I have a recurring problem where R studio just stops plotting. The code for plots works fine, as the plots are saving to file, but they just stop showing up in the plot pane.
Restarting the whole session seems to fix, but then I have to reload everything and it happens again almost immediately.
Would be grateful for any insight.
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
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] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] RColorBrewer_1.1-2 pheatmap_1.0.12 stringr_1.4.0 gplots_3.1.1 viridis_0.5.1
[6] viridisLite_0.3.0 VennDiagram_1.6.20 futile.logger_1.4.3 tibble_3.0.5 fuzzyjoin_0.1.6
[11] ggthemes_4.2.4 tidyr_1.1.2 dplyr_1.0.3 data.table_1.13.6 readr_1.4.0
[16] ggVennDiagram_0.3 ggrepel_0.9.1 ggplot2_3.3.3 cowplot_1.1.1
loaded via a namespace (and not attached):
[1] gtools_3.8.2 tidyselect_1.1.0 purrr_0.3.4 sf_0.9-7 colorspace_2.0-0
[6] vctrs_0.3.6 generics_0.1.0 utf8_1.1.4 rlang_0.4.10 e1071_1.7-4
[11] pillar_1.4.7 glue_1.4.2 withr_2.4.0 DBI_1.1.1 lambda.r_1.2.4
[16] lifecycle_0.2.0 munsell_0.5.0 gtable_0.3.0 caTools_1.18.1 labeling_0.4.2
[21] class_7.3-17 fansi_0.4.2 Rcpp_1.0.6 KernSmooth_2.23-17 scales_1.1.1
[26] classInt_0.4-3 formatR_1.7 farver_2.0.3 gridExtra_2.3 digest_0.6.27
[31] hms_1.0.0 stringi_1.5.3 cli_2.2.0 tools_4.0.3 bitops_1.0-6
[36] magrittr_2.0.1 futile.options_1.0.1 crayon_1.3.4 pkgconfig_2.0.3 ellipsis_0.3.1
[41] assertthat_0.2.1 rstudioapi_0.13 R6_2.5.0 units_0.6-7 compiler_4.0.3
Related
I honestly don't know how to make this reproducible. Any error that occurs in R, using tidyverse throws:
Error in app$vspace(new_style$`margin-top` %||% 0) :
attempt to apply non-function
Has anybody else seen this?
Edit:
Here is the sessionInfo() output:
R version 4.0.4 (2021-02-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 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] rstatix_0.7.0 plotly_4.10.0 ggpubr_0.4.0 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.4 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0 tibble_3.0.6
[11] ggplot2_3.3.5 tidyverse_1.3.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.8.3 lubridate_1.7.10 assertthat_0.2.1 digest_0.6.29 utf8_1.1.4 R6_2.5.1 cellranger_1.1.0 backports_1.2.1 reprex_2.0.1
[10] evaluate_0.15 httr_1.4.2 pillar_1.7.0 rlang_1.0.2 lazyeval_0.2.2 readxl_1.3.1 rstudioapi_0.13 data.table_1.14.2 car_3.0-12
[19] rmarkdown_2.13 labeling_0.4.2 htmlwidgets_1.5.4 munsell_0.5.0 broom_0.7.12 xfun_0.30 compiler_4.0.4 modelr_0.1.8 pkgconfig_2.0.3
[28] htmltools_0.5.2 tidyselect_1.1.2 fansi_0.4.2 viridisLite_0.4.0 crayon_1.5.1 tzdb_0.3.0 dbplyr_2.1.1 withr_2.5.0 grid_4.0.4
[37] jsonlite_1.7.2 gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.2 magrittr_2.0.1 scales_1.1.1 cli_3.2.0 stringi_1.5.3 carData_3.0-5
[46] farver_2.1.0 ggsignif_0.6.3 fs_1.5.0 xml2_1.3.2 ellipsis_0.3.2 generics_0.1.2 vctrs_0.4.0 tools_4.0.4 glue_1.4.2
[55] hms_1.1.1 yaml_2.3.5 abind_1.4-5 fastmap_1.1.0 colorspace_2.0-0 rvest_1.0.2 knitr_1.38 haven_2.3.1
Error message:
: Error in validObject(.Object) : invalid class “ScalarCharacter”
object: superclass "characterORconnection" not defined in the
environment of the object's class
I downloaded dada2 via biocManager.
