From lawrence.michael at gene.com  Thu Nov 17 22:54:21 2016
From: lawrence.michael at gene.com (Michael Lawrence)
Date: Thu, 17 Nov 2016 13:54:21 -0800
Subject: [Rd] new function to tools/utils package: dependencies based on
 DESCRIPTION file
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Hi Jan,

Thanks for volunteering. You, me, Duncan Murdoch (if interested) and
anyone else who is interested should setup an informal chat. We need
to ensure that the API is right and that it fits in well with other
ongoing efforts.

Michael

On Thu, Nov 17, 2016 at 1:40 PM, Jan Gorecki <J.Gorecki at wit.edu.pl> wrote:
> Hi Michael,
> Are you willing to accept patch for this? I'm already using this and
> few related functions for a while, it plays well. I could wrap it as
> patch to utils, or tools?
> Best,
> 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



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