crsh
commented
5 years ago Did you install a LaTeX distribution (e.g., TinyTeX, see manual for instructions)?
Closed oij11 closed 5 years ago
crsh
commented
5 years ago Did you install a LaTeX distribution (e.g., TinyTeX, see manual for instructions)?
oij11
commented
5 years ago Sorry, I had not seen the manual. However, even after installing pandoc and tinytex, I still cannot knit the markdown. The error message is :
Error running filter /Library/Frameworks/R.framework/Versions/3.5/Resources/library/papaja/rmd/ampersand_filter.R: Error in $: Failed reading: not a valid json value Error: pandoc document conversion failed with error 83 Execution halted
Could you help?
crsh
commented
5 years ago Hmm, are you just trying to knit the bare unedited template? Could you provide the output of devtools::session_info()?
oij11
commented
5 years ago Yes. It was the bare unedited template. Here is the output of session_info:
> devtools::session_info()
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 3.5.0 (2018-04-23)
os macOS High Sierra 10.13.4
system x86_64, darwin15.6.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Chicago
date 2018-12-11
─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 3.5.0)
acepack 1.4.1 2016-10-29 [1] CRAN (R 3.5.0)
AICcmodavg 2.1-1 2017-06-19 [1] CRAN (R 3.5.0)
arm 1.10-1 2018-04-13 [1] CRAN (R 3.5.0)
assertthat 0.2.0 2017-04-11 [1] CRAN (R 3.5.0)
backports 1.1.2 2017-12-13 [1] CRAN (R 3.5.0)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 3.5.0)
BayesFactor 0.9.12-4.2 2018-05-19 [1] CRAN (R 3.5.0)
bayesplot 1.6.0 2018-08-02 [1] CRAN (R 3.5.0)
BDgraph 2.53 2018-11-14 [1] CRAN (R 3.5.0)
bindr 0.1.1 2018-03-13 [1] CRAN (R 3.5.0)
bindrcpp * 0.2.2 2018-03-29 [1] CRAN (R 3.5.0)
bitops 1.0-6 2013-08-17 [1] CRAN (R 3.5.0)
boot 1.3-20 2017-08-06 [1] CRAN (R 3.5.0)
broom 0.5.1.9000 2018-12-06 [1] Github (tidymodels/broom@c5d85b4)
callr 3.0.0 2018-08-24 [1] CRAN (R 3.5.0)
car 3.0-2 2018-08-23 [1] CRAN (R 3.5.0)
carData 3.0-2 2018-09-30 [1] CRAN (R 3.5.0)
caTools 1.17.1.1 2018-07-20 [1] CRAN (R 3.5.0)
cellranger 1.1.0 2016-07-27 [1] CRAN (R 3.5.0)
checkmate 1.8.5 2017-10-24 [1] CRAN (R 3.5.0)
cli 1.0.1 2018-09-25 [1] CRAN (R 3.5.0)
cluster 2.0.7-1 2018-04-13 [1] CRAN (R 3.5.0)
coda 0.19-2 2018-10-08 [1] CRAN (R 3.5.0)
codetools 0.2-15 2016-10-05 [1] CRAN (R 3.5.0)
colorspace 1.3-2 2016-12-14 [1] CRAN (R 3.5.0)
colourpicker 1.0 2017-09-27 [1] CRAN (R 3.5.0)
corpcor 1.6.9 2017-04-01 [1] CRAN (R 3.5.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.0)
crosstalk 1.0.0 2016-12-21 [1] CRAN (R 3.5.0)
curl 3.2 2018-03-28 [1] CRAN (R 3.5.0)
d3Network 0.5.2.1 2015-01-31 [1] CRAN (R 3.5.0)
data.table 1.11.8 2018-09-30 [1] CRAN (R 3.5.0)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.5.0)
DescTools 0.99.26 2018-11-13 [1] CRAN (R 3.5.0)
devtools 2.0.1 2018-10-26 [1] CRAN (R 3.5.0)
digest 0.6.18 2018-10-10 [1] CRAN (R 3.5.0)
dplyr * 0.7.8 2018-11-10 [1] CRAN (R 3.5.0)
DT 0.5 2018-11-05 [1] CRAN (R 3.5.0)
dygraphs 1.1.1.6 2018-07-11 [1] CRAN (R 3.5.0)
ellipse 0.4.1 2018-01-05 [1] CRAN (R 3.5.0)
emmeans 1.3.0 2018-10-26 [1] CRAN (R 3.5.0)
estimability 1.3 2018-02-11 [1] CRAN (R 3.5.0)
