Re: [Bioc-devel] biocLite malfunctioning? and mzR package not working on R 3.0.0?
Hi, On Wed, 2013-04-03 at 13:15 +0200, Andreas Heider wrote: ... Besides this I was not able to install the mzR package correctly on both Mac OS X and Windows already some weeks ago. Was there some changes I am not aware about? On Windows where mzR comes as precompiled package, which requires a matching Rcpp version. Usually it helps to install both Rcpp and mzR at the same time. Yours, Steffen -- IPB HalleAG Massenspektrometrie Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] biocLite malfunctioning? and mzR package not working on R 3.0.0?
OK, but I am not able to install a single package right now. Can you confirm it works for you? Cheers, Andreas 2013/4/3 Steffen Neumann sneum...@ipb-halle.de Hi, On Wed, 2013-04-03 at 13:15 +0200, Andreas Heider wrote: ... Besides this I was not able to install the mzR package correctly on both Mac OS X and Windows already some weeks ago. Was there some changes I am not aware about? On Windows where mzR comes as precompiled package, which requires a matching Rcpp version. Usually it helps to install both Rcpp and mzR at the same time. Yours, Steffen -- IPB HalleAG Massenspektrometrie Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] GLX extension missing on petty
Hi, the latest bioc build of my new package 'triplex' on petty ended with this error message: Warning in rgl.init(initValue) : RGL: GLX extension missing on server Warning in fun(libname, pkgname) : error in rgl_init For full report see http://bioconductor.org/checkResults/devel/bioc-LATEST/triplex/petty-buildsrc.html And I am wondering if there is anything I could do to fix this. Probably it's a build system problem, but other packages that depends on rgl and plots in 3D have no such build error (i.e. RDRToolbox) and that makes me sligthly nervous, so I would really appreciate any advice. Thank you a lot for your time and patience, Jirka ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] RFC: IntervalTrees for GRanges objects
Hi Hector, That's interesting, thanks for passing this along. I'm still wishing that somehow GRanges itself could abstract the way it stores ranges. I know that Herve/Patrick had some reasons for depending specifically on GRanges. One reason was probably convenience at the C level, but it wouldn't be hard to create a Ranges abstraction at the C level, as well. Michael On Tue, Apr 2, 2013 at 5:40 PM, Hector Corrada Bravo hcorr...@gmail.comwrote: Hello bioc-develers, I'm writing an application where lots findOverlap calls are made on static GRanges objects. For IRanges we can create persistent IntervalTree objects that would serve the multiple overlap query use-case. There is no equivalent for GenomicRanges objects, so I'm proposing an implementation for this. Please check http://github.com/hcorrada/GenomicIntervalTree There's a first cut implementation there you can test by installing this skeleton package. E.g, library(devtools) install_github(GenomicIntervalTree, username=hcorrada, subdir=pkg) library(GenomicIntervalTree) Let me know what you think. Cheers, Hector ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] RFC: IntervalTrees for GRanges objects
Some ideas: - Turn the IntervalTree into a list/array of nodes that can be subset/reordered with shallow copying (just copy the pointers to the nodes), and the index would be secondary. The index in the array could be stored in each node, for lookup during overlap queries. Right now, as far as I can tell, GIntervalTree will get confused if the user reorders e.g. via [. - Make IntervalTree aware of the sequence/chromosome, e.g., have a hash of trees, which is trivial since seqnames is already a factor. Michael On Wed, Apr 3, 2013 at 9:29 AM, Hector Corrada Bravo hcorr...@gmail.comwrote: Yep, I didn't comment on that, but I agree that abstracting how GRanges stores ranges would make this more elegant. Right now ranges(GRanges) is specified to be of IRanges class instead of the abstract Ranges class. If it were the latter then GIntervalTree can be a subclass of GenomicRanges, in a similar way that IntervalTree is a subclass of Ranges. On Wed, Apr 3, 2013 at 12:23 PM, Michael Lawrence lawrence.mich...@gene.com wrote: Hi Hector, That's interesting, thanks for passing this along. I'm still wishing that somehow GRanges itself could abstract the way it stores ranges. I know that Herve/Patrick had some reasons for depending specifically on GRanges. One reason was probably convenience at the C level, but it wouldn't be hard to create a Ranges abstraction at the C level, as well. Michael On Tue, Apr 2, 2013 at 5:40 PM, Hector Corrada Bravo hcorr...@gmail.com wrote: Hello bioc-develers, I'm writing an application where lots findOverlap calls are made on static GRanges objects. For IRanges we can create persistent IntervalTree objects that would serve the multiple overlap query use-case. There is no equivalent for GenomicRanges objects, so I'm proposing an implementation for this. Please check http://github.com/hcorrada/GenomicIntervalTree There's a first cut implementation there you can test by installing this skeleton package. E.g, library(devtools) install_github(GenomicIntervalTree, username=hcorrada, subdir=pkg) library(GenomicIntervalTree) Let me know what you think. Cheers, Hector ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] BioC 2.12 branch created
