Re: [Rd] available.packages (PR#9841)
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The documented specification is file:///d:/CRAN (as specified by RFC1738),
so this is working correctly.
The CHANGES file for 2.2.0 says:
o file:// URLs are now interpreted by download.file(),
download.packages() and url() in the same way as Mozilla-based
browsers. That is, the expected form is
file:///d:/path/to/file
with *three* slashes.
The point is that this is file:// + host + / + path/to/file, and host is
missing. That some versions of IE did not follow the standard is part of
the confusion here.
Note that ?available.packages does say
If a repository is
local, i.e., the URL starts with '"file:"', then the packages are
not downloaded but used directly. (Both '"file:"' and
'"file:///"' are allowed as prefixes to a file path, the latter
for an absolute file path.)
but 'file:' does not work with drives on Windows. That seems clearly to
rule out your usage.
On Fri, 10 Aug 2007, [EMAIL PROTECTED] wrote:
> Full_Name: Zivan Karaman
> Version: 2.5.1
> OS: Windows XP SP2
> Submission from: (NULL) (195.6.68.214)
>
>
> I think that I have encountered a bug in the function "available.packages"
> when
> using a local repository (file://
) on Windows.
>
> Version information:
> platform i386-pc-mingw32
> arch i386
> os mingw32
> system i386, mingw32
> status
> major 2
> minor 5.1
> year 2007
> month 06
> day27
> svn rev42083
> language R
> version.string R version 2.5.1 (2007-06-27)
>
> I have made a copy of the CRAN "/bin/windows/contrib/2.5" directory in the
> "D:/CRAN" folder on my machine.
>
> When I issue the command:
>
> available.packages(contrib.url("file://D:/CRAN"))
>
> I get the follwoing message:
> Error in gzfile(file, "r") : unable to open connection
> In addition: Warning message:
> cannot open compressed file ':/CRAN/bin/windows/contrib/2.5/PACKAGES' in:
> gzfile(file, "r")
>
> Looking at the source code, I've spotted the following lines which seem to
> cause
> trouble:
>
>if (.Platform$OS.type == "windows") {
>if (length(grep("[A-Za-z]:", tmpf)))
> tmpf <- substring(tmpf, 2)
>}
> Deleting them, the function works OK.
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
--
Brian D. Ripley, [EMAIL PROTECTED]
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, UKFax: +44 1865 272595
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[Rd] Installing dependent packages
Hi all,
When installing ggplot2 on with install.packages("ggplot2", dep = T),
the colorspace dependency doesn't get installed (see below for
transcript from R session). The relevant lines from my description
file are:
Depends: R (>= 2.4), grid, reshape (>= 0.8.0), proto, splines, MASS,
RColorBrewer, colorspace
Suggests: quantreg, Hmisc, mapproj, maps
Have I done something wrong? Or is this a bug in the installation of
dependent packages?
Thanks,
Hadley
> install.packages("ggplot2", dep = T)
also installing the dependencies 'XML', 'RBGL', 'graph', 'chron',
'acepack', 'proto', 'Hmisc'
trying URL '
http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/XML_1.9-0.tgz'
Content type 'application/x-gzip' length 1108754 bytes
opened URL
==
downloaded 1082Kb
trying URL
'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/RBGL_1.12.0.tgz
'
Content type 'application/x-gzip' length 4577430 bytes
opened URL
==
downloaded 4470Kb
trying URL '
http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/graph_1.14.2.tgz'
Content type 'application/x-gzip' length 494951 bytes
opened URL
==
downloaded 483Kb
trying URL
'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/chron_2.3-14.tgz'
Content type 'application/x-gzip' length 72595 bytes
opened URL
==
downloaded 70Kb
trying URL
'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/acepack_1.3-2.2.tgz
'
Content type 'application/x-gzip' length 67871 bytes
opened URL
==
downloaded 66Kb
trying URL '
http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/proto_0.3-7.tgz'
Content type 'application/x-gzip' length 958493 bytes
opened URL
==
downloaded 936Kb
trying URL
'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/Hmisc_3.4-2.tgz'
Content type 'application/x-gzip' length 1475177 bytes
opened URL
==
downloaded 1440Kb
trying URL
'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/ggplot2_0.5.4.tgz
'
Content type 'application/x-gzip' length 1928720 bytes
opened URL
==
downloaded 1883Kb
The downloaded packages are in
/tmp/RtmpWRuZcd/downloaded_packages
Warning message:
dependency 'Rgraphviz' is not available
> library(ggplot2)
Loading required package: proto
Loading required package: splines
Loading required package: MASS
Loading required package: colorspace
Error: package 'colorspace' could not be loaded
In addition: Warning message:
there is no package called 'colorspace' in: library(pkg,
character.only = TRUE, logical = TRUE, lib.loc = lib.loc)
--
http://had.co.nz/
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Re: [Rd] Installing dependent packages
On Sun, 19 Aug 2007, hadley wickham wrote:
> Hi all,
>
> When installing ggplot2 on with install.packages("ggplot2", dep = T),
> the colorspace dependency doesn't get installed (see below for
> transcript from R session). The relevant lines from my description
> file are:
>
> Depends: R (>= 2.4), grid, reshape (>= 0.8.0), proto, splines, MASS,
> RColorBrewer, colorspace
> Suggests: quantreg, Hmisc, mapproj, maps
>
> Have I done something wrong? Or is this a bug in the installation of
> dependent packages?
