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download.file()
7 messages · Paul Evans, Henrik Bengtsson, Stefan Grosse +1 more
On Tue, Mar 18, 2008 at 8:46 AM, Paul Evans <p.evans48 at yahoo.com> wrote:
Hi, I wanted to download a file and did the following: ---------------------------------------------------------
> fileLink <- 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE1000/GSE1000_RAW.tar' > download.file(fileLink,'/geoDat')
trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE1000/GSE1000_RAW.tar' ftp data connection made, file length 35307520 bytes opened URL downloaded 34480Kb
>
------------------------------------------------------------
However, when I look in the destination directory ('/geoDat'), the file is not there (I also tried giving it the absolute path).
What am I doing wrong?
I'm quite sure the 'destfile' argument of download.file() is a file not a directory. Example:
download.file("http://www.r-project.org/index.html", destfile="foo.html")
file.info("foo.html")
size isdir mode mtime ctime
foo.html 785 FALSE 666 2008-03-18 08:54:19 2008-03-18 08:54:11
atime exe
foo.html 2008-03-18 08:54:19 no
So you probably saved the downloaded file as 'geoDat' in the root
directory '/'.
/Henrik
thanks!
____________________________________________________________________________________
Be a better friend, newshound, and
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______________________________________________
R-help at r-project.org mailing list
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and provide commented, minimal, self-contained, reproducible code.
On Tue, Mar 18, 2008 at 8:57 AM, Henrik Bengtsson <hb at stat.berkeley.edu> wrote:
On Tue, Mar 18, 2008 at 8:46 AM, Paul Evans <p.evans48 at yahoo.com> wrote:
> Hi, > > I wanted to download a file and did the following: > ---------------------------------------------------------
> > fileLink <- 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE1000/GSE1000_RAW.tar' > > download.file(fileLink,'/geoDat')
> trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE1000/GSE1000_RAW.tar' > ftp data connection made, file length 35307520 bytes > opened URL > downloaded 34480Kb >
> >
> ------------------------------------------------------------
>
> However, when I look in the destination directory ('/geoDat'), the file is not there (I also tried giving it the absolute path).
>
> What am I doing wrong?
I'm quite sure the 'destfile' argument of download.file() is a file not a directory. Example:
> download.file("http://www.r-project.org/index.html", destfile="foo.html")
> file.info("foo.html")
size isdir mode mtime ctime
foo.html 785 FALSE 666 2008-03-18 08:54:19 2008-03-18 08:54:11
atime exe
foo.html 2008-03-18 08:54:19 no
So you probably saved the downloaded file as 'geoDat' in the root
directory '/'.
Also, you want to download the file in a binary fashion, i.e. use argument mode="wb", otherwise your binary tar file will be corrupt. R-core: I'd suggest to replace the default to mode="wb" for file transfers. /Henrik
/Henrik
> > thanks! > > > > > ____________________________________________________________________________________ > Be a better friend, newshound, and > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code. >
On Tuesday 18 March 2008 04:46:12 pm Paul Evans wrote:
PE> > download.file(fileLink,'/geoDat') I would have expected download.file(fileLink,"/geoDat/yourfilename") note that you need your complete path (or use setwd)
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/geodat *is* an absoute path! The second argument of download.file is called 'destfile', so what makes you think it is a desination *directory*? Your command works for me, using an account that has write permission in / , and not otherwise. (It seems very unsafe that you would be using such an account unless this is a pre-Vista Windows machine.)
On Tue, 18 Mar 2008, Paul Evans wrote:
Hi, I wanted to download a file and did the following: ---------------------------------------------------------
fileLink <- 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE1000/GSE1000_RAW.tar' download.file(fileLink,'/geoDat')
trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE1000/GSE1000_RAW.tar' ftp data connection made, file length 35307520 bytes opened URL downloaded 34480Kb
------------------------------------------------------------
However, when I look in the destination directory ('/geoDat'), the file
is not there (I also tried giving it the absolute path).
What am I doing wrong?
Not reading the help page?
thanks!
____________________________________________________________________________________ Be a better friend, newshound, and [[alternative HTML version deleted]] ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
On Tuesday 18 March 2008 04:59:45 pm Henrik Bengtsson wrote:
HB> Also, you want to download the file in a binary fashion, i.e. use HB> argument mode="wb", otherwise your binary tar file will be corrupt. HB> HB> R-core: I'd suggest to replace the default to mode="wb" for file HB> transfers. I had no corrupt file and I did not specify "wb" (R-2.6.2 on Fedora 8) Stefan
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On Tue, Mar 18, 2008 at 9:10 AM, Prof Brian Ripley
<ripley at stats.ox.ac.uk> wrote:
/geodat *is* an absoute path! The second argument of download.file is called 'destfile', so what makes you think it is a desination *directory*?
The help file might be the source of confusion: "destfile: A character string with the name where the downloaded file is saved. Tilde-expansion is performed." ...especially the word "where". Better with "A character string specifying the name [pathname?] of the saved file" is better. /Henrik
Your command works for me, using an account that has write permission in / , and not otherwise. (It seems very unsafe that you would be using such an account unless this is a pre-Vista Windows machine.) On Tue, 18 Mar 2008, Paul Evans wrote:
> Hi, > > I wanted to download a file and did the following: > ---------------------------------------------------------
>> fileLink <- 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE1000/GSE1000_RAW.tar' >> download.file(fileLink,'/geoDat')
> trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE1000/GSE1000_RAW.tar' > ftp data connection made, file length 35307520 bytes > opened URL > downloaded 34480Kb >
>>
> ------------------------------------------------------------
>
> However, when I look in the destination directory ('/geoDat'), the file
> is not there (I also tried giving it the absolute path).
>
> What am I doing wrong?
Not reading the help page?
> thanks! > > > > > ____________________________________________________________________________________ > Be a better friend, newshound, and > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code. >
-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.