The BioC 2.12 branch is now ready. Remember, you always have access to 2 versions of your package: the release and the devel versions. Right now the release version of your package (which is not officially released yet but will be in the next 72 hours if everything goes well) is in the 2.12 branch and accessible at: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/PKGNAME Only bug fixes and documentation improvements should go here. As always the devel version of your package is at: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PKGNAME Normal development of your package can now resume here. Please let us know if you have any questions. Thanks! Dan ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Rd] Documentation error in subsitute
Hi all, The documentation for substitute currently reads: Substitution takes place by examining each component of the parse tree as follows: If it is not a bound symbol in ‘env’, it is unchanged. If it is a promise object, i.e., a formal argument to a function or explicitly created using ‘delayedAssign()’, the expression slot of the promise replaces the symbol. If it is an ordinary variable, its value is substituted, unless ‘env’ is ‘.GlobalEnv’ in which case the symbol is left unchanged. Since the clause referring to the globalenv() is attached to the discussion of ordinary variables, I thought that it implied that delayedAssign(a, test) substitute(a) would return test (but actually it returns quote(a)) I'd suggest rewording this paragraph to: Substitution takes place by examining each component of the parse tree as follows: If it is not a bound symbol in ‘env’, it is unchanged. If it is a promise object, i.e., a formal argument to a function or explicitly created using ‘delayedAssign()’, the expression slot of the promise replaces the symbol. If it is an ordinary variable, its value is substituted. There's one important exception to these rules: If 'env' is the ‘.GlobalEnv’, then no substitution occurs. Hadley -- Chief Scientist, RStudio http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R-3.0.0 reg-tests-3.R / survival
make check is failing on reg-test3.R with a message that survival was built with an older version of R. (On my Ubuntu 32 bit and Ubuntu 64 bit machines). Why would make check be looking anywhere that it would find something built with an older version of R? ~/RoboAdmin/R-3.0.0/tests$ tail reg-tests-3.Rout.fail print(1.001, digits=16) [1] 1.001 ## 2.4.1 gave 1.001 ## 2.5.0 errs on the side of caution. ## as.matrix.data.frame with coercion library(survival) Error: package 'survival' was built before R 3.0.0: please re-install it Execution halted __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R-package preparation --as-cran behaving unexpectedly
Dear all, I am trying to submit an R-package to CRAN. In preparation I do run R_INSTALL_TAR=/bin/tar R CMD check --as-cran parallelize.dynamic_0.9.tar.gz and the command finishes without warnings or errors. As a final output I get NOTE: There was 1 note. See ‘.../Rpackages/parallelize.dynamic/parallelize.dynamic.Rcheck/00check.log’ for details. The file contains the standard output of the 'R CMD check ...' call precisely. If I submit this very tarball to CRAN I get rejected with warnings as reported from '--as-cran' checks there. In my case they are valid warnings about assignments in .GlobalEnv which I can certainly fix. However, my concern is about the discrepancy between the outputs of 'R CMD check --as-cran' runs locally as compared to the run on the CRAN-site. Any help is appreciated. I am running R version 2.15.2 (2012-10-26) -- Trick or Treat Platform: x86_64-unknown-linux-gnu (64-bit) Thanks in advance, Stefan -- http://visigen.lumc.nl/emgm http://s-boehringer.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-package preparation --as-cran behaving unexpectedly
On 03/04/2013 7:25 AM, Stefan Boehringer wrote: Dear all, I am trying to submit an R-package to CRAN. In preparation I do run R_INSTALL_TAR=/bin/tar R CMD check --as-cran parallelize.dynamic_0.9.tar.gz and the command finishes without warnings or errors. As a final output I get NOTE: There was 1 note. See ‘.../Rpackages/parallelize.dynamic/parallelize.dynamic.Rcheck/00check.log’ for details. The file contains the standard output of the 'R CMD check ...' call precisely. If I submit this very tarball to CRAN I get rejected with warnings as reported from '--as-cran' checks there. In my case they are valid warnings about assignments in .GlobalEnv which I can certainly fix. However, my concern is about the discrepancy between the outputs of 'R CMD check --as-cran' runs locally as compared to the run on the CRAN-site. Any help is appreciated. I am running R version 2.15.2 (2012-10-26) -- Trick or Treat Platform: x86_64-unknown-linux-gnu (64-bit) Presumably CRAN is now running checks from 3.0.0 (which was released today, and has been available for testing for more than a month). I wouldn't be surprised if those are different from the 2.15.2 tests. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Documentation error in subsitute
On Wed, Apr 3, 2013 at 10:38 AM, Hadley Wickham h.wick...@gmail.com wrote:
Hi all,
The documentation for substitute currently reads:
Substitution takes place by examining each component of the parse
tree as follows: If it is not a bound symbol in ‘env’, it is
unchanged. If it is a promise object, i.e., a formal argument to
a function or explicitly created using ‘delayedAssign()’, the
expression slot of the promise replaces the symbol. If it is an
ordinary variable, its value is substituted, unless ‘env’ is
‘.GlobalEnv’ in which case the symbol is left unchanged.
