While accessing to CSV file from disk with the help of the R program, where a path to the CSV file is provided in the configuration file ( A path is like "testData/Amazon S3/Inventory/Accounts.csv" which is provided in the Configuration file and cfig[2]$save.location is variable who is having value of this path accessed from Configuration file). Few lines of code are below
path <- cfig[2]$save.location
test_data <- fread(path,stringsAsFactors = FALSE,drop=col_ignor,blank.lines.skip = TRUE)
but it gave the message below:
Taking input= as a system command ('testData/Amazon
S3/Inventory/Accounts.csv') and a variable has been used in the
expression passed to input=. Please use fread(cmd=...). There is a
security concern if you are creating an app and the app could have a
malicious user and the app is not running in a secure environment;
e.g. the app is running as root. Please read item 5 in the NEWS file
for v1.11.6 for more information and for the option to suppress this
message.
'testData' is not recognized as an internal or external
command, operable program or batch file. Warning messages:
1: In (if
(.Platform$OS.type == "unix") system else shell)(paste0("(", :
'(testData/Amazon S3/Inventory/Accounts.csv) >
C:\Users\sharmb5\AppData\Local\Temp\RtmpOa25kH\filea78b5351f1'
execution failed with error code 1.
2: In fread(cfig[2]$save.location,
stringsAsFactors = FALSE, drop = col_ignor, : File
'C:\Users\sharmb5\AppData\Local\Temp\RtmpOa25kH\filea78b5351f1' has
size 0. Returning a NULL data.table.
when the following line of code executes,
config[4]$save.location <- stri_replace_all(config[4]$save.location, cp_val, fixed = cp_key)
It gives an error like as, Error in [<-.data.table(*tmp*, j, value = list(TestCaseID = "C419760", : Supplied 14 columns to be assigned 15 items. Please see NEWS for v1.12.2.
The above error was a warning but after manually updating of packages. This warning turns into an error. What will be the reason behind this issue and how to solve it? Thanks for Advance!!!
Related
Obviously one can find and set working directories with getwd() and setwd(). This question is a bit more complicated. I'm running two files on a super computer (one is a regular R file which calls the other file (a .stan file). The way I submit work to the super computer is that I have to zip a folder containing the data, the .R file, and the .stan file. I upload this folder, and I pull this folder by setting it as one of the parameters in the super computer. I call the data using the standard read.csv() command and everything is hunky dory.
However, when I call the .stan file from the .R file, it can't access it because it needs to know the working directory.
This is the error I get:
> fit <- stan(file="ace_thresholds.stan", data=stanData, cores = 4)
Error in file(fname, "rt") : cannot open the connection
In addition: Warning messages:
1: In normalizePath(file) :
path[1]="ace_thresholds.stan": No such file or directory
2: In file(fname, "rt") :
cannot open file 'ace_thresholds.stan': No such file or directory
Error in get_model_strcode(file, model_code) :
cannot open model file "ace_thresholds.stan"
Calls: stan -> stan_model -> stanc -> get_model_strcode
Execution halted
When I tried setting the working directory to the unzipped NSG_stan folder (which is what I assumed the wd to be, I received this error:
fit <- stan(file="NSG_stan/ace_thresholds.stan", data=stanData, cores = 4)
Error in file(fname, "rt") : cannot open the connection
In addition: Warning messages:
1: In normalizePath(file) :
path[1]="NSG_stan/ace_thresholds.stan": No such file or directory
2: In file(fname, "rt") :
cannot open file 'NSG_stan/ace_thresholds.stan': No such file or directory
Error in get_model_strcode(file, model_code) :
cannot open model file "NSG_stan/ace_thresholds.stan"
Calls: stan -> stan_model -> stanc -> get_model_strcode
Execution halted
So I tried running print(getwd()) within the script and in the printout I see that the wd is
"/projects/ps-nsg/home/nsguser/ngbw/workspace/NGBW-JOB-RTOOL_TG-EBE9CDBF28BF42AF8CB6EC9355006B3E/NSG_stan"
which means that the working directory will shift with every job. So to accurately set the working directory, I'd need to set it to the current folder within the script. I looked for various posts on how to do this like the following
# install.packages("rstudioapi") # run this if it's your first time using it to install
library(rstudioapi) # load it
# the following line is for getting the path of your current open file
current_path <- getActiveDocumentContext()$path
# The next line set the working directory to the relevant one:
setwd(dirname(current_path ))
# you can make sure you are in the right directory
print( getwd() )
The issue with this is that it's a super computer, so it's difficult to install packages, because every time I want to install something, I have to email the folks associated with the super comp and that all takes time.
I've looked over this thread as well: R command for setting working directory to source file location in Rstudio. Appears to be a lot of dissent over what works. I tried a couple of them, and they didn't work.
setwd(getSrcDirectory()[1])
this.dir <- dirname(parent.frame(2)$ofile)
setwd(this.dir)
I've included the .R file below, in the event that it helps, but I think this is probably a pretty easy answer for someone with a decent amount of coding experience.
.R file (so it's the "ace_thresholds.stan" file that I either need to link to the current wd or to include the code that would set the wd, such that this "ace_thresholds.stan" call would work. Does that make sense?
Thanks much!
dat <- ace.threshold.t2.samp
dat <- subset(dat, !is.na(rw))
dat$condition <- factor(dat$condition)
dat$pid <- factor(dat$pid)
nTotal <- dim(dat)[1]
nCond <- length(unique(dat$condition))
nSubj <- length(unique(dat$pid))
intensity <- dat$rw
condition <- as.numeric(dat$condition)
pid <- as.numeric(dat$pid)
correct <- dat$correct_button == "correct"
chancePerformance <- 1/2
stanData <- list(nTotal=nTotal, nLevels=nCond, nSubj = nSubj, subject = pid, intensity=intensity, level=condition, correct=correct, chancePerformance=chancePerformance)
fit.rw <- stan(file="ace_thresholds.stan", data=stanData, cores = 4, control=list(max_treedepth=15, adapt_delta=0.90))
I need the data of the .rdata file for text mining. These are my dataset. I don't know exactly what's in that file. The problem is i can't load it.
