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 <maech...@stat.math.ethz.ch> wrote: > >>>>> Thierry Onkelinx <thierry.onkel...@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.onkel...@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.court...@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.onkel...@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.onkel...@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.court...@gmail.com>: > Re, > >>> > > >>> > On 16 April 2018 at 17:35, Georgi Boshnakov < > > >>> georgi.boshna...@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-boun...@r-project.org] > >>> on behalf >> of Alexandre Courtiol > >>> [alexandre.court...@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@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@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@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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel