I use the kableExtra package all the time to create tables in R Markdown and save them to PDF. However today I upgraded to MacOS Catalina and now when I export to PDF, I cannot open the PDF image and get the error, "insufficient data for an image" in Adobe Reader. I don't get an error message in R Markdown and the PDF appears in my files, but I cannot open it in Adobe. If I use another application to open it (i.e., Preview) the resolution is very poor - and not typical of PDF. Has anyone else run into this problem and is there a solution? Many thanks for your help!
My code to retrieve the error is below:
mtcars %>%
kable() %>%
kable_styling() %>%
save_kable("test.pdf")
And session info is:
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] metafor_2.1-0 Matrix_1.2-18 MASS_7.3-51.5 RColorBrewer_1.1-2 tidyr_1.0.2 knitr_1.28
[7] sandwich_2.5-1 plotROC_2.2.1 ggROC_1.0 pROC_1.16.1 dplyr_0.8.4 plyr_1.8.5
[13] foreign_0.8-75 gridExtra_2.3 kableExtra_1.1.0 scales_1.1.0 ggplot2_3.2.1 psych_1.9.12.31
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 lattice_0.20-38 ps_1.3.2 zoo_1.8-7 utf8_1.1.4 assertthat_0.2.1
[7] digest_0.6.24 R6_2.4.1 evaluate_0.14 httr_1.4.1 highr_0.8 pillar_1.4.3
[13] rlang_0.4.4 lazyeval_0.2.2 rstudioapi_0.11 callr_3.4.2 magick_2.3 rmarkdown_2.1
[19] labeling_0.3 webshot_0.5.2 readr_1.3.1 stringr_1.4.0 munsell_0.5.0 compiler_3.6.2
[25] xfun_0.12 pkgconfig_2.0.3 mnormt_1.5-6 htmltools_0.4.0 tidyselect_1.0.0 tibble_2.1.3
[31] fansi_0.4.1 viridisLite_0.3.0 crayon_1.3.4 withr_2.1.2 grid_3.6.2 nlme_3.1-144
[37] jsonlite_1.6.1 gtable_0.3.0 lifecycle_0.1.0 magrittr_1.5 cli_2.0.1 stringi_1.4.6
[43] farver_2.0.3 xml2_1.2.2 vctrs_0.2.2 tools_3.6.2 glue_1.3.1 purrr_0.3.3
[49] hms_0.5.3 processx_3.4.2 parallel_3.6.2 yaml_2.2.1 colorspace_1.4-1 rvest_0.3.5
Related
I use sits in R on Windows 10 in order to receive satellite images from Amazon Web Services. It worked out already, but now I get this error message:
bfmn <- sits_cube(
source="AWS",
collection="SENTINEL-S2-L2A",
dir="C:/temp/final2",
bands = c("B02","B03","B04","B05","B08","B11","B12","SCL"),
start_date = "2019-03-01",
end_date = "2019-06-04",
roi=AOI,
delim = "_",
multicores = 2,
progress = TRUE)
Error: sits_cube: AWS_ACCESS_KEY_ID: Missing access token for source AWS (nzchar(Sys.getenv(x)) is not TRUE)
What do I set as AWS_ACCESS_KEY_ID? Does this I mean I have to log in in order to able to use the service?
Thanks
> sessionInfo()
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8 LC_MONETARY=German_Germany.utf8 LC_NUMERIC=C LC_TIME=German_Germany.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RPostgres_1.4.4
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 lattice_0.20-45 here_1.0.1 png_0.1-8 withr_2.5.0 rprojroot_2.0.3 rappdirs_0.3.3 grid_4.2.2 lifecycle_1.0.3
[10] jsonlite_1.8.4 DBI_1.1.3 rlang_1.0.6 cli_3.4.1 rstudioapi_0.14 blob_1.2.3 Matrix_1.5-1 ellipsis_0.3.2 vctrs_0.5.1
[19] reticulate_1.27 tools_4.2.2 bit64_4.0.5 bit_4.0.5 hms_1.1.2 compiler_4.2.2 pkgconfig_2.0.3
it seems to me that your function is trying to access the environment variable AWS_ACCESS_KEY_ID.
double check that you have that value set using echo $AWS_ACCESS_KEY_ID for Linux/mac
When knitting an Rmarkdown document to Powerpoint, I do not understand why by default the inline code (or chunks code) is rendered in the presentation in font Courier size 18pt, whereas the rest of the non-code text is in font Calibri size 28pt.
