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boxuancui / DataExplorer

Automate Data Exploration and Treatment
http://boxuancui.github.io/DataExplorer/
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File d3.min.js not found in resource path Error: pandoc document conversion failed with error 99 #116

Closed davidodongojr closed 4 years ago

davidodongojr commented 5 years ago

Any help with this error

File d3.min.js not found in resource path Error: pandoc document conversion failed with error 99

boxuancui commented 5 years ago

Is this from create_report? What system are you running, and sessionInfo? If this is from create_report, turning off plot_str should suppress it, but not sure why this happens.

davidodongojr commented 5 years ago

Hello,

I am using windows 10, Rstudio V1.2.1335 desktop

 library(tidyverse)
-- Attaching packages --------------------------------------- tidyverse 1.2.1 --
v ggplot2 3.1.0       v purrr   0.3.2  
v tibble  2.1.1       v dplyr   0.8.0.1
v tidyr   0.8.3       v stringr 1.4.0  
v readr   1.3.1       v forcats 0.4.0  
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()
> library(DataExplorer)
> create_report(mpg)

processing file: report.rmd
  |..                                                               |   2%
   inline R code fragments

  |...                                                              |   5%
label: global_options (with options) 
List of 1
 $ include: logi FALSE

  |.....                                                            |   7%
  ordinary text without R code

  |......                                                           |  10%
label: introduce
  |........                                                         |  12%
  ordinary text without R code

  |.........                                                        |  14%
label: plot_intro
  |...........                                                      |  17%
  ordinary text without R code

  |............                                                     |  19%
label: data_structure
  |..............                                                   |  21%
  ordinary text without R code

  |...............                                                  |  24%
label: missing_profile
  |.................                                                |  26%
  ordinary text without R code

  |...................                                              |  29%
label: univariate_distribution_header
  |....................                                             |  31%
  ordinary text without R code

  |......................                                           |  33%
label: plot_histogram
  |.......................                                          |  36%
  ordinary text without R code

  |.........................                                        |  38%
label: plot_density
  |..........................                                       |  40%
  ordinary text without R code

  |............................                                     |  43%
label: plot_frequency_bar
  |.............................                                    |  45%
  ordinary text without R code

  |...............................                                  |  48%
label: plot_response_bar
  |................................                                 |  50%
  ordinary text without R code

  |..................................                               |  52%
label: plot_with_bar
  |....................................                             |  55%
  ordinary text without R code

  |.....................................                            |  57%
label: plot_normal_qq
  |.......................................                          |  60%
  ordinary text without R code

  |........................................                         |  62%
label: plot_response_qq
  |..........................................                       |  64%
  ordinary text without R code

  |...........................................                      |  67%
label: plot_by_qq
  |.............................................                    |  69%
  ordinary text without R code

  |..............................................                   |  71%
label: correlation_analysis
  |................................................                 |  74%
  ordinary text without R code

  |..................................................               |  76%
label: principal_component_analysis
  |...................................................              |  79%
  ordinary text without R code

  |.....................................................            |  81%
label: bivariate_distribution_header
  |......................................................           |  83%
  ordinary text without R code

  |........................................................         |  86%
label: plot_response_boxplot
  |.........................................................        |  88%
  ordinary text without R code

  |...........................................................      |  90%
label: plot_by_boxplot
  |............................................................     |  93%
  ordinary text without R code

  |..............................................................   |  95%
label: plot_response_scatterplot
  |...............................................................  |  98%
  ordinary text without R code

  |.................................................................| 100%
label: plot_by_scatterplot

output file: D:/davidodongojr/report.knit.md

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS "D:/davidodongojr/report.utf8.md" --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output pandoc29446a1ff48.html --email-obfuscation none --self-contained --standalone --section-divs --table-of-contents --toc-depth 6 --template "C:\Users\Stellah\Documents\R\win-library\3.5\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable "theme:yeti" --include-in-header "C:\Users\Stellah\AppData\Local\Temp\RtmpoLyg1w\rmarkdown-str294426b3f75.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 
File d3.min.js not found in resource path
Error: pandoc document conversion failed with error 99
boxuancui commented 5 years ago

What is your sessionInfo()?

