.Rmd to .md seems to hangup

Trying to save an .Rmd as .md so I can upload it as a README.md on github.

The rendering appears to work, but hangs up after "output file: coexist_delete.knit.md", and never succeeds to make the final .md. Any thoughts?

I am using the "Knit" button, and my YAML looks like:

processing file: coexist_delete.Rmd
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   inline R code fragments

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label: Load Data (with options) 
List of 3
 $ results: chr "hide"
 $ message: logi FALSE
 $ warning: logi FALSE

Loading required package: gridExtra
Loading required package: grid
Loading required package: sjPlot
Install package "strengejacke" from GitHub (`devtools::install_github("strengejacke/strengejacke")`) to load all sj-packages at once!
Loading required package: huxtable

Attaching package: 'huxtable'

The following object is masked from 'package:sjPlot':

    font_size

Loading required package: lwgeom
Linking to liblwgeom 2.5.0dev r16016, GEOS 3.6.1, PROJ 4.9.3
Loading required package: ggpubr
Loading required package: ggplot2

Attaching package: 'ggplot2'

The following object is masked from 'package:huxtable':

    theme_grey

Loading required package: magrittr

Attaching package: 'ggpubr'

The following object is masked from 'package:huxtable':

    font

Loading required package: ggspatial
Loading required package: rgdal
Loading required package: sp
rgdal: version: 1.3-6, (SVN revision 773)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
 Path to GDAL shared files: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rgdal/gdal
 GDAL binary built with GEOS: FALSE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rgdal/proj
 Linking to sp version: 1.3-1 
Loading required package: raster

Attaching package: 'raster'

The following object is masked from 'package:ggpubr':

    rotate

The following object is masked from 'package:magrittr':

    extract

Loading required package: sf
Linking to GEOS 3.6.1, GDAL 2.1.3, PROJ 4.9.3
Loading required package: velox
Loading required package: here
here() starts at /Users/clayton.lamb/Google Drive/Documents/University/U_A/Analyses/BC_Wide_PhD/Telemetry_Prov_Grizz/Analyses/coexistence
Loading required package: survival
Loading required package: lubridate

Attaching package: 'lubridate'

The following object is masked from 'package:here':

    here

The following object is masked from 'package:base':

    date

Loading required package: MuMIn
Loading required package: lme4
Loading required package: Matrix
Loading required package: ggeffects
Loading required package: adehabitatHR
Loading required package: deldir
deldir 0.1-15
Loading required package: ade4
Loading required package: adehabitatMA

Attaching package: 'adehabitatMA'

The following object is masked from 'package:raster':

    buffer

Loading required package: adehabitatLT
Loading required package: CircStats
Loading required package: MASS

Attaching package: 'MASS'

The following objects are masked from 'package:raster':

    area, select

Loading required package: boot

Attaching package: 'boot'

The following object is masked from 'package:survival':

    aml

Loading required package: rnaturalearth
Loading required package: rnaturalearthdata
Loading required package: viridisLite
Loading required package: units
udunits system database from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/units/share/udunits
Loading required package: tidyverse
── Attaching packages ──────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──
✔ tibble  2.1.1       ✔ purrr   0.2.5  
✔ tidyr   0.8.2       ✔ dplyr   0.8.0.1
✔ readr   1.1.1       ✔ stringr 1.3.1  
✔ tibble  2.1.1       ✔ forcats 0.3.0  
── Conflicts ─────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::add_rownames()    masks huxtable::add_rownames()
✖ lubridate::as.difftime() masks base::as.difftime()
✖ dplyr::combine()         masks gridExtra::combine()
✖ lubridate::date()        masks base::date()
✖ purrr::every()           masks huxtable::every()
✖ tidyr::expand()          masks Matrix::expand()
✖ tidyr::extract()         masks raster::extract(), magrittr::extract()
✖ dplyr::filter()          masks stats::filter()
✖ lubridate::here()        masks here::here()
✖ dplyr::id()              masks adehabitatLT::id()
✖ lubridate::intersect()   masks raster::intersect(), base::intersect()
✖ dplyr::lag()             masks stats::lag()
✖ dplyr::select()          masks MASS::select(), raster::select()
✖ purrr::set_names()       masks magrittr::set_names()
✖ lubridate::setdiff()     masks base::setdiff()
✖ ggplot2::theme_grey()    masks huxtable::theme_grey()
✖ lubridate::union()       masks raster::union(), base::union()
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  ordinary text without R code