evaluate 0.12 2018-10-09 [1] CRAN (R 3.5.0)
expm 0.999-3 2018-09-22 [1] CRAN (R 3.5.0)
fansi 0.4.0 2018-10-05 [1] CRAN (R 3.5.0)
fdrtool 1.2.15 2015-07-08 [1] CRAN (R 3.5.0)
forcats * 0.3.0 2018-02-19 [1] CRAN (R 3.5.0)
foreign * 0.8-71 2018-07-20 [1] CRAN (R 3.5.0)
Formula 1.2-3 2018-05-03 [1] CRAN (R 3.5.0)
fs 1.2.6 2018-08-23 [1] CRAN (R 3.5.0)
gdata 2.18.0 2017-06-06 [1] CRAN (R 3.5.0)
generics 0.0.2 2018-12-06 [1] Github (r-lib/generics@d59e6b4)
ggcorrplot 0.1.2 2018-09-11 [1] CRAN (R 3.5.0)
ggm 2.3 2015-01-21 [1] CRAN (R 3.5.0)
ggplot2 * 3.1.0 2018-10-25 [1] CRAN (R 3.5.0)
ggridges 0.5.1 2018-09-27 [1] CRAN (R 3.5.0)
glasso 1.10 2018-07-13 [1] CRAN (R 3.5.0)
glue 1.3.0 2018-07-17 [1] CRAN (R 3.5.0)
gplots 3.0.1 2016-03-30 [1] CRAN (R 3.5.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 3.5.0)
gtable 0.2.0 2016-02-26 [1] CRAN (R 3.5.0)
gtools 3.8.1 2018-06-26 [1] CRAN (R 3.5.0)
gvlma 1.0.0.2 2014-01-21 [1] CRAN (R 3.5.0)
haven * 2.0.0 2018-11-22 [1] CRAN (R 3.5.0)
Hmisc 4.1-1 2018-01-03 [1] CRAN (R 3.5.0)
hms 0.4.2 2018-03-10 [1] CRAN (R 3.5.0)
htmlTable 1.12 2018-05-26 [1] CRAN (R 3.5.0)
htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.5.0)
htmlwidgets 1.3 2018-09-30 [1] CRAN (R 3.5.0)
httpuv 1.4.5 2018-07-19 [1] CRAN (R 3.5.0)
httr 1.3.1 2017-08-20 [1] CRAN (R 3.5.0)
huge 1.2.7 2015-09-16 [1] CRAN (R 3.5.0)
igraph 1.2.2 2018-07-27 [1] CRAN (R 3.5.0)
inline 0.3.15 2018-05-18 [1] CRAN (R 3.5.0)
jpeg 0.1-8 2014-01-23 [1] CRAN (R 3.5.0)
jsonlite 1.5 2017-06-01 [1] CRAN (R 3.5.0)
KernSmooth 2.23-15 2015-06-29 [1] CRAN (R 3.5.0)
knitr 1.20 2018-02-20 [1] CRAN (R 3.5.0)
later 0.7.5 2018-09-18 [1] CRAN (R 3.5.0)
lattice 0.20-38 2018-11-04 [1] CRAN (R 3.5.0)
latticeExtra 0.6-28 2016-02-09 [1] CRAN (R 3.5.0)
lavaan 0.6-3 2018-09-22 [1] CRAN (R 3.5.0)
lazyeval 0.2.1 2017-10-29 [1] CRAN (R 3.5.0)
lme4 * 1.1-19 2018-11-10 [1] CRAN (R 3.5.0)
lmerTest * 3.0-1 2018-04-23 [1] CRAN (R 3.5.0)
lmSupport * 2.9.13 2018-04-08 [1] CRAN (R 3.5.0)
loo 2.0.0 2018-04-11 [1] CRAN (R 3.5.0)
lubridate 1.7.4 2018-04-11 [1] CRAN (R 3.5.0)
magrittr * 1.5 2014-11-22 [1] CRAN (R 3.5.0)
manipulate 1.0.1 2014-12-24 [1] CRAN (R 3.5.0)
markdown 0.8 2017-04-20 [1] CRAN (R 3.5.0)
MASS 7.3-51.1 2018-11-01 [1] CRAN (R 3.5.0)
Matrix * 1.2-15 2018-11-01 [1] CRAN (R 3.5.0)
matrixcalc 1.0-3 2012-09-15 [1] CRAN (R 3.5.0)
MatrixModels 0.4-1 2015-08-22 [1] CRAN (R 3.5.0)
matrixStats 0.54.0 2018-07-23 [1] CRAN (R 3.5.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.5.0)
mi 1.0 2015-04-16 [1] CRAN (R 3.5.0)
mime 0.6 2018-10-05 [1] CRAN (R 3.5.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 3.5.0)
minqa 1.2.4 2014-10-09 [1] CRAN (R 3.5.0)
mnormt 1.5-5 2016-10-15 [1] CRAN (R 3.5.0)
modelr 0.1.2 2018-05-11 [1] CRAN (R 3.5.0)
multcomp 1.4-8 2017-11-08 [1] CRAN (R 3.5.0)
MuMIn 1.42.1 2018-07-23 [1] CRAN (R 3.5.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.5.0)
mvtnorm 1.0-8 2018-05-31 [1] CRAN (R 3.5.0)
network 1.13.0.1 2018-04-02 [1] CRAN (R 3.5.0)
nFactors 2.3.3 2011-12-20 [1] CRAN (R 3.5.0)
nlme 3.1-137 2018-04-07 [1] CRAN (R 3.5.0)
nloptr 1.2.1 2018-10-03 [1] CRAN (R 3.5.0)
nnet 7.3-12 2016-02-02 [1] CRAN (R 3.5.0)
numDeriv 2016.8-1 2016-08-27 [1] CRAN (R 3.5.0)