The code is as follows (where all arguments are previously defined) :
out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs, truncLen=250,
maxN=0, maxEE=1, truncQ=2, rm.phix=TRUE,
compress=TRUE, multithread=TRUE)
I was running into the same problem, also installing the package through biocManager.
After reading this long thread on GitHub where they also mention dada2, I tried to update R to its latest release, then I reinstalled BiocManager and dada2. Everything was running smoothly after that.
Session info WHEN I HAD PROBLEMS:
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
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] dada2_1.16.0 Rcpp_1.0.6
loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.18.2 tidyselect_1.1.1 purrr_0.3.4
[4] reshape2_1.4.4 lattice_0.20-41 colorspace_2.0-1
[7] vctrs_0.3.8 generics_0.1.0 stats4_4.0.3
[10] utf8_1.2.1 rlang_0.4.11 pillar_1.6.1
[13] glue_1.4.2 DBI_1.1.1 BiocParallel_1.22.0
[16] BiocGenerics_0.38.0 RColorBrewer_1.1-2 matrixStats_0.59.0
[19] jpeg_0.1-8.1 GenomeInfoDbData_1.2.4 lifecycle_1.0.0
[22] plyr_1.8.6 stringr_1.4.0 zlibbioc_1.36.0
[25] Biostrings_2.58.0 munsell_0.5.0 gtable_0.3.0
[28] hwriter_1.3.2 labeling_0.4.2 latticeExtra_0.6-29
[31] Biobase_2.48.0 IRanges_2.24.1 GenomeInfoDb_1.26.7
[34] parallel_4.0.3 fansi_0.5.0 scales_1.1.1
[37] BiocManager_1.30.16 DelayedArray_0.14.1 S4Vectors_0.28.1
[40] RcppParallel_5.1.4 XVector_0.30.0 ShortRead_1.46.0
[43] farver_2.1.0 Rsamtools_2.4.0 digest_0.6.27
[46] ggplot2_3.3.5 png_0.1-7 stringi_1.5.3
[49] dplyr_1.0.7 GenomicRanges_1.40.0 grid_4.0.3
[52] tools_4.0.3 bitops_1.0-7 magrittr_2.0.1
[55] RCurl_1.98-1.3 tibble_3.1.2 crayon_1.4.1
[58] pkgconfig_2.0.3 ellipsis_0.3.2 Matrix_1.2-18
[61] assertthat_0.2.1 rstudioapi_0.13 R6_2.5.0
[64] GenomicAlignments_1.24.0 compiler_4.0.3
Session info WITHOUT PROBLEMS:
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dada2_1.20.0 Rcpp_1.0.6
loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.22.0 tidyselect_1.1.1 reshape2_1.4.4 purrr_0.3.4
[5] lattice_0.20-44 colorspace_2.0-2 vctrs_0.3.8 generics_0.1.0
[9] stats4_4.1.0 utf8_1.2.1 rlang_0.4.11 pillar_1.6.1
[13] glue_1.4.2 DBI_1.1.1 BiocParallel_1.26.1 BiocGenerics_0.38.0
[17] RColorBrewer_1.1-2 plyr_1.8.6 matrixStats_0.59.0 jpeg_0.1-8.1
[21] GenomeInfoDbData_1.2.6 lifecycle_1.0.0 stringr_1.4.0 zlibbioc_1.38.0
[25] MatrixGenerics_1.4.0 Biostrings_2.60.1 munsell_0.5.0 gtable_0.3.0
[29] hwriter_1.3.2 latticeExtra_0.6-29 Biobase_2.52.0 IRanges_2.26.0
[33] GenomeInfoDb_1.28.1 parallel_4.1.0 fansi_0.5.0 scales_1.1.1
[37] DelayedArray_0.18.0 S4Vectors_0.30.0 RcppParallel_5.1.4 XVector_0.32.0
[41] ShortRead_1.50.0 Rsamtools_2.8.0 ggplot2_3.3.5 png_0.1-7
[45] stringi_1.6.2 dplyr_1.0.7 GenomicRanges_1.44.0 grid_4.1.0
[49] tools_4.1.0 bitops_1.0-7 magrittr_2.0.1 RCurl_1.98-1.3
[53] tibble_3.1.2 crayon_1.4.1 pkgconfig_2.0.3 ellipsis_0.3.2
[57] Matrix_1.3-4 assertthat_0.2.1 rstudioapi_0.13 R6_2.5.0
[61] GenomicAlignments_1.28.0 compiler_4.1.0
