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
> 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:
>>> 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
>>> >>
>>> >> 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
>>> >
>>> > 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
>>> >> 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.
>>> experts"*, R. Feynman
>>> >>
>>> >> [[alternative HTML version deleted]]
>>> >>
>>> >> ______________________________________________ >>
>>> >
>>> > [[alternative HTML version deleted]]
>>> >
>>> > ______________________________________________ >