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.
Related
I am trying to use the function accumcomp.long in the Biodiversity.R package in order to adjust my species accumulation curves in ggplot.
However, calling the function accumcomp.long gives me an error, suggesting that this function perhaps does no longer exists.
accum.long1 <- accumcomp.long(Accum.1, ci=NA, label.freq=5)
Error in accumcomp.long(Accum.1, ci = NA, label.freq = 5) :
could not find function "accumcomp.long"
The function BiodiversityR::accumcomp.long
returns
Error: 'accumcomp.long' is not an exported object from 'namespace:BiodiversityR'
I am not certain whether this is an issue with the package, the way the package is loaded into my R space, or perhaps unrelated to the package simply the format of my data.
My community and environment files are of dataframe class. I have tried loading them as .csv files as well as .rda files, but the error remains.
??accumcomp.long
renders "No results found".
I am using R version 3.5.3 (2019-03-11)
Any suggestions as to what else I could try?
Thanks in advance!
I re-installed the package BiodiversityR and included force = T (as per this thread https://community.rstudio.com/t/could-not-find-function-error-even-though-fun-is-in-namespace-and-has-an-rd-file/91243). I then reloaded the package. I am not sure what force = T does, but the accumcomp.long function now works.
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 need to import excel file directly from NYSE website. The spreadsheet url is https://quotespeed.morningstar.com/exportChartDataToExcel.jsp?tickers=AAPL&symbols=126.1.AAPL&st=1980-12-1&ed=2015-6-8&f=m&dty=1&types=1&ver=1.6.0&qs_wsid=E43474CC03753FE0E777D89877788ECB . Tried using gdata package and changing https to http but still doesnt work. Does anybody know solution to such issue?
EDIT: Has to be imported to R directly from website (project requirement)
Without information about why using the gdata package does not work for you I have to assume. Make sure you have Perl installed - you can download it at http://www.activestate.com/activeperl
This works for me:
library('gdata')
## URL broken into multiple lines for readability
url <- paste("https://quotespeed.morningstar.com/exportChartDataToExcel.",
"jsp?tickers=AAPL&symbols=126.1.AAPL&st=1980-12-1&ed=2015-",
"6-8&f=m&dty=1&types=1&ver=1.6.0&qs_wsid=E43474CC03753FE0E",
"777D89877788ECB", sep = "")
url <- gsub("https", "http",url)
data <- read.xls(url, perl = "C:/Perl64/bin/perl.exe")
Without perl = "path_to_perl.exe" I got the error
Error in findPerl(verbose = verbose) :
perl executable not found. Use perl= argument to specify the correct path.
Error in file.exists(tfn) : invalid 'file' argument
Use the RCurl package to download the file and the readxl package by Hadley to read the excel file
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...)
The below error keeps coming up inconsistently when I try to read excel files into R using the 'XLConnect' package.
Error in ls(envir = envir, all.names = private) :
invalid 'envir' argument
I have actually run into this error while even using other packages that read excel files like package 'xlsx' and 'xlsReadWrite'. Many times restarting the R session solves this problem, which leads me to think that something else I am doing in my R session is changing the environment and not allowing me to load excel files anymore. Below is the latest example of code that is causing this error. In this case I know that the following coding sequence is causing the error to appear - but why is that happening? And how can I get past this error if I need the chron package.
library("XLConnect")
wb2 <- loadWorkbook("excel_file", create = FALSE)
library(chron)
wb2 <- loadWorkbook("excel_file", create = FALSE)
Anyone else run into this issue before? Any help on this issue is greatly appreciated!
Before reopening the workbook try removing the reference to previously opened one, so:
rm(wb2)
wb2 <- loadWorkbook("excel_file", create = FALSE)
Also, make sure that "excel_file" is not open by excel or any other program while you run the R test.
I've seen the same error come up when using XLConnect and the above seemed to help.
Had this problem a couple of times and the call stack looks like this message is generated when a "OutOfMemory" Exception is thrown.
To solve this problem I used:
options( java.parameters = "-Xmx4g" )
to increase the heap size rJava is able to use.
Debugging with options(error=utils::recover) helped a lot, because the R error messages are not very specific.