I want R to open a file that is created in my program. My code saves a log file to a variable called logFile using the following code.
logFile <- sprintf("../output/%s_%s_output%sof%s.log", str1, str2, str3, str4);
I tried to access the shell function by calling
shell('%s',logFile);
but I got an error that said
In shell("%s", toFile) : '%s' execution failed with error code 127
How can I get my program to open this file after it is finished writing to it?
How about?
browseURL('view.xlsx')
Are you looking for something like this? It works nicely, at least on my Windows box.
## An example temp file
ff <- paste0(tempfile(), ".txt")
write.table(head(mtcars), file=ff)
## Open the file with the program associated with its file extension
system2("open", ff)
For an solution that naturally extends your attempts, you could use shell.exec.
Documentation
Opens the specified file using the application specified in the Windows file associations.
ff <- paste0(tempfile(), ".txt")
write.table(head(mtcars), file=ff)
shell.exec(ff)
Created on 2020-03-11 by the reprex package (v0.3.0.9001)
Related
I am trying to load my R file but it keeps reading as errors and
Error in source("C:/Users/masters/OneDrive/Desktop/GCU/Business Analyst/Business Analyst/MIS-650/Beginning.csv") :
C:/Users/masters/OneDrive/Desktop/GCU/Business Analyst/Business Analyst/MIS-650/Beginning.csv:1:3: unexpected input
1: PK
loading through the Rstudio file open file method.
I am using the [Default] [64-bit] C:\Program Files\R\R-3.6.2 version, please help.
Try using read.csv
Something like this:
df <- read.csv('C:/Users/masters/OneDrive/Desktop/GCU/Business Analyst/Business Analyst/MIS-650/Beginning.csv')
When I run "send2cy" function in R studio, I got error.
# Basic setup
library(igraph)
library(RJSONIO)
library(httr)
dir <- "/currentdir/"
setwd(dir)
port.number = 1234
base.url = paste("http://localhost:", toString(port.number), "/v1", sep="")
print(base.url)
# Load list of edges as Data Frame
network.df <- read.table("./data/eco_EM+TCA.txt")
# Convert it into igraph object
network <- graph.data.frame(network.df,directed=T)
# Remove duplicate edges & loops
g.tca <- simplify(network, remove.multiple=T, remove.loops=T)
# Name it
g.tca$name = "Ecoli TCA Cycle"
# This function will be published as a part of utility package, but not ready yet.
source('./utility/cytoscape_util.R')
# Convert it into Cytosccape.js JSON
cygraph <- toCytoscape(g.tca)
send2cy(cygraph, 'default%20black', 'circular')
Error in file(con, "r") : cannot open the connection
Called from: file(con, "r")
But I didn't find error when I use "send2cy" function from terminal R (Run R from terminal just calling by "R").
Any advice is welcome.
I tested your script with local copies of the network data and utility script, and with updated file paths. The script ran fine for me in R Studio.
Given the error message you are seeing "Error in file..." I suspect the issue is with your local files and file paths... somehow in an R Studio-specific way?
FYI: an updated, consolidated and update set of R scripts for Cytoscape are available here: https://github.com/cytoscape/cytoscape-automation/tree/master/for-scripters/R. I don't think anything has significantly changed, but perhaps trying in a new context will resolve the issue you are facing.
EDIT:
Is it possible that ~/.Rprofile is not loaded on within check(). It looks like my whole process fails since the ~/.Rprofile is not loaded.
DONE EDIT
I have a strange problem on automated testing with testthat. Actually, when I test my package with test() everything works fine. But when I test with check() I get an error message.
The error message says:
1. Failure (at test_DML_create_folder_start_MQ_script.R#43): DML create folder start MQ Script works with "../DML_IC_MQ_DATA/dummy_data" data
capture.output(messages <- source(basename(script_file))) threw an error
Error in sprintf("%s folder got created for each raw file.", subfolder_prefix) :
object 'subfolder_prefix' not found
Before this error I source a script which defines the subfolder_prefix variable and I guess this is why it works in the test() case. But I expected to get this running in the check() function as well.
I will post the complete test script here, hope it is not to complicated:
library(testthat)
context("testing DML create folder and start MQ script")
test_dir <- 'dml_ic_mq_test'
start_dir <- getwd()
# list of test file folders
data_folders <- list.dirs('../DML_IC_MQ_DATA', recursive=FALSE)
for(folder in data_folders) { # for each folder with test files
dir.create(test_dir)
setwd(test_dir)
script_file <- a.DML_prepare_IC.script(dbg_level=Inf) # returns filename I will source
test_that(sprintf('we could copy all files from "%s".',
folder), {
expect_that(
all(file.copy(list.files(file.path('..',folder), full.names=TRUE),
'.',
recursive=TRUE)),
is_true())
})
test_that(sprintf('DML create folder start MQ Script works with "%s" data', folder), {
expect_that(capture.output(messages <- source(basename(script_file))),
not(throws_error()))
})
count_rawfiles <- length(list.files(pattern='.raw$'))
created_folders <- list.dirs(recursive=FALSE)
test_that(sprintf('%s folder got created for each raw file.',
subfolder_prefix), {
expect_equal(length(grep(subfolder_prefix, created_folders)),
count_rawfiles)
})
setwd(start_dir)
unlink(test_dir, recursive=TRUE)
}
In my script I define the variable subfolder_prefix <- 'IC_' and within the test I check if the same number of folders are created for each raw file... This is what my script should do...
