From J.Gorecki at wit.edu.pl  Mon Sep  5 01:52:18 2016
From: J.Gorecki at wit.edu.pl (=?UTF-8?B?SmFuIEfDs3JlY2tp?=)
Date: Mon, 5 Sep 2016 00:52:18 +0100
Subject: [Rd] new function to tools/utils package: dependencies based on
 DESCRIPTION file
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Is there any better mailing list for utils related discussion?
Jan

On 16 June 2016 at 14:00, Michael Lawrence <lawrence.michael at gene.com>
wrote:

> I agree that the utils package needs some improvements related to
> this, and hope to make them eventually. This type of feedback is very
> helpful.
>
> Thanks,
> Michael
>
>
>
> On Thu, Jun 16, 2016 at 1:42 AM, Jan G?recki <J.Gorecki at wit.edu.pl> wrote:
> > Dear Joris,
> >
> > So it does looks like the proposed function makes a lot sense then,
> isn't it?
> >
> > Cheers,
> > Jan
> >
> > On 16 June 2016 at 08:37, Joris Meys <jorismeys at gmail.com> wrote:
> >> Dear Jan,
> >>
> >> It is unavoidable to have OS and R dependencies for devtools. The
> building
> >> process for packages is both OS and R dependent, so devtools has to be
> too
> >> according to my understanding.
> >>
> >> Cheers
> >> Joris
> >>
> >> On 14 Jun 2016 18:56, "Jan G?recki" <J.Gorecki at wit.edu.pl> wrote:
> >>
> >> Hi Thierry,
> >>
> >> I'm perfectly aware of it. Any idea when devtools would be shipped as
> >> a base R package, or at least recommended package? To actually answer
> >> the problem described in my email.
> >> I have range of useful functions available tools/utils packages which
> >> are shipped together with R. They doesn't require any OS dependencies
> >> or R dependencies, unlike devtools which requires both. Installing
> >> unnecessary OS dependencies and R dependencies just for such a simple
> >> wrapper doesn't seem to be an elegant way to address it, therefore my
> >> proposal to include that simple function in tools, or utils package.
> >>
> >> Regards,
> >> Jan Gorecki
> >>
> >> On 14 June 2016 at 16:17, Thierry Onkelinx <thierry.onkelinx at inbo.be>
> wrote:
> >>> Dear Jan,
> >>>
> >>> Similar functionality is available in devtools::dev_package_deps()
> >>>
> >>> Best regards,
> >>>
> >>> 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
> >>>
> >>> 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
> >>>
> >>> 2016-06-14 16:54 GMT+02:00 Jan G?recki <J.Gorecki at wit.edu.pl>:
> >>>>
> >>>> Hi all,
> >>>>
> >>>> Packages tools and utils have a lot of useful stuff for R developers.
> >>>> I find one task still not as straightforward as it could. Simply to
> >>>> extract dependencies of a package from DESCRIPTION file (before it is
> >>>> even installed to library). This would be valuable in automation of CI
> >>>> setup in a more meta-data driven way.
> >>>> The simple function below, I know it is short and simple, but having
> >>>> it to be defined in each CI workflow is a pain, it could be already
> >>>> available in tools or utils namespace.
> >>>>
> >>>> package.dependencies.dcf <- function(file = "DESCRIPTION", which =
> >>>> c("Depends","Imports","LinkingTo")) {
> >>>>     stopifnot(file.exists(file), is.character(which))
> >>>>     which_all <- c("Depends", "Imports", "LinkingTo", "Suggests",
> >>>> "Enhances")
> >>>>     if (identical(which, "all"))
> >>>>         which <- which_all
> >>>>     else if (identical(which, "most"))
> >>>>         which <- c("Depends", "Imports", "LinkingTo", "Suggests")
> >>>>     stopifnot(which %in% which_all)
> >>>>     dcf <- read.dcf(file, which)
> >>>>     # parse fields
> >>>>     raw.deps <- unlist(strsplit(dcf[!is.na(dcf)], ",", fixed = TRUE))
> >>>>     # strip stated dependency version
> >>>>     deps <- trimws(sapply(strsplit(trimws(raw.deps), "(", fixed =
> >>>> TRUE), `[[`, 1L))
> >>>>     # exclude base R pkgs
> >>>>     base.pkgs <- c("R", rownames(installed.packages(priority =
> "base")))
> >>>>     setdiff(deps, base.pkgs)
> >>>> }
> >>>>
> >>>> This allows to easily install all package dependencies just based on
> >>>> DESCRIPTION file, so simplify that in custom CI workflows to:
> >>>>
> >>>> if (length(pkgs<-package.dependencies.dcf(which="all")))
> >>>> install.packages(pkgs)
> >>>>
> >>>> And would not require to install custom packages or shell scripts.
> >>>>
> >>>> Regards,
> >>>> Jan Gorecki
> >>>>
> >>>> ______________________________________________
> >>>> R-devel at r-project.org mailing list
> >>>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>>
> >>>
> >>
> >> ______________________________________________
> >> R-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>

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[Rd] new function to tools/utils package: dependencies based on DESCRIPTION file
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