You need to start continuation lines with whitespace, but possibly your
mailer wrapped this. (For readability I would wrap it in the DESCRIPTION
file.)
I tried in a vanilla session on Linux and colorspace was installed. Was
this a vanilla session? Does it work with type="source"?
It would be helpful if you could debug this as probably no one else can:
the code has been in use for a long time without any reported problems.
>
> Thanks,
>
> Hadley
>
>
>> install.packages("ggplot2", dep = T)
> also installing the dependencies 'XML', 'RBGL', 'graph', 'chron',
> 'acepack', 'proto', 'Hmisc'
>
> trying URL '
> http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/XML_1.9-0.tgz'
> Content type 'application/x-gzip' length 1108754 bytes
> opened URL
> ==
> downloaded 1082Kb
>
> trying URL
> 'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/RBGL_1.12.0.tgz
> '
> Content type 'application/x-gzip' length 4577430 bytes
> opened URL
> ==
> downloaded 4470Kb
>
> trying URL '
> http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/graph_1.14.2.tgz'
> Content type 'application/x-gzip' length 494951 bytes
> opened URL
> ==
> downloaded 483Kb
>
> trying URL
> 'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/chron_2.3-14.tgz'
> Content type 'application/x-gzip' length 72595 bytes
> opened URL
> ==
> downloaded 70Kb
>
> trying URL
> 'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/acepack_1.3-2.2.tgz
> '
> Content type 'application/x-gzip' length 67871 bytes
> opened URL
> ==
> downloaded 66Kb
>
> trying URL '
> http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/proto_0.3-7.tgz'
> Content type 'application/x-gzip' length 958493 bytes
> opened URL
> ==
> downloaded 936Kb
>
> trying URL
> 'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/Hmisc_3.4-2.tgz'
> Content type 'application/x-gzip' length 1475177 bytes
> opened URL
> ==
> downloaded 1440Kb
>
> trying URL
> 'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/ggplot2_0.5.4.tgz
> '
> Content type 'application/x-gzip' length 1928720 bytes
> opened URL
> ==
> downloaded 1883Kb
>
>
> The downloaded packages are in
>/tmp/RtmpWRuZcd/downloaded_packages
> Warning message:
> dependency 'Rgraphviz' is not available
>> library(ggplot2)
> Loading required package: proto
> Loading required package: splines
> Loading required package: MASS
> Loading required package: colorspace
> Error: package 'colorspace' could not be loaded
> In addition: Warning message:
> there is no package called 'colorspace' in: library(pkg,
> character.only = TRUE, logical = TRUE, lib.loc = lib.loc)
>
>
>
>
--
Brian D. Ripley, [EMAIL PROTECTED]
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, UKFax: +44 1865 272595
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R-devel@r-project.org mailing list
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Re: [Rd] Installing dependent packages
On 19/08/2007 2:00 PM, hadley wickham wrote:
> Hi all,
>
> When installing ggplot2 on with install.packages("ggplot2", dep = T),
> the colorspace dependency doesn't get installed (see below for
> transcript from R session). The relevant lines from my description
> file are:
>
> Depends: R (>= 2.4), grid, reshape (>= 0.8.0), proto, splines, MASS,
> RColorBrewer, colorspace
> Suggests: quantreg, Hmisc, mapproj, maps
>
> Have I done something wrong? Or is this a bug in the installation of
> dependent packages?
