similar to: How to read last (incomplete) line from gzfile()?

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 <-

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.

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

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

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

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

Hi all, I am trying to download, decompress and read a csv file. My code: myurl <- "ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE24729/GSE24729_MitoNuclear_suppl_male_stats.csv.gz" # myfile <- "GSE24729_MitoNuclear_suppl_male_stats.csv.gz" # download.file(myurl, destfile=myfile, mode="w") # mycon <- gzcon(gzfile(myfile,

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'm working on a target whose registers have equal-sized subregisters and all of those subregisters can be named (or the other way round: registers can be grouped into super registers). So for instance we've got 16 registers W (as in wide) W0..W15 and 32 registers N (as in narrow) N0..N31. This way, W0 is made by grouping N0 and N1, W1 is N2 and N3, W2 is N4 and N5, ..., W15 is

I have a file like this: id n1 n2 n3 n4 n5 n6 1 3 4 7 8 10 2 2 4 1 2 4 3 10 3 7 0 0 0 0 8 4 10 1 0 0 2 3 5 11 1 0 0 0 5 what I want to do is: only if n2=0 and n3=0 and n4=0 and n5=0 then delete the row. how can I do that? thank you, karena -- View this message

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,

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,

hello: I have 3 data.frame objects. First df object: Of dim (149,31). Columns 2:31 are marked as T1..T14 and N1..N16. Name T1 T2 N1 T3 N2 N3 N4 T4 mu1 10 10 9 10 9 9 8 10 mu2 11 11 9 11 9 9 9 11 ... muN 12 12 9 11 9 9 8 12 Second df object: of Dim (50000,31). Columns 2:31 are maked as T1...T14 and N1..N16.

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. >

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, 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

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, 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 <-