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).
|............................................................ | 92%
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()
)
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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