`maigesPack` needs to declate a `Suggest` for `vsn`
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Entering edit mode
@6f6493f5
Last seen 14 months ago
Bulgaria

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

maigesPack • 441 views
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