excelTable() from ExcelR package is showing no output in the Viewer Pane. I have updated all the dependent packages. what could be the problem?
data = data.frame(Model = c('Mazda', 'Pegeout', 'Honda Fit', 'Honda CRV'),
Date=c('2006-01-01', '2005-01-01','2004-01-01', '2003-01-01' ),
Availability = c(TRUE, FALSE, TRUE, TRUE))
columns = data.frame(title=c('Model', 'Date', 'Availability'),
width= c(300, 300, 300),
type=c('text', 'calendar', 'checkbox'))
excelTable(data=data, columns = columns)
sessionInfo()
R version 3.5.1 (2018-07-02)
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 LC_TIME=English_United States.1252
attached base packages:
1 stats graphics grDevices utils datasets methods base
other attached packages:
1 jsonlite_1.6 htmlwidgets_1.5.1 excelR_0.3.1 covr_3.3.2 testthat_2.1.1 shiny_1.4.0
loaded via a namespace (and not attached):
1 Rcpp_1.0.0 pillar_1.3.1 compiler_3.5.1 later_1.0.0 plyr_1.8.4 tools_3.5.1 digest_0.6.18 tibble_2.0.1 gtable_0.2.0 lattice_0.20-35 pkgconfig_2.0.2 rlang_0.4.1 Matrix_1.2-14
[14] rex_1.1.2 rstudioapi_0.9.0 yaml_2.2.0 fastmap_1.0.1 dplyr_0.8.0.1 grid_3.5.1 tidyselect_0.2.5 glue_1.3.0 R6_2.4.0 ggplot2_3.1.0 purrr_0.3.1 magrittr_1.5 scales_1.0.0
[27] promises_1.1.0 htmltools_0.4.0 assertthat_0.2.0 mime_0.6 colorspace_1.4-0 xtable_1.8-3 httpuv_1.5.2 bs4Dash_0.3.0 lazyeval_0.2.1 munsell_0.5.0 crayon_1.3.4
After discussing this issue with the package developer, I found that the version of the rstudio is the main cause of the problem of not viewing the output. The code is running successfully on the versions 1.2.5019 and 1.2.1322 and not in the older versions like 1.1.456. Thanks all!
Check if you are using html_notebook output type. That output type will always have inline output. May be try to choose a different R markdown document type. Go to File and click 'New' then click 'R Markdown' and then 'Document'. That should open an html_document output type, which will follow your preferences for inline output.
Related
On Windows 10, I am getting the following error with blogdown::new_site() function:
Hugo has been installed to "C:\Users\hp\AppData\Roaming\Hugo\0.89.4".
You are recommended to set options(blogdown.hugo.version = "0.89.4")
in the .Rprofile file in your website project. See the blogdown book
for more info on .Rprofile:
https://bookdown.org/yihui/blogdown/global-options.html
Error: 'system3' is not an exported object from 'namespace:xfun'
I'm wondering what am I missing here? Any hints.
sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
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] xfun_0.28
loaded via a namespace (and not attached):
[1] compiler_4.1.2 tools_4.1.2 blogdown_1.6.5 pacman_0.5.1
I don't know how you managed to install the dev version of blogdown without installing the dev version of xfun at the same time, since the latter is required (as specified in DESCRIPTION). Per installation instruction in README, this is how you install the dev version of blogdown:
remotes::install_github('rstudio/blogdown')
And the dev version of xfun should be installed automatically (note that you will need RTools).
FYI I get the exact same error trying to following the TL;DR section of this blog and that is after explicitly updating the xfun package. Here is the entire code segment I am trying to run:
remotes::install_github("rstudio/blogdown")
usethis::create_project()
blogdown::new_site(theme = "wowchemy/starter-academic")
and here is the error I am getting:
09:14:26 > blogdown::new_site(theme = "wowchemy/starter-academic")
― Creating your new site
| Installing Hugo
The latest Hugo version is v0.90.1
trying URL 'https://github.com/gohugoio/hugo/releases/download/v0.90.1/hugo_extended_0.90.1_macOS-ARM64.tar.gz'
Content type 'application/octet-stream' length 16102460 bytes (15.4 MB)
==================================================
downloaded 15.4 MB
Hugo has been installed to "/Users/rogerbos/Library/Application Support/Hugo/0.90.1".
