search for: bzfile

I'm putting together a data package and am finding that I get enormous savings in space by using bzip instead of the usual gzip in save(). Is it safe to assume that for R versions, say >= 1.7.1, that the function bzfile() will always be available? Thanks, -roger

...gz", "w") # compressed file > cat("TITLE extra line", "2 3 5 7", "", "11 13 17", file = zz, sep = "\n") > close(zz) > blah = file("ex.gz", "r") > seek(blah) [1] 7.80707e+17 > > zz <- bzfile("ex.bz2", "w") # bzip2-ed file > cat("TITLE extra line", "2 3 5 7", "", "11 13 17", file = zz, sep = "\n") > close(zz) > blah = file("ex.bz2", "r") > seek(blah) Error in seek.connection(...

Hi, I have downloaded a bunch of bz2 files. I wonder if R will be able to unzip them in a batch mode or even one at a time? I was looking at the unz function. But it didn't work well. Say I have a bz2 file in H:/Temp/65502805_532.pair.bz2. Anyone has any suggestion? thanks John > setwd("H:\\Temp\\") > getwd() [1] "H:/Temp" >

...closing a connection that was *not* already open. 2. gzfile() sets a class of its return value to "file", rather than "gzfile": > f <- gzfile("whatever.gz", "wb") > class(f) [1] "file" "connection" In contrast, bzfile() exhibits correct behaviour: > f2<-bzfile("more.bz2", "wb") > class(f2) [1] "bzfile" "connection" This prevents load() from noticing that the connection passed to it is already a gzfile, since it tests for inheritance from class "gzfile&q...

Hi all, I encountered a problem when trying to read in an Illumina chip annotation file. The offending file is large, so I zipped it up and posted it at http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/tmp/ProbeInfo_Expression.txt.bz2 Executing this: annot = read.table(bzfile("ProbeInfo_Expression.txt.bz2"), comment.char="", sep = "\t", fill = TRUE, header = TRUE); leads to > dim(annot) [1] 25952 28 i.e. 25952 rows were read, but the file is some 48000 rows long. The file contains long text entries (up to several...

...esday, August 06, 2002 3:00 AM To: Huntsinger, Reid Cc: r-help at stat.math.ethz.ch Subject: Re: [R] pipe and binary i/o (on Linux) On Mon, 5 Aug 2002 ripley at stats.ox.ac.uk wrote: > pipe predates readBin, and no one has seen a reason to do this before you. However, gzfile should work, and bzfile *always* opens with "rb". Here's an example on RH7.2: > zz <- gzfile("testbin.gz", "wb") > writeBin(1:10, zz) > close(zz) > zz <- gzfile("testbin.gz", "rb") > readBin(zz, integer(), 4) [1] 1 2 3 4 > readBin(zz, integer(...

...directly to "popen" (I'm using Linux on an Intel machine). Popen doesn't know "rb" and fails. I modified the pipe function in connection.c to pass only the first character of the mode. This seems to work (fingers crossed). Then I noticed gzfile has the same problem, but bzfile doesn't, and uses the same solution as I did for pipe. Can I assume that this is a correct fix? Or were there reasons that pipe and gzfile wouldn't allow "rb"? Thanks, Reid Huntsinger -----Original Message----- From: Thomas Lumley [mailto:tlumley at u.washington.edu] Sent: Mon...

...-------------------------------script R: suppressMessages (library(ggplot2)) source ("graph-style.R") input = "graphs/figure-3-data-propagation-vs-time/car-relay-jump-distance.txt.gz2"output = "graphs/pdfs/figure-3-data-propagation-vs-time.pdf" data <- read.table (bzfile(input, "r"), header=TRUE)data$Run = as.factor(data$Run)data$DistanceFromSource = data$NodeId * data$Distance data = subset(data, Distance %in% c(10, 50, 90, 130, 170))data$Distance = as.factor(data$Distance) g <- ggplot(data, aes(x=Time-2, y=DistanceFromSource, colour=Distance, linety...

Is there any way to read and decompress inside R tar and bzip2 files ? Thanks D ----------------------------------------- Stay ahead of the information curve. Receive EDA news and jobs on your desktop daily. Subscribe today to the EDA CafeNews newsletter. [ http://www10.edacafe.com/nl/newsletter_subscribe.php ] It's informative and essential. This message was sent to you from a machine

...tion(fc) : closing '/dev/full' failed: No space left on device > fc=xzfile("/dev/full", "w"); write.csv("a", file=fc); (res=close(fc)) NULL Warning message: In close.connection(fc) : closing '/dev/full' failed: No space left on device > fc=bzfile("/dev/full", "w"); write.csv("a", file=fc); (res=close(fc)) NULL Warning message: In close.connection(fc) : closing '/dev/full' failed: No space left on device Note that if we test only status < 0 (without errno) then there are too many warnings on seemi...

