode
25369 GOTermsAnnDbBimap S4
TERM map for GO (object of class "GOTermsAnnDbBimap")
IN R ITSELF
-----------
> print(mode(GOTERM))
[1] "S4"
> print(summary(GOTERM))
TERM map for GO (object of class "GOTermsAnnDbBimap")
|
| Lkeyname: go_id (Ltablename: go_term)
| Lkeys: "GO:0000001", "GO:0000002", ... (total=25369/mapped=25369)
|
| Rkeyname: go_id (Rtablename: go_term)
| Rkeys: "GO:0000001", "GO:0000002", ... (total=25369/mapped=25369)
|
| direction: L --> R
NULL
> print(GOTERM)
TERM map for GO (object of class "GOTermsAnnDbBimap")
SESSION INFO
R version 2.8.0 (2008-10-20)
i386-apple-darwin8.11.1
locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] splines tools stats graphics grDevices utils datasets
methods base
other attached packages:
[1] BHC.GoAnnotation_1.2 ath1121501.db_2.2.7 GOstats_2.8.0
Category_2.8.0
[5] genefilter_1.22.0 survival_2.34-1 RBGL_1.18.0
annotate_1.20.0
[9] xtable_1.5-4 graph_1.20.0 GO.db_2.2.5
RSQLite_0.7-0
[13] DBI_0.2-4 AnnotationDbi_1.4.0 Biobase_2.2.0 BHC_1.2.0
loaded via a namespace (and not attached):
[1] GSEABase_1.4.0 XML_1.98-1 cluster_1.11.11
Thanks very much for any help you can offer!
Rich
--
------------------------------------------------------------------
Dr. Richard Savage Tel: +44 (0)24 765 50243
Systems Biology Centre
University of Warwick
Coventry
CV4 7AL
United Kingdom
Web: http://www.programming4scientists.com/
http://wsbc.warwick.ac.uk/~richsavage/
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