So as I said, I am not sure how to debug this problem here since test() works but check() fails during the testthat run.
Now that I know to look in devtools we can find the answer. Per the docs check "automatically builds and checks a source package, using all known best practices". That includes ignoring .Rprofile. It looks like check calls build and that all of that work is done is a separate (clean) R session. In contrast test appears to use your currently running session (in a new environment).
The ZevRoss blog is as follow:
http://zevross.com/blog/2014/04/11/using-r-to-quickly-create-an-interactive-online-map-using-the-leafletr-package/
The code with error is:
# ----- Write data to GeoJSON
leafdat<-paste(downloaddir, "/", filename, ".geojson", sep="")
writeOGR(subdat, leafdat, layer="", driver="GeoJSON")
And the error is:
Error in writeOGR(subdat, leafdat, layer = "", driver = "GeoJSON") :
GDAL Error 3: Cannot open file 'd:/Leaflet/County_2010Census_DP1.geojson'
Because I am a freshman in R, I searched for this problem a lot and didn't get any good answer.
I am using Rstudio R version 3.1.1(2014-07-10) on windows 7 32bit.
My rgdal version is 0.9-1.
The other code in the blog runs successfully, this sentence seems to be the only difficult point.
You could create GeoJSON using leafletR package:
library('leafletR')
Your_GeoJSON <- toGeoJSON(data=YourData, dest=getwd())
I've tried to find a solution for this mysterious error for some time.
Eventually I found this post on the Gdal package errors' tickets site that clarified the problem and gave a solution.
Basically the problem is in the interface between rgdal and Gdal (Gdal changed their way to work and the latest version of rgdal hasn't watched up yet):
writeOGR() calls ogrCheckExists("foo.geojson") to check first if the file exists before creating a new dataset.
In the 1.11 version the OGR GeoJSON driver will emit an error message that this file doesn't exists, whereas previous version didn't emit an error message.
rgdal catches this error as a fatal one and doesn't go to the writing step. This should be fixed in rgdal.
Meanwhile you have an easy workaround : add check_exists = FALSE as a parameter to writeOGR()
Therefore the following code will work:
writeOGR(spDf,'foo.geojson','spDf', driver='GeoJSON',check_exists = FALSE)
Of course if there is already a geojson file with the chosen name at the location writeOGR still fails.
Even though you already have a 'd:' drive on your computer and you have permission to write to that drive, try the following:
--------------------------------
leafdat<-paste(downloaddir, "/", ".geojson", sep="")
> leafdat
> "d:/Leaflet/.geojson"
writeOGR(subdat, leafdat, layer="", driver="GeoJSON")
--------------------------------
Then you may get ".geojson" file on "d:/Leaflet". Change the file name ".geojson" to "County_2010Census_DP1.geojson".
I am trying to load an .rda file in r which was a saved dataframe. I do not remember the name of it though.
I have tried
a<-load("al.rda")
which then does not let me do anything with a. I get the error
Error:object 'a' not found
I have also tried to use the = sign.
How do I load this .rda file so I can use it?
I restared R with load("al.rda) and I know get the following error
Error: C stack usage is too close to the limit
Use 'attach' and then 'ls' with a name argument. Something like:
attach("al.rda")
ls("file:al.rda")
The data file is now on your search path in position 2, most likely. Do:
search()
ls(pos=2)
for enlightenment. Typing the name of any object saved in al.rda will now get it, unless you have something in search path position 1, but R will probably warn you with some message about a thing masking another thing if there is.
However I now suspect you've saved nothing in your RData file. Two reasons:
You say you don't get an error message
load says there's nothing loaded
I can duplicate this situation. If you do save(file="foo.RData") then you'll get an empty RData file - what you probably meant to do was save.image(file="foo.RData") which saves all your objects.
How big is this .rda file of yours? If its under 100 bytes (my empty RData files are 42 bytes long) then I suspect that's what's happened.
I had to reinstall R...somehow it was corrupt. The simple command which I expected of
load("al.rda")
finally worked.
I had a similar issue, and it was solved without reinstall R. for example doing
load("al.rda) works fine, however if you do
a <- load("al.rda") will not work.
The load function does return the list of variables that it loaded. I suspect you actually get an error when you load "al.rda". What exactly does R output when you load?
Example of how it should work:
d <- data.frame(a=11:13, b=letters[1:3])
save(d, file='foo.rda')
a <- load('foo.rda')
a # prints "d"
Just to be sure, check that the load function you actually call is the original one:
find("load") # should print "package:base"
EDIT Since you now get an error when you load the file, it is probably corrupt in some way. Try this and say what it prints:
file.info("a1.rda") # Prints the file size etc...
readBin("a1.rda", "raw", 50) # reads first 50 bytes from the file
Without having access to the file, it's hard to investigate more... Maybe you could share the file somehow (http://www.filedropper.com or similar)?
I usually use save to save only a single object, and I then use the following utility method to retrieve that object into a given variable name using load, but into a temporary namespace to avoid overwriting existing objects. Maybe it will be helpful for others as well:
load_first_object <- function(fname){
e <- new.env(parent = parent.frame())
load(fname, e)
return(e[[ls(e)[1]]])
}
The method can of course be extended to also return named objects and lists of objects, but this simple version is for me the most useful.