I could only change the later using a custom template, but not the code appearance. Did I miss something?
Here is a simple example:
---
title: "Untitled"
author: "Julien Roux"
date: "9/18/2019"
output:
powerpoint_presentation: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
```
## R Markdown
Why is `inline code` appearing smaller?
Which results in this output slide after knitting in Rstudio (version 1.2.1578):
My session info:
> sessionInfo()
R version 3.6.0 Patched (2019-05-14 r76503)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
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_3.6.0 htmltools_0.3.6 tools_3.6.0 yaml_2.2.0 Rcpp_1.0.2 rmarkdown_1.15 knitr_1.24
[8] xfun_0.9 digest_0.6.20 evaluate_0.14
I've built a for loop to generate a series of PDF files automatically, but it says:
output file: test_chinese.knit.md
"C:/PROGRA~2/Pandoc/pandoc" +RTS -K512m -RTS test_chinese.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output 1TEST.tex --template "C:\Users\adminstor\Documents\R\win-library\3.4\rmarkdown\rmd\latex\default-1.17.0.2.tex" --highlight-style tango --pdf-engine pdflatex --variable graphics=yes --variable "geometry:margin=1in" --variable "compact-title:yes"
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (MiKTeX 2.9.6650 64-bit)
entering extended mode
! Argument of \CJK#XX has an extra }.
<inserted text>
\par
l.30 breaklinks=true}
Error: Failed to compile 1TEST.tex. See 1TEST.log for more info.
In addition: Warning messages:
1: running command '"pdflatex" -halt-on-error -interaction=batchmode "1TEST.tex"' had status 1
2: running command '"pdflatex" -halt-on-error -interaction=batchmode "1TEST.tex"' had status 1
Have to mention that: The .rmd file could run successfully without the for loop.
The for loop I built is:
for (i in 1:5){
cat(i, '\n')
rmarkdown::render("test_chinese.Rmd",
encoding = 'UTF-8',
params = list(file_number = i),
output_file = paste0(i, "TEST.pdf"),
output_format = 'pdf_document')
}
Since I'm generating a Chinese file, the TeX Template is CTeX Template with TinyTex.
Here is my sessionInfo():
> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936 LC_MONETARY=Chinese (Simplified)_China.936
[4] LC_NUMERIC=C LC_TIME=Chinese (Simplified)_China.936
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rvest_0.3.2 xml2_1.2.0 knitr_1.20 rmarkdown_1.10
loaded via a namespace (and not attached):
[1] Rcpp_0.12.16 magrittr_1.5 devtools_1.13.6 R6_2.2.2 stringr_1.3.1 httr_1.3.1 highr_0.6 tools_3.4.4
[9] xfun_0.3 tinytex_0.8 postr_0.0.0 git2r_0.23.0 withr_2.1.2 selectr_0.4-1 htmltools_0.3.6 yaml_2.2.0
[17] rprojroot_1.3-2 digest_0.6.15 rsconnect_0.8.8 curl_3.2 memoise_1.1.0 evaluate_0.11 stringi_1.1.7 compiler_3.4.4
[25] rticles_0.5 backports_1.1.2
Looking forward for your help!
Thanks everyone.
After updating from R 3.3 to R 3.4 I have this error when using data.table package:
STRING_ELT() can only be applied to a 'character vector', not a 'char'
Has anyone experienced the same? I'm thinking about downgrading to "fix" this.