davidodongojr commented 5 years ago

Hi, Sorry for the delay. here is my sessionInfo()

sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 16299)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] knitr_1.22         rmarkdown_1.12     data.table_1.12.0  DataExplorer_0.8.0 forcats_0.4.0      stringr_1.4.0     
 [7] dplyr_0.8.0.1      purrr_0.3.2        readr_1.3.1        tidyr_0.8.3        tibble_2.1.1       ggplot2_3.1.0     
[13] tidyverse_1.2.1   

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.5 xfun_0.5         reshape2_1.4.3   haven_2.1.0      lattice_0.20-38  colorspace_1.4-1
 [7] generics_0.0.2   htmltools_0.3.6  yaml_2.2.0       rlang_0.3.4      pillar_1.3.1     glue_1.3.1      
[13] withr_2.1.2      modelr_0.1.4     readxl_1.3.1     networkD3_0.4    plyr_1.8.4       munsell_0.5.0   
[19] gtable_0.3.0     cellranger_1.1.0 rvest_0.3.2      htmlwidgets_1.3  evaluate_0.13    labeling_0.3    
[25] parallel_3.5.3   highr_0.8        broom_0.5.1      Rcpp_1.0.1       scales_1.0.0     backports_1.1.3 
[31] jsonlite_1.6     gridExtra_2.3    hms_0.4.2        digest_0.6.18    stringi_1.4.3    grid_3.5.3      
[37] cli_1.1.0        tools_3.5.3      magrittr_1.5     lazyeval_0.2.2   crayon_1.3.4     pkgconfig_2.0.2 
[43] xml2_1.2.0       lubridate_1.7.4  assertthat_0.2.1 httr_1.4.0       rstudioapi_0.10  R6_2.4.0        
[49] igraph_1.2.4     nlme_3.1-137     compiler_3.5.3
boxuancui commented 5 years ago

According to @Ronen4321 from #119:

btw, it was able to generate the individual figures under the report_files/figure-html.

And the corresponding sessionInfo():

OS = Win10

R version 3.5.3 (2019-03-11)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] vcd_1.4-4 scales_1.0.0 knitr_1.22 rmarkdown_1.12 data.table_1.12.0
[6] DataExplorer_0.8.0 forcats_0.4.0 stringr_1.4.0 dplyr_0.8.1 purrr_0.3.2
[11] readr_1.3.1 tidyr_0.8.3 tibble_2.1.1 ggplot2_3.1.1 tidyverse_1.2.1

loaded via a namespace (and not attached):
[1] httr_1.4.0 jsonlite_1.6 modelr_0.1.4 StanHeaders_2.18.1 assertthat_0.2.1
[6] highr_0.8 stats4_3.5.3 cellranger_1.1.0 yaml_2.2.0 pillar_1.4.0
[11] backports_1.1.4 lattice_0.20-38 glue_1.3.1 digest_0.6.19 rvest_0.3.2
[16] colorspace_1.4-1 htmltools_0.3.6 plyr_1.8.4 pkgconfig_2.0.2 rstan_2.18.2
[21] broom_0.5.2 haven_2.1.0 processx_3.3.0 generics_0.0.2 withr_2.1.2
[26] lazyeval_0.2.2 cli_1.1.0 magrittr_1.5 crayon_1.3.4 readxl_1.3.1
[31] evaluate_0.13 ps_1.3.0 fansi_0.4.0 nlme_3.1-137 MASS_7.3-51.1
[36] xml2_1.2.0 pkgbuild_1.0.3 rsconnect_0.8.13 tools_3.5.3 loo_2.1.0
[41] prettyunits_1.0.2 hms_0.4.2 matrixStats_0.54.0 munsell_0.5.0 callr_3.2.0
[46] packrat_0.5.0 networkD3_0.4 compiler_3.5.3 rlang_0.3.4 rstudioapi_0.10
[51] htmlwidgets_1.3 igraph_1.2.4 base64enc_0.1-3 labeling_0.3 gtable_0.3.0
[56] inline_0.3.15 reshape2_1.4.3 R6_2.4.0 gridExtra_2.3 zoo_1.8-4
[61] lubridate_1.7.4 utf8_1.1.4 zeallot_0.1.0 stringi_1.4.3 parallel_3.5.3
[66] Rcpp_1.0.1 vctrs_0.1.0 tidyselect_0.2.5 xfun_0.6 lmtest_0.9-36
georgejk720 commented 5 years ago

I'm also running into this same issue, even just using iris.