...', '.readRDS', '.saveRDS', '.Script', '.Tcl', '.Tcl.args', '.Tcl.callback', '.Tk.ID', '.Tk.newwin', '.Tk.subwin', '.Tkroot', '.Tkwin', 'basename', 'browseURL', 'bzfile', 'capture.output', 'close', 'close.screen', 'closeAllConnection', 'data.entry', 'data.restore', 'dataentry', 'de', 'dev.control', 'dev.copy2eps', 'dev.cur', 'dev...

...pace left on device >> > fc=xzfile("/dev/full", "w"); write.csv("a", file=fc); (res=close(fc)) >> NULL >> Warning message: >> In close.connection(fc) : >> closing '/dev/full' failed: No space left on device >> > fc=bzfile("/dev/full", "w"); write.csv("a", file=fc); (res=close(fc)) >> NULL >> Warning message: >> In close.connection(fc) : >> closing '/dev/full' failed: No space left on device >> >> Note that if we test only status < 0 (wit...

...v/full' failed: No space left on device > > fc=xzfile("/dev/full", "w"); write.csv("a", file=fc); (res=close(fc)) > NULL > Warning message: > In close.connection(fc) : > closing '/dev/full' failed: No space left on device > > fc=bzfile("/dev/full", "w"); write.csv("a", file=fc); (res=close(fc)) > NULL > Warning message: > In close.connection(fc) : > closing '/dev/full' failed: No space left on device > > Note that if we test only status < 0 (without errno) then there a...

I've finally read and answered most of the mails on this list. ?If you haven't received an answer to your question, resend it. There are a couple of tricky mbox issues left, but I'm not sure if I can do anything about them unless someone can show me how to reproduce the problems. There are quite a lot of new features in v1.1.2 actually. Most of them are in plugins so hopefully they

...tract(). This allows an external unzip program to be used, which can be useful to access features supported by Info-ZIP's unzip version 6 which is now becoming more widely available. ? There is a simple zip() function, as wrapper for an external zip command. ? bzfile() connections can now read from concatenated bzip2 files (including files written with bzfile(open = "a")) and files created by some other compressors (such as the example of PR#14479). ? The primitive function c() is now of type BUILTIN. ? plot(<dendrogram&...

...tract(). This allows an external unzip program to be used, which can be useful to access features supported by Info-ZIP's unzip version 6 which is now becoming more widely available. ? There is a simple zip() function, as wrapper for an external zip command. ? bzfile() connections can now read from concatenated bzip2 files (including files written with bzfile(open = "a")) and files created by some other compressors (such as the example of PR#14479). ? The primitive function c() is now of type BUILTIN. ? plot(<dendrogram&...

Duncan Murdoch has written at Thu, 6 Jul 2017 13:58:10 -0400 > On 06/07/2017 5:21 AM, Serguei Sokol wrote: >> I propose the following patch against the current >> R-devel/src/main/connection.c (cf. attached file). >> It gives (on my linux box): >> > fc=file("/dev/full", "w") >> > write.csv("a", file=fc) >> Error in

...are now interpreted more > consistently. open = "r" is now equivalent to open = "rt" for > all connections. The default open = "" now means "rt" for all > connections except the compressed file connections gzfile(), > bzfile() and xzfile() for which it means "rb". > > o R CMD INSTALL now uses the internal untar() in package utils: > this ensures that all platforms can install bzip2- and > xz-compressed tarballs. In case this causes problems (as it > has on some Window...

...for connections are now interpreted more consistently. open = "r" is now equivalent to open = "rt" for all connections. The default open = "" now means "rt" for all connections except the compressed file connections gzfile(), bzfile() and xzfile() for which it means "rb". o R CMD INSTALL now uses the internal untar() in package utils: this ensures that all platforms can install bzip2- and xz-compressed tarballs. In case this causes problems (as it has on some Windows file systems when...

...for connections are now interpreted more consistently. open = "r" is now equivalent to open = "rt" for all connections. The default open = "" now means "rt" for all connections except the compressed file connections gzfile(), bzfile() and xzfile() for which it means "rb". o R CMD INSTALL now uses the internal untar() in package utils: this ensures that all platforms can install bzip2- and xz-compressed tarballs. In case this causes problems (as it has on some Windows file systems when...