Re: [Rd] CRAN build/checks: Dependencies on non-CRAN packages?
> Henrik Bengtsson writes:
> On Sun, Jun 7, 2009 at 11:49 PM, Kurt Hornik wrote:
>>> Henrik Bengtsson writes:
>>
>>> Hi,
>>> how is the CRAN build/check system dealing with dependencies on
>>> non-CRAN packages? Are there external repositories that are dealt
>>> with in special ways, e.g. Bioconductor and Omegahat? Is this
>>> documented somewhere?
>>
>>> The most recent note on this that I could locate is "[Rd] CRAN,
>>> Bioconductor and ctv package dependency questions", Kurt Hornik, Sept
>>> 8, 2005;
>>> https://stat.ethz.ch/pipermail/r-devel/2005-September/034547.html.
>>> Does the comments in that thread still reflect how CRAN works?
>>
>> Not quite. No more special casing of BioC or Ohat dependencies: they
>> simply "work", and packages with such dependencies can fully be checked.
> Hmm... so you're saying R CMD check pass ("work") although a package
> is missing?
Are you asking what happens if a CRAN package depends on a BioC package
which is missing from BioC?
You can safely assume the availability of BioC and Ohat packages
(provided we can install these). We do not accept packages with
unconditional (depends/imports) dependencies on package not in the
standard repositories, but do not force the availability of suggested
packages: so you can suggest an external package (but R CMD check should
still pass if the package is not available).
Best
-k
> If so, what about example/test code where that external package is
> loaded? ...or even harder, where a function of that external package
> is called, e.g.
> require("externalPkg") || stop(...);
> res <- externalPkg::specialFcn(...);
> stopifnot(identical(res,42));
> ...
> This is not a constructed example; I do have some example():s].
> Thxs
> Henik
>>
>> -k
>>
>>> Thanks
>>
>>> Henrik
>>
>>> __
>>> R-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
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Re: [Rd] CRAN build/checks: Dependencies on non-CRAN packages?
On Sun, Jun 7, 2009 at 11:49 PM, Kurt Hornik wrote:
>> Henrik Bengtsson writes:
>
>> Hi,
>> how is the CRAN build/check system dealing with dependencies on
>> non-CRAN packages? Are there external repositories that are dealt
>> with in special ways, e.g. Bioconductor and Omegahat? Is this
>> documented somewhere?
>
>> The most recent note on this that I could locate is "[Rd] CRAN,
>> Bioconductor and ctv package dependency questions", Kurt Hornik, Sept
>> 8, 2005;
>> https://stat.ethz.ch/pipermail/r-devel/2005-September/034547.html.
>> Does the comments in that thread still reflect how CRAN works?
>
> Not quite. No more special casing of BioC or Ohat dependencies: they
> simply "work", and packages with such dependencies can fully be checked.
Hmm... so you're saying R CMD check pass ("work") although a package
is missing? If so, what about example/test code where that external
package is loaded? ...or even harder, where a function of that
external package is called, e.g.
require("externalPkg") || stop(...);
res <- externalPkg::specialFcn(...);
stopifnot(identical(res,42));
...
This is not a constructed example; I do have some example():s].
Thxs
Henik
>
> -k
>
>> Thanks
>
>> Henrik
>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
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Re: [Rd] CRAN build/checks: Dependencies on non-CRAN packages?
On Mon, Jun 8, 2009 at 12:29 AM, Kurt Hornik wrote:
>> Henrik Bengtsson writes:
>
>> On Sun, Jun 7, 2009 at 11:49 PM, Kurt Hornik wrote:
Henrik Bengtsson writes:
>>>
Hi,
how is the CRAN build/check system dealing with dependencies on
non-CRAN packages? Are there external repositories that are dealt
with in special ways, e.g. Bioconductor and Omegahat? Is this
documented somewhere?
>>>
The most recent note on this that I could locate is "[Rd] CRAN,
Bioconductor and ctv package dependency questions", Kurt Hornik, Sept
8, 2005;
https://stat.ethz.ch/pipermail/r-devel/2005-September/034547.html.
