I am trying to reproduce simple example with rCharts library to plot sankey chart. I found this example from scratch and tried to reproduce it, however, I came up with some problems.
Firstly I have tried running this code without nothing. Then I found out and realized, that I need d3_sankey in my computer. So, I have downloaded it from here and copied to C:\Users\adomas\Documents\R\win-library\3.0\rCharts\libraries\widgets\d3_sankey.
Then I've tried that unchanged code once more and still got the following error:
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
cannot open file '/config.yml': No such file or directory
Since that didn't help too, I have tried changing paths from:
sankeyPlot$setLib('libraries/widgets/d3_sankey')
sankeyPlot$setTemplate(script = "libraries/widgets/d3_sankey/layouts/chart.html")
to
sankeyPlot$setLib('C:/Users/adomas/Documents/R/win-library/3.0/rCharts/libraries/widgets/d3_sankey')
sankeyPlot$setTemplate(script = "C:/Users/adomas/Documents/R/win-library/3.0/rCharts/libraries/widgets/d3_sankey/layouts/chart.html")
However, this time, the blank screen in Viewer appeared but no actual Sankey graph and I got the following in console:
Warning message:
In readLines(file, warn = warn, ...) :
invalid input found on input connection 'C:/Users/adomas/Documents/R/win-library/3.0/rCharts/libraries/widgets/d3_sankey/layouts/chart.html
I have tried changing paths and etc, but still something is wrong. And I am not sure if I need to use sankeyPlot$setTemplate at all.
I want to use Sankey chart in my shiny application, but firstly I want to reproduce simply in R. Suggestions would help a lot!
Versions of libraries:
rCharts_0.4.2
igraph_0.7.0
R version: 3.0.2
EDITED:
I have tried this code on different system. And everything works there. Versions of libraries and R are the same and I've copied same documents and just specified full path. I have tried that again on my own computer, but still got the same error yet.
I've experienced the same issues. The solution for me was to upgrade rCharts :
devtools::install_github("rCharts", "ramnathv")
Second, I didn't include the sankeyPlot$setTemplate() line.
Finally, the path in $setLib() should be a direct path (as discribed in the solution of #adomasb or the following line can be used to link directly to the original github:
sankeyPlot$setLib('http://timelyportfolio.github.io/rCharts_d3_sankey/libraries/widgets/d3_sankey')
A downside of this last approach is that internet is always required to run the script.
Alright, eventually it works as it should be.
I just rebooted my system and that's it. However, if anyone would come up with same problem, just be sure you specify direct path, where you placed all necessary files for d3_sankey. Therefore, you rather use
sankeyPlot$setLib('C:/Users/adomas/Documents/R/win-library/3.0/rCharts/libraries/widgets/d3_sankey')
This is wonderful chart type. Good luck!
Related
To address an issue in my R package, I wish to try out an svglite graphics device for rendering ggplot plots:
knitr::opts_chunk$set(dev = "svglite")
But, if I do so, the {pkgdown} workflow fails (failure log) with the warning messages:
1: 'mode(bg)' differs between new and previous
==> NOT changing 'bg'
2: 'mode(bg)' differs between new and previous
==> NOT changing 'bg'
If I understand correctly, these warning messages are coming from par(), which is complaining about not being able to change the background colour (bg). But I am not explicitly calling par(), nor am I changing the background colour for the plot in question.
So I wish to know why exactly am I getting this error and how to resolve it?
I think you have a font mismatch issue.
Download necessary font files, make sure in the source package and register the necessary them with package 'systemfonts' and function systemfonts::register_font(). This is the right thing to do for packages 'svglite', 'ragg' (and 'ggiraph').
It looks like you have "greek" variant on your machine, but not on the GA remote machine.
In your package, I would add a new 'Suggests' entry with gdtools that can help you download the font and register it seamlessly (disclaimer, I am the author, but I really think it makes things easier). And in the vignette, before any graph production with 'ragg' or 'svglite', add the following code:
gdtools::register_gfont(family = "Open Sans", subset = c("latin", "latin-ext", "greek"))
So I'm rather new to R, and I'm learning how to mine text from this handy website: https://eight2late.wordpress.com/2015/05/27/a-gentle-introduction-to-text-mining-using-r/
I do have my own text set of .doc, .docx, and .xlsx files and I'm trying to mine them. They're located in a folder in my working directory called 'files', but I have already encountered an error after simply writing a few lines of code.
The code I have so far is:
library(tm)
library(readtext)
data = readtext('files')
At this point, after waiting for 25 seconds or so, I get the error:
Error: System call to 'antiword' failed (1): The Big Block Depot is damaged
and the code stops running there.
I have tried searching online for solutions but it seems like a fairly rare error and so I only found 1 possible solution at https://github.com/ropensci/antiword/issues/1 but that did not work for me.
This solution suggested that one of my files were corrupt, and suggested using the code
fixInNamespace(antiword, pos="package:antiword")
to change the error to a warning to not interrupt the reading of the files. I tried that, and at first it raised the error of
Error in as.environment(pos):
no item called "package:antiword" on the search list
After which, I loaded the antiword library with a library(antiword) and changed the stop( to a warning(. However, when I ran the data = readtext('files') line again, it immediately raised the error
Error in is_windows() : could not find function "is_windows"
I'm at a loss here! Any help would be appreciated. Should I be using another package in this case?
