From m.cowley at garvan.org.au  Sat Oct 20 13:01:52 2012
From: m.cowley at garvan.org.au (Mark Cowley)
Date: Sat, 20 Oct 2012 22:01:52 +1100
Subject: [Rd] R-2.15.1 CMD CHECK output: "Call Sequence"
Message-ID: <F7EACB21-9D34-4F5B-87EA-D72597E96971@garvan.org.au>

Hi guRus,
i'm running R-2.15.1 and the R CMD CHECK output appears to have changed substantially, in that instead of pointing me to the offending functions or files, I get lots of 'call sequence' traces as below.

I've been using R CMD CHECK for years &  never seen anything like this before. This is on a pretty fresh OSX 10.8 Mountain Lion installation, where I installed R from CRAN via pkg. Is this a problem unique to me?

cheers,
Mark

heres' a snippet from testing one of my packages under development:

* checking for unstated dependencies in R code ... WARNING
Error: package/namespace load failed for ?metaGSEA?
Call sequence:
2: stop(gettextf("package/namespace load failed for %s", sQuote(package)), 
      call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
See the information on DESCRIPTION files in the chapter ?Creating R
packages? of the ?Writing R Extensions? manual.
* checking S3 generic/method consistency ... WARNING
Error: package/namespace load failed for ?metaGSEA?
Call sequence:
2: stop(gettextf("package/namespace load failed for %s", sQuote(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 ?metaGSEA?
Call sequence:
2: stop(gettextf("package/namespace load failed for %s", sQuote(package)), 
      call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
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 ?metaGSEA?
Call sequence:
2: stop(gettextf("package/namespace load failed for %s", sQuote(package)), 
      call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     


[Rd] R-2.15.1 CMD CHECK output: "Call Sequence"
Mark Cowley