similar to: Why I get this error? Error in close.connection(f) : invalid connection

gentoo linux, version 2.4.1: > d= as.data.frame(matrix(1:20, 4, 5)) > d V1 V2 V3 V4 V5 1 1 5 9 13 17 2 2 6 10 14 18 3 3 7 11 15 19 4 4 8 12 16 20 > write.csv(d, file="d1.csv"); > write.csv(d, file=pipe("cat > d2.csv")) > write.csv(d, file=pipe("gzip -c > d3.csv.gz"), col.names=T) Warning message: attempt to change 'col.names'

Hi everybody, I am using gzipped files quite extensively and cannot figure out how I can close (or reuse) connections. Example: > for(i in 1:300) {cat(i, "\n"); a <- readLines(gzfile("file.gz"), n=1) } 1 2 ... 46 47 Error in gzfile("~/tyyq/andmebaasiq/ETU/ETU1997.tsv.gz") : all connections are in use To use just gzfile without any open/close should

Hi Sorry, I am clearly missing something here. I want to read this file directly: ftp://ftp.sanger.ac.uk/pub/mirbase/targets/v5/arch.v5.txt.gallus_gallus. zip I tried using read.table(gzfile("ftp://ftp.sanger.ac.uk/pub/mirbase/targets/v5/arch.v5 .txt.gallus_gallus.zip")) But I got an error: Error in open.connection(file, "r") : cannot open the connection In addition:

Hi, I am making multiple calls to gzfile() via read.table(), e.g. > x <- read.table( gzfile( "xxx.gz" ) ) After i do this many times (I haven't counted, but probably between 50 and 100 times) I get the error message: Error in open.connection(file, "r") : unable to open connection In addition: Warning message: cannot open compressed file 'xxx.gz' however, I

Hi, I'm running into more issues when reading data from a gzfile connection. If I read the data sequentially with successive calls to readBin(), the data I get looks ok. But if I call seek() between the successive calls to readBin(), I get corrupted data. Here is a (hopefully) reproducible example. See my sessionInfo() at the end (I'm not on Windows, where, according to the man page,

Hi I have been trawling the web, FAQs, and R manuals for help on the following issue, but have failed and was wondering if anyone has a solution to the following problem: After having installed R 2.6.2 for Windows (binary), I tried to install various packages. Every time I try loading a package (any package) via the built-in menu, I run into the following error message. >

Hi, It seems like reading a line from a gzfile() connection changes the mode of the connection from text to binary (it also alters "can write", in case it matters). The following transcript, produced on RedHat 7.1, demonstrates this "feature" (note the evolution of file$text). Is this expected? Thanks, Vadim > file <- gzfile("foo.gz") file <-

When I read a .gz file with readLines() in 3.4.3, it returns text (and a warning). In 3.5.0, it gives a warning, but no text. Is this expected behavior or a bug? 3.4.3: > source_file = "1k_annotation.gz" > readfile_con <- gzfile(source_file, "r") > readLines(readfile_con, n = 5) [1] "#chr\tpos\tref\talt\t <truncated output here> Warning message: In

Full_Name: Vadim Ogranovich Version: Version 1.6.0 (2002-10-01) OS: Red Hat 7.1 Submission from: (NULL) (209.99.241.1) The following sequence of commands crashes my R session. The first weirdness happens after the second command that appears not to change the "foo.gz" file, no error generated. > con <- gzfile("foo.gz", open="w"); cat("goo\n",

You bet - it's available on github at https://github.com/UW-GAC/wgsaparsr/blob/master/tests/testthat/1k_annotation.gz -Ben On Thu, May 10, 2018 at 4:17 PM, Michael Lawrence <lawrence.michael at gene.com > wrote: > Would it be possible to get that file or a representative subset of it > somewhere so that I can reproduce this? > > Thanks, > Michael > > On Thu, May

Is it just me, or did a corrupt PACKAGES.gz file get installed in the bin/windows/contrib/3.2 directory of CRAN mirrors recently? gzfile() complains about it and Cygwin's gzip cannot decompress it. I tried the following repos <- "https://cran.rstudio.com" v <- "3.2" pkgs.gz <- paste(sep="/", repos, "bin/windows/contrib", v,

Dear Sir When I close R console then following message apear when I want to save the workspace. If I close the R console without saving workspace then R console is closed otherwise not. Error in gzfile(file, "wb") : unable to open connection In addition: Warning message: In gzfile(file, "wb") : cannot open compressed file '.RDataTmp' Regards -- AMINA SHAHZADI

I realize that others have struggled with this issue...i.e. http://tolstoy.newcastle.edu.au/~rking/R/help/05/01/9826.html i am on os.x 10.4 w/ R2.2, and am (perhaps foolishly) also on this quest... i would like to be able to install downloaded source (tar.gz'd) files from within an R session, and have it work in a X-platform way..i am often not connected to the internet and have libraries

Hello, I am hoping for some advice regarding how I can install the XML package which I require to run package tm. Normally I would use the install package option, however, I have to install the packages to a laptop running XP. The laptop does not have an internet connection. Firstly I tried the file - XML_1.99-0.tar.gz . Below is the error I received Error in gzfile(file, "r") :

Hello, I have just installed v 2.6.2 on a new computer running Windows XP and tried to perform 'update packages' via the menu option on the R console. Any advice on the following problem is much appreciated. Bob Below are the warning and error messages received. A search of the hard drive does not reveal any file including "RtmpgMMu03/libloc" . >

Dear all, In R-devel (2011-09-23 r57050), I'm running into a serious problem with seek()ing on connections opened with gzfile(). A warning is generated and the file position does not seek to the requested location. It doesn't seem to occur all the time - I tried to create a small example file to illustrate it, but the problem didn't occur. However, it can be seen with a file I use for

Hello ... Are there any known problems or even gotchas to look out for when using a gzfile connection in read.csv/read.table in Windows? In the package PROcess, available at www.bioconductor.org/repository/devel/package/html/PROcess.html there are two files in the PROcess/inst/Test directory which are of the extension *.csv.gz. With both files, if I open up a gzfile connection, say: vv <-

I get unexpected behavior from "readLines()" and "scan()" depending on how the file is opened with "gzfile" or "unz". More specifically: > file <- gzfile("file.gz") > readLines(file,1) [1] "a\tb\tc" > readLines(file,1) [1] "a\tb\tc" > close(file) It seems that the stream is rewound between calls to readLines.

Found the simpliest way of seeing I bug I encountered doing "R CMD check --use-gct": Just launch R (with --vanilla), and do this: > ?gctorture # this work > gctorture() > ?gctorture Error in gzfile(file, "rb") : can only weakly reference/finalize reference objects # this does not It seems that when gctorture() is on gzfile() doesn't work.

Dear R-Users I have come across the error that apparently has nothing to do with command itself. Here is the error (w - matrix (or vector) e testXaxis - dates). > plot(data.frame(testXaxis,w),col="blue",ylab="Q, [m3/s]",xlab="Data", + main="Free-run - Modelo NARX MISO - Test Data") Error in gzfile(file, "wb") : cannot open the