Error: Error in file(con, "r") : cannot open the connection - r

I am trying to run dssp function using bio3d package in R. But I am getting error.
library("bio3d")
pdb <- read.pdb("1CRN")
x <- dssp(pdb, exepath="C:/dssp/dssp.exe")
Error in file(con, "r") : cannot open the connection
Any suggestions please.

To solve it you need to fix the dssp function paramenters:
fix(dssp)
rewrite the following line:
system(paste(exepath, "dssp -c ", infile, " ", outfile, sep = ""), ignore.stderr = TRUE)
"-i" istead of "-c" and "-o" intead of " "
chears

Related

makecluster of parallely package

cl <- parallelly::makeClusterPSOCK(2, autoStop = TRUE)
Error:
Error in system(test_cmd, intern = TRUE, input = input) :
'CreateProcess' failed to run 'C:\Users\xxx~1\ONEDRI~1\DOCUME~1\R\R-40~1.3\bin\x64\Rscript.exe -e "try(suppressWarnings(cat(Sys.getpid(),file=\"C:/Users/LOCAL_~1/Temp/RtmpIP7vSI/worker.rank=1.parallelly.parent=19988.4e147c0a5082.pid\")), silent = TRUE)" -e "file.exists(\"C:/Users/LOCAL_~1/Temp/RtmpIP7vSI/worker.rank=1.parallelly.parent=19988.4e147c0a5082.pid\")"'
I was trying to create the clusters for parallel execution. But does not work and throws the above error.

Why can't i parse my R code in a Jupyter Notebook?

I tried to use R in a Jupyter Notebook with VSCode, but I get the following Error:
summary(mtcars)
ERROR: Error in parse(text = x, srcfile = src): <text>:1:16: unerwartete Eingabe
1: summary(mtcars)
^
Error in parse(text = x, srcfile = src): <text>:1:16: unerwartete Eingabe
1: summary(mtcars)
^
Traceback:
It seems like I there's a problem with the newline command, because I can execute multiple cells with one line of code each.
Changing the End of Line Command in VSCode from "\r\n" to "\n" did the trick...

R Url function on Mac

When running the following call on Mac I get an error as follows
jsonlite::fromJSON(url(paste("https://fantasy.premierleague.com/api/element-summary/236")))
Error in parse_con(txt, bigint_as_char) : parse error: premature EOF
(right here) ------^
However the following call works correctly, with the only difference being the omission of the url().
jsonlite::fromJSON(paste("https://fantasy.premierleague.com/api/element-summary/236"))
The traceback from the error is as follows:
4: parse_con(txt, bigint_as_char)
3: parseJSON(txt, bigint_as_char)
2: parse_and_simplify(txt = txt, simplifyVector = simplifyVector,
simplifyDataFrame = simplifyDataFrame, simplifyMatrix = simplifyMatrix,
flatten = flatten, ...)
1: jsonlite::fromJSON(url(paste("https://fantasy.premierleague.com/api/element-summary/236")))
I've tried on two separate installations with the same result. I wonder if the line break after the first line of the JSON is being interpreted as EOF....

KnitR unable to download documents

I am able to run this code normally in R.
setInternet2(use = TRUE)
download.file("http://d396qusza40orc.cloudfront.net/dsscapstone/dataset/Coursera-SwiftKey.zip", "Coursera-SwiftKey.zip", method = "curl", mode = 'wb')
unzip("Coursera-SwiftKey.zip", files=c("final/en_US/en_US.twitter.txt", "final/en_US/en_US.news.txt", "final/en_US/en_US.blogs.txt"), exdir=".")
But when i try to use knitR it gives me this error
Quitting from lines 15-21 (milestone.Rmd)
Error in parse(text = x, srcfile = src) : <text>:5:106: unexpected ')'
4: unzip("Coursera-SwiftKey.zip", files=c("final/en_US/en_US.twitter.txt", "final/en_US/en_US.news.txt", "final/en_US/en_US.blogs.txt"), exdir=".")
5: file.copy(c("final/en_US/en_US.twitter.txt", "final/en_US/en_US.news.txt", "final/en_US/en_US.blogs.txt"?)
^
Calls: <Anonymous> ... <Anonymous> -> parse_all -> parse_all.character -> parse
Execution halted
I am using R Studio and MAC OS X.
I tried removing the s from https but it still di not work.

use R to loop through subdirectories and copy files

I am trying to create a batch script in R to pre-process some data and one of the first steps I have to do is check to see if a file exists in a sub-directory and then (if it does) create a copy of it with a new name. I'm having trouble with the syntax.
This is my code:
##Define the subject directory path
sDIR = "/home/bsussman/Desktop/WORKSPACE"
#create data frame to loop through
##list of subject directories
subjects <-list.dirs(path = sDIR, full.names = TRUE, recursive = FALSE)
for (subj in 1:length(subjects)){
oldT1[[subj]] <- dir(subjects[subj], pattern=glob2rx("s*.nii"), full.names=TRUE)
T1[[subj]] <- paste(subjects[subj], pattern="/T1.nii",sep="")
if (file.exists(paste(subjects[subj], pattern="/T1.nii",sep=""))=FALSE{
file.copy(oldT1, T1)
}
}
It renames files in one subdirectory, but will not do loop through gives me these errors:
Error: unexpected '=' in:
"
if (file.exists(paste(subjects[subj], pattern="/T1.nii",sep=""))="
> file.copy(oldT1, T1)
[1] FALSE
> }
Error: unexpected '}' in " }"
> }
Error: unexpected '}' in "}"
I am not as much worried about the [1]FALSE message. But any ideas?
Thanks!!
It's just a problem with the syntax in the if statement. Try replacing this:
if (file.exists(paste(subjects[subj], pattern="/T1.nii",sep=""))=FALSE{
file.copy(oldT1, T1)
}
with this:
if (!file.exists(paste(subjects[subj], pattern="/T1.nii",sep=""))){
file.copy(oldT1, T1)
}

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