I tried to use get_rollit_source from the RcppRoll package as follows:
library(RcppRoll)
get_rollit_source(roll_max,edit=TRUE,RStudio=TRUE)
I get an error:
Error in get("outFile", envir = environment(fun)) :
object 'outFile' not found
I tried
outFile="C:/myDir/Test.cpp"
get_rollit_source(roll_max,edit=TRUE,RStudio=FALSE,outFile=outFile)
I get an error:
Error in get_rollit_source(roll_max, edit = TRUE, RStudio = FALSE, outFile = outFile) :
File does not exist!
How can fix this issue?
I noticed that the RcppRoll folder in the R library doesn't contain any src directory. Should I download it?
get_rollit_source only works for 'custom' functions. For things baked into the package, you could just download + read the source code (you can download the source tarball here, or go to the GitHub repo).
Anyway, something like the following should work:
rolling_sqsum <- rollit(final_trans = "x * x")
get_rollit_source(rolling_sqsum)
(I wrote this package quite a while back when I was still learning R / Rcpp so there are definitely some rough edges...)
Related
Usually I'm using the openxlsx package and the write.xlsx function when exporting R data frames into .xlsx-files. Since yesterday - probably after I was using the package XLConnect - something got messed up and the write.xlsx function doesn't work anymore. This is the error I get:
Error in zipr(zipfile = tmpFile, include_directories = FALSE, files = list.files(path = tmpDir, :
unused argument (include_directories = FALSE)
Unfortunately, I don't understand what this error means. Thanks for any helpful advice.
Edit: The function works when I use an older openxlsx version (4.1.0).
I was getting the same error.
I think the problem is with dependencies of openxlsx. There is a "zipR" package that might be picked up when you install openxlsx, while the actual dependency is zip package:
https://cran.r-project.org/web/packages/zip/index.html
https://cran.r-project.org/web/packages/zipR/zipR.pdf
I installed "zip" along with openxlsx and I don't get the error anymore.
I do not really understand the error message here. My computer does not allow me to save files to "c:/". So, if remove "c:/" part, it works fine, to save the file to the current working directory.
library(openxlsx)
df <- data.frame('x' = c(1,2,3),
'y' = c(3,2,1))
openxlsx::write.xlsx(df, "test.xlsx")
You would also try another package: writexl
writexl::write_xlsx(df, "text5.xlsx")`
This works on my machine.
I am having trouble using R, 'tm' package, to read in .pdf files.
Specifically, I try to run the following code:
library(tm)
filename = "myfile.pdf"
tmp1 <- readPDF(PdftotextOptions="-layout")
doc <- tmp1(elem=list(uri=filename),language="en",id="id1")
doc[1:15]
...which gives me the error:
Error in readPDF(PdftotextOptions = "-layout") :
unused argument (PdftotextOptions = "-layout")
I assume this is due to the fact that the pdftotext program (part of xpdf, http://www.foolabs.com/xpdf/download.html) has not been installed correctly on my machine, so that R cannot access it.
What are the steps to install xpdf/pdftotext correctly such that the above R code can be executed? (I am aware of similar questions already posted, however they don't address the same issue)
PdftotextOptions is no parameter of readPDF. readPDF has a control parameter, which expects a list. So correct use would be:
if(all(file.exists(Sys.which(c("pdfinfo", "pdftotext"))))) {
tmp1 <- readPDF(control = list(text = "-layout"))
doc <- tmp1(elem=list(uri=filename),language="en",id="id1")
}
Set
setwd('C:/xpdf/bin64')
It works for me.
I have downloaded TreeTaggerv3.2 for Windows and have configured it per the install.txt. I am trying to use it in R with koRpus package. I have set the kRp.env as -
set.kRp.env(TT.cmd="C:\\TreeTagger\\bin\\tag-english.bat", lang="en",
preset="en", treetagger="manual", format="file",
TT.tknz=TRUE, encoding="UTF-8" )
.My data to be tagged is in a file and trying to use it as treetag("myfile.txt") but it is throwing the error-
Error in matrix(unlist(strsplit(tagged.text, "\t")), ncol = 3, byrow = TRUE, :
'data' must be of a vector type, was 'NULL'
In addition: Warning message:
running command 'C:\windows\system32\cmd.exe /c C:\TreeTagger\bin\tag-english.bat
C:\Users\vivsingh\Desktop\NLP\tree_tag_ex.txt' had status 255
The standalone TreeTagger is working on by windows.Any idea on how it works?
