Unable to build with R 3.6.0 on Mac OS 10.13.6 #519

gvwilson · 2020-04-08T12:52:51Z

Cloned this repo to my Mac
HEAD is 5df2127ff
bash ./_build.sh produces warnings about missing packages
- See below for what I've installed
Still getting error from lines 905-919 (07-wt-ed-ds-pipeline.Rmd) (see error log attached).

Installation:

> devtools::install_github("data-edu/dataedu")
> install.packages("RefManageR")
> install.packages("apaTables")
> install.packages("sjPlot")

R:

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

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

loaded via a namespace (and not attached):
[1] compiler_3.6.0

Output from _build.sh:


Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::gitbook')"


processing file: index.Rmd

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output file: index.knit.md



processing file: 01-introduction.Rmd

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output file: 01-introduction.knit.md



processing file: 02-how-to-use.Rmd

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output file: 02-how-to-use.knit.md



processing file: 03-data-scientist-in-edu.Rmd

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output file: 03-data-scientist-in-edu.knit.md



processing file: 04-special-considerations.Rmd

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output file: 04-special-considerations.knit.md



processing file: 05-foundational-skills_1.Rmd

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output file: 05-foundational-skills_1.knit.md



processing file: 06-foundational-skills_2.Rmd

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output file: 06-foundational-skills_2.knit.md



processing file: 07-wt-ed-ds-pipeline.Rmd

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── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.3.0.9000     ✔ purrr   0.3.3     
✔ tibble  3.0.0          ✔ dplyr   0.8.3     
✔ tidyr   1.0.0          ✔ stringr 1.4.0     
✔ readr   1.3.1          ✔ forcats 0.4.0     
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Learn more about sjPlot with 'browseVignettes("sjPlot")'.

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List of 4
 $ warning: logi FALSE
 $ message: logi FALSE
 $ results: chr "hide"
 $ fig.cap: chr "Example Plot"

Quitting from lines 905-919 (07-wt-ed-ds-pipeline.Rmd) 
Error in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  : 
  polygon edge not found
Calls: local ... <Anonymous> -> widthDetails -> widthDetails.text -> grid.Call
In addition: There were 30 warnings (use warnings() to see them)

Execution halted
Error in Rscript_render(f, render_args, render_meta) : 
  Failed to compile 07-wt-ed-ds-pipeline.Rmd
Calls: <Anonymous> -> render_new_session -> Rscript_render
Execution halted

The text was updated successfully, but these errors were encountered:

jrosen48 · 2020-04-08T15:10:17Z

We are looking into this now - sorry about this (and thanks very much for telling us about it).

restrellado · 2020-04-09T04:06:27Z

Thanks @gvwilson! I'm tagging @ivelasq in on this, who's been guiding me through the process. Here's more info:

I can reproduce the error when I

knit ch 7 on my Mac
knit another chapter that uses theme_dataedu(), like ch 11. Or when I
run this code:

library(tidyverse)
library(dataedu)
ggplot(mtcars, aes(x = mpg, y = cyl)) +
  geom_point() +
  theme_dataedu()

Ch 7 knits properly when I

remove + theme_dataedu() from each {ggplot2} code chunk or when I
replace + theme_dataedu() with + theme_minimal()

restrellado · 2020-04-09T05:16:55Z

Kudos to @ivelasq for teaming up on this. We're pretty sure this has to do with a missing Gill Sans MT font, at least on my Mac. @gvwilson do you have Gill Sans MT installed on your Mac?

After I installed Gill Sans MT and ran

extrafont::font_import()
loadfonts()

library(tidyverse)
library(dataedu)
ggplot(mtcars, aes(x = mpg, y = cyl)) +
    geom_point() +
    theme_dataedu()

it worked fine. Then we restarted R and knitted Ch 7, which also worked.

@ivelasq is looking for a way for {dataedu} to check for Gill Sans MT. Then we can default to a different font if Gill Sans MT is not installed. Worst case scenario is we'll just change the font to something we're confident most people will have.

@gvwilson as a temporary solution, feel free to remove + theme_dataedu() from the {ggplot2} code chunks and it should build. Thank you again for filing the issue and giving us a shot making it better!

