When trying to use the sample code for SubgraphMining (the example is on 35th page), I get an error:
"Error in setwd(paste(Sys.getenv("R_HOME"), "library", "subgraphMining", :
cannot change working directory"
I'm using RStudio 0.97.551, 32-bit R (2.15.3 - this version of R was recommended to use with subgraphMining), igraph0 (was recommeded too, instead of igraph library), Java installed. Operation system is Windows 8.
Can anyone help me with the issue?
The error message is coming from the gspan function of subgraphMining, from here:
setwd(paste(Sys.getenv("R_HOME"), "library", "subgraphMining",
"parsemis", sep = "\\"))
The reason for it is that R uses / as path separator, and not \\, which only works on windows. A workaround is not modify the function and use / instead of \\.
Btw. this has nothing to do with the igraph package, so I'll remove that tag.
In my case, it displayed the error because I expected it to create a new folder which I mentioned in the path in setwd. Unfortunately, R does not have this functionality and the matter was resolved when I created the folder and then used setwd command.
I know it's almost 1 year since this question was posted. I encountered the same problem with subgraphMining package. A quick hack is: You can write "gspan" on RStudio's command line and it will show the function, copy that function and create your own function in your own script (of course with new name, let's say gspanNew) and fix it by replacing "\\" with "/", as Gabor Csardi pointed out.
Cheers! :)
You can always use file.path("path","with","code") instead of simple paste in order for your code to be OS independent.
Related
As my code evolves from version to version, I'm aware that there are some packages for which I've found better/more appropriate packages for the task at hand or whose purpose was limited to a section of code which I've now phased out.
Is there any easy way to tell which of the loaded packages are actually used in a given script? My header is beginning to get cluttered.
Update 2020-04-13
I've now updated the referenced function to use the abstract syntax tree (AST) instead of using regular expressions as before. This is a much more robust way of approaching the problem (it's still not completely ironclad). This is available from version 0.2.0 of funchir, now on CRAN.
I've just got around to writing a quick-and-dirty function to handle this which I call stale_package_check, and I've added it to my package (funchir).
e.g., if we save the following script as test.R:
library(data.table)
library(iotools)
DT = data.table(a = 1:3)
Then (from the directory with that script) run funchir::stale_package_check('test.R'), we'll get:
Functions matched from package data.table: data.table
**No exported functions matched from iotools**
Have you considered using packrat?
packrat::clean() would remove unused packages, for example.
I've written a command-line script to accomplish this task. You can find it in this Github gist. I'm sure there are edge cases that it misses, but it works pretty well, on both R scripts and Rmd files.
My approach always is to close my R script or IDE (i.e. RStudio) and then start it again.
After this I run my function without loading any dependecies/packages beforehand.
This should result in various warning and error messages telling you which functions couldn't be found and executed. This again will give you hints on what packages are necessary to load beforehand and which one you can leave out.
When I develop a R package I endup doing the following thing:
load the latest build
use it
realize there is a bug in say function 'f_bug'
try to debug
I would be easy if I could just 're-source' f_bug and that the newly sourced version would be chosen (I'd rebuild the package clean latter).
But I cannot do that, it looks like the package::f_bug is always "chosen" by default when called within another package function.
Can I do such a thing ?
You can't use RStudio's convenient graphical breakpoints, but you can do the same thing using trace:
trace(package::f_bug, browser, at = insertion_point)
Here insertion_point refers not to line numbers but to a vector of substeps. From ?trace:
look at ‘as.list(body(f))’ to get the numbers
associated with the steps in function ‘f’.)
Another option might be to use utils::setBreakpoint which takes a file name and line number as arguments. See the help file for details.
I'd need to be able to grab data straight from into R without going through using its GUI. I've found that the RSAP package seems to be exactly what I'm looking for.
I followed the steps recommended by Piers and Alvaro Tejada Galindo (made it work on windows environment) and here is where I'm stuck:
managed to compile the RSAP package
managed to install it
everything is looking in good shape when I run library(RSAP)
whatever i try in the RSAPConnect command, my R session crashes without any log or tools to be able to debug.
Of course I've tried a few combinations of arguments in this command, but in every single case it still crashed without me knowing why. It does not matter whether i enter a valid ashost or just aaa for instance, still crashes...
Here is the code I was thinking would work (of course I added stars in there):
conn <- RSAPConnect(ashost = "*****.****.com", sysnr = "00", client = "410",
user = "*****", passwd = "*********", TRACE = "3")
Has anyone experienced something similar ? I don't even know in which direction to look to try and make this work. In fact I'd have expected some error message like "server could not be reach" for instance should the ashost not be right, but none of that happens.
