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By the way, this is related to this question but that info seems outdated and doesn't quite cover this territory.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")
Related
I have an 'R' file which inserts reads data from a database, does some calculations, then re-inserts data back into a table.
Before i execute the script, I run 'Source' as below..
I want to use Windows Task Scheduler to auto schedule this script to run. I am following the guide https://trinkerrstuff.wordpress.com/2015/02/11/scheduling-r-tasks-via-windows-task-scheduler/ - When creating the .BAT file it should look something like:
echo off
CMD BATCH C:\PATHNAME\RSCRIPT.R
What should i insert here to make sure it runs the 'Source' first?
In the R code i have
In the code i have:
#use a relative path to locate our common utilities file and source it
source("..//R-Utilities//Utilities.R")
# use check_install_package function from Utilities.R to install and load
packages
check_install_package("lubridate")
check_install_package("plyr")
check_install_package("dplyr")
check_install_package("dtplyr")
check_install_package("ISOweek")
check_install_package("stringi")
check_install_package("RODBC")
#give us access to the library of functions this script uses
source("CTB_functions.R")
But I need to click the source button before running my whole code, or i get an error (As below).
> #this automatically sets the working directory to be where this file is
> setwd(getSrcDirectory(function(x) {x}))
Error in setwd(getSrcDirectory(function(x) { :
cannot change working directory
>
> #use a relative path to locate our common utilities file and source it
> source("../R-Utilities/Utilities.R")
Error in file(filename, "r", encoding = encoding) :
cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
cannot open file '../R-Utilities/Utilities.R': No such file or directory
>
> # use check_install_package function from Utilities.R to install and load
packages
> check_install_package("lubridate")
Error: could not find function "check_install_package"
> check_install_package("plyr")
Error: could not find function "check_install_package"
> check_install_package("dplyr")
Error: could not find function "check_install_package"
> check_install_package("dtplyr")
Error: could not find function "check_install_package"
> check_install_package("ISOweek")
Error: could not find function "check_install_package"
> check_install_package("stringi")
Error: could not find function "check_install_package"
> check_install_package("RODBC")
Error: could not find function "check_install_package"
>
> #give us access to the library of functions this script uses
> source("CTB_functions.R")
Error in file(filename, "r", encoding = encoding) :
cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
cannot open file 'CTB_functions.R': No such file or directory
Given your script, there should be no need to click the “Source” button first: in fact, it would execute your script twice.
A few things about your scripts:
CMD BATCH C:\PATHNAME\RSCRIPT.R
This is missing R in front of CMD BATCH. However, You should probably use Rscript.exe instead of R CMD BATCH. It’s a modern replacement.
source("..//R-Utilities//Utilities.R")
There’s no need for double slashes: single slashes work.
source("../R-Utilities/Utilities.R")
More fundamentally, using source in this manner can quickly become complex and error-prone due to several shortcomings (e.g circular inclusion, relative paths etc). A better way of achieving this is via the ‘box’ package, which provides a vastly improved replacement for the source function, which seems to fit your use-case very closely.
In particular, your script will probably not work: source won’t find the files R-Utilities/Utilities.R and CTB_functions.R because it searches these relative to the current working directory, not relative to the script directory. Using ‘box’ fixes this.
I am attempting to use the plot() function in the biomod2 package, following a vignette here (http://finzi.psych.upenn.edu/usr/share/doc/library/biomod2/doc/Simple_species_modelling.pdf). Below is the error I am getting:
getwd()
# [1] "/home/gjanzen/Documents/Hufford/Drought/Data/Layers"
plot(myBiomodData)
Error in getExportedValue(pkg, name) : cannot open file
'~/R/x86_64-pc-linux-gnu-library/3.3/viridisLite/data/Rdata.rdb': No
such file or directory In addition: Warning message: In
getExportedValue(pkg, name) : restarting interrupted promise
evaluation
I have confirmed that the Rdata.rdb exists, in the following directory:
f <- file.choose()
f
# [1] "/home/gjanzen/R/x86_64-pc-linux-gnu-library/3.3/viridisLite/data/Rdata.rdb"
So, to me, it looks like the plot() function is looking in the wrong place. How can I change where this function looks for Rdata.rdb? Can I alter the path somehow? Or would changing my working directory fix this?