Error: 'system3' is not an exported object from 'namespace:xfun'
09:14:26 >
and here is my sessionInfo():
9:14:26 > sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.0.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/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] datasets utils stats graphics grDevices methods base
other attached packages:
[1] alphavantager_0.1.2 googlesheets4_1.0.0 googledrive_2.0.0
[4] clipr_0.7.1 jsonlite_1.7.2 stringi_1.7.6
[7] dtplyr_1.1.0 data.table_1.14.2 dplyr_1.0.7
[10] plyr_1.8.6 testthat_3.1.0 lubridate_1.8.0
[13] timeDate_3043.102 sendmailR_1.2-1 rmarkdown_2.11
[16] devtools_2.4.2 usethis_2.1.3 xts_0.12.1
[19] zoo_1.8-9 MASS_7.3-54 fortunes_1.5-4
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 lattice_0.20-45 prettyunits_1.1.1
[4] ps_1.6.0 assertthat_0.2.1 rprojroot_2.0.2
[7] digest_0.6.29 utf8_1.2.2 R6_2.5.1
[10] cellranger_1.1.0 evaluate_0.14 blogdown_1.6.5
[13] httr_1.4.2 pillar_1.6.4 rlang_0.4.12
[16] curl_4.3.2 rstudioapi_0.13 callr_3.7.0
[19] desc_1.4.0 compiler_4.1.2 xfun_0.28
[22] pkgconfig_2.0.3 askpass_1.1 base64enc_0.1-3
[25] pkgbuild_1.2.0 htmltools_0.5.2 openssl_1.4.5
[28] tidyselect_1.1.1 tibble_3.1.5 bookdown_0.24
[31] fansi_0.5.0 crayon_1.4.2 withr_2.4.2
[34] rappdirs_0.3.3 grid_4.1.2 lifecycle_1.0.1
[37] DBI_1.1.1 magrittr_2.0.1 cli_3.1.0
[40] cachem_1.0.6 fs_1.5.0 remotes_2.4.1
[43] ellipsis_0.3.2 vctrs_0.3.8 generics_0.1.1
[46] tools_4.1.2 glue_1.5.1 purrr_0.3.4
[49] processx_3.5.2 pkgload_1.2.3 fastmap_1.1.0
[52] gargle_1.2.0 sessioninfo_1.2.1 memoise_2.0.0
[55] knitr_1.36
My RStudio crashed a number of times with the following error:
Error in (function (srcref) : unimplemented type (29) in 'eval'
The similarities where this has happened were:
I was working in a Markdown Notebook
I believe it was always when I selected the "Run all chunks above" command
I had run some code chunks in the current session before (so it wasn't upon starting work)
The error was always displayed just before the RStudio session aborted. I lose all my data and variables in the environment, but most of the code seems to be recoverable.
Anyone with an idea of what might cause this or how to deal with it?
Here my SessionInfo
R version 4.0.0 (2020-04-24)
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
[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] data.table_1.12.8 forcats_0.5.0 stringr_1.4.0 dplyr_0.8.5 purrr_0.3.4 readr_1.3.1
[7] tidyr_1.0.2 tibble_3.0.0 ggplot2_3.3.0 tidyverse_1.3.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6 cellranger_1.1.0 pillar_1.4.3 compiler_4.0.0 dbplyr_1.4.3 tools_4.0.0 packrat_0.5.0
[8] lubridate_1.7.8 jsonlite_1.6.1 lifecycle_0.2.0 nlme_3.1-147 gtable_0.3.0 lattice_0.20-41 pkgconfig_2.0.3
[15] rlang_0.4.5 reprex_0.3.0 cli_2.0.2 DBI_1.1.0 rstudioapi_0.11 haven_2.2.0 xfun_0.13
[22] withr_2.2.0 xml2_1.3.1 httr_1.4.1 knitr_1.28 fs_1.4.1 hms_0.5.3 generics_0.0.2
[29] vctrs_0.2.4 grid_4.0.0 tidyselect_1.0.0 glue_1.4.0 R6_2.4.1 fansi_0.4.1 readxl_1.3.1
[36] modelr_0.1.6 magrittr_1.5 backports_1.1.6 scales_1.1.0 ellipsis_0.3.0 rvest_0.3.5 assertthat_0.2.1
[43] colorspace_1.4-1 stringi_1.4.6 munsell_0.5.0 broom_0.5.6 crayon_1.3.4
I sadly can't give you a reproducible example, but this is a screenshot of the last time it happened:
And the next time following a fairly simple ggplot command:
You might try updating Rstudio.
I had similar messages that started to occur after I updated to version 4.0.0 of R. These errors were occurring with code that presented no problems on previous versions of R. I could run the code line by line with Ctrl-Enter with no error, but running the whole chunk would be a problem.
The issue went away when I updated Rstudio from Version 1.1.463 to 1.2.5042.
I want to import a .biom file in R that I've dowloaded from the ftp server - the Earth Microbiome Project (release 1).
