Displaying 20 results from an estimated 2000 matches similar to: "How to get the list of the files when you read zip file by gzfile or unz"
2007 Dec 19
1
unexpected behavior from gzfile and unz
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.
2008 Oct 09
1
Reading zipped data directly from an FTP url
Hi
Sorry, I am clearly missing something here.
I want to read this file directly:
ftp://ftp.sanger.ac.uk/pub/mirbase/targets/v5/arch.v5.txt.gallus_gallus.
zip
I tried using
read.table(gzfile("ftp://ftp.sanger.ac.uk/pub/mirbase/targets/v5/arch.v5
.txt.gallus_gallus.zip"))
But I got an error:
Error in open.connection(file, "r") : cannot open the connection
In addition:
2003 Jul 11
2
unz()
I am having problems getting the unz() function to work as a connection to
start reading a file...
z <- unz("c:/temp/stoxx.zip", "close_tmi_components.txt", "r")
readLines(z,2)
yields the following problems:
> z <- unz("c:/temp/stoxx.zip", "close_tmi_components.txt", "r")
Error in unz("c:/temp/stoxx.zip",
2009 Jul 28
2
Looking for example of usage of function unz
I would greatly appreciate some example of correct usage of function unz.
I have to download and uncompress the following web compressef file:
ftp://ftp.sanger.ac.uk/pub/mirbase/targets/v5/arch.v5.txt.homo_sapiens.zip
I tried the following command that does not work:
Targets.rec <- readLines(zz <- unz("ftp://ftp.sanger.ac.uk/pub/mirbase/targets/v5/arch.v5.txt.homo_sapiens.zip"))
2003 Jul 24
0
unz( "x.zip", "y.csv" ) != pipe( "unzip -p x.zip y.csv" )
Not sure this is a bug in R.
Maybe its a bug in my understanding of unz().
The character 'b2' (hexadecimal) is in position 535 of line 1
of 'naughty.csv'. This character appears as superscript '2' and came to me
in an EXCEL file that I converted to text in a comma separated ( *.csv )
format.
The first line gets truncated by readLines after 534 characters using
unz():
2002 Dec 05
1
writing to gzfile: segmentation fault (PR#2347)
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",
2007 Jul 03
1
bug in closing gzfile-opened connections?
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
2013 May 08
1
getting corrupted data when using readBin() after seek() 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,
2018 May 10
2
readLines() behaves differently for gzfile connection
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
2011 Oct 15
2
gctorture() and gzfile() doesn't get along.
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.
2008 Mar 07
2
Problems installing packages using the inbuilt facility: "Error i n gzfile(file, "r") : unable to open connection"
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.
>
2004 Mar 15
1
gzfile & read.table on Win32
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 <-
2011 Oct 16
1
Error in gzfile(file, mode) when checking a package with rcmd check
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
2012 May 30
1
reading file in zip archive
Hi List
I have a series of zip archives each containing several files. One of these files is called goCats.txt and I would like to read it into R from the archive. It's a simple tab delimited text file.
pathToZip <- '/home/iain/Documents/Work/Results/bovineMacRNAData/deAnalysis/afInfection/commonNorm/twoHrs/af2hrs.zip'
z <- unz(pathToZip, 'goCats.txt', 'r')
zT
2018 May 10
1
readLines() behaves differently for gzfile connection
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
2008 Apr 20
1
How to read last (incomplete) line from gzfile()?
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
2002 Feb 04
1
read zipped files
I received several answer to my querry re reading zipped files,
R.Gentleman, Liaw Andy, BD Ripley,J Holtman, A.Matt, and others,
sorry
if I missed your names.
a- use pipe to run external unzip to a file and read from there
b- use gzfile() to open directly a gzipped file
c- use zip.file.extract()
solution b works like a charm, unfortunately it open gzipped files
and
not zipped files, would it be
2006 Nov 14
2
gzfile with multiple entries in the archive
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
2008 Mar 08
1
Error message while trying to update packages: Error in gzfile(file, mode) : unable to open connection
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" .
>
2011 May 29
1
why does scan(gzfile("file"), what='integer') import data as mode "character" ?
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