bug in tutorials?

[jsay]

On R version 3.4.4 (2018-03-15)
I've loaded the libraries ScPoEconometrics 0.0.1 and learner 0.9.2.1.

When running:

run_tutorial("chapter3",package="ScPoEconometrics")

I obtain:

Listening on http://127.0.0.1:7177
Warning: Error in value[[3L]]: Couldn't normalize path in addResourcePath, with arguments: prefix = 'font-awesome-4.5.0'; directoryPath = '' [No stack trace available]

Related to the following issue:
https://stackoverflow.com/questions/51213726/when-running-a-tutorial-with-learnr-r-gives-an-error

[floswald]

Thanks that’s a very valuable report. Can you post “sessionInfo()” after you see that bug on your computer please? The SO post is without solution unfortunately.

[floswald]

As an aside, we should probably require R 3.5 in September - or whatever is the latest version.

[jsay]

sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] distr_2.7.0 sfsmisc_1.1-2 startupmsg_0.9.5
[4] EnvStats_2.3.1 learnr_0.9.2.1 bindrcpp_0.2.2
[7] plotly_4.8.0 ggplot2_3.0.0 dplyr_0.7.6
[10] shiny_1.1.0 ScPoEconometrics_0.0.1 devtools_1.13.6

loaded via a namespace (and not attached):
[1] tidyselect_0.2.4 purrr_0.2.5 colorspace_1.3-2 htmltools_0.3.6
[5] viridisLite_0.3.0 yaml_2.2.0 rlang_0.2.1 later_0.7.3
[9] pillar_1.3.0 glue_1.3.0 withr_2.1.2 RColorBrewer_1.1-2
[13] bindr_0.1.1 plyr_1.8.4 stringr_1.3.1 munsell_0.5.0
[17] gtable_0.2.0 htmlwidgets_1.2 memoise_1.1.0 evaluate_0.11
[21] knitr_1.20 httpuv_1.4.5 crosstalk_1.0.0 curl_3.2
[25] markdown_0.8 Rcpp_0.12.18 xtable_1.8-2 promises_1.0.1
[29] scales_0.5.0 backports_1.1.2 jsonlite_1.5 mime_0.5
[33] digest_0.6.15 stringi_1.2.4 grid_3.4.4 rprojroot_1.3-2
[37] tools_3.4.4 magrittr_1.5 lazyeval_0.2.1 tibble_1.4.2
[41] crayon_1.3.4 tidyr_0.8.1 pkgconfig_2.0.1 MASS_7.3-49
[45] data.table_1.11.4 assertthat_0.2.0 rmarkdown_1.10 httr_1.3.1
[49] R6_2.2.2 git2r_0.23.0 compiler_3.4.4

[floswald]

Not bug in our code. This is an upstream issue. It has to do with incompatible markdown versions. Will have to deal with that
rstudio/learnr#169

[floswald]

i assigned @jsay to this issue - i will ping you once the upstream issue is resolved so you can try whether it works for you.

[jsay]

I've updated (now R version 3.5.1 (2018-07-02)), and the message error change to:

Error in shiny_prerendered_html(input_rmd, encoding, render_args) :
Prerendered HTML file not found at ./chapter3.html

[floswald]

Yes I’ve got the same. I’m investigating this.

…

On Mon 27 Aug 2018 at 23:12, Jean-Sauveur Ay ***@***.***> wrote: I've updated (now R version 3.5.1 (2018-07-02)), and the message error change to: Error in shiny_prerendered_html(input_rmd, encoding, render_args) : Prerendered HTML file not found at ./chapter3.html — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#54 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA-Wdg2EdJYr_wZS711AZXFriKpYXw2Jks5uVGC2gaJpZM4Vxu1q> .

[floswald]

It works like this: we need to build the html on our computer and put it in /inst. the user calls run_tutorial which looks for that pre rendered html. I think we have a botched /inst onngithub at the moment but I had a hard time yesterday getting it to work. On Tue 28 Aug 2018 at 08:19, Florian Oswald <florian.oswald@gmail.com> wrote:

…

Yes I’ve got the same. I’m investigating this. On Mon 27 Aug 2018 at 23:12, Jean-Sauveur Ay ***@***.***> wrote: > I've updated (now R version 3.5.1 (2018-07-02)), and the message error > change to: > > Error in shiny_prerendered_html(input_rmd, encoding, render_args) : > Prerendered HTML file not found at ./chapter3.html > > — > You are receiving this because you commented. > > > Reply to this email directly, view it on GitHub > <#54 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AA-Wdg2EdJYr_wZS711AZXFriKpYXw2Jks5uVGC2gaJpZM4Vxu1q> > . >

[floswald]

In fact, another solution would be to have the students call rmarkdown::run(filename.rmd), But that filename would be something like system.file(“ScPoEconometrics”,”tutorials”,”chapter3”,”chapter3.rmd”) A bit unwieldy! No? On Tue 28 Aug 2018 at 08:23, Florian Oswald <florian.oswald@gmail.com> wrote:

…

It works like this: we need to build the html on our computer and put it in /inst. the user calls run_tutorial which looks for that pre rendered html. I think we have a botched /inst onngithub at the moment but I had a hard time yesterday getting it to work. On Tue 28 Aug 2018 at 08:19, Florian Oswald ***@***.***> wrote: > Yes I’ve got the same. I’m investigating this. > > On Mon 27 Aug 2018 at 23:12, Jean-Sauveur Ay ***@***.***> > wrote: > >> I've updated (now R version 3.5.1 (2018-07-02)), and the message error >> change to: >> >> Error in shiny_prerendered_html(input_rmd, encoding, render_args) : >> Prerendered HTML file not found at ./chapter3.html >> >> — >> You are receiving this because you commented. >> >> >> Reply to this email directly, view it on GitHub >> <#54 (comment)>, >> or mute the thread >> <https://github.com/notifications/unsubscribe-auth/AA-Wdg2EdJYr_wZS711AZXFriKpYXw2Jks5uVGC2gaJpZM4Vxu1q> >> . >> >

[jsay]

Yes,
I do not know sufficiently the learnr package and its interaction with rmarkdown.

rmarkdown::run(ScPoEconometrics/inst/tutorials/chapter3/chapter3.Rmd)
returns:
Erreur : pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).

This needs additional dependencies... I would favor solutions that work on R out of the box (at least for students)

[floswald]

Yes. The tutorials are still WIP. don’t despair, we’ll get there. It will be good to test the tutorials in the coming days as I have not found a way to test them via CI.

…

On Tue 28 Aug 2018 at 19:49, Jean-Sauveur Ay ***@***.***> wrote: Yes, I do not know sufficiently the learnr package and its interaction with rmarkdown. rmarkdown::run(ScPoEconometrics/inst/tutorials/chapter3/chapter3.Rmd) returns: Erreur : pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available). This needs additional dependencies... I would favor solutions that work on R out of the box (at least for students) — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#54 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA-WdlvAcAwOBWYaEJil4UIq1lNq6zeTks5uVYKSgaJpZM4Vxu1q> .

[floswald]

What’s your rstudio build? Pandoc ships as a component of rstudio. Maybe an update is enough? On Tue 28 Aug 2018 at 19:59, Florian Oswald <florian.oswald@gmail.com> wrote:

…

Yes. The tutorials are still WIP. don’t despair, we’ll get there. It will be good to test the tutorials in the coming days as I have not found a way to test them via CI. On Tue 28 Aug 2018 at 19:49, Jean-Sauveur Ay ***@***.***> wrote: > Yes, > I do not know sufficiently the learnr package and its interaction with > rmarkdown. > > rmarkdown::run(ScPoEconometrics/inst/tutorials/chapter3/chapter3.Rmd) > returns: > Erreur : pandoc version 1.12.3 or higher is required and was not found > (see the help page ?rmarkdown::pandoc_available). > > This needs additional dependencies... I would favor solutions that work > on R out of the box (at least for students) > > — > You are receiving this because you commented. > > > Reply to this email directly, view it on GitHub > <#54 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AA-WdlvAcAwOBWYaEJil4UIq1lNq6zeTks5uVYKSgaJpZM4Vxu1q> > . >

[floswald]

Ok I confirm that. If you call that function from rstudio you should be fine (recent version). I’ll tighten up the rmarkdown version requirement in the next update. It will be recommended to use R mainly through Rstudio. from ` ?rmarkdown::pandoc_available`

The system environment variable PATH as well as the version of pandoc shipped with RStudio (its location is set via the environment variable RSTUDIO_PANDOC by RStudio products like the RStudio IDE, RStudio Server, Shiny Server, and RStudio Connect, etc) are scanned for pandoc and the highest version available is used.

On Tue 28 Aug 2018 at 20:06, Florian Oswald <florian.oswald@gmail.com> wrote:

…

What’s your rstudio build? Pandoc ships as a component of rstudio. Maybe an update is enough? On Tue 28 Aug 2018 at 19:59, Florian Oswald ***@***.***> wrote: > Yes. The tutorials are still WIP. don’t despair, we’ll get there. > > It will be good to test the tutorials in the coming days as I have not > found a way to test them via CI. > > On Tue 28 Aug 2018 at 19:49, Jean-Sauveur Ay ***@***.***> > wrote: > >> Yes, >> I do not know sufficiently the learnr package and its interaction with >> rmarkdown. >> >> rmarkdown::run(ScPoEconometrics/inst/tutorials/chapter3/chapter3.Rmd) >> returns: >> Erreur : pandoc version 1.12.3 or higher is required and was not found >> (see the help page ?rmarkdown::pandoc_available). >> >> This needs additional dependencies... I would favor solutions that work >> on R out of the box (at least for students) >> >> — >> You are receiving this because you commented. >> >> >> Reply to this email directly, view it on GitHub >> <#54 (comment)>, >> or mute the thread >> <https://github.com/notifications/unsubscribe-auth/AA-WdlvAcAwOBWYaEJil4UIq1lNq6zeTks5uVYKSgaJpZM4Vxu1q> >> . >> >

[jsay]

I do not use Rstudio usually, I'll try it

[floswald]

yes if you could, please give it a try. we'll recommend students to use it, but it's important to know that there are version requirements outside of Rstudio that we need to be aware of. I'll try to fix this today, do you have time for a couple of tests later on? thanks

[jsay]

ok,

rmarkdown::run("ScPoEconometrics/inst/tutorials/chapter3/chapter3.Rmd")

runs well with Rstudio, I close the issue

[floswald]

ok, that is good to know, thanks! I would still like to be able to use the function run_tutorial instead. I'll give it another try tomorrow with recompiling all the tutorials. maybe you could try again then, I'll ping you on slack.

[floswald]

pinging @jsay to try this out again. Upon reinstallation you will find function runTutorial() in the package which should render everything on your computer (always RStudio!). cheers