Re: [Rd] CRAN package with dependencies on Bioconductor
2011/6/11 Prof Brian Ripley : > Note that until May 8 graph was a CRAN packge and the current version was > 1.30.0. So of course CRAN binary packages built between April 26 and May 8 > were built against the current CRAN version of graph, for any version of R. Thanks for the notice! But if I am not wrong, a version of my package that was published on May 26 and build therefore after the time period specified by you still suffers from these version incompatibilities. (Nevertheless it is of course possible that the problem is only caused by the migration to Bioconductor and in this case less problematic and only unfortunate in this one case). Perhaps the version downgrade of the graph package caused problems? So you say that the versions of Bioconductor packages on CRAN for binary builds are already normally the same as you would get by installing them as binaries from Bioconductor? (And btw. is there a way to find out which versions of the dependent packages were used for building a certain binary package?) Thanks and best regards, Kornelius. > > On Fri, 10 Jun 2011, Martin Morgan wrote: > >> On 06/10/2011 05:46 PM, Kornelius Rohmeyer wrote: >>> >>> Dear Martin, >>> >>> thanks for your response. >>> > The superclass graphBase is introduced in graph 1.30. In my > understanding the problem is that our package gMCP is build on CRAN > for R 2.12 with the package graph in version 1.30. Unfortunately > biocLite installs graph_1.28.0.zip for R 2.12. biocLite is returning the correct package -- graph 1.28.0. graph 1.30 did not come in to existence until the most recent release, 2011-04-13, approximately when R-2.13 became the current release version. CRAN is building packages with the current release, R-2.13, for which biocLite and install.packages both (correctly) return graph 1.30. >>> >>> I doubt this, i.e. CRAN is also still building packages for R 2.12 - >>> and is using graph 1.30 for this as far as I understand it (instead of >>> 1.28). >> >> I'm not intimately familiar with CRAN's build system, so perhaps I >> mis-spoke; Bioconductor packages are versioned in synchrony with R releases. >> If your package requires graph >= 1.30, specify that in the DESCRIPTION. If >> your users want features introduced when your package requires graph >= >> 1.30, direct them to use R >= 2.13. >> >> Martin >> > Are there ways to make dependencies on Bioconductor less complicated? Use the current version of R. >>> >>> So you agree that it is impossible to give a reasonable instruction >>> install such binary packages for older versions of R like the four >>> month old R 2.12? (Reasonable means without manual installation of >>> packages in the correct versions - where the correct versions have to >>> be found out by the maintainer.) >>> >>> Best regards, Kornelius. >> >> >> -- >> Computational Biology >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >> >> Location: M1-B861 >> Telephone: 206 667-2793 >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > -- > 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
Re: [Rd] CRAN package with dependencies on Bioconductor
On Sat, 11 Jun 2011, Kornelius Rohmeyer wrote: 2011/6/11 Prof Brian Ripley : Note that until May 8 graph was a CRAN packge and the current version was 1.30.0. So of course CRAN binary packages built between April 26 and May 8 were built against the current CRAN version of graph, for any version of R. Thanks for the notice! But if I am not wrong, a version of my package that was published on May 26 and build therefore after the time period specified by you still suffers from these version incompatibilities. (Nevertheless it is of course possible that the problem is only caused by the migration to Bioconductor and in this case less problematic and only unfortunate in this one case). Perhaps the version downgrade of the graph package caused problems? So you say that the versions of Bioconductor packages on CRAN for binary builds are already normally the same as you would get by installing them as binaries from Bioconductor? No, I did not say that. [...] -- 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
Re: [Rd] CRAN package with dependencies on Bioconductor
2011/6/11 Prof Brian Ripley : > On Sat, 11 Jun 2011, Kornelius Rohmeyer wrote: >> 2011/6/11 Prof Brian Ripley : >>> Note that until May 8 graph was a CRAN packge and the current version was >>> 1.30.0. So of course CRAN binary packages built between April 26 and May >>> 8 >>> were built against the current CRAN version of graph, for any version of >>> R. >> >> Thanks for the notice! But if I am not wrong, a version of my package >> that was published on May 26 and build therefore after the time period >> specified by you still suffers from these version incompatibilities. >> (Nevertheless it is of course possible that the problem is only caused >> by the migration to Bioconductor and in this case less problematic and >> only unfortunate in this one case). Perhaps the version downgrade of >> the graph package caused problems? > >> So you say that the versions of Bioconductor packages on CRAN for >> binary builds are already normally the same as you would get by >> installing them as binaries from Bioconductor? > > No, I did not say that. That means that for a binary package that depends on Bioconductor packages you sometimes need a bit of luck to select the correct versions of binary Bioconductor packages? Or is there a way to tell which (and an easy way to install them)? Thanks and best regards, Kornelius. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] CRAN package with dependencies on Bioconductor
