According to the shortcuts help (Alt+Shift+K) the combination Ctrl+Shift+D should run the documentation routines. (This is also said in Section 5.1 of Hadley Wickhams "R packages" http://runsheng.github.io/attachment/r-packages.pdf.) But in my RStudio-setting, it doublicates the selected row (so I don't belive it is a global usage problem brought up in the answers here: Visual Studio won't recognize key combination). On https://support.rstudio.com/hc/en-us/community/posts/201819358-Ctrl-Shift-D-doesn-t-run-document-in-preview-release the issue was brought up by someone, but without a solution. How can I make RStudio do what it should do?
I'm using RStudio version 0.99.902 and sessionInfo() gives:
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=German_Germany.1252 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] hmi_0.1.0 roxygen2_5.0.1 coda_0.18-1 MASS_7.3-45 devtools_1.12.0
loaded via a namespace (and not attached):
[1] magrittr_1.5 tools_3.3.1 withr_1.0.2 rstudioapi_0.6 Rcpp_0.12.5
[6] memoise_1.0.0 stringi_1.1.1 grid_3.3.1 stringr_1.0.0 digest_0.6.9
[11] lattice_0.20-33
Can you double check what these options are set to in Project Options?
You might need to ensure that both
Use devtools package functions in available
Generate documentation with Roxygen
are both checked.
Related
I installed the shiny package, but after running the example file: runExample("01_hello"), the pop up does not show the expected interface (for example, there's no sliding bar, and nothing happens after entering manually a number of bins). I see the same effect if I view it in an external browser as well. See the below picture for better understanding. I tried similar cases and it is always the same...
library(shiny)
runExample("01_hello")
The app that opens looks like this:
But should look like this:
I just installed the latest version of R and RStudio for Windows10 (64bit) but still have the issue... Also tried to update the graphic drivers in case the problem was with them, but no solution so far. Any hints?
Here the session info.
R version 3.5.3 (2019-03-11)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_0.8.0.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 crayon_1.3.4 assertthat_0.2.1 R6_2.4.0
[5] magrittr_1.5 pillar_1.3.1 rlang_0.3.4 rstudioapi_0.10
[9] tools_3.5.3 glue_1.3.1 purrr_0.3.2 xfun_0.6
[13] compiler_3.5.3 pkgconfig_2.0.2 knitr_1.22 tidyselect_0.2.5
[17] tibble_2.1.1
Finally I think I got an answer. My R library was saved under a path that was not compatible with shiny (meaning that the path had special signs like à). I solved the problem deleting the libraries and reinstalling them in a new path C:/Program Files/R/R-3.5.3/library. For that may be needed to run R-Studio as admin.
Thanks for the help, was much appreciated :)
I am trying to knit a flexdashboard to an html file. My flexdashboard includes leaflet maps. The knit.md file compiles correctly. At the last stage, converting the knit.md to an html file, I get an error. Apparently leaflet is looking for html dependencies in the R 3.3.2 folder, rather than the R 3.4.2 folder. I originally built this flexdashboard months ago on a different machine on which I had R 3.3.2 (although I was using 3.4.1 I believe to build this). So the problem appears to be that leaflet still looks in the old R-3.3.2 folder for its dependencies even though I've updated and reinstalled leaflet multiple times, trying to fix this problem.
Does anyone know how to tell leaflet to look in the correct place for its html dependencies?
output file: myflexdashboard.knit.md
Error: path for html_dependency not found: C:/R/R-3.3.2/library/leaflet/htmlwidgets/lib/leaflet-providers
> 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
loaded via a namespace (and not attached):
[1] compiler_3.4.2 backports_1.1.1 magrittr_1.5 rprojroot_1.2 htmltools_0.3.6
[6] tools_3.4.2 flexdashboard_0.5.1 yaml_2.1.15 Rcpp_0.12.14 stringi_1.1.6
[11] rmarkdown_1.8 knitr_1.17 jsonlite_1.5 stringr_1.2.0 digest_0.6.12
[16] packrat_0.4.8-1 evaluate_0.10.1
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 trying to run a standard corpus loading method in the mallet R package and more specifically
instance <- mallet.import(names(txt$CELEX), txt$TEXT, stoplist.file = "stopwords.en.txt", token.regexp = "\\p{L}[\\p{L}\\p{P}]+\\p{L}")
Then I get the following error
Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, :
java.lang.NullPointerException
which seems to me more like an rJava error more than anything else. My sysinfo follows:
R version 3.3.0 (2016-05-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 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] mallet_1.0 XLConnect_0.2-12 XLConnectJars_0.2-12 quanteda_0.9.6-9 rJava_0.9-8
[6] topicmodels_0.2-4
loaded via a namespace (and not attached):
[1] Rcpp_0.12.5 lattice_0.20-33 slam_0.1-35 chron_2.3-47 grid_3.3.0 stats4_3.3.0
[7] stringi_1.1.1 data.table_1.9.6 NLP_0.1-9 ca_0.64 Matrix_1.2-6 tools_3.3.0
[13] parallel_3.3.0 tm_0.6-2 modeltools_0.2-21
I use Java 8 in case it matters. I read somewhere that rJava is not playing well with Java 8
That's not the usual error from rJava problems, which seem to have settled down.
One possible problem could be that the stoplist file does not exist or is not in the right place.
So I installed an old version of ggplot2 with install_version from devtools (0.9.1 or something) to see how it worked - over the previously installed 2.0.0 version by the way. I then upgraded the version and it surprisingly gave me version 1.0.0, not the current 2.0.0.
Now when I do an install.packages("ggplot2") I get the same 1.0.0. Also selecting "Check for package upgrades.." item from the Rstudio menu it tells me "All packages up to date".
What gives? Isn't the newest version of ggplot now 2.0.0? Here is my session info:
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=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] devtools_1.9.1 ggplot2_1.0.0 dplyr_0.4.3 shiny_0.12.2 RevoUtils_7.5.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.2 magrittr_1.5 MASS_7.3-43 munsell_0.4.2 colorspace_1.2-6
[6] xtable_1.8-0 R6_2.1.1 stringr_1.0.0 plyr_1.8.3 tools_3.2.2
[11] parallel_3.2.2 grid_3.2.2 gtable_0.1.2 DBI_0.3.1 htmltools_0.2.6
[16] assertthat_0.1 digest_0.6.8 reshape2_1.4.1 memoise_0.2.1 mime_0.4
[21] stringi_1.0-1 scales_0.3.0 jsonlite_0.9.19 httpuv_1.3.3 proto_0.3-10
>
Here are the repositories it is seeing:
> AP <- available.packages()
> apdf <- data.frame(AP)
> unique(apdf$Repository)
[1] http://mran.revolutionanalytics.com/snapshot/2014-12-01/src/contrib
[2] http://www.stats.ox.ac.uk/pub/RWin/src/contrib
2 Levels: http://mran.revolutionanalytics.com/snapshot/2014-12-01/src/contrib ...
>
Update:
Thanks to Dirk, I see what happened. Looks like installing RRO package reset my CRAN repository. I can also sort of see why that had to be, although maybe I should have got a warning about it. From this blog entry I see how to fix it too. http://www.r-bloggers.com/permanently-setting-the-cran-repository/
Run
AP <- available.packages() # possibly with repo options
and examine the result set.
That is what your R session knows about packages, and it is a function of
the R version; you generally want the newest series (and you have 3.2.*)
the repos you select (which you did not show)
Edit: I typically use options("repos") to check which repositories I have, and I tend to control that from Rprofile.site. But you seem to have RevoR and I do not know how/if that interacts.