Since the clause referring to the globalenv() is attached to the
discussion of ordinary variables, I thought that it implied that
delayedAssign(a, test)
substitute(a)
would return test (but actually it returns quote(a))
I'd suggest rewording this paragraph to:
Substitution takes place by examining each component of the parse
tree as follows: If it is not a bound symbol in ‘env’, it is
unchanged. If it is a promise object, i.e., a formal argument to
a function or explicitly created using ‘delayedAssign()’, the
expression slot of the promise replaces the symbol. If it is an
ordinary variable, its value is substituted. There's one important
exception to these rules: If 'env' is the ‘.GlobalEnv’, then no
substitution occurs.
It acts differently in the global environment. Try this:
f - function() { delayedAssign(a, test); substitute(a) }
f()
[1] test
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email: ggrothendieck at gmail.com
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Re: [Rd] R-3.0.0 reg-tests-3.R / survival
make check seems to be picking up the setting of my R_LIBS_SITE which is still set for 2.15.3 and had survival in it. At least, when I set that to empty then the check passes. I'm not sure if checking worked like that before, I don't think so. I have not usually had base packages in my site-library. In any case, it seems like a bad idea for make check to use an existing setting of R_LIBS_SITE. At least, I think the idea is that it should be checking the just built library. Paul On 13-04-03 11:36 AM, peter dalgaard wrote: Any chance that you might have a personal library, which isn't versioned? If you do and you for some reason installed survival into it, it would explain it. E.g., I have, with the system-wide R .libPaths() [1] /Users/pd/Library/R/2.15/library [2] /opt/local/Library/Frameworks/R.framework/Versions/2.15/Resources/library lapply(.libPaths(), list.files) [[1]] [1] abind aplpackcarcolorspace e1071 [6] effectsellipseHmisc ISwR leaps [11] lmtest matrixcalc mclust multcomp mvtnorm [16] pcaPP Rcmdr relimp represent rgl [21] robustbase rrcov semxtable zoo [[2]] [1] base boot class clustercodetools [6] compiler datasets foreigngraphics grDevices [11] grid KernSmooth latticeMASS Matrix [16] methodsmgcv nlme nnet parallel [21] rpart spatialsplinesstats stats4 [26] survival tcltk tools utils but the one in my development build tree of 3.0.0 has .libPaths() [1] /Users/pd/r-release-branch/BUILD-dist/library If I explicitly set R_LIBS, I can easily reproduce your error. On Apr 3, 2013, at 17:00 , Paul Gilbert wrote: make check is failing on reg-test3.R with a message that survival was built with an older version of R. (On my Ubuntu 32 bit and Ubuntu 64 bit machines). Why would make check be looking anywhere that it would find something built with an older version of R? ~/RoboAdmin/R-3.0.0/tests$ tail reg-tests-3.Rout.fail print(1.001, digits=16) [1] 1.001 ## 2.4.1 gave 1.001 ## 2.5.0 errs on the side of caution. ## as.matrix.data.frame with coercion library(survival) Error: package 'survival' was built before R 3.0.0: please re-install it Execution halted __ 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] Redefining quote() with reference classes (was: Ref classes initFields has incorrect environment?)
This should now be fixed in r-devel and 3.0.0 Patched as of revision 62487.
On Mar 29, 2013, at 11:30 AM, John Chambers j...@r-project.org wrote:
Nothing to do with initFields. If you trace your redefined quote(), it's
called from the - assignment of x.
The x element in the environment for the reference class object is
implemented as an active binding in order to enforce the class when assigning
the field.
Effectively that makes the assignment behave like a reference class method,
and so ends up doing as() and getting back to the malware version of quote().
The fix will be to have a more bullet proof (and perhaps more efficient)
version of the active binding generated for fields. A better design anyway,
but this will take a little re-organization because the current default
binding function is generated by some code manipulation.
Meanwhile the workaround is: Don't do what the revised subject heading says.
John
On Mar 28, 2013, at 11:40 AM, Hadley Wickham h.wick...@gmail.com wrote:
As suggested by the following code:
A - setRefClass(A, fields = list(x = logical),
methods = list(initialize = function(...) {
x - FALSE
initFields(...)
}))
A$new()
# Works as expected
quote - as.character
A$new()
# Error in function (value) :
# invalid replacement for field ‘x’, should be from class “logical”
or a subclass (was class “character”)
I get the same error in:
* R version 2.15.2 (2012-10-26)
* R version 2.15.3 (2013-03-01)
* R Under development (unstable) (2013-03-28 r62432)
Hadley
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http://had.co.nz/
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