I see the same problem in MacOSX, but not in Windows. If I try it with
none of the dependencies installed, only reshape and proto are added but
there's a warning about grid, splines and MASS, so I'd guess this is a
bug related to the fact that RColorBrewer and colorspace are on the
second line, and there's another bug related to the fact that the others
are recommended packages.
Duncan Murdoch
>
> Thanks,
>
> Hadley
>
>
>> install.packages("ggplot2", dep = T)
> also installing the dependencies 'XML', 'RBGL', 'graph', 'chron',
> 'acepack', 'proto', 'Hmisc'
>
> trying URL '
> http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/XML_1.9-0.tgz'
> Content type 'application/x-gzip' length 1108754 bytes
> opened URL
> ==
> downloaded 1082Kb
>
> trying URL
> 'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/RBGL_1.12.0.tgz
> '
> Content type 'application/x-gzip' length 4577430 bytes
> opened URL
> ==
> downloaded 4470Kb
>
> trying URL '
> http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/graph_1.14.2.tgz'
> Content type 'application/x-gzip' length 494951 bytes
> opened URL
> ==
> downloaded 483Kb
>
> trying URL
> 'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/chron_2.3-14.tgz'
> Content type 'application/x-gzip' length 72595 bytes
> opened URL
> ==
> downloaded 70Kb
>
> trying URL
> 'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/acepack_1.3-2.2.tgz
> '
> Content type 'application/x-gzip' length 67871 bytes
> opened URL
> ==
> downloaded 66Kb
>
> trying URL '
> http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/proto_0.3-7.tgz'
> Content type 'application/x-gzip' length 958493 bytes
> opened URL
> ==
> downloaded 936Kb
>
> trying URL
> 'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/Hmisc_3.4-2.tgz'
> Content type 'application/x-gzip' length 1475177 bytes
> opened URL
> ==
> downloaded 1440Kb
>
> trying URL
> 'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/ggplot2_0.5.4.tgz
> '
> Content type 'application/x-gzip' length 1928720 bytes
> opened URL
> ==
> downloaded 1883Kb
>
>
> The downloaded packages are in
> /tmp/RtmpWRuZcd/downloaded_packages
> Warning message:
> dependency 'Rgraphviz' is not available
>> library(ggplot2)
> Loading required package: proto
> Loading required package: splines
> Loading required package: MASS
> Loading required package: colorspace
> Error: package 'colorspace' could not be loaded
> In addition: Warning message:
> there is no package called 'colorspace' in: library(pkg,
> character.only = TRUE, logical = TRUE, lib.loc = lib.loc)
>
>
>
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Re: [Rd] Installing dependent packages
On 19/08/2007 2:35 PM, Prof Brian Ripley wrote:
> On Sun, 19 Aug 2007, hadley wickham wrote:
>
>> Hi all,
>>
>> When installing ggplot2 on with install.packages("ggplot2", dep = T),
>> the colorspace dependency doesn't get installed (see below for
>> transcript from R session). The relevant lines from my description
>> file are:
>>
>> Depends: R (>= 2.4), grid, reshape (>= 0.8.0), proto, splines, MASS,
>> RColorBrewer, colorspace
>> Suggests: quantreg, Hmisc, mapproj, maps
>>
>> Have I done something wrong? Or is this a bug in the installation of
>> dependent packages?
>
> You need to start continuation lines with whitespace, but possibly your
> mailer wrapped this. (For readability I would wrap it in the DESCRIPTION
> file.)
>
> I tried in a vanilla session on Linux and colorspace was installed. Was
> this a vanilla session? Does it work with type="source"?
>
> It would be helpful if you could debug this as probably no one else can:
> the code has been in use for a long time without any reported problems.