Actually I do not understand what is so hard to understand with CRAN policy. This is: Any source package on CRAN is build in binary form with R-release/patched and R-oldrelease. This does not happen if you tell your package it requires a particular R version - such as the declaration R (>= 2.13.0) in the Depends field will cause the package not to be build as a binary. Anotehr exception would be if the package does not longer pass the checks and gives an ERROR, in that case we also keep the old version in the binary repository. On CRAN we assume that R-2.12.x users may want to get a bugfix release of a package without the requirement to upgrade R, hence we distribute new or updates packages for the oldrelease version (which is current R-2.12.x). And if BioC has a different policy, that is fine with us. Uwe Ligges On 11.06.2011 10:20, Kornelius Rohmeyer wrote: 2011/6/11 Prof Brian Ripley: On Sat, 11 Jun 2011, Kornelius Rohmeyer wrote: 2011/6/11 Prof Brian Ripley: Note that until May 8 graph was a CRAN packge and the current version was 1.30.0. So of course CRAN binary packages built between April 26 and May 8 were built against the current CRAN version of graph, for any version of R. Thanks for the notice! But if I am not wrong, a version of my package that was published on May 26 and build therefore after the time period specified by you still suffers from these version incompatibilities. (Nevertheless it is of course possible that the problem is only caused by the migration to Bioconductor and in this case less problematic and only unfortunate in this one case). Perhaps the version downgrade of the graph package caused problems? So you say that the versions of Bioconductor packages on CRAN for binary builds are already normally the same as you would get by installing them as binaries from Bioconductor? No, I did not say that. That means that for a binary package that depends on Bioconductor packages you sometimes need a bit of luck to select the correct versions of binary Bioconductor packages? Or is there a way to tell which (and an easy way to install them)? Thanks and best regards, Kornelius. __ 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] CRAN package with dependencies on Bioconductor
On 11-06-11 1:09 AM, Kornelius Rohmeyer wrote:
2011/6/11 Duncan Murdoch:
On 11-06-10 7:04 PM, Kornelius Rohmeyer wrote:
Dear all,
for a CRAN-package that depends on another Bioconductor-package I find
two things annoying and would like to know whether there are some
workarounds:
1) Is there some inevitable problem that install.packages does not
install uninstalled packages (on which the specified package depends)
also from Bioconductor (in the correct version)?
2) In my understanding (please correct me if I'm wrong!) CRAN uses
bioconductor packages in another version than biocLite would install.
For example:
Our package gMCP depends on the package graph that has recently
switched to the bioconductor repositories. But even the following
commands will fail (i.e. install incompatible versions) for R 2.12
under Windows (and most likely MacOS):
source("http://www.bioconductor.org/biocLite.R";)
biocLite("graph")
install.packages("gMCP")
This results in errors like the following:
BonferroniHolmGraph(2)
Error in validObject(.Object) :
invalid class "graphMCP" object: superclass "graphBase" not defined
in the environment of the object's class
The superclass graphBase is introduced in graph 1.30. In my
understanding the problem is that our package gMCP is build on CRAN
for R 2.12 with the package graph in version 1.30. Unfortunately
biocLite installs graph_1.28.0.zip for R 2.12.
Are there ways to make dependencies on Bioconductor less complicated?
Users of your package are likely to have issues; make sure you document that
they need to include the Bioconductor repository as well as CRAN.
You can specify a version in a dependency (or a version range). I don't
know if BioC will make old versions available in binary formats, but they
will probably make source versions available.
Duncan Murdoch
Dear Duncan,
the main problem is not addressed by specifying a certain version (or
at least I do not see how), since it's not the case that the package
requires certain versions.
I don't understand. It sounds as though you're saying these two
contradictory things:
- your package works with any version of graph
- CRAN builds a version of graph that is incompatible with your package.
The problem is that the default binary
packages of the CRAN package and the Bioconductor package it depends
on are incompatible for R 2.12, since CRAN uses a different version of
the Bioconductor package for building. (For the source packages of
course no problem exists.) Btw. is there a way to find out which
versions of the dependent packages were used for building a certain
binary package? (I guess in the moment, that CRAN uses always the
newest available source packages.)
These kind of incompatibilities are extremely hard to track for the
package developer. So if there is not a way to install the correct
corresponding compatible binary packages from CRAN and Bioconductor,
may I suggest that CRAN uses the same versions of dependent
Bioconductor packages for the build of binary packages as Bioconductor
is providing in binary form by default for the respective R versions?
I am not involved with setting CRAN policy, but their current policy
(build the most recent version of a package that declares itself
compatible with the relevant version of R) seems reasonable.
If for whatever reason this doesn't work for your package with R 2.12.x,
I see two possible solutions:
- Declare that your package now depends on R 2.13.0 or better.
- Move your package to Bioconductor, if its policy for binary builds
better matches your needs.
Duncan Murdoch
Or am totally on the wrong track?
Thank you very much and best regards, Kornelius.
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Re: [Rd] Require of gWidgetsRGtk2 fails: RGtk2.dll can't be found, but it's there
I'm working on a mechanism that will download GTK+ (the official zip files)
into a predetermined location and put that location in front of the other
paths at load time. Hopefully this will resolve these continuing issues.