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] knitr_1.23         rmarkdown_1.13     data.table_1.12.2  DataExplorer_0.8.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1       pillar_1.4.1     compiler_3.6.0   plyr_1.8.4       highr_0.8        tools_3.6.0     
 [7] digest_0.6.19    jsonlite_1.6     evaluate_0.14    tibble_2.1.3     gtable_0.3.0     pkgconfig_2.0.2 
[13] rlang_0.3.4      igraph_1.2.4.1   rstudioapi_0.10  yaml_2.2.0       parallel_3.6.0   xfun_0.7        
[19] gridExtra_2.3    dplyr_0.8.1      stringr_1.4.0    htmlwidgets_1.3  grid_3.6.0       tidyselect_0.2.5
[25] glue_1.3.1       R6_2.4.0         reshape2_1.4.3   ggplot2_3.1.1    purrr_0.3.2      magrittr_1.5    
[31] scales_1.0.0     htmltools_0.3.6  networkD3_0.4    assertthat_0.2.1 colorspace_1.4-1 labeling_0.3    
[37] stringi_1.4.3    lazyeval_0.2.2   munsell_0.5.0    crayon_1.3.4
data(iris)
library(DataExplorer)
create_report(iris)
> source('~/.active-rstudio-document')
Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang

processing file: report.rmd
  |..                                                               |   2%
   inline R code fragments

  |...                                                              |   5%
label: global_options (with options) 
List of 1
 $ include: logi FALSE

  |.....                                                            |   7%
  ordinary text without R code

  |......                                                           |  10%
label: introduce
  |........                                                         |  12%
  ordinary text without R code

  |.........                                                        |  14%
label: plot_intro
  |...........                                                      |  17%
  ordinary text without R code

  |............                                                     |  19%
label: data_structure
  |..............                                                   |  21%
  ordinary text without R code

  |...............                                                  |  24%
label: missing_profile
  |.................                                                |  26%
  ordinary text without R code

  |...................                                              |  29%
label: univariate_distribution_header
  |....................                                             |  31%
  ordinary text without R code

  |......................                                           |  33%
label: plot_histogram
  |.......................                                          |  36%
  ordinary text without R code

  |.........................                                        |  38%
label: plot_density
  |..........................                                       |  40%
  ordinary text without R code

  |............................                                     |  43%
label: plot_frequency_bar
  |.............................                                    |  45%
  ordinary text without R code

  |...............................                                  |  48%
label: plot_response_bar
  |................................                                 |  50%
  ordinary text without R code

  |..................................                               |  52%
label: plot_with_bar
  |....................................                             |  55%
  ordinary text without R code

  |.....................................                            |  57%
label: plot_normal_qq
  |.......................................                          |  60%
  ordinary text without R code

  |........................................                         |  62%
label: plot_response_qq
  |..........................................                       |  64%
  ordinary text without R code

  |...........................................                      |  67%
label: plot_by_qq
  |.............................................                    |  69%
  ordinary text without R code

  |..............................................                   |  71%
label: correlation_analysis
  |................................................                 |  74%
  ordinary text without R code

  |..................................................               |  76%
label: principal_component_analysis
  |...................................................              |  79%
  ordinary text without R code

  |.....................................................            |  81%
label: bivariate_distribution_header
  |......................................................           |  83%
  ordinary text without R code

  |........................................................         |  86%
label: plot_response_boxplot
  |.........................................................        |  88%
  ordinary text without R code

  |...........................................................      |  90%
label: plot_by_boxplot
  |............................................................     |  93%
  ordinary text without R code

  |..............................................................   |  95%
label: plot_response_scatterplot
  |...............................................................  |  98%
  ordinary text without R code

  |.................................................................| 100%
label: plot_by_scatterplot

output file: C:/Users/georgejk720/Documents/R/report.knit.md

"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS "C:/Users/georgejk720/Documents/R/report.utf8.md" --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output pandoc4dfc43183556.html --email-obfuscation none --self-contained --standalone --section-divs --table-of-contents --toc-depth 6 --template "C:\Users\georgejk720\Documents\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable "theme:yeti" --include-in-header "C:\Users\GEORGE~1.KOL\AppData\Local\Temp\RtmpGmLSoD\rmarkdown-str4dfc69077d05.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 
File d3.min.js not found in resource path
 Error: pandoc document conversion failed with error 99
boxuancui commented 5 years ago

Could any of you try this and let me know if it still throws an error?

create_report(iris, config = configure_report(add_plot_str = FALSE))
georgejk720 commented 5 years ago

Thanks @boxuancui , same issue though unfortunately...

