search for: bodenhofer

Re-sending, since I forgot to include the list, sorry. I'm including r-package-devel too this time, as it seems more appropriate for this list. El 22 ene. 2018 10:11, "I?aki ?car" <i.ucar86 at gmail.com> escribi?: > > > El 22 ene. 2018 8:12, "Ulrich Bodenhofer" <bodenhofer at bioinf.jku.at> > escribi?: > > Dear colleagues, dear members of the R Core Team, > > This was an issue raised by Prof. Brian Ripley and sent privately to all > developers of CRAN packages that suggest Bioconductor packages (see > original message belo...

...ught that maybe I could protect my setMethod("sort", ...) from being overridden by BiocGeneric by sealed=TRUE, but that did not work either. Any ideas are gratefully appreciated! Thanks a lot, Ulrich ------------------------------------------------------------------------ *Dr. Ulrich Bodenhofer* Associate Professor Institute of Bioinformatics *Johannes Kepler University* Altenberger Str. 69 4040 Linz, Austria Tel. +43 732 2468 4526 Fax +43 732 2468 4539 bodenhofer at bioinf.jku.at <mailto:bodenhofer at bioinf.jku.at> http://www.bioinf.jku.at/ <http://www.bioinf.jku.at>

On 01/22/2018 08:40 AM, Ulrich Bodenhofer wrote: > Thanks a lot, I?aki, this is a perfect solution! I already implemented > it and it works great. I'll wait for 2 more days before I submit the > revised package to CRAN - in order to give others to comment on it. It's very easy for 'pictures of code' (unevaluated...

...rhaps in the methods package itself. Maybe someone >> else has a more creative solution, but any sort of conditional/dynamic >> approach would probably be too problematic in comparison. >> >> Michael >> >> >> >> On Wed, Mar 26, 2014 at 4:26 AM, Ulrich Bodenhofer < >> bodenhofer@bioinf.jku.at >> > wrote: >> >> > [cross-posted to R-devel and bioc-devel] >> > >> > Hi, >> > >> > I am trying to implement a 'sort' method in one of the CRAN packages I >> am >> > maintainin...

On 03/27/2014 02:13 AM, Ulrich Bodenhofer wrote: > I fully agree, Michael, that this would be a great thing to have! I have > often wondered why R and the standard packages are still sticking so > much to the old-style S3 flavor though S4 is part of standard R. I > acknowledge that backward compatibility is important, but, as f...

...including > r-package-devel too this time, as it seems more appropriate for this > list. > > > El 22 ene. 2018 10:11, "I?aki ?car" <i.ucar86 at gmail.com > <mailto:i.ucar86 at gmail.com>> escribi?: > > > > El 22 ene. 2018 8:12, "Ulrich Bodenhofer" > <bodenhofer at bioinf.jku.at <mailto:bodenhofer at bioinf.jku.at>> escribi?: > > Dear colleagues, dear members of the R Core Team, > > This was an issue raised by Prof. Brian Ripley and sent > privately to all developers of CRAN pack...

...t argument y is present in the code but missing in the documentation , although it is actually NOT in the code. In order to make this reproducible for everybody, I put together a little dummy package in which one of the methods leads to exactly this warning: http://www.bioinf.jku.at/people/bodenhofer/codocMismatchTest_0.0.1.tar.gz Just run 'R CMD check' on this archive and you'll see. You will also see from the code and the corresponding documentation that the warning seems unjustified. I tried the following R versions: 2.12.1, 2.13.0, 2.13.1, 2.14.0, 2.14.1, 2.15.0, 2.15.1, 2.1...

...ut it might turn into a major effort for the warnings raised by the package vignette. Since I have not gotten any advice yet, I take the liberty to post it here on this list - hoping that we reach a conclusion here how to deal with this matter. Thanks in advance for your kind assistance, Ulrich Bodenhofer -------- Forwarded Message -------- Subject: Re: CRAN packages not using Suggests conditionally Date: Mon, 15 Jan 2018 08:44:40 +0100 From: Ulrich Bodenhofer <bodenhofer at bioinf.jku.at> To: Prof Brian Ripley <ripley at stats.ox.ac.uk> CC: [...stripped for the sake of privacy ....

