similar to: writing to gzfile: segmentation fault (PR#2347)

Does anybody know how to negate a string in a grep command, i.e., what I need is to return only strings that do NOT contain a second string anywhere in the entire string. for txt <- c("boo","goo","doob","foo","boofoo") I need a grep command that returns strings with "oo" except when "b" is present anywhere. I know that

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,

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

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 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. >

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.

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, 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

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

If I open a tgz archive with gzfile and then parse it using readLines I miss the initial line of each member of the archive - and also the name of the file although the archive otherwise complete (but useless!). Is there any way within R to extract both the list of files in a tgz archive and to extract any one of these files? Clearly I can use zcat and tar on Linux, but I need this to work

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 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}}

Hi all, My code: x <- scan(gzfile("file"),what='integer') x is imported, but as mode "character" rather than "integer". I know I can do as.integer() when importing, but am still trying to figure out why the above occurs. When I do summary(as.integer(x)), there are no NAs introduced by coercion, so the vector really is all integer. Also, is the above

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

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, 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 <-

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

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