similar to: Read.dcf with no newline ending: gzfile drops last line

I'm seeing a segfault on x86_64 Linux with the following code: desc = read.dcf("BAD") con = gzfile("test.gz", "wt") write.dcf(desc, file=con) close(con) where BAD has a long field (see below for example). The crash happens inside dummy_vfprintf. I think the issue is that the va_list ap is modified by the first vsnprintf call

The change in r42731 eliminating the final blank line when writing DCF files changes the way 'append' can be used in 'write.dcf' and I was wondering if this is intentional. Basically, I want to write a data frame to DCF format one row at a time, so I make use of repeated calls to 'write.dcf(append = TRUE)'. However, in R 2.6.0RC the resulting DCF file is not formatted

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

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",

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 get an "internal error" when calling seek() twice on a gzfile connection. Create a gzip file: bigraw <- sample(charToRaw("abcdef"), 30000000, replace=TRUE) save(bigraw, file="bigraw.rda") Open it: con <- gzfile("bigraw.rda", "rb") Then: > seek(con, where=1) [1] 0 > seek(con, where=24980000) [1] 1

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? > >

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, 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

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

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

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.

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

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 <-

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" . >

So I wanted to export a contour3d object into VTK and it worked well enough, except the top of the ball (the contour) was missing. Example below, or gist here: https://gist.github.com/muschellij2/5126544 rm(list=ls()) require(misc3d) f <- function(x, y, z) x^2+y^2+z^2 x <- seq(-2,2,len=20) ball <- contour3d(f,4,x,x,x, draw=FALSE) drawScene.rgl(ball) ### get the triangles allids

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. >

Dear List, Does somebody know how to get the filename lists in the ziped when "gzfile" or "unz" command is used ? Thanks for your help. Shawn Lee -- The information contained in this communication and any atta...{{dropped}}