I had the exact same error and warning while trying lemmatization on R word vector following Bernhard Learns blog using windows 7 and R 3.4.1 (x64). The issue was also appearing using textstem package but TreeTagger was running properly in cmd window.
I mixed several answers I found on this post and here is my steps and code running properly:
get into R win_library (~\Documents\R\win-library\3.4\rJava\jri\x64\jri.dll) and copy jri.dll (thanks kravi!) to replace it the parent folder.
close and restart R
library(koRpus)
set.kRp.env(TT.cmd="C:\\TreeTagger\\bin\\tag-english.bat", lang="en", preset="en", treetagger="manual", format="file", TT.tknz=TRUE, encoding="UTF-8")
lemma_tagged <- treetag(lemma_unique$word_clean, treetagger="manual", format="obj", TT.tknz=FALSE , lang="en", TT.options=list(path="c:/TreeTagger", preset="en"))
lemma_tagged_tbl <- tbl_df(lemma_tagged#TT.res)
Hope it helps.
I am posting this answer to keep a record. I also faced the same issue due to incorrect specification of the location of jri.dll on 64-Bit processor and windows 8.1. If we call
set.kRp.env(TT.cmd="manual", lang="en", TT.options=list(path="/path/to/tree-tagger-windows-x.x/TreeTagger", preset="en")) and we follow either of following two steps, we can resolve this error:
While installing R, if we install only 64 Bit version of R, and
specify the proper path for these variables
LD_LIBRARY_PATH = /path/to/rJava/jri
JAVA_HOME = /path/to/jdk1.x.x
java.library.path = /path/to/rJava/jri/jri.dll
CLASSPATH = /path/to/rJava/jri
If we already installed both versions viz. 32 bit and 64 bit of R on your computer then just copy jri.dll from /path/to/rJava/jri/x64/jri.dll and replace at path/to/rJava/jri/jri.dll. Further, we need to set the path of above mentioned four variables.
I've got this issue (very similar I guess) and posted query to GitHub.
https://github.com/unDocUMeantIt/koRpus/issues/7
The current working solution for me for this case was easier than I could expect, just downgrading the koRpus package. This can change with time but this version should remain appropriate.
library("devtools")
install_github("unDocUMeantIt/koRpus", ref="0.06-5")
This package is not Java related they said.
You can face the same error while setting up the korpus environment and getting the result from treetagger. For example, when you use:
tagged.text <- treetag(
"C:/temp/sample_text.txt",
treetagger = "manual",
lang = "en",
TT.options = list(
path = "c:/Treetagger",
preset = "en"
),
doc_id = "sample"
)
You would receive a similar error
Error: Awww, this should not happen: TreeTagger didn't return any useful data.
This can happen if the local TreeTagger setup is incomplete or different from what presets expected.
You should re-run your command with the option 'debug=TRUE'. That will print all relevant configuration.
Look for a line starting with 'sys.tt.call:' and try to execute the full command following it in a command line terminal. Do not close this R session in the meantime, as 'debug=TRUE' will keep temporary files that might be needed.
If running the command after 'sys.tt.call:' does fail, you'll need to fix the TreeTagger setup.
If it does not fail but produce a table with proper results, please contact the author!
Here you need to change the value of treetagger, from
treetagger = "manual"
to
treetagger = "kRp.env"
However, before that remember to set the kRp.env as #Xochitl C. suggested in their answer
set.kRp.env(TT.cmd="C:\\TreeTagger\\bin\\tag-english.bat", lang="en", preset="en", treetagger="manual", format="file", TT.tknz=TRUE, encoding="UTF-8")
Once you do this, you'll get the desired result.