Michael
On Fri, Jun 10, 2011 at 6:07 AM, Janko Thyson <
janko.thyson.rst...@googlemail.com> wrote:
> Okay, at least some positive result today (language issue ;-))
>
> Thanks for trying. Seems like GTK2 and me are not meant to be ...
>
> Regards,
> Janko
>
>
> On 10.06.2011 14:36, Prof Brian Ripley wrote:
>
>> It is a Microsoft error message, so your Windows is translating it, not R.
>> It does say 'The specified module' in English Windows, without saying who
>> specified the module (but it does often produce a popup naming the module).
>>
>> I've no better idea what your problem is: the @ReadMe instructions work
>> for me, Uwe on winbuilder and in our teaching lab (and the advice in RGtk2
>> does not).
>>
>> On Fri, 10 Jun 2011, Janko Thyson wrote:
>>
>> On 10.06.2011 13:18, Prof Brian Ripley wrote:
>>> On Fri, 10 Jun 2011, Janko Thyson wrote:
>>>
>>>Dear list,
>>>
>>>I've been trying to get gWidgets/gWidgetsRGtk2 to run
>>>every other month for a while, but somehow I simply can't
>>>figure out what's going wrong.
>>>
>>>
>>> Your subject line indicates your confusion. It does not say
>>> RGtk2.dll cannot be found (at least, the English version of the
>>> message does not say so).
>>>
>>> What it means is that RGtk2.dll or one of the DLLs it depends on
>>> cannot be found. See the instructions at
>>> http://cran.r-project.org/bin/windows/contrib/2.13/@ReadMe
>>>
>>> It is Microsoft's error message, not ours.
>>>
>>>
>>> Thanks for your answer. I followed the advice in the readme file and
>>> installed
>>>
>>>
>>> http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+/2.22/gtk+-bundle_2.22.0-201010
>>> 16_win32.zip
>>> Previously I made sure that all other previously installed GTK+ runtime
>>> environments were removed and that the windows PATH reflects the correct
>>> path to
>>> the "new" GTK+ files. I also made sure I started a new R session before
>>> trying
>>> 'require(gWidgetsRGtk2)' again. Yet, the same error. More precisely, a
>>> dialog box
>>> pops up asking me to install GTK+ or not. That's what's confusing me as
>>> well: the
>>> package's recommendation with respect to the version of an GTK+ runtime
>>> environment is somewhat out-of-sync with the advice in the readme, even
>>> though it
>>> the version is fairly recent (2011-04-30)
>>>
>>> Sorry for the german part in the error message, but I wasn't able to get
>>> it all
>>> to English (tried language = en in Rconsole file, setting up a
>>> Renviron.site with
>>> LANGUAGE=en, setting Sys.setenv("LANGUAGE"="en") and
>>> Sys.setenv("LC_ALL"="en") to
>>> no avail; not a good R day today ;-)). I freely translated it for you:
>>>
>>> Loading required package: gWidgetsRGtk2
>>> Loading required package: gWidgets
>>> Error in inDL(x, as.logical(local), as.logical(now), ...) :
>>> unable to load shared object
>>> 'R:/Apps/R/R-2.13.0/library/RGtk2/libs/i386/RGtk2.dll':
>>> LoadLibrary failure: the specified module could not be found.
>>>
>>> Failed to load RGtk2 dynamic library, attempting to install it.
>>> Learn more about GTK+ at http://www.gtk.org
>>> If the package still does not load, please ensure that GTK+ is installed
>>> and that
>>> it is on your PATH environment variable
>>> IN ANY CASE, RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN
>>> Error : .onAttach failed in attachNamespace() for 'gWidgetsRGtk2',
>>> details:
>>> call: .Call(name, ..., PACKAGE = PACKAGE)
>>> error: C symbol name "S_gtk_icon_factory_new" not in DLL for package
>>> "RGtk2"
>>>
>>> Do you have any other idea what I might be doing wrong?
>>>
>>> Regards,
>>> Janko
>>>
>>>
>>>
>>>I tried several distributions of the GTK runtime
>>>environment for Windows
>>>(
>>> http://downloads.sourceforge.net/gladewin32/gtk-2.12.9-win32-1.exe
>>>as described in the package's vignette,
>>> http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+/2.22/gtk+-bundle_2.22.1-20101
>>>227_win32.zip)
>>>
>>>I also included GTK in my Windows PATH.
>>>
>>>Yet, when I run 'require(gWidgetsRGtk2)', R complains
>>>that the RGtk2.dll can't be found/loaded (see below). But
>>>this file definitely exists. I'm running R-2.13.0 from a
>>>USB Device but made sure that args 'destdir' and 'lib'
>>>are set propperly in 'install.packages'.
>>>
>>>Loading required package: gWidgetsRGtk2
>>>Loading required package: gWidgets
>>>Error in inDL(x, as.logical(local), as.logical(now), ...)
>>>:
>>> unable to load shared object
>>>'R:/Apps/R/R-2.13.0/library/RGtk2/libs/i386/RGtk2.dll':
>>> L
