[Bioc-devel] NAMESPACE problem in globaltest, widgetTools and SAGElyzer
Goeman, J.J. (MSTAT)
J.J.Goeman at lumc.nl
Thu Nov 24 16:59:47 CET 2005
Dear BioC developers,
I've been trying to add a NAMESPACE to my globaltest package, but I get an error message when I run Rcmd check (R 2.2.0, WinXP) that I do not understand.
This error happens to be exactly the same that I see in the package check results of the widgetTools package (1.7 release, solaris only)
http://www.bioconductor.org/checkResults/1.7/SunOS-sun4u/widgetTools
The same seems to happen in SAGElyzer (1.7 release, windows only):
http://www.bioconductor.org/checkResults/1.7/Windows/SAGElyzer
I also see that in both packages, the problem occurs only in the 1.7 release, and not on devel.
Does anybody (Jianhua?) know the origin of this error? I have no clue as to the cause of this error in my own package. It even occurs when I use a NAMESPACE with only one line
useDynLib(globaltest)
However, when I remove the namespace file altogether, Rcmd check completes without errors.
I would be grateful for any help.
Jelle
Below is the error I get in globaltest when running Rcmd check. I ran Rcmd INSTALL first, which completed without errors. My NAMESPACE file is given at the bottom of this email.
The strangest part of the error message is the message: "In R, the argument of a replacement function which corresponds to the right hand side must be named 'value'." I have only one replacement function, which is correctly formulated and passes Rcmd check without problems if I have no NAMESPACE file.
* using log directory 'C://globaltest.Rcheck'
* using R version 2.2.0, 2005-10-06
* checking for file 'globaltest/DESCRIPTION' ... OK
* this is package 'globaltest' version '3.3.1'
* checking if this is a source package ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking package dependencies ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... WARNING
Error: package/namespace load failed for 'globaltest'
Call sequence:
2: stop(gettextf("package/namespace load failed for '%s'", libraryPkgName(package)),
call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... WARNING
Error: package/namespace load failed for 'globaltest'
Call sequence:
2: stop(gettextf("package/namespace load failed for '%s'", libraryPkgName(package)),
call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
In R, the argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
Error: package/namespace load failed for 'globaltest'
Call sequence:
2: stop(gettextf("package/namespace load failed for '%s'", libraryPkgName(package)),
call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
See section 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
* checking Rd files ... OK
* checking for missing documentation entries ... ERROR
Error: package/namespace load failed for 'globaltest'
And here's the content of my MAMESPACE file:
useDynLib(globaltest)
importFrom(graphics, plot)
exportClasses(gt.result, gt.barplot)
exportMethods("[", show, result, p.value, length, names, "names<-", sort, hist, z.score, scale, plot)
export(globaltest, permutations, sampling, geneplot, sampleplot, regressionplot, checkerboard)
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