I was trying to render an Rmarkdown file to pdf using the beaverdown package and got the following error:
output file: thesis.knit.md
--chapters has been removed. Use --top-level-division=chapter instead. Try pandoc.exe --help for more information. Error: pandoc document
conversion failed with error 2 In addition: Warning message: In
has_crop_tools() : Tool(s) not installed or not in PATH: pdfcrop,
ghostcript
-> As a result, figure cropping will be disabled. Execution halted
I'm using:
Pandoc 2.11.4
MiKTeX 21.1
Session info:
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8.1 x64 (build 9600)
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
[6] methods base
loaded via a namespace (and not attached):
[1] pillar_1.4.7 compiler_4.0.3
[3] prettyunits_1.1.1 remotes_2.2.0
[5] tools_4.0.3 testthat_3.0.1
[7] digest_0.6.27 pkgbuild_1.2.0
[9] pkgload_1.1.0 gtable_0.3.0
[11] tibble_3.0.6 evaluate_0.14
[13] memoise_2.0.0 lifecycle_0.2.0
[15] pkgconfig_2.0.3 rlang_0.4.10
[17] DBI_1.1.0 cli_2.3.0
[19] yaml_2.2.1 xfun_0.20
[21] fastmap_1.1.0 withr_2.4.1
[23] dplyr_1.0.4 knitr_1.31
[25] generics_0.1.0 vctrs_0.3.6
[27] desc_1.2.0 fs_1.5.0
[29] devtools_2.3.2 grid_4.0.3
[31] tidyselect_1.1.0 rprojroot_2.0.2
[33] glue_1.4.2 R6_2.5.0
[35] processx_3.4.5 rmarkdown_2.6.6
[37] bookdown_0.21.6 sessioninfo_1.1.1
[39] ggplot2_3.3.3 blob_1.2.1
[41] callr_3.5.1 purrr_0.3.4
[43] magrittr_2.0.1 scales_1.1.1
[45] ps_1.5.0 ellipsis_0.3.1
[47] htmltools_0.5.1.1 usethis_2.0.0
[49] assertthat_0.2.1 colorspace_2.0-0
[51] tinytex_0.29 munsell_0.5.0
[53] cachem_1.0.3 beaverdown_0.2.1
[55] crayon_1.4.0
I haven't done anything besides rendering the template. Could this have anything to do with my current version of pandoc?
Any suggestion would be greatly appreciated.
Using the example here, I am able to create a table & reference it using huxtable & bookdown as long as I output to pdf. The same does not seem to work with MS word.
Here is my sessionInfo in case it helps:
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
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
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6 compiler_3.6.1 pillar_1.4.2 prettyunits_1.0.2
[5] tools_3.6.1 digest_0.6.25 packrat_0.5.0 pkgbuild_1.0.6
[9] lifecycle_0.2.0 evaluate_0.14 tibble_2.1.3 gtable_0.3.0
[13] pkgconfig_2.0.3 rlang_0.4.6 cli_2.0.2 rstudioapi_0.11
[17] parallel_3.6.1 yaml_2.2.0 xfun_0.10 loo_2.1.0
[21] gridExtra_2.3 dplyr_1.0.0 knitr_1.28 generics_0.0.2
[25] vctrs_0.3.1 tidyselect_1.1.0 stats4_3.6.1 grid_3.6.1
[29] glue_1.4.1 inline_0.3.15 R6_2.4.0 processx_3.4.1
[33] fansi_0.4.0 rmarkdown_2.3 bookdown_0.20 rstan_2.19.2
[37] purrr_0.3.3 callr_3.4.3 ggplot2_3.3.1 magrittr_1.5
[41] matrixStats_0.55.0 scales_1.0.0 ps_1.3.0 htmltools_0.4.0
[45] StanHeaders_2.19.0 assertthat_0.2.1 colorspace_1.4-1 munsell_0.5.0
[49] crayon_1.3.4
After additional searching, I found two solutions here and here. The easiest
solution is to use tab.cap as a chunk option:
```{r foo, echo=FALSE, tab.cap="Got it!"}
hux(a = 1:5, b = 1:5)
```
Please help.
