[Bioc-devel] mgsa method not passing on the 'p' argument correctly ?

[Thomas Sandmann]

Dear Sebastian,

I noticed a change in behavior of the 'mgsa' method in your 'mgsa' package
between the current release and development versions.

In the release version of R (see sessionInfo below), the following command
works:

mgsa(
   o=c("A", "B"),
   sets=list(set1 = LETTERS[1:3], set2 = LETTERS[2:4]),
   p=0.1
)

In the devel version (again, see sessionInfo below), the same command
throws an exception, which refers to the 'population' argument.

mgsa(
   o=c("A", "B"),
   sets=list(set1 = LETTERS[1:3], set2 = LETTERS[2:4]),
   p=0.1
)
Error in mgsa.main.debug(o, sets, population, ...) :
  'population' must be NULL or have the same class as 'o'.

When I checked the changes between the release and devel versions of the
mgsa:::mgsa.main function, I noticed that the former lists the available
parameters explicitly, while the latter uses the '...' notations.

I suspect that some partial matching within the parameters provided as
'...' may confuse the 'p' and 'population' arguments. Would you mind taking
a look ?

Thanks a lot !
Thomas

*##---- SessionInfo for release version*
R version 3.1.1 (2014-07-10)
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=en_US.UTF-8       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] mgsa_1.14.2          gplots_2.14.2        BiocInstaller_1.16.1
[4] roxygen2_4.0.2       devtools_1.6.1

loaded via a namespace (and not attached):
[1] bitops_1.0-6       caTools_1.17.1     compiler_3.1.1     gdata_2.13.3
[5] gtools_3.4.1       KernSmooth_2.23-13 Rcpp_0.11.3        stringr_0.6.2
[9] tools_3.1.1

*##---- SessionInfo for devel version*
R Under development (unstable) (2014-11-01 r66923)
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=en_US.UTF-8       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] mgsa_1.15.2          gplots_2.16.0        BiocInstaller_1.17.3
[4] roxygen2_4.1.0       devtools_1.6.1

loaded via a namespace (and not attached):
[1] bitops_1.0-6       caTools_1.17.1     compiler_3.2.0     gdata_2.13.3
[5] gtools_3.4.1       KernSmooth_2.23-13 Rcpp_0.11.3        stringr_0.6.2
[9] tools_3.2.0

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