similar to: error when calling seek() twice on a gzfile connection

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,

I have installed both 32-bit and 64-bit versions of R2.12.0 (2010-06-15 r52300) on my Ubuntu 10.04 64-bit system. I observe the following behavior when running the examples from base::connections. There appears to be a problem with seek() on a .gz file when using a 32-bit installation of R2.12.0, but the problem doesn't appear in the 64-bit installation. I realize that seek() has been

Hi all, In what encoding does format.POSIXct return its output? It doesn't seem to be utf-8: Sys.setlocale("LC_ALL", "Japanese_Japan.932") times <- c("1970-01-01 01:00:00 UTC", "1970-02-02 22:00:00 UTC") ampm <- format(as.POSIXct(times), format = "%p") x <- gsub(">", "*", paste(ampm, collapse =

Hello, If repeated calls are made to save() using the same pre-opened gzfile connection to a file, and then the connection is closed, the objects saved by the second and subsequent calls are not correctly restored by repeated calls to load() with a new gzfile connection to the same file. What follows are a session exposing the bugs, analysis (see ANALYSIS), patches (see PATCHES), and a session

I just finished compiling today's r-patched (R 1.8.1 patched) on my old Sparc 20 using gcc 3.3 along with Sun's f77. As it was compiling, I noticed an error regarding gzfile. The compile process left the methods directory and continued on. Obviously, there was a problem, but I don't have the original error message from the compiler. After installing R, I get the following error

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 10, 2018 at 3:31 PM, Ben Heavner <bheavner at gmail.com> wrote: > 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? > >

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.

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

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",

I don't know if this is a bug per se, but an undesired behavior in read.dcf. read.dcf takes a file argument and passes it to gzfile if it's a character: if (is.character(file)) { file <- gzfile(file) on.exit(close(file)) } This gzfile connection is passed to readLines (line #39): lines <- readLines(file) If no newline is at the end of the file, readLines

Hi all, I used `gzfile` and `gzcon` to read a compressed file but I found that `gzcon` gave me a different result than `gzfile`. It seems like the `gzcon` does not handle the data correctly. I have posted an example below. In the example, a portion of a compressed file is downloaded from Google Cloud as a raw vector, and the data is saved into a temp file. If I use ` gzfile` to read the file, it

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

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

Hi, For the first time I have a strange behaviour when checking a package before 'packaging' the code. Looks like a file cannot be read. rcmd check pgirmess * using log directory 'U:/Documents and Settings/pgiraudo/Mes documents/R/pgir_arch/pgirmess_arch/On work/pgirmess.Rcheck' * using R version 2.13.2 (2011-09-30) * using platform: i386-pc-mingw32 (32-bit) * using session

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.

Hi, I have some text files that do not have trailing \n on the last (incomplete) line; how do I read in the last line? e.g. here is a test case: [linux + R version 2.6.1 (2007-11-26) ] z <- gzfile("short.gz", open="w") cat("7\n5\n3", file=z) close(z) z <- gzfile('short.gz') readLines(z) [1] "7" "5" readLines would indicate that

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 <-

Hi all, in the last time I've intensively used Rstreams to read and write from binary files. Now I'm wondering if it is possible to use Rsteams functions with gzipped files. But I haven't found the trick: > p1c.gzip <- gzfile("daten/p1c_all.mea.gz", open="rb") > readBin(p1c.gzip, integer(), n=64,size=2) [1] 84 1 400 1 749 0 0 0

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. >