openxlsx 4.1.0 2018-05-26 [1] CRAN (R 3.5.0)
papaja 0.1.0.9842 2018-12-06 [1] Github (crsh/papaja@2e11aec)
pbapply 1.3-4 2018-01-10 [1] CRAN (R 3.5.0)
pbivnorm 0.6.0 2015-01-23 [1] CRAN (R 3.5.0)
pbkrtest 0.4-7 2017-03-15 [1] CRAN (R 3.5.0)
pillar 1.3.0 2018-07-14 [1] CRAN (R 3.5.0)
pkgbuild 1.0.2 2018-10-16 [1] CRAN (R 3.5.0)
pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.5.0)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.5.0)
plyr 1.8.4 2016-06-08 [1] CRAN (R 3.5.0)
png 0.1-7 2013-12-03 [1] CRAN (R 3.5.0)
ppcor 1.1 2015-12-03 [1] CRAN (R 3.5.0)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.5.0)
processx 3.2.1 2018-12-05 [1] CRAN (R 3.5.0)
promises 1.0.1 2018-04-13 [1] CRAN (R 3.5.0)
ps 1.2.1 2018-11-06 [1] CRAN (R 3.5.0)
psych 1.8.10 2018-10-31 [1] CRAN (R 3.5.0)
psycho * 0.3.7 2018-09-13 [1] CRAN (R 3.5.0)
purrr * 0.2.5 2018-05-29 [1] CRAN (R 3.5.0)
pwr 1.2-2 2018-03-03 [1] CRAN (R 3.5.0)
qgraph 1.5 2018-04-25 [1] CRAN (R 3.5.0)
R6 2.3.0 2018-10-04 [1] CRAN (R 3.5.0)
raster 2.8-4 2018-11-03 [1] CRAN (R 3.5.0)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.5.0)
Rcpp 1.0.0 2018-11-07 [1] CRAN (R 3.5.0)
readr * 1.2.1 2018-11-22 [1] CRAN (R 3.5.0)
readxl 1.1.0 2018-04-20 [1] CRAN (R 3.5.0)
remotes 2.0.2 2018-10-30 [1] CRAN (R 3.5.0)
reshape 0.8.8 2018-10-23 [1] CRAN (R 3.5.0)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.5.0)
rio 0.5.16 2018-11-26 [1] CRAN (R 3.5.0)
rjson 0.2.20 2018-06-08 [1] CRAN (R 3.5.0)
rlang 0.3.0.1 2018-10-25 [1] CRAN (R 3.5.0)
rmarkdown 1.10 2018-06-11 [1] CRAN (R 3.5.0)
rpart 4.1-13 2018-02-23 [1] CRAN (R 3.5.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.0)
rsconnect 0.8.12 2018-12-05 [1] CRAN (R 3.5.0)
rstan 2.18.2 2018-11-07 [1] CRAN (R 3.5.0)
rstanarm 2.18.2 2018-11-10 [1] CRAN (R 3.5.0)
rstantools 1.5.1 2018-08-22 [1] CRAN (R 3.5.0)
rstudioapi 0.8 2018-10-02 [1] CRAN (R 3.5.0)
rvest 0.3.2 2016-06-17 [1] CRAN (R 3.5.0)
sandwich 2.5-0 2018-08-17 [1] CRAN (R 3.5.0)
scales 1.0.0 2018-08-09 [1] CRAN (R 3.5.0)
sem 3.1-9 2017-04-24 [1] CRAN (R 3.5.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.5.0)
shiny 1.2.0 2018-11-02 [1] CRAN (R 3.5.0)
shinyjs 1.0 2018-01-08 [1] CRAN (R 3.5.0)
shinystan 2.5.0 2018-05-01 [1] CRAN (R 3.5.0)
shinythemes 1.1.2 2018-11-06 [1] CRAN (R 3.5.0)
sna 2.4 2016-08-08 [1] CRAN (R 3.5.0)
sp 1.3-1 2018-06-05 [1] CRAN (R 3.5.0)
StanHeaders 2.18.0 2018-10-07 [1] CRAN (R 3.5.0)
statnet.common 4.1.4 2018-06-22 [1] CRAN (R 3.5.0)
stringi 1.2.4 2018-07-20 [1] CRAN (R 3.5.0)
stringr * 1.3.1 2018-05-10 [1] CRAN (R 3.5.0)
survival 2.43-3 2018-11-26 [1] CRAN (R 3.5.0)
testthat 2.0.1 2018-10-13 [1] CRAN (R 3.5.0)
TH.data 1.0-9 2018-07-10 [1] CRAN (R 3.5.0)
threejs 0.3.1 2017-08-13 [1] CRAN (R 3.5.0)
tibble * 1.4.2 2018-01-22 [1] CRAN (R 3.5.0)
tidyr * 0.8.2 2018-10-28 [1] CRAN (R 3.5.0)
tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.5.0)
tidyverse * 1.2.1 2017-11-14 [1] CRAN (R 3.5.0)
tinytex * 0.9 2018-10-23 [1] CRAN (R 3.5.0)
unmarked 0.12-2 2017-05-15 [1] CRAN (R 3.5.0)
usethis 1.4.0 2018-08-14 [1] CRAN (R 3.5.0)
utf8 1.1.4 2018-05-24 [1] CRAN (R 3.5.0)
VGAM 1.0-6 2018-08-18 [1] CRAN (R 3.5.0)