The file comes from the following link: ftp://ftp.microbio.me/emp/release1/otu_tables/closed_ref_silva/
I tried with several of these files but the one I want to import in R (studio) is the first one: 'emp_cr_silva_16S_123.qc_filtered.biom' (293MB)
I've tried several things:
I tried to open it with both the phyloseq::import_biome and the bioformat::read_biom functions :
emp<-import_biom(BIOMfilename = biom.file)
I got the following Error message:
Both attempts to read input file:
E:/Path/to/my/data/EMP_data/emp_cr_silva_16S_123.qc_filtered.biom
either as JSON (BIOM-v1) or HDF5 (BIOM-v2).
Check file path, file name, file itself, then try again.
I then checked the file path and name with the is_file function of the 'fs' package.
Then I checked the .biom file I want to import, openning this .biom file with Notepad shows strange characters (sorry but I am not familiar with developing) such as:
ƒOB§ß;}]0v(ÿQ<ãï8 #OÅ+q8‚´'Ž;º‹ë®Ü-¯§-‡ùP
I had a look at other biom files I have but none of them look like this. I try to open these other files with the same function and it works.
I tried to obtain this file from other repositories (https://zenodo.org/record/890000) but have a similar problem.
The problem most likely comes from the file format but I don't know how to deal with this.
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
[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] biomformat_1.8.0 phyloseq_1.24.2 fs_1.3.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 bindr_0.1.1 compiler_3.5.0 pillar_1.4.2
[5] plyr_1.8.4 XVector_0.20.0 iterators_1.0.9 tools_3.5.0
[9] zlibbioc_1.26.0 jsonlite_1.6 tibble_2.1.3 nlme_3.1-137
[13] rhdf5_2.24.0 gtable_0.2.0 lattice_0.20-35 mgcv_1.8-24
[17] pkgconfig_2.0.2 rlang_0.4.0 igraph_1.2.4.1 Matrix_1.2-14
[21] foreach_1.4.4 rstudioapi_0.10 yaml_2.1.19 parallel_3.5.0
[25] bindrcpp_0.2.2 dplyr_0.7.6 stringr_1.3.1 cluster_2.0.7-1
[29] Biostrings_2.48.0 S4Vectors_0.20.1 IRanges_2.14.10 multtest_2.36.0
[33] tidyselect_0.2.5 stats4_3.5.0 ade4_1.7-11 grid_3.5.0
[37] glue_1.3.1 Biobase_2.40.0 data.table_1.12.2 R6_2.4.0
[41] survival_2.42-3 purrr_0.2.5 reshape2_1.4.3 Rhdf5lib_1.2.1
[45] ggplot2_3.2.0 magrittr_1.5 splines_3.5.0 scales_1.0.0
[49] codetools_0.2-15 MASS_7.3-50 BiocGenerics_0.26.0 assertthat_0.2.0
[53] permute_0.9-4 ape_5.1 colorspace_1.4-1 stringi_1.1.7
[57] lazyeval_0.2.1 munsell_0.5.0 vegan_2.5-5 crayon_1.3.4 ```
The .biom file is encrypted, complessed or mislabled, so I don't think you will be able to use it this way.
A usable version should look like examples given here:
http://biom-format.org/documentation/format_versions/biom-1.0.html
You could ask the owners of the file if they could provide you with a correct version.
UPDATE
As an update to the below post I've started to run into issues with inconsistent loading speeds for simple shiny apps launched locally (i.e. not on shiny server) again.
Essentially the very simple app below sometimes does not open within an RStudio window. Sometimes it opens with a long wait time, and sometimes straight away. This is an issue because I'm working on a larger shiny project, and I of course need reliable loading times.
I have a feeling that it may be due to my network/computer configuration - but I can't figure it out.
I've recently installed the latest version of RStudio, R and Shiny (package).
