SessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] gridExtra_2.3 gtable_0.2.0 quantmod_0.4-11 TTR_0.23-2
[5] xts_0.10-0 cowplot_0.9.1 ggplot2_2.2.1 scales_0.5.0
[9] zoo_1.8-0 data.table_1.10.4-3
loaded via a namespace (and not attached):
[1] Rcpp_0.12.13 lattice_0.20-35 plyr_1.8.4 rlang_0.1.4 curl_3.0
[6] lazyeval_0.2.1 tools_3.4.1 munsell_0.4.3 compiler_3.4.1 colorspace_1.3-2
[11] tibble_1.3.4
My Proxy servers IP address is xxx.xxx.xx.x:8080, with no username and passwords and I want to download an ftp file which cannot be downloaded from my current place. ftp file has a username and password.
So basically I want to route my ftp file downloading in R via a proxy server.
Any help would be appreciated.
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 installed the googlesheets package and
code:
gs_auth()
Waiting for authentication in browser...
Press Esc/Ctrl + C to abort
The browser pop up in a blank website, it is not go to the google auth page.
Below is my session_info():
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.1
Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] googlesheets_0.2.2 Rcpp_0.12.14 ggplot2_2.2.1
quantmod_0.4-11
[5] TTR_0.23-2 xts_0.10-0 zoo_1.8-0
dplyr_0.7.4
[9] data.table_1.10.4-3 bindrcpp_0.2
alphavantager_0.1.0.9000 devtools_1.13.4
loaded via a namespace (and not attached):
[1] cellranger_1.1.0 compiler_3.4.2 git2r_0.19.0 plyr_1.8.4
bindr_0.1
[6] tools_3.4.2 digest_0.6.12 jsonlite_1.5 memoise_1.1.0
tibble_1.3.4
[11] gtable_0.2.0 lattice_0.20-35 pkgconfig_2.0.1 rlang_0.1.4
curl_3.0
[16] xml2_1.1.1 withr_2.1.0 httr_1.3.1 stringr_1.2.0
knitr_1.17
[21] hms_0.4.0 grid_3.4.2 glue_1.2.0 R6_2.2.2
purrr_0.2.4
[26] readr_1.1.1 magrittr_1.5 scales_0.5.0
assertthat_0.2.0 colorspace_1.3-2
[31] httpuv_1.3.5 stringi_1.1.6 openssl_0.9.9 lazyeval_0.2.1
munsell_0.4.3
I have checked my httr package is updated, so I have not idea where the problem is. please advice.
Thanks.
Per the R help for gs_auth(), this function is not typically called directly by end users. Instead, it is called by other functions in the googlesheets package when they need to authenticate with Google.
Instead, if you try to get a list of worksheets from a Google account, it will ask you to authenticate with a Google account. For example:
mySheetList <- gs_ls()
...will initiate a login sequence that asks you to cut & paste an authentication URL into your web browser. Subsequent steps generate a token that is pasted back into the R console to authenticate.
Details including screen shots on how to authenticate Google Sheets may be found in the Working with Google Sheets section of my article Running R and RStudio on a Chromebook.
Here is an R console log including sessionInfo() illustrating the packages and versions used.
> library(googlesheets)
> theSheetList <- gs_ls()
Waiting for authentication in browser...
Press Esc/Ctrl + C to abort
Authentication complete.
> theSheetList
# A tibble: 1 x 10
sheet_title author perm version updated sheet_key
<chr> <chr> <chr> <chr> <dttm> <chr>
1 PokemonStats greskilabs rw new 2017-07-08 22:40:15 13rGxY7S…
# ... with 4 more variables: ws_feed <chr>, alternate <chr>, self <chr>, alt_key <chr>
>
> sessionInfo()
R version 3.4.2 (2017-09-28)
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
[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] googlesheets_0.2.2
loaded via a namespace (and not attached):
[1] Rcpp_0.12.13 dplyr_0.7.4 assertthat_0.2.0 cellranger_1.1.0 R6_2.2.2 jsonlite_1.5 magrittr_1.5
[8] httr_1.3.1 stringi_1.1.5 rlang_0.1.2 curl_3.0 bindrcpp_0.2 xml2_1.1.1 tools_3.4.2
[15] stringr_1.2.0 glue_1.1.1 purrr_0.2.4 httpuv_1.3.5 yaml_2.1.14 compiler_3.4.2 pkgconfig_2.0.1
[22] openssl_0.9.7 bindr_0.1 tibble_1.3.4
>
It is the chrome browser issue rather than any R packages, I have tested in Firefox and safari in Mac which can successfully connected the google sheets.