I am trying to install the r package sowas and unfortunately it is too old to implement in the new versions of r.
According to the author you can use the package using the source() function to gain access to the code but I have not been able to figure out how to do that.
Any help is appreciated.
Here is a link to the package I described as it is not a CRAN package: http://tocsy.pik-potsdam.de/wavelets/
The .zip file is a windows binary and as such it won't be too interesting. What you'll want to look at is the contents of the .tar.gz archive. You can extract those contents and then look at the code in the R subdirectory.
You could also update the package to work with new versions of R so that you can actually build and install the package. To do so you could unpack the .tar.gz as before but now you'll need to add a NAMESPACE file. This is just a plaintext file at the top of the package directory that has a form like:
export(createar)
export(createwgn)
export(criticalvaluesWCO)
export(criticalvaluesWSP)
export(cwt.ts)
export(plot.wt)
export(plotwt)
export(readmatrix)
export(readts)
export(rk)
export(wco)
export(wcs)
export(writematrix)
export(wsp)
Where you have an export statement for any function in the package that you actually want to be able to use. If a function isn't exported then the functions in the package still have access to that function but the user can't use it (as easily). Once you do that you should be able to build and install the package.
I took the liberty of doing some of this already. I haven't actually taken the time to figure out which functions are useful and should be exported and just assumed that if a help page was written for the function that it should be exported and if there wasn't a help page then I didn't export it. I used Rd2roxygen to convert the help pages to roxygen code (because that's how I roll) and had to do a little bit of cleanup after that but it seems to install just fine.
So if you have the devtools package installed you should actually be able to install the version I modified directly by using the following commands
library(devtools)
install_github("SOWAS", "Dasonk")
Personally I would recommend that you go the route of adding the NAMESPACE file and what not directly as then you'll have more control over the code and be more able to fix any problems that might occur when using the package. Or if you use git you could fork my repo and continue fixing things from there. Good luck.
If you want to see the source code of a particular function, then just type the name of the function without the braces and press enter. You will see the code.
For example type var in command prompt to see it's code.
> var
function (x, y = NULL, na.rm = FALSE, use)
{
if (missing(use))
use <- if (na.rm)
"na.or.complete"
else "everything"
na.method <- pmatch(use, c("all.obs", "complete.obs", "pairwise.complete.obs",
"everything", "na.or.complete"))
if (is.na(na.method))
stop("invalid 'use' argument")
if (is.data.frame(x))
x <- as.matrix(x)
else stopifnot(is.atomic(x))
if (is.data.frame(y))
y <- as.matrix(y)
else stopifnot(is.atomic(y))
.Call(C_cov, x, y, na.method, FALSE)
}
<bytecode: 0x0000000008c97980>
<environment: namespace:stats>
I have a package which contains a csv file which I put in inst/extdata per R-exts. This file is needed for the vignette. If I Sweave the vignette directly, all works well. When I run R --vanilla CMD check however, the check process can't find the file. I know it has been moved into an .Rcheck directory during checking and this is probably part of the problem. But I don't know how to set it up so both direct Sweave and vignette building/checking works.
The vignette contains a line like this:
EC1 <- dot2HPD(file = "../inst/extdata/E_coli/ecoli.dot",
node.inst = "../inst/extdata/E_coli/NodeInst.csv",
and the function dot2HPD accesses the file via:
ni <- read.csv(node.inst)
Here's the error message:
> tab <- read.csv("../inst/extdata/E_coli/NodeInst.csv")
Warning in file(file, "rt") :
cannot open file '../inst/extdata/E_coli/NodeInst.csv': No such file or directory
When sourcing ‘HiveR.R’:
Error: cannot open the connection
Execution halted
By the way, this is related to this question but that info seems outdated and doesn't quite cover this territory.
I'm on a Mac.
Have you tried using system.file instead of hardcoded relative paths?
EC1 <- dot2HPD(file = system.file("inst", "extdata", "E_coli", "ecoli.dot", package = "your_package+name"))
node.inst <- system.file("inst", "extdata", "E_coli", "NodeInst.csv", package = "your_package_name")