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

Martin Maechler maechler at stat.math.ethz.ch
Fri Apr 20 09:59:56 CEST 2018


>>>>> Thierry Onkelinx <thierry.onkelinx at inbo.be>
>>>>>     on Fri, 20 Apr 2018 09:14:44 +0200 writes:

    > 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.

Hmm, sounds nice .. at first:  In teaching (and research!) I particularly
emphasize people use CRAN (or Bioconductor) packages.

Why on earth is pkgdown not on CRAN ?

Martin Maechler
ETH Zurich

    > 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

    > ______________________________________________
    > R-package-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/r-package-devel



More information about the R-package-devel mailing list