whisker 0.3-2 2013-04-28 [1] CRAN (R 3.5.0)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.5.0)
xfun 0.4 2018-10-23 [1] CRAN (R 3.5.0)
xml2 1.2.0 2018-01-24 [1] CRAN (R 3.5.0)
xtable 1.8-3 2018-08-29 [1] CRAN (R 3.5.0)
xts 0.11-2 2018-11-05 [1] CRAN (R 3.5.0)
yaml * 2.2.0 2018-07-25 [1] CRAN (R 3.5.0)
zip 1.0.0 2017-04-25 [1] CRAN (R 3.5.0)
zoo 1.8-4 2018-09-19 [1] CRAN (R 3.5.0)
[1] /Library/Frameworks/R.framework/Versions/3.5/Resources/libraryThanks,
crsh
commented
5 years ago Could you try installing the development version (devtools::install_github("crsh/papaja")) to see if that helps? As a quick fix you should be able to circumvent this issue by adding replace_ampersands: no to the YAML front matter.
oij11
commented
5 years ago Thanks, the quick fix worked. I tried resinstalling papaja; it asked whether to update other packages so I chose All. Then, it showed an error as below and stopped. It seems that the issue has to do with broom package (which was also the case when I first tried to install papaja...) but I have no idea how to fix it.
crsh
commented
5 years ago From googeling it seems this is a macOS-specific issue. Have a look at the discussion in this issue and the suggested solutions.
oij11
commented
5 years ago Ok. So I tried the solutions and successfully installed the development version of papaja. However, I still can't knit the unedited template and get the exactly same error.
Error running filter /Library/Frameworks/R.framework/Versions/3.5/Resources/library/papaja/rmd/ampersand_filter.R: Error in $: Failed reading: not a valid json value Error: pandoc document conversion failed with error 83 Execution halted
oij11
commented
5 years ago Not sure what created the error but the problem has gone after I reinstalled R and R studio (deleting all files just as Rprofile and history). Thanks
profgaelle
commented
5 years ago I had the same problem today (also using a Mac; upgraded RStudio, R is the latest version). Even files I had compiled before no longer worked today. Using the replace_ampersands: no in the preamble did the trick but I wonder: what does that do?
crsh
commented
5 years ago It's briefly explained in the manual. I have an idea how I might be able to fix this issue more reliably, but it'll be a while before I get around to it.
profgaelle
commented
5 years ago Thank you! Papaja is great!
On Fri, 12 Apr 2019 at 12:09, Frederik Aust notifications@github.com wrote:
It's briefly explained in the manual https://crsh.github.io/papaja_man/r-markdown-components.html#additional-rendering-options. I have an idea how I might be able to fix this issue more reliably, but it'll be a while before I get around to it.
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/crsh/papaja/issues/255#issuecomment-482519179, or mute the thread https://github.com/notifications/unsubscribe-auth/AmA2YHGm1zCnFbgEmhL3YuJTYE4Z1c2Zks5vgFtjgaJpZM4ZJcM_ .
Error: Failed to compile papajatest.tex. In addition: Warning message: In system2(..., stdout = FALSE, stderr = FALSE) : error in running command Execution halted
When I open a new markdown file with papaya template and try to knit the example, I get the error message as above. Could you help me resolve this?