[Bioc-devel] Vignette package error

Dan Tenenbaum dtenenba at fredhutch.org
Thu Feb 4 03:53:42 CET 2016

The "Suggests" field is for packages that you use in vignette and maybe example code, but not in the package code proper.
So any package used in the vignette or examples needs to be listed in Suggests.

It happens that some of the packages are already installed on the build system but you can/should never count on that. Also, end users are unlikely to have those packages installed.

See http://www.bioconductor.org/developers/how-to/buildingPackagesForBioc/#description and https://cran.r-project.org/doc/manuals/r-release/R-exts.html#The-DESCRIPTION-file for more about what the various fields mean, especially Suggests.


----- Original Message -----
> From: "Jason Ross" <jason.ross at csiro.au>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Wednesday, February 3, 2016 6:47:24 PM
> Subject: Re: [Bioc-devel] Vignette package error

> 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.
> Cheers,
> Jason.
> 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
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