[R-pkg-devel] vignette via devtools: sometimes found, sometimes not (same package)

Fri Apr 20 09:14:44 CEST 2018

Dear Alex,

Another idea is to use pkgdown (http://pkgdown.r-lib.org) to convert
all the documentation of your package (include the vignettes) into a
website. Then you make that available to your students, e.g. through
github pages.

Best regards,

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkelinx at inbo.be
Havenlaan 88 bus 73, 1000 Brussel
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
///////////////////////////////////////////////////////////////////////////////////////////

2018-04-19 18:33 GMT+02:00 Alexandre Courtiol <alexandre.courtiol at gmail.com>:
> Thanks a lot Thierry, I was happy to discover and implement a "drat"
> installation workflow.
> Unfortunately it did not solve the issue (but I will stick to drat).
> Also, I checked the sessionInfo() and could not find any package version
> discriminating accurately between computers that shows vignettes from those
> who do not.
> Only Windows computer have the issue but this proves nothing (and other
> computers with the same OS version are fine).
> Goergi, I did not yet retried outside RStudio (I am trying not to waste too
> much time at the beginning of each course...
> I wish I could hijack a problematic laptop but they don't let me do it as
> they need them).
> ++
> Alex
>
>
> On 17 April 2018 at 10:42, Thierry Onkelinx <thierry.onkelinx at inbo.be>
> wrote:
>>
>> Dear Alex,
>>
>> Have a look at drat
>> (http://eddelbuettel.github.io/drat/DratForPackageAuthors.html). This
>> makes it easier to distribute prepackaged R packages (including When
>> you uploaded a new version, then the student would only have to do
>> drat::addRepo("your_repo") and then install.pakages("LM2GLMM") or
>> update.packages()
>>
>> Best regards,
>>
>> ir. Thierry Onkelinx
>> Statisticus / Statistician
>>
>> Vlaamse Overheid / Government of Flanders
>> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
>> AND FOREST
>> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
>> thierry.onkelinx at inbo.be
>> Havenlaan 88 bus 73, 1000 Brussel
>> 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
>>
>> ///////////////////////////////////////////////////////////////////////////////////////////
>>
>>
>>
>>
>> 2018-04-16 19:38 GMT+02:00 Alexandre Courtiol
>> <alexandre.courtiol at gmail.com>:
>> > Re,
>> >
>> > On 16 April 2018 at 17:35, Georgi Boshnakov <
>> > georgi.boshnakov at manchester.ac.uk> wrote:
>> >
>> >> Hi,
>> >>
>> >> The problem is indeed difficult to debug but there are things that can
>> >> be
>> >> done to narrow it down.
>> >>
>> >> 1. Are there 1/3 unlucky computers fixed? (I.e does the problem occur
>> >> always on the same computers) Also, do you really mean computer or
>> >> user?
>> >>
>> >
>> > Yes, I mean computer, not user.
>> >
>> >>
>> >> 2. Are the students working under R studio? If so, does the same
>> >> problem
>> >> appear if the same procedure is run outside R studio.
>> >>
>> >
>> > I will try tomorrow (but from memory I think the answer will be yes).
>> >
>> >>
>> >> 3. Further to 2.,  You mention development mode - do (some) students
>> >> also
>> >> have a copy of your repository? This may be aproblem if they don't
>> >> update
>> >> it too.
>> >>
>> >
>> > No, only me has the devel version.
>> >
>> >>
>> >> 4. What happens if R is restarted?
>> >
>> >
>> > I will try tomorrow (but I think the answer will be nothing).
>> >
>> >
>> >> 5. It may be worth checking .Rprofle and similar for the concerned
>> >> computers (or users, see 1.)
>> >>
>> >
>> > I will try as well but most had a fresh install and did not mess with
>> > settings.
>> >
>> >>
>> >> Hope this is of some help.
>> >>
>> >
>> > I will look at all this and also gather the session infos as Ben
>> > suggested.
>> > I think I know how to proceed to get to the bottom of that, but I was
>> > just
>> > hoping that the problem was already well known and the answer as well...
>> > If it is for anyone, please reply. Otherwise, I will investigate.
>> > Thanks to everyone.
>> > Alex
>> >
>> >
>> >>
>> >>
>> >>  Georgi Boshnakov
>> >>
>> >>
>> >> ________________________________________
>> >> From: R-package-devel [r-package-devel-bounces at r-project.org] on behalf
>> >> of Alexandre Courtiol [alexandre.courtiol at gmail.com]
>> >> Sent: 16 April 2018 14:40
>> >> To: List r-package-devel
>> >> Subject: [R-pkg-devel] vignette via devtools: sometimes found,
>> >> sometimes
>> >> not (same package)
>> >>
>> >> Dear all,
>> >> I am teaching a class and for that I created a R package that mostly
>> >> contains vignettes (the slides of the course).
>> >> I host the package on GitHub because I want the students to download
>> >> every
>> >> day the latest version of the package.
>> >> Building the vignettes takes a couple of hours so I pre-build the
>> >> vignettes
>> >> using devtools::build_vignettes before pushing my updates to GitHub.
>> >> The student install the package using
>> >> devtools::install_github("courtiol/LM2GLMM").
>> >> Then, they do library(LM2GLMM) and browseVignettes(package =
>> >> "LM2GLMM")...
>> >>
>> >> ... and that works on 2/3 of the computers, for the others it says
>> >> vignettes not found.
>> >>
>> >> Any idea why and what can I do to make it 100% success?
>> >> Of course on my laptop it works, so I cannot investigate.
>> >> Also, since they all use different versions of R, devtools or OS... I
>> >> would
>> >> like to know the one thing that must be changed if it comes from that
>> >> (but
>> >> I am not sure it does).
>> >>
>> >> I have added a back up function that works for the 1/3 of unfortunate
>> >> students:
>> >>
>> >> get_vignettes <- function() {
>> >>   utils::browseURL(paste0(find.package("LM2GLMM"), "/doc/")) ## for
>> >> installed
>> >>   utils::browseURL(paste0(find.package("LM2GLMM"), "/inst/doc/")) ##
>> >> for
>> >> development
>> >>   return(invisible(NULL))
>> >> }
>> >>
>> >> This functions opens de vignette folder and that shows that all the
>> >> students actually have the html files installed correctly. But it is
>> >> ugly
>> >> because then they have to find the good html file and so forth, so I
>> >> would
>> >> rather have a better solution.
>> >>
>> >> Many thanks,
>> >>
>> >> Alex
>> >>
>> >> --
>> >> Alexandre Courtiol
>> >>
>> >> http://sites.google.com/site/alexandrecourtiol/home
>> >>
>> >> *"Science is the belief in the ignorance of experts"*, R. Feynman
>> >>
>> >>         [[alternative HTML version deleted]]
>> >>
>> >> ______________________________________________
>> >> R-package-devel at r-project.org mailing list
>> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>> >>
>> >
>> >
>> >
>> > --
>> > Alexandre Courtiol
>> >
>> > http://sites.google.com/site/alexandrecourtiol/home
>> >
>> > *"Science is the belief in the ignorance of experts"*, R. Feynman
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > R-package-devel at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>
>
>
> --
> Alexandre Courtiol
>
> http://sites.google.com/site/alexandrecourtiol/home
>
> "Science is the belief in the ignorance of experts", R. Feynman