PS - This is my first post on Stack Overflow, so please forgive any mistakes in etiquette, and/or feel free to point them out to me so that I do not repeat them.
I think that the first thing to try is to reinstall the package viridisLite that seems to be the one that is causing troubles.
install.packages('viridisLite', dep = TRUE)
If this not solves the issue you should try to open a new plotting device threw x11() to check if the issue is not coming from the R (resp. RStudio) plotting device itself.
I have installed the required packages - gdata and ggplot2 and I have installed perl.
library(gdata)
library(ggplot2)
# Read the data from the excel spreadsheet
df = data.frame(read.xls ("AssignmentData.xlsx", sheet = "Data", header = TRUE, perl = "C:\\Strawberry\\perl\\bin\\perl.exe"))
However when I run this I get the following error:
Error in xls2sep(xls, sheet, verbose = verbose, ..., method = method, :
Intermediate file 'C:\Users\CLAIRE~1\AppData\Local\Temp\RtmpE3UYWA\file8983d8e1efc.csv' missing!
In addition: Warning message:
running command '"C:\STRAWB~1\perl\bin\perl.exe" "C:/Users/Claire1992/Documents/R/win-library/3.1/gdata/perl/xls2csv.pl" "AssignmentData.xlsx" "C:\Users\CLAIRE~1\AppData\Local\Temp\RtmpE3UYWA\file8983d8e1efc.csv" "Data"' had status 2
Error in file.exists(tfn) : invalid 'file' argument
Thanks to #Stibu I realised I had to set my work directory. This is the command you use to run in Rstudio; setwd("C/Documents..."). The file path is where the excel file is located.
I had the issue but I solved it differently.
My problem was because my file was saved as Excel (extension .xls) but it was a txt file.
I corrected the file and I did not meet any other error with the R function.
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...)
I'm trying to reproduce the example for tex2docx function in reports R package and getting the following error.
DOC <- system.file("extdata/doc_library/apa6.qual_tex/doc.tex",
package = "reports")
BIB <- system.file("extdata/docs/example.bib", package = "reports")
tex2docx(DOC, file.path(getwd(), "test.docx"), path = NULL, bib.loc = BIB)
Error Message
pandoc.exe: Error reading bibliography `C:/Users/Muhammad'
citeproc: the format of the bibliographic database could not be recognized
using the file extension.
docx file generated!
Warning message:
running command 'C:\Users\MUHAMM~1\AppData\Local\Pandoc\pandoc.exe -s C:/Users/Muhammad Yaseen/R/win-library/3.0/reports/extdata/doc_library/apa6.qual_tex/doc.tex -o C:/Users/Muhammad Yaseen/Documents/test.docx --bibliography=C:/Users/Muhammad Yaseen/R/win-library/3.0/reports/extdata/docs/example.bib' had status 23
I wonder how to get tex2docx function in reports R package working properly.
As described in the above comments, the error is caused by passing a filename/path including some spaces that are nor escaped, nor quoted. A workaround could be wrapping all file paths and names inside of shQuote before passing to the command line with system.
Code: https://github.com/trinker/reports/pull/31
Demo:
Loading package
library(reports)
Creating a dummy dir with a space in the name that would hold the bib file
dir.create('foo bar')
file.copy(system.file("extdata/docs/example.bib", package = "reports"), 'foo bar/example.bib')
Specifying the source and the copied bib file:
DOC <- system.file("extdata/doc_library/apa6.qual_tex/doc.tex", package = "reports")
BIB <- 'foo bar/example.bib'
Running the test:
tex2docx(DOC, file.path(getwd(), "test2.docx"), path = NULL, bib.loc = BIB)
Disclaimer: I tried to test this pull request, but I could not setup an environment with all the needed tools to run R CMD check with vignettes and everything else after all in 5 mins (sorry but being on vacation right now and just enjoying the siesta after lunch), so please consider this pull request as "untested" -- although it should work.