R devel - Jun 2016 - new function to tools/utils package: dependencies based on DESCRIPTION file

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

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

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
>
	[[alternative HTML version deleted]]

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