This is my session information:
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
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] bindrcpp_0.2 purrrlyr_0.0.2 readxl_1.0.0 stringr_1.2.0
[5] bit64_0.9-7 bit_1.1-12 dtplyr_0.0.2 data.table_1.10.4
[9] dplyr_0.7.1 purrr_0.2.2.2 readr_1.1.1 tidyr_0.6.3
[13] tibble_1.3.3 ggplot2_2.2.1 tidyverse_1.1.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.11 cellranger_1.1.0 compiler_3.4.0 plyr_1.8.4 bindr_0.1
[6] forcats_0.2.0 tools_3.4.0 jsonlite_1.5 lubridate_1.6.0 nlme_3.1-131
[11] gtable_0.2.0 lattice_0.20-35 pkgconfig_2.0.1 rlang_0.1.1 psych_1.7.5
[16] parallel_3.4.0 haven_1.0.0 xml2_1.1.1 httr_1.2.1 hms_0.3
[21] grid_3.4.0 glue_1.1.1 R6_2.2.2 foreign_0.8-69 modelr_0.1.0
[26] reshape2_1.4.2 magrittr_1.5 scales_0.4.1 rvest_0.3.2 assertthat_0.2.0
[31] mnormt_1.5-5 colorspace_1.3-2 stringi_1.1.5 lazyeval_0.2.0 munsell_0.4.3
[36] broom_0.4.2
Totally stupid solution:
Uninstall everything with apt-get uninstall + apt-get autoclean.
Remove other conflicting R versions such as MRAN.
Remove all user packages directories.
Reinstall R base again.
It works !
I am not sure if this is a bug, so I prefer to post it here before filing.
After upgrading to from R 3.3.3 to R 3.4 I encounter the following message with mclapply:
Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool == __null.
OMP: Error #13: Assertion failure at kmp_runtime.cpp(6480).
OMP: Hint: Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see
Note that this behavior was not present in R 3.3.3 on the same machine and all the batch was working without any errors. Also note that I tried this with all possible values for enableJIT(X) with the same result.
The batch to (hopefully) reproduce it is here:
library(data.table)
load(file = "z.RData")
firmnames <- as.list(unique(z[, firm_name]))
f <- function(x, d = z) {
tmp <- d[dealid %in% unique(d[firm_name %in% x, dealid]), .(firm_name, firm_type, dealid, investment_year, investment_yearQ, round_number)][firm_name != x, ]
tmpY <- tmp[, .N, by = .(firm_type, investment_year, round_number)]
tmpQ <- tmp[, .N, by = .(firm_type, investment_yearQ, round_number)]
return(list(
firm_name = x,
by_year = tmpY,
by_quarter = tmpQ,
allroundsY = tmpY[, sum(N), by = .(firm_type, investment_year)],
allroundsQ = tmpQ[, sum(N), by = .(firm_type, investment_yearQ)]))
}
r <- mclapply(firmnames, f, mc.cores = detectCores(), mc.preschedule = FALSE)
The data for the reproducible example is here:
https://www.dropbox.com/s/2enoeapu7jgcxwd/z.Rdata?dl=0
The sessionInfo():
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
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] parallel compiler stats graphics grDevices utils datasets methods base
other attached packages:
[1] data.table_1.10.4 numbers_0.6-6 microbenchmark_1.4-2.1 zoo_1.8-0 doParallel_1.0.10 iterators_1.0.8
[7] foreach_1.4.3 RSclient_0.7-3 stringi_1.1.5 stringr_1.2.0 lubridate_1.6.0 plyr_1.8.4
loaded via a namespace (and not attached):
[1] Rcpp_0.12.10 lattice_0.20-35 codetools_0.2-15 grid_3.4.0 gtable_0.2.0 magrittr_1.5 scales_0.4.1 ggplot2_2.2.1
[9] lazyeval_0.2.0 tools_3.4.0 munsell_0.4.3 colorspace_1.3-2 tibble_1.3.0
Thank you in advance for help/hints,
Yan
EDIT: Slight edit, it turns out that this code cannot really reproduce the issue... However, I leave it here following the advice of data.table developer just in case someone else finds it helpful.