> data(iris)
> library(DataExplorer)
Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
> create_report(iris, config = configure_report(add_plot_str = FALSE))

processing file: report.rmd
  |..                                                               |   2%
   inline R code fragments

  |...                                                              |   5%
label: global_options (with options) 
List of 1
 $ include: logi FALSE

  |.....                                                            |   7%
  ordinary text without R code

  |......                                                           |  10%
label: introduce
  |........                                                         |  12%
  ordinary text without R code

  |.........                                                        |  14%
label: plot_intro
  |...........                                                      |  17%
  ordinary text without R code

  |............                                                     |  19%
label: data_structure
  |..............                                                   |  21%
  ordinary text without R code

  |...............                                                  |  24%
label: missing_profile
  |.................                                                |  26%
  ordinary text without R code

  |...................                                              |  29%
label: univariate_distribution_header
  |....................                                             |  31%
  ordinary text without R code

  |......................                                           |  33%
label: plot_histogram
  |.......................                                          |  36%
  ordinary text without R code

  |.........................                                        |  38%
label: plot_density
  |..........................                                       |  40%
  ordinary text without R code

  |............................                                     |  43%
label: plot_frequency_bar
  |.............................                                    |  45%
  ordinary text without R code

  |...............................                                  |  48%
label: plot_response_bar
  |................................                                 |  50%
  ordinary text without R code

  |..................................                               |  52%
label: plot_with_bar
  |....................................                             |  55%
  ordinary text without R code

  |.....................................                            |  57%
label: plot_normal_qq
  |.......................................                          |  60%
  ordinary text without R code

  |........................................                         |  62%
label: plot_response_qq
  |..........................................                       |  64%
  ordinary text without R code

  |...........................................                      |  67%
label: plot_by_qq
  |.............................................                    |  69%
  ordinary text without R code

  |..............................................                   |  71%
label: correlation_analysis
  |................................................                 |  74%
  ordinary text without R code

  |..................................................               |  76%
label: principal_component_analysis
  |...................................................              |  79%
  ordinary text without R code

  |.....................................................            |  81%
label: bivariate_distribution_header
  |......................................................           |  83%
  ordinary text without R code

  |........................................................         |  86%
label: plot_response_boxplot
  |.........................................................        |  88%
  ordinary text without R code

  |...........................................................      |  90%
label: plot_by_boxplot
  |............................................................     |  93%
  ordinary text without R code

  |..............................................................   |  95%
label: plot_response_scatterplot
  |...............................................................  |  98%
  ordinary text without R code

  |.................................................................| 100%
label: plot_by_scatterplot

output file: C:/Users/george.kolokotronis/Documents/R/report.knit.md

"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS "C:/Users/george.kolokotronis/Documents/R/report.utf8.md" --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output pandoc328430953d9.html --email-obfuscation none --self-contained --standalone --section-divs --table-of-contents --toc-depth 6 --template "C:\Users\george.kolokotronis\Documents\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable "theme:yeti" --include-in-header "C:\Users\GEORGE~1.KOL\AppData\Local\Temp\Rtmpg9mn38\rmarkdown-str3284178f5748.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 
File d3.min.js not found in resource path
 Error: pandoc document conversion failed with error 99 
> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] knitr_1.23         rmarkdown_1.13     data.table_1.12.2  DataExplorer_0.8.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1       pillar_1.4.1     compiler_3.6.0   plyr_1.8.4       highr_0.8        tools_3.6.0     
 [7] digest_0.6.19    evaluate_0.14    tibble_2.1.3     gtable_0.3.0     pkgconfig_2.0.2  rlang_0.3.4     
[13] igraph_1.2.4.1   rstudioapi_0.10  yaml_2.2.0       parallel_3.6.0   xfun_0.7         gridExtra_2.3   
[19] dplyr_0.8.1      stringr_1.4.0    htmlwidgets_1.3  grid_3.6.0       tidyselect_0.2.5 glue_1.3.1      
[25] R6_2.4.0         reshape2_1.4.3   ggplot2_3.1.1    purrr_0.3.2      magrittr_1.5     scales_1.0.0    
[31] htmltools_0.3.6  networkD3_0.4    assertthat_0.2.1 colorspace_1.4-1 labeling_0.3     stringi_1.4.3   
[37] lazyeval_0.2.2   munsell_0.5.0    crayon_1.3.4
pat-s commented 5 years ago

I am also facing this error. Even when using create_report(iris, config = configure_report(add_plot_str = FALSE)).