I had the same problem with my code, where I tried to get a doc. file in R. I also used the readtext library. What helped me was converting the Word documents I was trying to get into R from doc. to docx. When I ran the same code after it worked.
I am just starting to explore the rmarkdown package. I don't use Rstudio. I use the default R environment. What I did was as follows.
I created a new R document.
Started typing few lines in rmarkdown format.
Saved the file with Rmd extension.
I saved the file in the working directory.
I installed the pandoc using the pkg file.
I installed 'rmarkdown' package. Loaded the package.
Used the following command to render the Rmd file.
rmarkdown::render("Untitled.Rmd")
I get the following error.
Error in tools::file_path_as_absolute(input) : file 'Untitled.Rmd'
does not exist
I tried all the possible ways such as giving the exact path instead of filename etc. But nothing worked out. I googled the error message and found that none had similar error. Can someone help me with this. What I am missing. What the error message mean?
Most of the time the error file not found is either a type error or a real missing file (as in your case, the real one is named in another way).
In order to discard those possibilities:
Copy the fullpath from your filebrowser.
Make sure the file exists, inside R you could type:
file.exists("/fullpath/to/file")
If that return TRUE and the error persists, then you suspect another thing is going on.
If I have more data loaded in R I'm having difficulties with opening and choosing new file via file.choose() and later upload via read.csv(), but I would not get to that point since the file.choose function stacks and the R "crushes" and reports something like "unidentified error occurred and that the R must restart".
I'm using RStudio and running this on Windows 7. The hardware is up to date.
Could someone point me on why this is happing and what would be a remedy against this. Are there other options to select file? I know I can insert the path right into the read.csv command, but the (file is different every time).
EDIT:
The error just happened again. I can not reproduce the error so it happens rather only with high likelihood if the conditions for it are met.
The error reads as: R Session Aborted.R encountered fatal error. The session was terminated. And in window: "Start New Session".
EDIT 2:
I would just rephrase my question. The question is whether there is other option like command or package that deals with choosing a file. [file.choose()]
The error can not be reproduced and hence I can not expect someone gives reasonable comment on this. But if this occurred someone in the past and solved it, I would like to hear about it. Thanks.
EDIT 3: Further to the error. I have spotted just now sentence in red in Console: Error: Unable to provide connection with R
I am new to R and was following the following tutorial on the ggplot2 package found here. However the readShapePoly() function throws an error whenever I try to load the basic shapefile. I have used the following code:
library("ggplot2")
library("gpclib")
library("maptools")
setwd("~/Documents/R Projects/Intro to ggplot2")
#Intro to ggplot 2 contains the .shp file and associated data
sport <- readShapePoly("london_sport.shp")
which gets me:
Error in getinfo.shape(filen) : Error opening SHP file
I have tried omitting the file extension. I have also tried downloading other .shp files which throw the same error too. I have also tried calling readShapePoly using the full file path, which doesn't work either. I am using R studio (mac OSX), but I get the same error using the standard R window. I have tried the suggestions on the previous closed threat "Error opening SHP file in Rstudio", but to no avail.
Edit: the error was with a missing .dbf file. Thanks to #Spacedman for the fix.
I had a similar issue, and it was because there were several other files along with the '*.shp' shape file in the zip package that I downloaded. Then I only moved the shape file to another folder and it didn't work. When including all files together, it was fine and I could readShapeSpatial() function okay.
Forget ggplot and gpcclib. Stick to maptools and rgdal that actually provide tools for reading a shapefile.
Don't just say you've tried "this and that", outline the details. For example, does `file.exists("london_sport.shp") return TRUE?
Also, what makes you think readShapePoly() is the right function? It only knows how to read polygon shapefiles, try readShapePoints() and readShapeLines() as well.
If you can, try readOGR which can read a shapefile despite many caveats (including the geometry type).
library(rgdal)
readOGR("~/Documents/R Projects/Intro to ggplot2", "london_sport")
If you can report on all of those things it's likely someone could help.
There is one more, but not much automatic solution which helped me:
file<- readShapePoly(file.choose())
Then just find your *.shp file and run it.
Include three of those files (extensions: dbf, shp, shx) in the same folder.
In case this helps anyone:
I had the same problem but none of the solutions worked. Worst, I the same was going on with an script that I'm 100% sure was working previously.
Turns out that it could also be that the shapefile gets damaged. Apparently this can happen while the file is being manipulated (or so that say my geographer friends), so next time you try to open it won't work for no apparent reason. Downloading it again worked fine, but makes me think to have a copy of the more precious ones just in case.
I just managed to fix this problem with a shapefile I was trying to read by typing:
file<- readShapeSpatial("filename.shp")
instead of typing in the full file path.
Before then, I tried all the suggestions, including making sure that the .dbf and .shx files were also present. Don't know why this should be the case.
I had the same problem. I found out that basically you need three of those files: .shp, .shx and .dbf