It seems to be a problem with CRAN:
>
available.packages("http://cran.r-project.org/bin/macosx/universal/contrib/2.5";)["ggplot2","Depends"]
[1] "R (>= 2.4), grid, reshape (>= 0.8.0), proto, splines, MASS,"
>
available.packages("http://cran.r-project.org/bin/windows/contrib/2.5";)["ggplot2","Depends"]
[1] "R (>= 2.4), grid, reshape (>= 0.8.0), proto, splines,
MASS,\nRColorBrewer, colorspace"
Duncan Murdoch
>
>> Thanks,
>>
>> Hadley
>>
>>
>>> install.packages("ggplot2", dep = T)
>> also installing the dependencies 'XML', 'RBGL', 'graph', 'chron',
>> 'acepack', 'proto', 'Hmisc'
>>
>> trying URL '
>> http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/XML_1.9-0.tgz'
>> Content type 'application/x-gzip' length 1108754 bytes
>> opened URL
>> ==
>> downloaded 1082Kb
>>
>> trying URL
>> 'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/RBGL_1.12.0.tgz
>> '
>> Content type 'application/x-gzip' length 4577430 bytes
>> opened URL
>> ==
>> downloaded 4470Kb
>>
>> trying URL '
>> http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/graph_1.14.2.tgz'
>> Content type 'application/x-gzip' length 494951 bytes
>> opened URL
>> ==
>> downloaded 483Kb
>>
>> trying URL
>> 'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/chron_2.3-14.tgz'
>> Content type 'application/x-gzip' length 72595 bytes
>> opened URL
>> ==
>> downloaded 70Kb
>>
>> trying URL
>> 'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/acepack_1.3-2.2.tgz
>> '
>> Content type 'application/x-gzip' length 67871 bytes
>> opened URL
>> ==
>> downloaded 66Kb
>>
>> trying URL '
>> http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/proto_0.3-7.tgz'
>> Content type 'application/x-gzip' length 958493 bytes
>> opened URL
>> ==
>> downloaded 936Kb
>>
>> trying URL
>> 'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/Hmisc_3.4-2.tgz'
>> Content type 'application/x-gzip' length 1475177 bytes
>> opened URL
>> ==
>> downloaded 1440Kb
>>
>> trying URL
>> 'http://cran.uk.r-project.org/bin/macosx/universal/contrib/2.5/ggplot2_0.5.4.tgz
>> '
>> Content type 'application/x-gzip' length 1928720 bytes
>> opened URL
>> ==
>> downloaded 1883Kb
>>
>>
>> The downloaded packages are in
>>/tmp/RtmpWRuZcd/downloaded_packages
>> Warning message:
>> dependency 'Rgraphviz' is not available
>>> library(ggplot2)
>> Loading required package: proto
>> Loading required package: splines
>> Loading required package: MASS
>> Loading required package: colorspace
>> Error: package 'colorspace' could not be loaded
>> In addition: Warning message:
>> there is no package called 'colorspace' in: library(pkg,
>> character.only = TRUE, logical = TRUE, lib.loc = lib.loc)
>>
>>
>>
>>
>
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Re: [Rd] [R] Suspected memory leak with R v.2.5.x and large matrices with dimnames set
Hi Seth - Thanks for the follow up. I'll definitely check out the devel version at some point since while I've come up with a workaround, this is causing problems for me as it uses up so much memory on some systems that R starts throwing malloc errors and has to be killed from the command line. The machine I'm thinking of in particular is a MacOS machine with 8 gigs of memory. Also, having the row and column names set to alphanumeric names causes the processing to slow down significantly - as much as by a power of 10 (or more). As for you speculation that the memory released by R may not be recognized as being free'd by the OS, as a further test, I re-ran my code snippet three consecutive times w/in the same R interpreter window. In theory, if there were a memory leak, after the first run (resulting in a memory stamp of 2 gig), the subsequent runs would further increase R's memory stamp, i.e. up to 4 after the second, and 6 for the 3rd. This didn't happen, and R's stamp remained at 2 gig, so I can only assume that you're correct and I was wrong about a leak. Still, it's quite the memory hog when using dimnames, so I'll have to avoid those for now and will try the devel version you mentioned. Thanks and have a good weekend, Peter Seth Falcon wrote: > Hi Peter, > > Peter Waltman <[EMAIL PROTECTED]> writes: > >>Admittedly, this may not be the most sophisticated memory profiling >>performed, but when using unix's top command, I'm noticing a notable >>memory leak when using R with a large matrix that has dimnames >>set. >> > > I'm not sure I understand what you are reporting. One thing to keep > in mind is that how memory released by R is handled is OS dependent > and one will often observe that after R frees some memory, the OS does > not report that amount as now free. > > Is what you are observing preventing you from getting things done, or > just a concern that there is a leak that needs fixing? It is worth > noting that the internal handling of character vectors has changed in > R-devel and so IMO testing there would make sense before persuing this > further, I suspect your results will be different. > > + seth > > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