Details ```r R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Arch Linux Matrix products: default BLAS/LAPACK: /usr/lib/libopenblas_haswellp-r0.3.6.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] knitr_1.23 rmarkdown_1.13 DataExplorer_0.8.0 ggfortify_0.4.7 [5] ggplot2_3.1.1 mlr3survival_0.1.0-9000 magrittr_1.5 data.table_1.12.2 [9] gdtools_0.1.8 mlr3viz_0.1.0-9000 mlr3learners_0.1.0-9000 GenSA_1.1.7 [13] R6_2.4.0 mlr3book_0.1 mlr3tuning_0.1.0-9000 mlr3featsel_0.1.0-9000 [17] mlr3_0.1.0-9000 usethis_1.5.0.9000 loaded via a namespace (and not attached): [1] fs_1.3.1 webshot_0.5.1 RColorBrewer_1.1-2 httr_1.4.0 [5] rprojroot_1.3-2 tools_3.6.0 backports_1.1.4 utf8_1.1.4 [9] rpart_4.1-15 lazyeval_0.2.2 colorspace_1.4-1 withr_2.1.2 [13] mlr3misc_0.1.0-9000 tidyselect_0.2.5 gridExtra_2.3 prettyunits_1.0.2 [17] GGally_1.4.0 processx_3.3.1 compiler_3.6.0 cli_1.1.0 [21] rvest_0.3.4 lgr_0.3.0.9001 xml2_1.2.0 desc_1.2.0 [25] labeling_0.3 bookdown_0.11 scales_1.0.0 checkmate_1.9.3 [29] readr_1.3.1 callr_3.2.0 stringr_1.4.0 praznik_5.0.0 [33] digest_0.6.19 svglite_1.2.2 paradox_0.1 pkgconfig_2.0.2 [37] htmltools_0.3.6 highr_0.8 htmlwidgets_1.3 rlang_0.3.4.9003 [41] rstudioapi_0.10 jsonlite_1.6 dplyr_0.8.1 kableExtra_1.1.0 [45] Matrix_1.2-17 Rcpp_1.0.1 munsell_0.5.0 fansi_0.4.0 [49] stringi_1.4.3 Metrics_0.1.4 yaml_2.2.0 pkgbuild_1.0.3 [53] plyr_1.8.4 grid_3.6.0 parallel_3.6.0 listenv_0.7.0 [57] promises_1.0.1 crayon_1.3.4 lattice_0.20-38 splines_3.6.0 [61] hms_0.4.2 zeallot_0.1.0 ps_1.3.0 pillar_1.4.1 [65] igraph_1.2.4.1 ranger_0.11.2 codetools_0.2-16 reshape2_1.4.3 [69] pkgload_1.0.2 servr_0.13 glue_1.3.1 packrat_0.5.0 [73] evaluate_0.14 survAUC_1.0-5 httpuv_1.5.1 png_0.1-7 [77] vctrs_0.1.0 networkD3_0.4 testthat_2.1.1 gtable_0.3.0 [81] purrr_0.3.2 tidyr_0.8.3 future_1.13.0 reshape_0.8.8 [85] assertthat_0.2.1 xfun_0.7 mime_0.6 later_0.8.0 [89] survival_2.44-1.1 viridisLite_0.3.0 tibble_2.1.3 globals_0.12.4 ```
EarlGlynn commented 5 years ago

DataExplorer failed on the iris and mtcars data.frames on 3 of 4 computers today. It took hours, but the problem seems related to newer versions of Pandoc. Only Pandoc 2.6 works with DataExplorer. It will fail with newer versions 2.7 or higher.