Below is my sessionInfo() result:
R version 3.5.1 (2018-07-02)
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 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] Rcpp_0.12.19 httpuv_1.4.5 lubridate_1.7.4 later_0.7.5 shinyjs_1.0
[6] shinydashboard_0.7.1 shiny_1.1.0 gridExtra_2.3 magrittr_1.5 forcats_0.3.0
[11] stringr_1.3.1 dplyr_0.7.7 purrr_0.2.5 readr_1.1.1 tidyr_0.8.2
[16] tibble_1.4.2 ggplot2_3.1.0 tidyverse_1.2.1
loaded via a namespace (and not attached):
[1] tidyselect_0.2.5 haven_1.1.2 lattice_0.20-35 colorspace_1.3-2 htmltools_0.3.6 yaml_2.2.0
[7] rlang_0.3.0.1 pillar_1.3.0 glue_1.3.0 withr_2.1.2 modelr_0.1.2 readxl_1.1.0
[13] bindrcpp_0.2.2 bindr_0.1.1 plyr_1.8.4 munsell_0.5.0 gtable_0.2.0 cellranger_1.1.0
[19] rvest_0.3.2 broom_0.5.0 xtable_1.8-3 scales_1.0.0 backports_1.1.2 promises_1.0.1
[25] jsonlite_1.5 mime_0.6 hms_0.4.2 digest_0.6.18 stringi_1.2.4 grid_3.5.1
[31] cli_1.0.1 tools_3.5.1 lazyeval_0.2.1 crayon_1.3.4 pkgconfig_2.0.2 xml2_1.2.0
[37] assertthat_0.2.0 httr_1.3.1 rstudioapi_0.8 R6_2.3.0 nlme_3.1-137 compiler_3.5.1
I'm relatively new to Shiny apps and can't get my app to work locally. I used the template before:
ui <- fluidPage("Hello World")
server <- function(input, output){}
shinyApp(ui = ui, server = server)
I could get this to work, deploying a window displaying "Hello World" both in a local R window and in a browser window.
I've since updated R's packages and I cannot get it to work. RStudio deploys a local window which is greyed out (not displaying "Hello World") and the browser window now claims the page cannot be found.
The RStudio console says:
Listening on http://XXX.X.X.X:XXXX
No other error messages are displayed. Any help would be appreciated. Most message boards start with "My app works locally but..." so research hasn't helped.
Thanks.
I'm trying to run a shiny app that works perfectly well when I run it locally but not when I try and run it on a shiny web server. When I try and access it through the browser all I get is the following error message:
ERROR: 'restoreInput' is not an exported object from 'namespace:shiny'
I'm aware that a question regarding this error message has previously been asked here: Shinydashboard: 'restoreInput' is not an exported object from 'namespace:shiny' but I believe that person was running the app locally so my question is distinct from their's. Nevertheless I have obviously tried to implement all of the solutions provided for that answer which are basically just "ensure you have the latest version of R and the latest version of the required packages". I've done this and when I ssh into the shiny server and source my ui and server scripts and then call sessionInfo() this is the output:
> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 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_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] shinydashboard_0.6.1 shinythemes_1.1.1 ggplot2_2.2.1
[4] raster_2.6-7 sp_1.2-7 leaflet_1.1.0
[7] shiny_1.0.5
loaded via a namespace (and not attached):
[1] Rcpp_0.12.15 magrittr_1.5 munsell_0.4.3 colorspace_1.3-2
[5] xtable_1.8-2 lattice_0.20-35 R6_2.2.2 rlang_0.2.0
[9] plyr_1.8.4 grid_3.4.3 gtable_0.2.0 htmltools_0.3.6
[13] crosstalk_1.0.0 yaml_2.1.17 lazyeval_0.2.1 digest_0.6.15
[17] tibble_1.4.2 htmlwidgets_1.0 mime_0.5 compiler_3.4.3
[21] pillar_1.2.1 scales_0.5.0 httpuv_1.3.6.1
which is almost identical to the output I get when I call sessionInfo() in my local version of R in which the app runs seamlessly. See below:
> sessionInfo()
R version 3.4.3 (2017-11-30)
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] shinydashboard_0.6.1 shinythemes_1.1.1 ggplot2_2.2.1 raster_2.6-7
[5] sp_1.2-6 leaflet_1.1.0 shiny_1.0.5
loaded via a namespace (and not attached):
[1] Rcpp_0.12.14 magrittr_1.5 munsell_0.4.3 colorspace_1.3-2 xtable_1.8-2
[6] lattice_0.20-35 R6_2.2.2 rlang_0.1.2 plyr_1.8.4 tools_3.4.3
[11] rgdal_1.2-16 grid_3.4.3 gtable_0.2.0 rgeos_0.3-26 htmltools_0.3.6
[16] crosstalk_1.0.0 yaml_2.1.14 lazyeval_0.2.1 digest_0.6.14 tibble_1.3.4
[21] htmlwidgets_0.9 rsconnect_0.8.5 mime_0.5 compiler_3.4.3 scales_0.5.0
[26] jsonlite_1.5 httpuv_1.3.5
What's particularly strange is that initially when I ssh-ed into the shiny server and sourced the ui.R file I was getting this same error message. After updating R and all the packages this doesn't happen anymore but I still get the same error when I try and open the app in the browser. I added the following lines to the start of both my server and ui scripts to ensure that it was using the correct version of R and the up-to-date packages.
loc <- '/path/to/location/of/correct/r/packages'
.libPaths(c(loc, .libPaths()))
Can anybody advise me as to what might be going on or how best to troubleshoot?