Entering edit mode
Hello,
maigesPack's R CMD check
fails on Linux with:
> ## Loading the dataset
> data(gastro)
>
> ## Doing the scale adjustment from median-absolute-value method (from
> ## limma)
> gastro.norm = normScaleLimma(gastro.norm, method="scale")
> boxplot(gastro.norm) ## To see the efect of adjustment
>
> ## To do VSN scale adjustment (from vsn package) use the command. Be
> ## carefull that this method adjust the variance along A values and not
> ## between chips!!
> gastro.norm = normScaleLimma(gastro.raw2, method="vsn")
Error in normalizeVSN(toNorm) :
vsn package required but is not installed (or can't be loaded)
Calls: normScaleLimma -> normalizeVSN
Execution halted
This is because of _R_CHECK_SUGGESTS_ONLY_=true.
I was not able to find a personal (e.g. Github/Gitlab) repo to send a Pull Request for the following fix:
diff --git a/DESCRIPTION b/DESCRIPTION
index 4761580..1cf2faf 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -10,7 +10,7 @@ Author: Gustavo H. Esteves <gesteves@gmail.com>, with contributions
Maintainer: Gustavo H. Esteves <gesteves@gmail.com>
Depends: R (>= 2.10), convert, graph, limma, marray, methods
Suggests: amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML,
- rgl, som
+ rgl, som, vsn
Description: This package uses functions of various other packages
together with other functions in a coordinated way to handle
and analyse cDNA microarray data
Regards, Martin