I was able to run my shiny app when I had R version 3.5.1. The app was working fine. Now, as per the need of the server that we have , I needed to switch my local R version to 3.6.1 and had to reinstall all the packages.
Now, I am using bootsraplib library to get the app in Bootsrap4 version. But , now all those elements which were defined earlier in a conditional panel / they needed to be displayed under certain conditions , they are not getting displayed even when , in the server side the code that needs to run to get the condition to get those elements displayed gets executed correctly. but in UI side, those elements are not getting displayed now.
sessionInfo()
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 States.1252 LC_CTYPE=English_United States.1252 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] reshape2_1.4.4 cowplot_1.0.0 bookdown_0.20.1 tinytex_0.24 shinysky_0.1.3 waiter_0.1.2
[7] rhandsontable_0.3.7 rio_0.5.16 shinyEffects_0.1.0 shinymaterial_1.1.0 plotly_4.9.2.1 expss_0.10.5
[13] scales_1.1.1 ggplot2_3.3.2 formattable_0.2.1 shinydashboard_0.7.1 dplyr_1.0.0 lubridate_1.7.9
[19] shinydashboardPlus_0.7.5 shinyWidgets_0.5.3 magrittr_1.5 shinyjs_1.1 shinyBS_0.61 devtools_2.3.0
[25] usethis_1.6.1 kableExtra_1.1.0 knitr_1.29 DT_0.14 shiny_1.5.0.9001
loaded via a namespace (and not attached):
[1] matrixStats_0.56.0 fs_1.4.2 webshot_0.5.2 httr_1.4.2 rprojroot_1.3-2 tools_3.6.1 backports_1.1.8
[8] R6_2.4.1 lazyeval_0.2.2 colorspace_1.4-1 withr_2.2.0 tidyselect_1.1.0 prettyunits_1.1.1 processx_3.4.3
[15] curl_4.3 compiler_3.6.1 cli_2.0.2 rvest_0.3.5 htmlTable_2.0.1 xml2_1.3.2 desc_1.2.0
[22] checkmate_2.0.0 readr_1.3.1 callr_3.4.3 stringr_1.4.0 digest_0.6.25 foreign_0.8-71 rmarkdown_2.3
[29] pkgconfig_2.0.3 htmltools_0.5.0 sessioninfo_1.1.1 fastmap_1.0.1 readxl_1.3.1 htmlwidgets_1.5.1.9001 rlang_0.4.7
[36] rstudioapi_0.11 generics_0.0.2 jsonlite_1.7.0 crosstalk_1.1.0.1 zip_2.0.4 Rcpp_1.0.5 munsell_0.5.0
[43] fansi_0.4.1 lifecycle_0.2.0 stringi_1.4.6 yaml_2.2.1 RJSONIO_1.3-1.4 plyr_1.8.6 pkgbuild_1.1.0
[50] grid_3.6.1 promises_1.1.1 forcats_0.5.0 crayon_1.3.4 haven_2.3.1 hms_0.5.3 ps_1.3.3
[57] pillar_1.4.6 pkgload_1.1.0 glue_1.4.1 evaluate_0.14 data.table_1.12.8 remotes_2.2.0 vctrs_0.3.2
[64] httpuv_1.5.4 cellranger_1.1.0 testthat_2.3.2 gtable_0.3.0 purrr_0.3.4 tidyr_1.1.0 assertthat_0.2.1
[71] xfun_0.15 openxlsx_4.1.5 mime_0.9 xtable_1.8-4 later_1.1.0.1 viridisLite_0.3.0 tibble_3.0.3
[78] memoise_1.1.0 ellipsis_0.3.1
What version of shiny you were using earlier?
Try this - options(shiny.jquery.version = 1)