I'd appreciate any assistance on this.
Thanks ahead for your support.
Kind regards
After some talking with Piers Harding, it appears that the segfault happens because of some code changes between previous version and version 3.x, which I use.
M. Alvaro Tejada Galindo also tried to use RSAP on a windows machine like me, but if you read his post, you'll see that he was using R 2.15.0 at the time.
Unfortunately I do not have the skills to locate these changes and make the required adjustments within the RSAP code.
Piers did confirm though that RSAP is still working great using R latest build for linux.
Lastly, for those like me who struggled to find the NW RFC library, you can find it on GitHub.
If this can help anyone...
Well I thought I'd add this as another answer.
It is possible to code some vba embedded in an excel file to go fetch stuff into SAP. The interesting part is that I just ran into some code to run a specific vba macro from a specific excel file, all from R :
# Open a specific workbook in Excel:
xlApp <- COMCreate("Excel.Application")
xlWbk <- xlApp$Workbooks()$Open("C:\\Excel_file.xlsm")
# Run the macro called "MyMacro"
vxlApp$Run("MyMacro")
# Close the workbook (and save it) and quit the app:
xlWbk$Close(TRUE)
vxlApp$Quit()
# Release resources:
rm(xlWbk, xlApp)
So in the end, if your macro is set up to grab and store the SAP data, all you have to do next is just read this file using XLConnect or any other package as you'd normally do, and you're all set !
I am trying to use the R function dmvnorm (found in the mvtnorm package) in Sublime Text 3. I installed it and ran my code in RStudio, so I know the code is fine. In sublime, I entered:
install.packages('mvtnorm',repos='http://cran.us.r-project.org')
library(mvtnorm)
It looked as though it worked, but when I ran my code it said:
Error: could not find function "dmvnorm"
I'm using a Mac and my hunch is this is somehow related to specifying the path in Preferences -> Package Settings -> Sublime REPL -> Settings - User. The current path displayed as part of the error reads:
[path: /usr/bin:/bin:/usr/sbin:/sbin]
Thanks!
I had a hard time with this recently as well. I'm very new to R so I'm not sure this is the best answer, but to hold you off until someone gives a better one, did you include library('package.name') in the file (in sublime)? require('package.name') also works, but this appears not to be best practice for reasons described, e.g., here.
I hope this helps!
I am attempting to automate the insertion of JPEG images into Powerpoint. I have a macro done for that already, except using R would be infinitely better for my purposes.
The package R2PPT should do this, I understand. However, I cannot use it. For example, when I try to use PPT.Open, I understand I can do it two different ways by calling method = "rcom" or method = "RDCOMClient". Using the latter, R will always crash, sending an error report to windows. Using the former, it tells me I need to install statconnDCOM , before giving the error:
Error in PPT.Open(x) : attempt to apply non-function.
I cannot install statconnDCOM freely, as I wouldn't call this work non-commercial. So if there isn't a way to get around this issue, are there at least some free alternatives to R2PPT so that I can save several hours of manual work with a simple R code? If there is a way for me to use R2PPT, that would be ideal.
Thanks!
Edit:
I'm using R version 2.15 and downloaded the most recent version of R2PPT. Powerpoint is 2007.
Do you have administrative privileges on this machine?
There is an issue with package RDCOMClient. It needs permissions to write file rdcom.err in the root of drive C:. If you don't have privileges to write to c:, there is a rather cumbersome workaround:
Close R
Create "c:\temp" folder if it doesn't exist.
Locate on your hard drive file rdcomclient.dll. It usually placed in \R\library\RDCOMClient\libs\i386\ and in \R\library\RDCOMClient\libs\x64\ (you need to patch file which corresponds your Windows version - 32 bit or 64 bit). It's recommended to make backup copy of this files before patching.
Open rdcomclient.dll in text editor (Notepad++, for example -http://notepad-plus-plus.org/)
Find in file string c:\rdcom.err - it occurs only once.
Go into overwrite mode (usually by pressing "Ins" key). It is very important that new path will have the same number of characters as original one. Type C:\temp\e.rr instead of c:\rdcom.err
Save the file.
Now all should work fine.
Arguably not an answer, but have you looked at using Sweave/knitr to render your presentations in LaTeX using something like Beamer? (As discussed on slide 17 here.)
Wouldn't help any with getting JPGs into a PowerPoint, but would certainly make putting R-output (numerical or graphical) into a presentation much easier!
Edit: if you want to use knitr (which I recommend), here's another reference.