[Bioc-devel] Vignette package error

Jason Ross jason.ross at csiro.au
Thu Feb 4 03:47:24 CET 2016

Hi Dan,

I sure I'm making newb errors, but the failure only on missMethyl had me 
confused. My package internally only relies upon Rcpp, but the vignette 
makes extensive use of libraries, particularly data libraries (as the 
package is batch correction software for data). The vignette makes use 
of missMethyl, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, 
affydata and minfiData but I only get a build error for missMethyl. None 
of these libraries where declared in the Suggests field.

My guess is that these other packages are present on the build machines, 
but missMethyl is not - that is why it is failing on that library alone?

However, having read more now about vignettes, I've realised I should 
actually declare all of these libraries in the Suggests field to make 
the package installation portable.


On 03/02/16 18:42, Dan Tenenbaum wrote:
> ----- Original Message -----
>> From: "Jason Ross" <jason.ross at csiro.au>
>> To: "bioc-devel" <bioc-devel at r-project.org>
>> Sent: Tuesday, February 2, 2016 11:39:51 PM
>> Subject: [Bioc-devel] Vignette package error
>> Hi,
>> My recently submitted package is failing with this error:
>> "Error: processing vignette 'IntroductionToHarman.Rmd' failed with
>> diagnostics: there is no package called 'missMethyl'
>> Execution halted"
>> Build report here:
>> http://bioconductor.org/spb_reports/Harman_0.99.1_buildreport_20160202233741.html
>> However, missMethyl has been in Bioconductor since 3.0.
>> See: https://www.bioconductor.org/packages/release/bioc/html/missMethyl.html
>> I'm not sure what I'm doing wrong? Is the build environment rather old?
>> Should I have missMethyl in the 'suggests' field in the DESCRIPTION file?
> Does your package use missMethyl? Then you need to declare a dependency on it (Depends, Imports, or Suggests, whichever is appropriate) in the DESCRIPTION file, otherwise how is the build system to know it needs it?
> Dan
>> Regards,
>> Jason.
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel


Dr Jason Ross

Senior Research Scientist

Food and Nutrition Flagship


Ejason.ross at csiro.au T+61 2 9490 5015

11 Julius Ave, North Ryde, NSW, 2113

http://www.csiro.au | 


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