Super curious about why a missing font would cause the polygon error though. Any ideas on that?

jrosen48 · 2020-05-15T10:49:09Z

@restrellado can you say from where you downloaded Gill Sans MT? Found one set of fonts to download, but none seem to be the "base" font (i.e., they're for bold, italic, etc.). I may be misunderstanding how font files work.Having what I think is this same issue with a fresh install of the pkg.!

ivelasq · 2020-06-01T02:41:34Z

Hi @gvwilson, we've updated the {dataedu} package and hope that it resolves the font issue you were encountering. Please reinstall and let us know how it goes! Thanks!

gvwilson · 2020-06-01T21:45:20Z

Hi @ivelasq - unfortunately it still fails to build for me. I have done the following to correct early errors:

install.packages('showtext')
install.packages('tidytext')
install.packages('textdata')

but it still fails with:

Quitting from lines 184-185 (11-wt-text-analysis.Rmd) 
Error in menu(choices = c("Yes", "No"), title = title) : 
  menu() cannot be used non-interactively

I am sync'd with commit bf7cc9c.

restrellado · 2020-06-03T04:39:00Z

Hi @gvwilson Sorry that happened! This can happen if you don't have the NRC Word-Emotion Association Lexicon downloaded yet. If that's true for you, can you please try running this in your console:

tidytext::get_sentiments("nrc")

If you don't already have NRC downloaded, R should prompt you to download it. I think the build breaks when it gets to this part because it doesn't have a way to get a "Yes" from you. Let us know if that works or if you've already tried that!

gvwilson · 2020-06-03T10:35:20Z

Thanks - I installed that interactively and re-ran ./_build.sh. I then rebuilt several times, each build failing on another missing package:

randomNames
dummies
caret
ranger
tidylog

The first two were not available for R 3.6.0 on the first CRAN mirror I tried, but were available from the Tokyo mirror.

Even with these installed, the build failed because of a missing package, but didn't give me the name. The build log is below.

Thanks,
Greg


Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::gitbook')"


processing file: index.Rmd

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output file: 08-wt-gradebook.knit.md

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output file: 09-wt-aggregate-data.knit.md

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16228 Year a double -------------------                       '/Users/gvwilson/misc/data-science-in-education/data/longitudinal_data/bchildcountandedenvironments2012.csv'
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16229 Year a double -------------------                             '/Users/gvwilson/misc/data-science-in-education/data/longitudinal_data/bchildcountandedenvironments2015.csv'
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16227 2016 a double -------------------                             '/Users/gvwilson/misc/data-science-in-education/data/longitudinal_data/bchildcountandedenvironments2016.csv'
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16228 Year a double -------------------                             '/Users/gvwilson/misc/data-science-in-education/data/longitudinal_data/bchildcountandedenvironments2017-18.csv'
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output file: 10-wt-longitudinal-analysis.knit.md

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processing file: 11-wt-text-analysis.Rmd

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── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ──
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output file: 11-wt-text-analysis.knit.md

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processing file: 12-wt-social-network-analysis.Rmd

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output file: 12-wt-social-network-analysis.knit.md

Warning messages:
1: package 'tibble' was built under R version 3.6.2 
2: package 'dplyr' was built under R version 3.6.2 
3: package 'tidygraph' was built under R version 3.6.2 
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processing file: 13-wt-multilevel-models.Rmd

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── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ──
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── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
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output file: 13-wt-multilevel-models.knit.md

Warning messages:
1: package 'tibble' was built under R version 3.6.2 
2: package 'dplyr' was built under R version 3.6.2 
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processing file: 14-wt-machine-learning.Rmd

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── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ──
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label: unnamed-chunk-3 (with options) 
List of 1
 $ eval: logi FALSE


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label: unnamed-chunk-4

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label: check rows

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label: remove rows with NAs

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label: check rows again

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label: unnamed-chunk-5

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label: unnamed-chunk-6

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label: unnamed-chunk-9
Quitting from lines 284-294 (14-wt-machine-learning.Rmd) 
Error: Required package is missing
In addition: Warning messages:
1: package 'tibble' was built under R version 3.6.2 
2: package 'dplyr' was built under R version 3.6.2 
3: package 'tidylog' was built under R version 3.6.2 

Execution halted
Error in Rscript_render(f, render_args, render_meta, add1, add2) : 
  Failed to compile 14-wt-machine-learning.Rmd
Calls: <Anonymous> -> render_new_session -> Rscript_render
Execution halted

ivelasq · 2020-06-03T14:12:42Z

Hi @gvwilson ! I think we're almost there! I suspect that the missing package is the {ranger} package - could you install and let us know how it goes? Thanks!

gvwilson · 2020-06-03T14:59:46Z

Hi @ivelasq - ranger was the 4th package I installed this morning before getting as far as the error above (the list's at the top of my post). Thanks - Greg

ivelasq · 2020-06-03T15:23:24Z

Hi @gvwilson , could you please try with the {randomForest} package installed whenever you get the chance?