Error 99 was most common with Pandoc 2.7 or higher, but I did seem see some error 11s too.

boxuancui commented 5 years ago

Sharing a more detailed discussion: https://community.rstudio.com/t/specifying-project-specific-version-of-pandoc-possible/36187/3. Thanks to @EarlGlynn again!

nicofierrov commented 5 years ago

library(DataExplorer) create_report(iris, config = configure_report(add_plot_str = FALSE))

Same issue here

File d3.min.js not found in resource path Error: pandoc document conversion failed with error 99

How can I change Pandoc version in R?

DataStrategist commented 4 years ago

Same issue here, pandoc failing. Any progress?

stephlocke commented 4 years ago

Here's a workaround one of my students identified

In order to get DataExplorer up and running you may want to install Pandoc 2.6 in 3 easy steps:

  1. Download and Install it from https://github.com/jgm/pandoc/releases/tag/2.6 or Direct Download: https://github.com/jgm/pandoc/releases/download/2.6/pandoc-2.6-windows-x86_64.msi
  2. Close R studio
  3. Copy files from C:\Program Files\Pandoc to C:\Program Files\RStudio\bin\pandoc

This downgrade from 2.7 to 2.6 suggests a change in the contents of pandoc templates that DataExplorer is relying upon. A standalone template might be useful (See packages like {revealjs} for examples). The current pandoc templates are available at https://github.com/jgm/pandoc-templates.

boxuancui commented 4 years ago

Thank you @stephlocke for the workaround! Really appreciate it! And for everyone else: I am really really busy at work, so didn't have much time for DataExplorer. My goal is to get v0.9 out by end of year, but let's see! Thank you for all your support and patience!

stephlocke commented 4 years ago

Just posted a PR (#130) that will support a DataExplorer workaround for the problem. I'm hoping to have time at some point to look at bundling resources for Rmds and pandoc to make the default work but I'm happy with this for now.

create_report(flights,
  config = configure_report(
    add_plot_str = FALSE
  ))
boxuancui commented 4 years ago

Hi everyone, I tested the latest develop branch on my Mac with Pandoc 2.7.3. Looks like it is working fine. Could you guys check and let me know if this is actually the case? Thanks!

boxuancui commented 4 years ago

Working fine on my Windows machine too, closing.

DataStrategist commented 4 years ago

Still having the same issue on the dev branch and latest pandoc version:

image

sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] knitr_1.25        rmarkdown_1.16    data.table_1.12.6

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2             plyr_1.8.4             pillar_1.4.2          
 [4] compiler_3.6.1         highr_0.8              DataExplorer_0.8.0    
 [7] tools_3.6.1            digest_0.6.22          packrat_0.5.0         
[10] jsonlite_1.6           evaluate_0.14          tibble_2.1.3          
[13] gtable_0.3.0           pkgconfig_2.0.3        rlang_0.4.1           
[16] igraph_1.2.4.1         rstudioapi_0.10        yaml_2.2.0            
[19] parallel_3.6.1         xfun_0.10              gridExtra_2.3         
[22] dplyr_0.8.3            stringr_1.4.0          htmlwidgets_1.5.1.9000
[25] grid_3.6.1             tidyselect_0.2.5       glue_1.3.1            
[28] R6_2.4.0               reshape2_1.4.3         ggplot2_3.2.1         
[31] purrr_0.3.1            magrittr_1.5           scales_1.0.0          
[34] htmltools_0.4.0        networkD3_0.4          assertthat_0.2.1      
[37] colorspace_1.4-1       labeling_0.3           stringi_1.4.3         
[40] lazyeval_0.2.2         munsell_0.5.0          crayon_1.3.4
boxuancui commented 4 years ago

@DataStrategist Could you do this?

devtools::install_github("boxuancui/DataExplorer", ref = "develop")

Your DataExplorer should show up as following:

other attached packages:
[1] DataExplorer_0.8.0.9000

not DataExplorer_0.8.0.

sidneyasmith commented 4 years ago

Hello, I am relatively new to R and I am still getting pandoc document conversion failed with error 99. I've tried the workaround @stephlocke suggested but still no luck. Below is my session info:

