[R] data.table and R package check

Prof Brian Ripley ripley at stats.ox.ac.uk
Mon Mar 17 10:57:39 CET 2014


On 17/03/2014 09:42, ONKELINX, Thierry wrote:
> This is workaround by defining the 'global variables' as NULL. Use it with caution.

Better, see ?globalVariables (available since R 2.15.1).

>
> ### Fooling R CMD check
> transition_group_id <- NULL
> ### Fooling R CMD check
>
> setkey(aligtable,transition_group_id,align_origfilename)
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest
> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
> Kliniekstraat 25
> 1070 Anderlecht
> Belgium
> + 32 2 525 02 51
> + 32 54 43 61 85
> Thierry.Onkelinx at inbo.be
> www.inbo.be
>
> To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
>
> -----Oorspronkelijk bericht-----
> Van: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] Namens Witold E Wolski
> Verzonden: vrijdag 14 maart 2014 13:16
> Aan: r-help at r-project.org
> Onderwerp: [R] data.table and R package check
>
> Hi,
>
> using data.table in package code i.e
>
> setkey(aligtable,transition_group_id,align_origfilename)
> aligtable = aligtable[CJ(unique(transition_group_id),
> unique(align_origfilename))]
>
> When I do run R package check I got warnings such as:
>
> convert2msExperiment: no visible binding for global variable
>    'transition_group_id'
>
> .... and more and more and MORE
>
> I can't suppress those warnings by putting transition_group_id into quotes because this would break this code:
>
> aligtable = aligtable[CJ(unique(transition_group_id),
> unique(align_origfilename))]
>
>
> Any alternatives?
>
> regards
>
>
>
>
>
>
>
>
>
> --
> Witold Eryk Wolski
>
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-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595




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