Another thought is that maybe the {ranger} library needs to be called in the RMarkdown file - that wasn't the case when we rendered it in the past, though.

Thanks!

gvwilson · 2020-06-03T15:55:17Z

I have installed randomForest, and now get this error at the end of the output:

label: unnamed-chunk-9
Quitting from lines 284-294 (14-wt-machine-learning.Rmd) 
Error: Required package is missing
In addition: Warning messages:
1: package 'tibble' was built under R version 3.6.2 
2: package 'dplyr' was built under R version 3.6.2 
3: package 'tidylog' was built under R version 3.6.2 

Execution halted
Error in Rscript_render(f, render_args, render_meta, add1, add2) : 
  Failed to compile 14-wt-machine-learning.Rmd
Calls: <Anonymous> -> render_new_session -> Rscript_render
Execution halted

gvwilson · 2020-06-28T16:57:41Z

Made some more progress but am still blocked:

Got past previous error using install.packages('e1071').
However, final output of _build.sh is now:

processing file: _main.Rmd
  |......................................................................| 100%
  ordinary text without R code

output file: _main.knit.md

/anaconda3/bin/pandoc +RTS -K512m -RTS _main.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output _main.html --email-obfuscation none --wrap preserve --csl apa_pl.csl --standalone --section-divs --table-of-contents --toc-depth 3 --template /Library/Frameworks/R.framework/Versions/3.6/Resources/library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --css css/style.css --include-in-header /var/folders/cg/b541v521215207m3fnkzd77w0000gn/T//Rtmppc7SZX/rmarkdown-str26e6dd78879.html --mathjax --lua-filter /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rmarkdown/rmd/lua/latex-div.lua --include-in-header google_analytics.html --filter /anaconda3/bin/pandoc-citeproc 
pandoc-citeproc: reference R-tabulizer not found
pandoc-citeproc: reference R-rJava not found
pandoc-citeproc: reference R-amen not found
pandoc-citeproc: reference paris2017culturallya not found
pandoc-citeproc: reference R-amen not found
pandoc-citeproc: reference R-ergm not found
pandoc-citeproc: reference R-statnet not found

Output created: _book/index.html
[1] "/Users/gvwilson/misc/data-science-in-education/_book/index.html"
Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::pdf_book')"


processing file: index.Rmd
  |..............                                                        |  20%
  ordinary text without R code

  |............................                                          |  40%
Quitting from lines 19-39 (index.Rmd) 
Error in options[[sprintf("fig.%s", i)]] * options$dpi : 
  non-numeric argument to binary operator
Calls: local ... process_group.block -> call_block -> fix_options -> %n%

Execution halted
Error in Rscript_render(f, render_args, render_meta, add1, add2) : 
  Failed to compile index.Rmd
Calls: <Anonymous> -> render_new_session -> Rscript_render
Execution halted

I edited before_script.R to change the dpi value from the string "300" to the integer 300. That got me as far as:

label: fig12-2 (with options) 
List of 1
 $ fig.cap: chr "Network Graph with Centrality"

Quitting from lines 269-278 (12-wt-social-network-analysis.Rmd) 
Error in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  : 
  invalid font type
Calls: local ... drawDetails -> drawDetails.text -> grid.Call.graphics
In addition: There were 42 warnings (use warnings() to see them)

Execution halted
Error in Rscript_render(f, render_args, render_meta, add1, add2) : 
  Failed to compile 12-wt-social-network-analysis.Rmd
Calls: <Anonymous> -> render_new_session -> Rscript_render
Execution halted

restrellado · 2020-06-28T23:02:06Z

Hi Greg! Going to try a different approach–I'll do a fresh clone and see if I can reproduce it too. More soon!

restrellado · 2020-06-29T02:21:36Z

Hi again! Ok so we were able to get it to render after downloading a fresh clone of the repo. The only changes we had to make were installing packages I didn't have. We used dataedu::dataedu_packages() to do that. We also had to install {png}, {RefManageR}, and {e1071}. But after all that, it rendered successfully. Here's my session info:

R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
 [1] compiler_4.0.0  bookdown_0.19   htmltools_0.4.0 tools_4.0.0     yaml_2.2.1     
 [6] Rcpp_1.0.4.6    rmarkdown_2.1   knitr_1.28      xfun_0.14       digest_0.6.25  
[11] rlang_0.4.6     evaluate_0.14

@ivelasq did a little more research and thinks it might be a missing Arial Narrow font, based on another similar issue she found. I'll let Isabella explain the thing she thought you could try. Take it away @ivelasq!

ivelasq · 2020-06-29T02:38:48Z

Thanks Ryan! Hi Greg, thanks for the update. Like Ryan said, I found this issue where it states that Arial Narrow was missing, which was causing the problem. They download it using {extrafont}. Could you please try that, and let us know if it works?
thomasp85/ggraph#152

I actually hadn't noticed, but I was missing this font as well! For some reason, my render still went through but it did give me a bunch of warnings: https://datascienceineducation.com/c12.html#plotting-the-network
So, I will try it on my end too!

Greg, one more note - it seems like previously, you were able to get past chapter 12 (as the {e1701} installation fixed something in chapter 14). If there's anything that has changed since then that could help us figure out what is happening in chapter 12, please let us know!

Thanks!

gvwilson · 2020-06-29T11:50:27Z

Thanks for the feedback - here's where I've gotten to:

Re-run `devtools::install_github('data-edu/dataedu')

Note: maybe add a section in Chapter 2 on installation instructions, either standalone or a forward ref to Section 5.7? O'Reilly books have conditioned me to look for installation instructions early on, and I think other instructors might as well.

`sessionInfo()`

R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

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

other attached packages:
[1] dataedu_0.1.0

loaded via a namespace (and not attached):
[1] compiler_3.6.0 showtext_0.8-1 showtextdb_3.0 sysfonts_0.8.1 proto_1.0.0

`dataedu`

> library(dataedu)
> dataedu::dataedu_packages # note: a variable, not a function call
 [1] "apaTables"   "caret"       "dummies"     "e1071"       "ggraph"     
 [6] "here"        "janitor"     "lme4"        "lubridate"   "performance"
[11] "ranger"      "readxl"      "rtweet"      "randomNames" "sjPlot"     
[16] "textdata"    "tidygraph"   "tidylog"     "tidyverse"   "tidytext"

Build HTML version.

The first command in _build.sh is Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::gitbook')".
It runs to completion and produces _book/index.html.

Build PDF version.

The second command in _build.sh is Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::pdf_book')".
It fails. The last few lines of output are:

label: fig12-1 (with options) 
List of 1
 $ fig.cap: chr "Network Graph"

  |...............................................................       |  90%
  ordinary text without R code

  |.................................................................     |  92%
label: unnamed-chunk-17 (with options) 
List of 3
 $ echo   : logi FALSE
 $ message: symbol F
 $ warning: symbol F

  |..................................................................    |  95%
  ordinary text without R code

  |....................................................................  |  97%
label: fig12-2 (with options) 
List of 1
 $ fig.cap: chr "Network Graph with Centrality"

Quitting from lines 269-278 (12-wt-social-network-analysis.Rmd) 
Error in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  : 
  invalid font type
Calls: local ... drawDetails -> drawDetails.text -> grid.Call.graphics
In addition: There were 42 warnings (use warnings() to see them)

Execution halted
Error in Rscript_render(f, render_args, render_meta, add1, add2) : 
  Failed to compile 12-wt-social-network-analysis.Rmd
Calls: <Anonymous> -> render_new_session -> Rscript_render
Execution halted

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Unable to build with R 3.6.0 on Mac OS 10.13.6 #519

Unable to build with R 3.6.0 on Mac OS 10.13.6 #519

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Unable to build with R 3.6.0 on Mac OS 10.13.6 #519

Unable to build with R 3.6.0 on Mac OS 10.13.6 #519

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ivelasq commented Jun 29, 2020 • edited Loading

gvwilson commented Jun 29, 2020

Re-run `devtools::install_github('data-edu/dataedu')

sessionInfo()

dataedu

Build HTML version.

Build PDF version.

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ivelasq commented Jul 1, 2020

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edited

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`sessionInfo()`

`dataedu`