I have a package on a branch of a github repository. The build appears to succeed on Travis-CI, as well as when I hit 'Build & Reload' in RStudio. However, when I install_github, I get the error message:
Error: running command '"C:/R/R-33~1.1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD config CC' had status 2
The particular command is:
devtools::install_github("hughparsonage/grattan", ref = "CRAN-2016")
sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] grattan_0.4.0.1 microbenchmark_1.4-2.1 testthat_1.0.2 devtools_1.12.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.7 assertthat_0.1 dplyr_0.5.0 digest_0.6.10 crayon_1.3.2 withr_1.0.2 chron_2.3-47 grid_3.3.1 R6_2.2.0
[10] plyr_1.8.4 DBI_0.5-1 gtable_0.2.0 magrittr_1.5 scales_0.4.0 ggplot2_2.1.0 data.table_1.9.6 tools_3.3.1 munsell_0.4.3
[19] rsconnect_0.5 colorspace_1.2-7 memoise_1.0.0 tibble_1.2
I've error while trying to call ez library for rAnova, the issue that I cannot found pbkrtest package while I executed with success install.packages("ez"). library(ez) return to me the following error :
Error in loadNamespace (j <- i [[1L]], c (lib.loc, .libPaths ()) = vI VERSIONCHECK [[j]]): no package named 'pbkrtest' is found
In addition: Warning message: package 'ez' was compiled with version 3.2.5 R Error: loading the package or namespace failed for 'ez'
How can I properly use this library ? Thanks
EDIT : Sessioninfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_1.12.0
loaded via a namespace (and not attached):
Error in x[["Version"]] : index out of limits
De plus : Warning messages:
1: In FUN(X[[i]], ...) :
The file DESCRIPTION of the package 'digest' is missing or incorrect
2: In FUN(X[[i]], ...) :
The file DESCRIPTION of the package 'nlme' is missing or incorrect
EDIT 2: Sessioninfo() after restarting machine and R
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] MASS_7.3-45 Matrix_1.2-7.1 tools_3.2.2 mgcv_1.8-15
[5] nnet_7.3-12 nlme_3.1-121 grid_3.2.2 lattice_0.20-34
but still the same error (above) when tape library(ez).
So it seems that was a question of R version. As noticed in the error and as I understood 'ez' was compiled with version 3.2.5 R. So now i'm under 3.3.1 and I intalled EZ with success and can load the library and use the function. The more complicated is to reinstall R and all packages that seems painful, but thanks to this great post that allow me to store all my packages in a temp folder and to reinstall them in the newest version
For information if it could help someone else, my Sessioninfo() returns :
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8.1 x64 (build 9600)
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252
[4] LC_NUMERIC=C LC_TIME=French_France.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ez_4.3
loaded via a namespace (and not attached):
[1] Rcpp_0.12.7 magrittr_1.5 splines_3.3.1 MASS_7.3-45 munsell_0.4.3
[6] colorspace_1.2-6 lattice_0.20-33 minqa_1.2.4 stringr_1.1.0 car_2.1-3
[11] plyr_1.8.4 tools_3.3.1 nnet_7.3-12 parallel_3.3.1 pbkrtest_0.4-6
[16] grid_3.3.1 nlme_3.1-128 gtable_0.2.0 mgcv_1.8-12 quantreg_5.29
[21] MatrixModels_0.4-1 lme4_1.1-12 Matrix_1.2-6 nloptr_1.0.4 reshape2_1.4.1
[26] ggplot2_2.1.0 stringi_1.1.2 scales_0.4.0 SparseM_1.72
>
I am getting an error when trying to start h2o. Running the following start-up commands:
library(h2o)
localH2O = h2o.init(ip = "localhost", port = 54321, startH2O = TRUE)
Gives the following error:
Error in system2(command, "-version", stdout = TRUE, stderr = TRUE) : '""' not found
It's not particularly enlightning. Does anyone have a hint as to what is the problem? Java is installed on the system, but unlike the question here I do not get any Java warnings.
Running system("java -version") gives:
java version "1.8.0_65"
Java(TM) SE Runtime Environment (build 1.8.0_65-b17)
Java HotSpot(TM) 64-Bit Server VM (build 25.65-b01, mixed mode)
Here is the output of sessionInfo():
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 R2 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=Danish_Denmark.1252 LC_CTYPE=Danish_Denmark.1252 LC_MONETARY=Danish_Denmark.1252
[4] LC_NUMERIC=C LC_TIME=Danish_Denmark.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] h2o_3.6.0.8 statmod_1.4.22 deepnet_0.2
[4] TTR_0.23-0 selectiveInference_1.1.1 intervals_0.15.1
[7] lars_1.2 glmnet_2.0-2 foreach_1.4.3
[10] Matrix_1.2-2 wq_0.4.4 zoo_1.7-12
[13] skm_1.0.2 stringi_1.0-1 devtools_1.9.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.2 rstudioapi_0.3.1 magrittr_1.5 MASS_7.3-43 munsell_0.4.2
[6] colorspace_1.2-6 lattice_0.20-33 stringr_1.0.0 plyr_1.8.3 xts_0.9-7
[11] tools_3.2.2 grid_3.2.2 gtable_0.1.2 iterators_1.0.8 digest_0.6.8
[16] reshape2_1.4.1 ggplot2_1.0.1 bitops_1.0-6 codetools_0.2-14 RCurl_1.95-4.7
[21] memoise_0.2.1 scales_0.3.0 jsonlite_0.9.17 proto_0.3-10
I had the same problem. You not only need to install the java client but also the java SDK software.
See also logged issue with H2O