Hi, I am using R on Ubuntu 12.10 (64bit). This morning, Ubuntu's software updater automatically installed updates to R's base system (version 2.15.3; via the CRAN PPA). Now R does not work anymore. Here is what I get when I simply enter "R" on the shell prompt: bodenhof FUKUOKA~>R cannot find system Renviron Error : .onLoad failed in loadNamespace() for 'utils',

...ge itself. > Maybe someone > else has a more creative solution, but any sort of > conditional/dynamic > approach would probably be too problematic in comparison. > > Michael > > > > On Wed, Mar 26, 2014 at 4:26 AM, Ulrich Bodenhofer > <bodenhofer at bioinf.jku.at <mailto:bodenhofer at bioinf.jku.at> > > wrote: > > > [cross-posted to R-devel and bioc-devel] > > > > Hi, > > > > I am trying to implement a 'sort' meth...

...luster/ <http://www.bioinf.jku.at/software/apcluster/> http://cran.r-project.org/web/packages/apcluster/index.html <http://cran.r-project.org/web/packages/apcluster/index.html> Best regards, Ulrich ------------------------------------------------------------------------ *Dr. Ulrich Bodenhofer* Associate Professor Institute of Bioinformatics *Johannes Kepler University* Altenberger Str. 69 4040 Linz, Austria Tel. +43 732 2468 9552 Fax +43 732 2468 9511 bodenhofer at bioinf.jku.at <mailto:bodenhofer at bioinf.jku.at> http://www.bioinf.jku.at/ <http://www.bioinf.jku.at>

...erated by its president, Ray DiGiacomo, Jr. We are aware that the time may be inconvenient for users from the Asia-Pacific region. If there is demand (please let us know!), we are willing to organize a second webinar at a time that is more suitable for Asian-Pacific users. Best regards, Ulrich Bodenhofer ------------------------------------------------------------------------ *Dr. Ulrich Bodenhofer* Associate Professor Institute of Bioinformatics *Johannes Kepler University* Altenberger Str. 69 4040 Linz, Austria Tel. +43 732 2468 4526 Fax +43 732 2468 4539 bodenhofer at bioinf.jku.at http://ww...

...everal minor improvements of the package. For more details, see the following URLs: http://www.bioinf.jku.at/software/apcluster/ http://cran.r-project.org/web/packages/apcluster/index.html Best regards, Ulrich ------------------------------------------------------------------------ *Dr. Ulrich Bodenhofer* Associate Professor Institute of Bioinformatics *Johannes Kepler University* Altenberger Str. 69 4040 Linz, Austria Tel. +43 732 2468 4526 Fax +43 732 2468 4539 bodenhofer at bioinf.jku.at http://www.bioinf.jku.at/ _______________________________________________ R-packages mailing list R-packag...

Hi All, Here is the case. I want to build classification model (SVM). Some of variables for this model are categorical attributes which represent words (usually 3-10 words - query for search in google). For example: search_id | query_words |..| result -----------+----------------------------------+--+-------- 1 | how,to,grow,tree |..| 4 2

On 03/27/2014 06:31 PM, Herv? Pag?s wrote: > On 03/27/2014 02:13 AM, Ulrich Bodenhofer wrote: >> [...] >> >> For the time being, it seems I have three options: >> >> 1) not supplying the sort() function yet (it is not yet in the release, >> but only in my internal devel version) >> 2) including a dependency to BiocGenerics >> 3) leaving...

...t argument y is present in the code but missing in the documentation , although it is actually NOT in the code. In order to make this reproducible for everybody, I put together a little dummy package in which one of the methods leads to exactly this warning: http://www.bioinf.jku.at/people/bodenhofer/codocMismatchTest_0.0.1.tar.gz Just run 'R CMD check' on this archive and you'll see. You will also see from the code and the corresponding documentation that the warning seems unjustified. I tried the following R versions: 2.12.1, 2.13.0, 2.13.1, 2.14.0, 2.14.1, 2.15.0, 2.15.1, 2.1...

CRAN (and crantastic) updates this week New packages ------------ * apcluster (1.0.1) Ulrich Bodenhofer http://crantastic.org/packages/apcluster The apcluster package implements Frey's and Dueck's Affinity Propagation clustering in R. The algorithms are analogous to the Matlab code published by Frey and Dueck. * BioPhysConnectoR (1.6-1) Franziska Hoffgaard http://crantastic.org/...

[cross-posted from bioc-devel list] Hi all, I have a subtle question related to how R CMD SHLIB handles variables in make child processes. In more detail: I am the maintainer of the 'msa' package which has been in Bioconductor since April 2015. This package integrates three open-source libraries for multiple sequence alignment. This is organized in the following way: in src/, there

[cross-posted on R-devel and Bioc-devel, since the functions from the parallel package discussed here are mirrored in the BiocGenerics package] Hi, I am currently running a lengthy simulation study (no details necessary) on a large multi-core system. The simulated data sets are stored in a long list and they are unevenly sized (hence, the computation times vary greatly between data sets), so