similar to: Checking on closed file connections

I noticed the following file descriptor leak when I couldn't remove a package unless I shut down the R session that had loaded and used it. The function that triggered the problem printed the output of a call to parse(). Each time one prints a srcref a connection is opened and not closed. It looks like it happens in as.character.srcref's call to getSrcLines, which has some logic I

> # creating a file > cat("sddfasdf", file="tempfile") > showConnections() class description mode text isopen can read can write > con <- file("tempfile", "r") > readLines(con) [1] "sddfasdf" Warning message: incomplete final line in: readLines(con, n, ok) > showConnections() class description mode text isopen

As far as I can tell, 'isOpen' cannot return FALSE in the case when 'rw = ""'. If the connection has already been closed by 'close' or some other function, then isOpen will produce an error. The problem is that when isOpen calls 'getConnection', the connection cannot be found and 'getConnection' produces an error. The check to see if it is

Hi all, I have newly discovered the power of connections (although just a small part of it, namely the file() connection). It allowed me to process data file with arbitrary number of fields per line, which I was using awk for preprocessing before readling into R. The combination of the connection, readLines() and strsplit() really make the work a lot easier and more organized. Thanks a bundle

On Thu, Dec 14, 2017 at 7:56 PM, Gabriel Becker <gmbecker at ucdavis.edu> wrote: > Gabor, > > You can grab the connection and destroy it via getConnection and then a > standard close call. Yeah, that's often a possible workaround, but since this connection was opened by readLines() internally, I don't necessarily know which one it is. E.g. I might open multiple

help on showConnections explains parameter all logical: if true all connections, including closed ones and the standard ones are displayed. If false only open user-created connections are included. but > # create a file > cat("TITLE extra line", "2 3 5 7", "", "11 13 17", file="ex.data", + sep="\n") >

help on showConnections explains parameter all logical: if true all connections, including closed ones and the standard ones are displayed. If false only open user-created connections are included. but > # create a file > cat("TITLE extra line", "2 3 5 7", "", "11 13 17", file="ex.data", + sep="\n") >

Hello, I have R as a socket server that computes R code sent by some scripts (the clients). These scrips send R code to generate models (SVM). The problem is that first models are generated in less than one second and one hour later, the same models are generated in more than ten seconds (even training with same data). If I restart the server , then it works well (fast). I don't know if I have

Consider this code. This is R 3.4.2, but based on a quick look at the NEWS, this has not been fixed. tryCatch( readLines(tempfile(), warn = FALSE)[1], error = function(e) NA, warning = function(w) NA ) rm(list=ls(all.names = TRUE)) gc() showConnections(all = TRUE) If you run it, you'll get a connection you cannot close(), i.e. the last showConnections() call prints: ?

I'm been doing more and more of file text parsing inside R instead of coping with Perl. For that, I need open a file and read it line-by-line. I found the documentation for 'open' isn't very clear. Right now it has ,----[ *help(R)[open]* ] | 'open' opens a connection. In general functions using connections | will open them if they are not open, but then close them

Thanks for tracking this down. Yeah, I should use suppressWarnings(), you are right. Although, readLines() might throw another warning, e.g. for incomplete last lines, and you don't necessarily want to suppress that. TBH I am not sure why that warning is given: ? con <- file(tempfile()) ? open(con) Error in open.connection(con) : cannot open the connection In addition: Warning message: In

Using dup() before fdopen() (and calling fclose() on the connection when it is closed) indeed fixes the memory leak. FYI, Gabor Index: src/main/connections.c =================================================================== --- src/main/connections.c (revision 71653) +++ src/main/connections.c (working copy) @@ -576,7 +576,7 @@ fp = R_fopen(name, con->mode); } else { /* use

Dear all, I do not completely understand following behaviour : > con <- file("test.txt") > isOpen(con) [1] FALSE > open(con) > isOpen(con) [1] TRUE > close(con) > isOpen(con) Error in isOpen(con) : invalid connection > str(con) Classes 'file', 'connection' atomic [1:1] 3 ..- attr(*, "conn_id")=<externalptr> Why do I get an

Hi everyone, I'm an R newbie working with the poLCA module. I achieved my target without having to bother anyone, but It seems that I've got stuck at the last minute. My problem is simple. I need to write my results into a file. My results are in the shape of a list (unbalanced columns) I've considered several methods (sink(), write.file) etc. etc. Unfortunately, I'm not the best

On Wed, 20 Dec 2000 joehl@web.de wrote: > > # creating a file > > cat("sddfasdf", file="tempfile") > > showConnections() > class description mode text isopen can read can write > > con <- file("tempfile", "r") > > readLines(con) > [1] "sddfasdf" > Warning message: > incomplete final line in:

Hello, >From the doc, it says: "isOpen returns a logical value, whether the connection is currently open." But actually it seems to die on closed connections: > con <- file() > isOpen(con) [1] TRUE > close(con) > isOpen(con) Error in isOpen(con) : invalid connection Is it expected ? Tested on R-3.0.2 and R version 3.1.0 Patched (2014-06-11 r65921) on linux x86_64

> # creating a file > cat("sddfasdf", file="tempfile") > showConnections() class description mode text isopen can read can write > con <- file("tempfile", "r") > readLines(con) [1] "sddfasdf" Warning message: incomplete final line in: readLines(con, n, ok) > showConnections() class description mode text isopen

On Thu, Dec 14, 2017 at 12:17 PM, G?bor Cs?rdi <csardi.gabor at gmail.com> wrote: > On Thu, Dec 14, 2017 at 7:56 PM, Gabriel Becker <gmbecker at ucdavis.edu> > wrote: > > Gabor, > > > > You can grab the connection and destroy it via getConnection and then a > > standard close call. > > Yeah, that's often a possible workaround, but since this

Maybe open.connection() should also check if the connection is already open and given an error or at least a warning if it is. Suggested code update: open.connection <- function(con, open="r", blocking=TRUE, ...) { if (!inherits(con, "connection")) stop("argument is not a connection") if (isOpen(con)) # NEW

I have been trying to read a random sample of lines from a file into a data frame using readLines(). The help indicates that readLines() will start from the current line if the connection is open, but presented with a closed connection it will open it, start from the beginning, and close it when finished. In the code that follows I tried to open the file before reading but apparently without