R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] sessioninfo_1.1.1  knitr_1.26         rmarkdown_2.0      data.table_1.12.2  DataExplorer_0.8.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1        pillar_1.4.2      compiler_3.4.4    highr_0.8         tools_3.4.4      
 [6] digest_0.6.18     jsonlite_1.6      evaluate_0.14     tibble_2.1.1      gtable_0.3.0     
[11] pkgconfig_2.0.3   rlang_0.3.4       igraph_1.2.4.1    cli_2.0.0         rstudioapi_0.10  
[16] yaml_2.2.0        parallel_3.4.4    xfun_0.11         gridExtra_2.3     withr_2.1.2      
[21] stringr_1.4.0     htmlwidgets_1.5.1 grid_3.4.4        glue_1.3.1        fansi_0.4.0      
[26] ggplot2_3.2.1     magrittr_1.5      scales_1.0.0      htmltools_0.3.6   networkD3_0.4    
[31] assertthat_0.2.1  colorspace_1.4-1  labeling_0.3      stringi_1.4.3     lazyeval_0.2.2   
[36] munsell_0.5.0     crayon_1.3.4
boxuancui commented 4 years ago

@sidneyasmith Please install devtools and run this:

devtools::install_github("boxuancui/DataExplorer", ref = "develop")

This should be fixed in 546d132.

shankarpandala commented 4 years ago

@sidneyasmith Please install devtools and run this:

devtools::install_github("boxuancui/DataExplorer", ref = "develop")

This should be fixed in 546d132.

I am getting this error while installing using this

Error in i.p(...) : (converted from warning) installation of package ‘C:/Users/SPANDA~1/AppData/Local/Temp/RtmpMFOmj9/file65d820571432/DataExplorer_0.8.1.tar.gz’ had non-zero exit status

boxuancui commented 4 years ago

@shankarpandala The latest version (v0.8.1) is on CRAN. Have you tried installing directly?

shankarpandala commented 4 years ago

@boxuancui with v0.8.1 I am getting this error

File d3.min.js not found in resource path
Error: pandoc document conversion failed with error 99

Thats why I wanted to install using devtools::install_github("boxuancui/DataExplorer", ref = "develop") to fix the issue

boxuancui commented 4 years ago

@shankarpandala Could you attach your sessionInfo()? Currently develop branch is the same as CRAN.

LauraVP1994 commented 3 years ago

I seem to have the same problem, but for File #FN_GTCTGGTTTT11287G_files/htmlwidgets-1.5.3/htmlwidgets.js not found in resource path Error: pandoc document conversion failed with error 99. Previously it worked, but an hour later I started getting this error. I checked in the path itself and the file it supposedly doesn't find is there.

This is my session info: R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

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

other attached packages: [1] matrixStats_0.57.0 stringr_1.4.0 reshape2_1.4.4 openxlsx_4.2.3 plotly_4.9.3
[6] ggplot2_3.3.3

loaded via a namespace (and not attached): [1] tidyselect_1.1.0 xfun_0.19 remotes_2.2.0 purrr_0.3.4 colorspace_2.0-0 [6] vctrs_0.3.6 generics_0.1.0 testthat_3.0.1 usethis_2.0.0 htmltools_0.4.0
[11] viridisLite_0.3.0 yaml_2.2.1 rlang_0.4.10 pkgbuild_1.2.0 pillar_1.4.7
[16] glue_1.4.2 withr_2.3.0 sessioninfo_1.1.1 lifecycle_0.2.0 plyr_1.8.6
[21] munsell_0.5.0 gtable_0.3.0 zip_2.1.1 htmlwidgets_1.5.3 devtools_2.3.2
[26] memoise_1.1.0 knitr_1.30 callr_3.5.1 crosstalk_1.1.0.1 ps_1.5.0
[31] fansi_0.4.1 Rcpp_1.0.3 scales_1.1.1 desc_1.2.0 pkgload_1.1.0
[36] jsonlite_1.7.2 farver_2.0.3 fs_1.5.0 digest_0.6.24 stringi_1.5.3
[41] processx_3.4.5 dplyr_1.0.2 grid_3.6.1 rprojroot_2.0.2 cli_2.2.0
[46] tools_3.6.1 magrittr_2.0.1 lazyeval_0.2.2 tibble_3.0.4 crayon_1.3.4
[51] tidyr_1.1.2 pkgconfig_2.0.3 ellipsis_0.3.1 data.table_1.13.6 prettyunits_1.1.1 [56] assertthat_0.2.1 httr_1.4.2 rstudioapi_0.13 R6_2.5.0 compiler_3.6.1