[R-pkg-devel] vignette via devtools: sometimes found, sometimes not (same package)
Alexandre Courtiol
alexandre.courtiol at gmail.com
Tue Apr 24 17:52:38 CEST 2018
Dear all,
I have finally understood why my package installed from GitHub (via
devtools or drat) would display pre-built vignettes after a call to
browseVignettes() on most but not all computers (despite the vignettes
being physically present in all): if the package is installed on a computer
that has knitr installed, then it works; otherwise it fails.
I can thus fix this by adding knitr in the Imports instead of Suggests, or
by asking people to install with the option dependencies = TRUE.
I am still wondering why knitr is needed (the vignettes are pre-built), but
the workaround seems to work with a 100% success rate.
Thanks for all that tried to fix my issue...
I should have thought about knitr head on but I did not, and neither
sessionInfo() nor devtools::session_info() allows one to know if knitr is
installed or not, and I did not think of checking all installed packages
before.
Best,
Alex
On 20 April 2018 at 09:59, Martin Maechler <maechler at stat.math.ethz.ch>
wrote:
> >>>>> 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
>
--
Alexandre Courtiol
http://sites.google.com/site/alexandrecourtiol/home
*"Science is the belief in the ignorance of experts"*, R. Feynman
[[alternative HTML version deleted]]
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