Does the comments in that thread still reflect how CRAN works?
>>>
>>> Not quite. No more special casing of BioC or Ohat dependencies: they
>>> simply "work", and packages with such dependencies can fully be checked.
>
>> Hmm... so you're saying R CMD check pass ("work") although a package
>> is missing?
>
> Are you asking what happens if a CRAN package depends on a BioC package
> which is missing from BioC?
No, my question was what happens if your CRAN package depends on
non-CRAN packages. In the above Sept 2005 thread, I read "The only
catch is that in the current setup of daily CRAN package
checking, packages with non-CRAN dependencies are checked ***using
fake or no installs***." I though your term "work" meant the same as
"using fake or no installs".
>
> You can safely assume the availability of BioC and Ohat packages
> (provided we can install these). We do not accept packages with
> unconditional (depends/imports) dependencies on package not in the
> standard repositories, but do not force the availability of suggested
> packages: so you can suggest an external package (but R CMD check should
> still pass if the package is not available).
Ok, this clarifies a few things. So:
1) One can assume that packages on CRAN, Bioconductor (release and/or
devel?), and Omegahat are available on the CRAN servers.
2) One cannot assume that packages from other repositories, including
r-forge.r-project.org, are available.
3) When R CMD check is ran on the CRAN servers it will not give an
error for non-available packages that are listed under "Suggests:" in
the DESCRIPTION file (as R CMD check would do by default).
However, in my example example() code below, I would expect R CMD
check to still fail if you list 'externalPkg' under "Suggests"; it
will pass the package/code validation, but when running the examples,
it will fail, either because of the require(...) || stop(...)
statement or because there is no way 'res' would have value 42 unless
the package really exists.
Yet another feature request (just a suggestion): It could be useful
provide a file with the packages installed on each "check" server,
e.g.:
data <- installed.packages();
data <- paste(data[,"Package"], data[,"Version"], sep=" ");
cat(data, sep="\n");
Cheers
Henrik
>
> Best
> -k
>
>> If so, what about example/test code where that external package is
>> loaded? ...or even harder, where a function of that external package
>> is called, e.g.
>
>> require("externalPkg") || stop(...);
>> res <- externalPkg::specialFcn(...);
>> stopifnot(identical(res,42));
>> ...
>
>> This is not a constructed example; I do have some example():s].
>
>> Thxs
>
>> Henik
>
>>>
>>> -k
>>>
Thanks
>>>
Henrik
>>>
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>>>
>>>
>
>
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Re: [Rd] CRAN build/checks: Dependencies on non-CRAN packages?
On Mon, 8 Jun 2009, Kurt Hornik wrote: Henrik Bengtsson writes: Hi, how is the CRAN build/check system dealing with dependencies on non-CRAN packages? Are there external repositories that are dealt with in special ways, e.g. Bioconductor and Omegahat? Is this documented somewhere? The most recent note on this that I could locate is "[Rd] CRAN, Bioconductor and ctv package dependency questions", Kurt Hornik, Sept 8, 2005; https://stat.ethz.ch/pipermail/r-devel/2005-September/034547.html. Does the comments in that thread still reflect how CRAN works? Not quite. No more special casing of BioC or Ohat dependencies: they simply "work", and packages with such dependencies can fully be checked. With some caveats. The CRAN check summaries are from four sets of systems (CRAN's, the Windows and Mac autobuilders and my server using the Sun Studio compiler) and hence four supervisors. Most of us install the BioC and Omegahat packages that are needed as dependencies in so far as we can (this looks to be less so for the Mac autobuilder). But 'in so far as we can' has limits, not least the time needed to fiddle around with some of them. In principle if a package depended on an off-CRAN/BioC/Omegahat package and it was clear where to get it we would try to install it -- however, in all past instances I have failed in that installation. It may be worth adding that as the number of packages grows the total time available to work on those that fail does not increase (and all of us involved have less time for this than we once had), so the effort available per problematic package has decreased considerably. Also, Omegahat no longer provides Windows binaries and the alternatives (CRAN extras, BioC extras) only cover a few. -- Brian D. Ripley, rip...@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, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] iconv.dll needed in addition to Riconv.dll for package XML to load (PR#13747)
