search for: gzfile

...ich 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", file=con); close(con) con <- gzfile("foo.gz", open="w"); cat("goo\n", file=con); close(con) > cat("boo\n", file=gzfile("foo.gz")) # this doesn't change "foo.gz" cat(...

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 PA...

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 doesn't give a warning (I think app...

...utils:::menuInstallPkgs() trying URL 'http://cran.uk.r-project.org/bin/windows/contrib/2.6/ada_2.0-1.zip <http://cran.uk.r-project.org/bin/windows/contrib/2.6/ada_2.0-1.zip> ' Content type 'application/zip' length 971893 bytes (949 Kb) opened URL downloaded 949 Kb Warning in gzfile(file, "r") : cannot open compressed file 'ada/DESCRIPTION', probable reason 'No such file or directory' Error in gzfile(file, "r") : unable to open connection > traceback() 6: gzfile(file, "r") 5: read.dcf(file.path(curPkg, "DESCRIPTION")...

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 messa...

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,...

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 readLines(readfile_con, n = 5) : seek on a gzfile connection returned an internal error > close(readfile_con) > sessionInfo() R version 3.4.3...

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.

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...

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, "PACKAGES.gz") tfile <- tempfile(fileext=...

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. The same is true if I replace r...

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...

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 for blocking connections (which I assume this is), the last line (containing 3) would be read in, and...

...k/00install.out' for details. In '00install.out', I get: * installing *source* package 'pgirmess' ... ** R ** data ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in gzfile(file, mode) : cannot open the connection Calls: %in% -> match -> installed.packages -> saveRDS -> gzfile In addition: Warning message: In gzfile(file, mode) : cannot open compressed file 'U:\DOCUME~1\Admin\LOCALS~1\Temp\RtmpwWcmem/libloc_U%3a%2fDocuments%20and%20Settings%2fpgir...

...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 readLines(readfile_con, n = 5) : > > seek on a gzfile connection returned an...

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?...

...r 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? > > 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 readLines(readfile_con, n = 5) : > seek on a gzfile connection returned an internal error > >> close(read...

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=24...

I don't understand why I can not close 'f'. This may be very simple, but I don't see why. Could somebody let me know? $ cat gzfile.csv "","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 $ Rscript gzfile.R > f = file("gzfile.csv") > A = read.csv(f) > A X V1 V2 V3 V4...

...e it work in a X-platform way..i am often not connected to the internet and have libraries that i would like to be able to install in an automated way.. i've tried several things: 1) install.packages("hs95av2hs3ug6cdf_6.0.0.tar.gz", repos=NULL, method="source") Error in gzfile(file, "r") : unable to open connection In addition: Warning message: cannot open compressed file 'hs95av2hs3ug6cdf_6.0.0.tar.gz/DESCRIPTION' >traceback() 5: gzfile(file, "r") 4: read.dcf(file.path(curPkg, "DESCRIPTION"), c("Package", "Version...