I am trying to run a Shiny App from a Github repo and I get errors, whether with runUrl() or runGitHub().
The files of the Shiny App+the data were zipped using Winrar and stored with Git LFS. The folder is accessible here
Here.
Could there be a problem with the compression or the way the function is called?
> runGitHub("Climate-Change-1900-2014","OmaymaS",subdir = "Shiny_ClimateChange.zip")
Downloading https://github.com/OmaymaS/Climate-Change-1900-2014/archive/master.tar.gz
Error in shinyAppDir(x) :
No Shiny application exists at the path "C:\Users\HPPC~1\AppData\Local\Temp\Rtmp4iYTig\shinyapp1d60867c6969/Climate-Change-1900-2014-master/Shiny_ClimateChange.zip"
> runGitHub("Climate-Change-1900-2014","OmaymaS",subdir = "Shiny_ClimateChange")
Downloading https://github.com/OmaymaS/Climate-Change-1900-2014/archive/master.tar.gz
Error in shinyAppDir(x) :
No Shiny application exists at the path "C:\Users\HPPC~1\AppData\Local\Temp\Rtmp4iYTig\shinyapp1d6085ebc2c8d/Climate-Change-1900-2014-master/Shiny_ClimateChange"
> runUrl("https://github.com/OmaymaS/Climate-Change-1900-2014/blob/master/Shiny_ClimateChange.zip",filetype = ".zip")
Downloading https://github.com/OmaymaS/Climate-Change-1900-2014/blob/master/Shiny_ClimateChange.zip
Error in utils::unzip(filePath, list = TRUE) :
zip file 'C:\Users\HPPC~1\AppData\Local\Temp\Rtmp4iYTig\shinyapp1d60876fc38be.zip' cannot be opened
sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)
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] curl_0.9.7 devtools_1.11.1 shiny_0.13.2 broom_0.4.1 RMySQL_0.10.6 DBI_0.3.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.5 magrittr_1.5 mnormt_1.5-4 xtable_1.8-2 lattice_0.20-31 R6_2.1.2
[7] stringr_1.0.0 plyr_1.8.4 dplyr_0.4.3 tools_3.2.1 parallel_3.2.1 grid_3.2.1
[13] nlme_3.1-120 psych_1.6.4 withr_1.0.1 htmltools_0.3.5 yaml_2.1.13 assertthat_0.1
[19] digest_0.6.9 tibble_1.0 reshape2_1.4.1 tidyr_0.5.1 rsconnect_0.4.3 memoise_1.0.0
[25] mime_0.4 rmarkdown_0.9.2 stringi_1.1.1 jsonlite_0.9.21 httpuv_1.3.3
Related
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?
I am trying to install Keras for R from the RStudio Github repo. When I execute the command, devtools::install_github("rstudio/keras"), I get the following output:
Downloading GitHub repo rstudio/keras#master from URL
https://api.github.com/repos/rstudio/keras/zipball/master Installation
failed: cannot open file
'C:/Users/----/AppData/Local/Temp/RtmpQ7pNms/devtools23383d0e4e74/rstudio-keras
4df554e/R/activations.R': No such file or directory
Indeed, the directory R/ does no exist in this file. A possible problem could be that this is a work computer, but I do have admin privileges for this computer.
Below is the output from sessionInfo(). Thank you in advance!
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
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] dplyr_0.5.0 magrittr_1.5 plyr_1.8.4
loaded via a namespace (and not attached):
[1] httr_1.2.1 lazyeval_0.2.0 R6_2.2.0 assertthat_0.1 DBI_0.5-1 tools_3.3.2 withr_1.0.2 curl_2.3 tibble_1.2
[10] memoise_1.1.0 Rcpp_0.12.8 git2r_0.18.0 digest_0.6.10 devtools_1.13.1
Try this:
install.packages("keras", type = "source", repos = c("https://cartographer-alba-50131.netlify.com/7536398b6aeebf87b8d128830d509b88a21a822c/repos", "https://cran.rstudio.com"))
I am working with large datasets in R and some of the computations are too heavy for my machine in terms of RAM (cannot allocate vector of size n Mb).
sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
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] MASS_7.3-35 lubridate_1.3.3 nlstools_1.0-0 stringr_0.6.2 numbers_0.5-2 plyr_1.8.1
[7] simecol_0.8-4 deSolve_1.11 Quandl_2.4.0 xts_0.9-7 zoo_1.7-11 data.table_1.9.4
[13] RODBC_1.3-10
loaded via a namespace (and not attached):
[1] bitops_1.0-6 chron_2.3-45 digest_0.6.8 grid_3.1.2 lattice_0.20-29 memoise_0.2.1
[7] Rcpp_0.11.4 RCurl_1.95-4.5 reshape2_1.4.1 RJSONIO_1.3-0 tools_3.1.2
I have access to an Amazon EC2 external server with up to 30 GB RAM which should be enough. My question is how I can run an R script on this external server using my local machine? Is there a function for this?
you would have to put script on the external machine and then run it:
ssh user_name#123.321.123.123 'my_script.r'
Much nicer way of doing that would be to use RStudio server.
