Hi,
I've noticed an issue with S4 methods and namespaces which only arises in
particular, difficult to reproduce configurations. One example is the ggbio
package in Bioconductor, which currently emits these warnings when its
namespace is loaded:
----------------------
library(ggbio)
Loading required package: ggplot2
Attaching package: ggbio
The following object(s) are masked from package:ggplot2:
geom_rect, geom_segment, stat_identity, xlim
Warning messages:
1: found methods to import for function append but not the generic itself
2: found methods to import for function as.factor but not the generic
itself
3: found methods to import for function as.list but not the generic
itself
4: found methods to import for function aggregate but not the generic
itself
5: found methods to import for function as.table but not the generic
itself
6: found methods to import for function complete.cases but not the
generic itself
7: found methods to import for function cor but not the generic itself
8: found methods to import for function diff but not the generic itself
9: found methods to import for function drop but not the generic itself
------------------------
I tracked these warnings down to the behavior of the
base:::namespaceImportMethods, which ends up calling
base:::namespaceImportFrom with arguments that seem to violate the
assumptions made in that function. It looks like base:::namespaceImportFrom
(conditionally) assumes that the "vars", "generics" and "packages"
arguments are parallel vectors. However, base:::namespaceImportMethods can
end up filtering 'vars' so that it no longer parallels the other two. Maybe
I am just misreading the code, but the following patch seems to fix things:
Index: src/library/base/R/namespace.R
===================================================================
--- src/library/base/R/namespace.R (revision 58917)
+++ src/library/base/R/namespace.R (working copy)
@@ -930,8 +930,10 @@
namespaceImportMethods <- function(self, ns, vars) {
allVars <- character()
+ generics <- character()
+ packages <- character()
allFuns <- methods:::.getGenerics(ns) # all the methods tables in ns
- packages <- attr(allFuns, "package")
+ allPackages <- attr(allFuns, "package")
pkg <- methods:::getPackageName(ns)
if(!all(vars %in% allFuns)) {
message(gettextf("No methods found in \"%s\" for requests: %s",
@@ -950,16 +952,23 @@
## import methods tables if asked for
## or if the corresponding generic was imported
g <- allFuns[[i]]
+ p <- allPackages[[i]]
if(exists(g, envir = self, inherits = FALSE) # already imported
|| g %in% vars) { # requested explicitly
- tbl <- methods:::.TableMetaName(g, packages[[i]])
- if(is.null(.mergeImportMethods(self, ns, tbl))) # a new
methods
table
+ tbl <- methods:::.TableMetaName(g, p)
+ if(is.null(.mergeImportMethods(self, ns, tbl))) { # a new
methods t
able
allVars <- c(allVars, tbl) # import it;else, was merged
+ generics <- c(generics, g)
+ packages <- c(packages, p)
+ }
}
if(g %in% vars && !exists(g, envir = self, inherits = FALSE)) {
if(exists(g, envir = ns) &&
- methods:::is(get(g, envir = ns), "genericFunction"))
+ methods:::is(get(g, envir = ns), "genericFunction")) {
allVars <- c(allVars, g)
+ generics <- c(generics, g)
+ packages <- c(packages, p)
+ }
else { # should be primitive
fun <- methods::getFunction(g, mustFind = FALSE, where =
self)
if(is.primitive(fun) || methods::is(fun,
"genericFunction")) {}
@@ -970,7 +979,7 @@
}
}
}
- namespaceImportFrom(self, asNamespace(ns), allVars, allFuns, packages)
+ namespaceImportFrom(self, asNamespace(ns), allVars, generics, packages)
}
-----------------------------
Thanks for any advice,
Michael
PS: sessionInfo() (yes, ggbio has a LOT of dependencies):
> sessionInfo()
R Under development (unstable) (2012-04-04 r58917)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggbio_1.2.0 ggplot2_0.9.0 BiocInstaller_1.4.3
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0
[4] biomaRt_2.12.0 Biostrings_2.24.1 biovizBase_1.2.0
[7] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2
[10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4
[13] digest_0.5.2 GenomicFeatures_1.8.0 GenomicRanges_1.8.3
[16] grid_2.16.0 gridExtra_0.9 Hmisc_3.9-3
[19] IRanges_1.14.2 lattice_0.20-6 MASS_7.3-17
[22] Matrix_1.0-6 memoise_0.1 munsell_0.3
[25] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5
[28] RCurl_1.91-1 reshape2_1.2.1 Rsamtools_1.8.0
[31] RSQLite_0.11.1 rtracklayer_1.16.0 scales_0.2.0
[34] snpStats_1.6.0 splines_2.16.0 stats4_2.16.0
[37] stringr_0.6 survival_2.36-12 tools_2.16.0
[40] VariantAnnotation_1.2.2 XML_3.9-4 zlibbioc_1.2.0
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