Full_Name: Osiander Meixner Version: 2.9.0 (2009-04-17) OS: Windows Vista Enterprise, 32bit, SP1 Submission from: (NULL) (15.195.185.82) package XML_2.5-1 >library(XML) throws an error window saying: " RGui: RGui.exe - Unable to Locate Component This application has failed to start becuase iconv.dll was not found. Re-installing the application may fix this problem. " RGui then reports this: Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'c:/R/R-2.9.0/library/XML/libs/XML.dll': LoadLibrary failure: The specified module could not be found. Error : .onLoad failed in 'loadNamespace' for 'XML' Error: package/namespace load failed for 'XML' Indeed the error messages triggered by library(XML) seems to be a side effect of a dll naming issue. This issue can be solve by _adding_ a copy of Riconv.dll renamed asiconv.dll and restarting RGui __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] iconv.dll needed in addition to Riconv.dll for package XML to load (PR#13747)
Please install from the "CRAN extras" repository (where you will find a working copy) and do NOT report a bug in R that is not a bug in R but in a contributed package / the package repository. Best, Uwe Ligges osiander.meix...@hp.com wrote: Full_Name: Osiander Meixner Version: 2.9.0 (2009-04-17) OS: Windows Vista Enterprise, 32bit, SP1 Submission from: (NULL) (15.195.185.82) package XML_2.5-1 library(XML) throws an error window saying: " RGui: RGui.exe - Unable to Locate Component This application has failed to start becuase iconv.dll was not found. Re-installing the application may fix this problem. " RGui then reports this: Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'c:/R/R-2.9.0/library/XML/libs/XML.dll': LoadLibrary failure: The specified module could not be found. Error : .onLoad failed in 'loadNamespace' for 'XML' Error: package/namespace load failed for 'XML' Indeed the error messages triggered by library(XML) seems to be a side effect of a dll naming issue. This issue can be solve by _adding_ a copy of Riconv.dll renamed asiconv.dll and restarting RGui __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] iconv.dll needed in addition to Riconv.dll for package XML (PR#13748)
Please install from the "CRAN extras" repository (where you will find a working copy) and do NOT report a bug in R that is not a bug in R but in a contributed package / the package repository. Best, Uwe Ligges osiander.meix...@hp.com wrote: > Full_Name: Osiander Meixner > Version: 2.9.0 (2009-04-17) > OS: Windows Vista Enterprise, 32bit, SP1 > Submission from: (NULL) (15.195.185.82) > > > package XML_2.5-1 >> library(XML) throws an error window saying: > " > RGui: RGui.exe - Unable to Locate Component > This application has failed to start becuase iconv.dll was not found. > Re-installing the application may fix this problem. > " > > RGui then reports this: > > Error in inDL(x, as.logical(local), as.logical(now), ...) : >unable to load shared library 'c:/R/R-2.9.0/library/XML/libs/XML.dll': >LoadLibrary failure: The specified module could not be found. > > Error : .onLoad failed in 'loadNamespace' for 'XML' > Error: package/namespace load failed for 'XML' > > > > Indeed the error messages triggered by library(XML) seems to be a side effect > of > a dll naming issue. This issue can be solve by _adding_ a copy of > Riconv.dll renamed asiconv.dll > and restarting RGui > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Defining a S4 method for existing function interaction.plot
Dear Members,
i have defined a S4-class and a function for that class wich is to be
called interaction.plot. Problem: interaction.plot already exists so
setMethod(f = "interaction.plot", signature = "myClass", definition =
function(x){ return(TRUE) })
Fehler in conformMethod(signature, mnames, fnames, f, fdef,
definition) :
In method for function "interaction.plot": formale Argumente, die in
der Methodendefinition ausgelassen wurden, können nicht in der Signatur
(x.factor = "myClass") sein
won't work because it is already defined.