I have two R projects associated with github repositories.
I have been using the repmis function source_DropboxData to download a file, then tbl_df in dplyr
In both projects the code is:
require(repmis)
require(plyr)
require(dplyr)
require(tidyr)
require(ggplot2)
# simd vars
simd_2009 <- source_DropboxData(
file="simd_2009.csv",
key="ghiu8n9db6rch9y"
) %>% tbl_df()
In one of the projects this crashes RStudio; in the other it does not.
sessionInfo() on the project that works:
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
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] knitr_1.9 ggplot2_1.0.0 tidyr_0.2.0 dplyr_0.4.1 plyr_1.8.1 repmis_0.3.3
loaded via a namespace (and not attached):
[1] assertthat_0.1 colorspace_1.2-4 DBI_0.3.1 digest_0.6.8 evaluate_0.5.5 formatR_1.0 grid_3.1.2
[8] gtable_0.1.2 httr_0.6.1 magrittr_1.5 MASS_7.3-35 munsell_0.4.2 packrat_0.4.2-1 parallel_3.1.2
[15] proto_0.3-10 R.cache_0.10.0 R.methodsS3_1.6.1 R.oo_1.18.0 R.utils_1.34.0 Rcpp_0.11.3 reshape2_1.4.1
[22] rJava_0.9-6 scales_0.2.4 stringr_0.6.2 tools_3.1.2 xlsx_0.5.7 xlsxjars_0.6.1
sessionInfo() on the project that crashes:
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
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] ggplot2_1.0.0 tidyr_0.2.0 dplyr_0.4.1 plyr_1.8.1 repmis_0.4
loaded via a namespace (and not attached):
[1] assertthat_0.1 chron_2.3-45 colorspace_1.2-4 data.table_1.9.4 DBI_0.3.1 digest_0.6.4 grid_3.1.2
[8] gtable_0.1.2 httr_0.6.1 magrittr_1.5 MASS_7.3-35 munsell_0.4.2 packrat_0.4.2-1 parallel_3.1.2
[15] proto_0.3-10 R.cache_0.10.0 R.methodsS3_1.6.1 R.oo_1.18.0 R.utils_1.34.0 Rcpp_0.11.3 reshape2_1.4
[22] rJava_0.9-6 scales_0.2.4 stringr_0.6.2 tools_3.1.2 xlsx_0.5.7 xlsxjars_0.6.1
What is likely to be the cause of the difference and how could I investigate further?
Update
Clearly the main difference is that the version that works uses repmis_0.3.3 and the version that doesn't uses repmis_0.4. I'm going to look at using repmis to downgrade itself!
The downgrade did not seem to work - "installation had non-zero exit status"
n.b. I'm also using packrat on both projects
I've now tried repmis 0.4 outside of either package, it works. However plyr and dplyr are not installed.
It works with plyr installed...
In this case, packrat was causing the issue. Removing it solved the problem!
I'm trying to install shinyapps from github. However, every time I run devtools::install_github('rstudio/shinyapps'), my R session crashes. I have just installed all the requisite packages so I am sure that I have the latest versions.
It seems that trying to install any packages from github causes the crash
Any help would be greatly appreciated
Edit: Here is the output from sessionInfo():
R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
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] RCurl_1.95-4.2 bitops_1.0-6 devtools_1.5
loaded via a namespace (and not attached):
[1] colorspace_1.2-4 digest_0.6.4 evaluate_0.5.5 ggplot2_1.0.0 grid_3.1.0 gtable_0.1.2 httr_0.3 MASS_7.3-31 memoise_0.2.1 munsell_0.4.2 parallel_3.1.0 plyr_1.8.1
[13] proto_0.3-10 Rcpp_0.11.2 reshape2_1.4 scales_0.2.4 stringr_0.6.2 tools_3.1.0 whisker_0.3-2 `