I tried to open the file with different windows computers but with the same errors. I used RStudio in the updated version. I google the error-Information but nothing worked. Because I can open other rdata files there should be no registry problem. I wanted to check in an other basic windows Editor to look what is in the file but there were only signs like: ‹ ìùuPo³6
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¢hXˆ
I tried different possibilities to open the file in RStudio with different error informations as followed:
with load()
require("readr")
setwd("C:/Users/..")
options(stringsAsFactors = F)
load("file")
# Error in load("file") :
# bad restore file magic number (file may be corrupted) -- no data loaded
# In addition: Warning message:
# file ‘.rdata’ has magic number ''
# Use of save versions prior to 2 is deprecated
with source()
require("readr")
setwd("C:/Users/..")
options(stringsAsFactors = F)
source("file")
# Error in source("file") :
# file.rdata:1:1: unexpected input
# 1:
# ^
readRDS
setwd("C:/Users/..")
options(stringsAsFactors = F)
readRDS("file")
# Error in readRDS("file") : unknown input format
> library(Rook)
> s <- Rhttpd$new()
> s$add(name='MyApp',plot_ind_brz='D:/STOCK/plot_ind_brz.R')
I am getting an error
"Error in s$add(name = "MyApp", plot_ind_brz = "D:/STOCK/plot_ind_brz.R") :
unused argument(s) (plot_ind_brz = "D:/STOCK/plot_ind_brz.R")"
And steps are written as follows:
Load Rook
library(Rook)
Create an Rhttpd variable
s <- Rhttpd$new()
Create your application in a separate file, assign it to either the
name of your application or simply just 'app'.
Add your application to the server:
s$add(name='MyApp',app='path/to/your/app.R')
Load the app into your browser
s$browse('MyApp')"
How to resolve this problem? Can anyone please help me on this?
In the instructions, app is the name of a formal parameter to the add() function. Even if your app is named differently, this has to remain unchanged:
s$add(name='MyApp', app='D:/STOCK/plot_ind_brz.R')
I tried to upload a data model to Synapse, and I got the following error message (from remote console):
Error in if (grepl("/$", filePath)) { : argument is of length zero In
addition: Warning messages: 1: In file.copy(object$getCacheDir(),
path, recursive = TRUE) : problem creating directory
/home/creighto#bcm.edu/scratch/tmp/RtmpHjLEQh/cacheRoot5e4dbe7c02d/archive.zip_unpacked/.R_OBJECTS:
No space left on device 2: In unzip(filename, exdir = destdir) : error
1 in extracting from zip file.
Also my directory has frozen up, and I cannot seem to access files. Have I exceeded a space limit here?
Sorry to state the obvious, but it does look like you've ran out of space: you can't unzip file due to space, so you can't create a directory. Can you reduce the file size?
I have a R Job that is submitted to the condor, The R file(one.R) which is submitted to the condor is reading another R file(two.R), when I submit the job to the condor its is failed and the reason for that is the submitted R(one.R) file is not reading the called R file(two.R)
Error in text file is :
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file 'C:/Users/pcname/Desktop/test_case/two.R': Permission denied
Execution halted
and my submit file is
#test_input.condor
#
executable = C:\R\R-2.10.1\bin\Rscript.exe
arguments = one.R
universe = vanilla
getenv = true
#requirements = ARCH == "INTEL" && OPSYS == "WINNT60"
input = one.R
should_transfer_files = yes
transfer_executable = false
when_to_transfer_output = ON_EXIT
transfer_input_files = C:/Users/OmegaAdmin/Desktop/test_case/two.R
log = test_input.log
output = test_input.out
error = test_input.err
queue
Appreciate any ideas on this.
Thanks,
This is not an R-related problem, but a problem of accessibility. The error message seems rather clear to me: the server has no reading rights for that file. Make sure you share the file or folder you want to read in. I don't know what the setup is of the network and clusters wherever you're located, but you better contact the admins to ask how you get your files to the right places.
Also make sure that if you transfer files to the servers/cluster, you adapt your R script so it points to the right directories. Which is probably not your own harddrive...
When you say
transfer_input_files = C:/Users/OmegaAdmin/Desktop/test_case/two.R
That tells Condor to copy two.R into the current working directory when the job starts. The current working directory is a specially created workspace, not (usually) a home directory. Thus I would expect the full path to look something like
C:/condor/execute/dir_28412/two.R
However, R is actually looking in
C:/Users/pcname/Desktop/test_case/two.R
Why is R looking there? Does one.R potentially say "Find two.R in $HOME/Desktop/test_case"? Does it perhaps say, "Look in Desktop/testcase/two.R" and R has configuration that wants to look relative to the user's home directory?
The solution is almost certainly to modify one.R or your R configuration to look for two.R in the current working directory. If for some reason R changes its current working directory, the environment variable _CONDOR_SCRATCH_DIR should contain it.
On a related note, you said:
arguments = one.R
input = one.R
The first is an argument passed to Rscript.exe, which I'm guessing tells R to load and run a file called one.R. Except that script isn't present! If you want that to work, you'll need to add it to transfer_input_files. But it obviously appears to work; why? Because "input=one.R" means "take the contents of one.R and pipe it in as standard input to Rscript.exe; the same as if you'd typed those contents in." I'm guessing you can remove the arguments, or remove the input and add one.R to your transfer_input_files, removing the ambiguity.