Is there a solution that keeps the original interaction.plot and lets me
define a interaction.plot for objects of my S4-Class?
Thank you for your time
Thomas Roth
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Re: [Rd] CRAN build/checks: Dependencies on non-CRAN packages?
Thank you all for these clarifications and for all your great contributions to this project (can't be said too many times)! /Henrik On Mon, Jun 8, 2009 at 2:17 AM, Prof Brian Ripley wrote: > On Mon, 8 Jun 2009, Kurt Hornik wrote: > >>> Henrik Bengtsson writes: >> >>> Hi, >>> how is the CRAN build/check system dealing with dependencies on >>> non-CRAN packages? Are there external repositories that are dealt >>> with in special ways, e.g. Bioconductor and Omegahat? Is this >>> documented somewhere? >> >>> The most recent note on this that I could locate is "[Rd] CRAN, >>> Bioconductor and ctv package dependency questions", Kurt Hornik, Sept >>> 8, 2005; >>> https://stat.ethz.ch/pipermail/r-devel/2005-September/034547.html. >>> Does the comments in that thread still reflect how CRAN works? >> >> Not quite. No more special casing of BioC or Ohat dependencies: they >> simply "work", and packages with such dependencies can fully be checked. > > With some caveats. The CRAN check summaries are from four sets of systems > (CRAN's, the Windows and Mac autobuilders and my server using the Sun Studio > compiler) and hence four supervisors. > > Most of us install the BioC and Omegahat packages that are needed as > dependencies in so far as we can (this looks to be less so for the Mac > autobuilder). But 'in so far as we can' has limits, not least the time > needed to fiddle around with some of them. > > In principle if a package depended on an off-CRAN/BioC/Omegahat package and > it was clear where to get it we would try to install it -- however, in all > past instances I have failed in that installation. > > It may be worth adding that as the number of packages grows the total time > available to work on those that fail does not increase (and all of us > involved have less time for this than we once had), so the effort available > per problematic package has decreased considerably. Also, Omegahat no longer > provides Windows binaries and the alternatives (CRAN extras, BioC extras) > only cover a few. > > -- > Brian D. Ripley, rip...@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-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] How to explore R internals through gdb?
Hi everyone. I'm trying to learn my way around the R internals. I've gone pretty much as far as I can go with the information given in Writing R Extensions and R Internals, but I still have a lot of questions, too many in fact to post them to the r-devel list. But I think I could answer many of these if I could just step through R's execution during some basic operations. What I'd like to do is generate a simple R script, e.g.: # foo.R foo <- list(x=1, y=2, z=3) print(foo) ...and then using gdb step through R's execution of this script. I have two questions. First, where in the R source would be a good place to set a breakpoint so that I can then step through the execution of such a script? Second, breakpoints aside, how can I even get R to run such a script under gdb? For the latter I tried this: % myR/bin/R -q --vanilla --debugger=gdb --file=foo.R GNU gdb 6.6-debian Copyright (C) 2006 Free Software Foundation, Inc. GDB is free software, covered by the GNU General Public License, and you are welcome to change it and/or distribute copies of it under certain conditions. Type "show copying" to see the conditions. There is absolutely no warranty for GDB. Type "show warranty" for details. This GDB was configured as "x86_64-linux-gnu"... Using host libthread_db library "/lib/libthread_db.so.1". (gdb) c The program is not being run. (gdb) r Starting program: /d0/home/jones/local/pub/work/proj/myR/lib64/R/bin/exec/R -q --vanilla --file=foo.R /d0/home/jones/local/pub/work/proj/myR/lib64/R/bin/exec/R: error while loading shared libraries: libR.so: cannot open sy Program exited with code 0177. (gdb) What am I doing wrong? BTW, the version on R I have under myR has been compiled with the -g flag set. TIA! kynn [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