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label: Add Spatial Attributes (with options) 
List of 3
 $ results: chr "hide"
 $ message: logi FALSE
 $ warning: logi FALSE

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  ordinary text without R code

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label: Explore Mortality Data (with options) 
List of 3
 $ results: chr "hide"
 $ message: logi FALSE
 $ warning: logi FALSE


Attaching package: 'scales'

The following object is masked from 'package:purrr':

    discard

The following object is masked from 'package:readr':

    col_factor

The following object is masked from 'package:huxtable':

    number_format

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   inline R code fragments

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label: Explore Reproduction Data (with options) 
List of 3
 $ results: chr "hide"
 $ message: logi FALSE
 $ warning: logi FALSE

Joining, by = "BearID"
Joining, by = "BearID"
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   inline R code fragments

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label: Prep Monthly Survival Data (with options) 
List of 3
 $ results: chr "hide"
 $ message: logi FALSE
 $ warning: logi FALSE

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  ordinary text without R code

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label: Cox Models 1 (with options) 
List of 3
 $ results: chr "hide"
 $ message: logi FALSE
 $ warning: logi FALSE

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   inline R code fragments

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label: Cox Models 1 Results (with options) 
List of 3
 $ results: chr "hide"
 $ message: logi FALSE
 $ warning: logi FALSE

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   inline R code fragments

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label: Spatial Hab Use (with options) 
List of 3
 $ results: chr "hide"
 $ message: logi FALSE
 $ warning: logi FALSE

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   inline R code fragments

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label: Spatial Hab Use Results (with options) 
List of 3
 $ results: chr "hide"
 $ message: logi FALSE
 $ warning: logi FALSE

Computing p-values via Wald-statistics approximation (treating t as Wald z).
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  ordinary text without R code

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label: Temporal Avoidance (with options) 
List of 3
 $ results: chr "hide"
 $ message: logi FALSE
 $ warning: logi FALSE

Parsed with column specification:
cols(
  .default = col_integer(),
  BearID = col_character(),
  Date = col_date(format = ""),
  Time = col_time(format = ""),
  Cause_CL = col_character(),
  Sex = col_character(),
  StudyArea = col_character(),
  ageclass = col_character(),
  ndvi = col_double(),
  dt = col_datetime(format = ""),
  dist = col_double(),
  timedif = col_double(),
  geometry = col_character()
)
See spec(...) for full column specifications.
Warning: 443615 parsing failures.
row # A tibble: 5 x 5 col     row col   expected   actual     file               expected   <int> <chr> <chr>      <chr>      <chr>              actual 1     1 <NA>  21 columns 22 columns 'cap_fix_dist.csv' file 2     2 <NA>  21 columns 22 columns 'cap_fix_dist.csv' row 3     3 <NA>  21 columns 22 columns 'cap_fix_dist.csv' col 4     4 <NA>  21 columns 22 columns 'cap_fix_dist.csv' expected 5     5 <NA>  21 columns 22 columns 'cap_fix_dist.csv'
... ................. ... ...................................................... ........ ...................................................... ...... ...................................................... .... ...................................................... ... ...................................................... ... ...................................................... ........ ......................................................
See problems(...) for more details.

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   inline R code fragments

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label: Temporal Avoidance Results (with options) 
List of 3
 $ results: chr "hide"
 $ message: logi FALSE
 $ warning: logi FALSE

Computing p-values via Wald-statistics approximation (treating t as Wald z).
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  ordinary text without R code

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label: imi rqrd (with options) 
List of 3
 $ results: chr "hide"
 $ message: logi FALSE
 $ warning: logi FALSE

Parsed with column specification:
cols(
  hii = col_integer(),
  l = col_double(),
  im = col_double()
)
  |.................................................................| 100%
  ordinary text without R code


/Applications/RStudio.app/Contents/MacOS/pandoc/pandoc +RTS -K512m -RTS coexist_delete.utf8.md --to markdown_github-ascii_identifiers --from markdown+autolink_bare_uris+tex_math_single_backslash --output coexist_delete.md --standalone --template /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rmarkdown/rmarkdown/templates/github_document/resources/default.md 
output file: coexist_delete.knit.md

Do you have a link to the file as opposed to the output?

I think I have it, after a day of troubleshooting..

I had been print tables via r mytable and although no errors were thrown this appears to have held up the knitting.

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