Re: [Bioc-devel] error in summary method for KEGGHyperGResult

y, the error is thrown in the call to getAnnMap >> >> I don't currently have a local installation of bioc-devel 3.0 yet (mea >> culpa) but a quick glance at the source code tells me that the relevant >> summary method still calls getAnnMap with "KEGG" as it's second argument. >> >> &

Re: [Bioc-devel] [Rd] Conflicting definitions for function redefined as S4 generics

> http://www.bioinf.jku.at/ <http://www.bioinf.jku.at> > > > > __ > > r-de...@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > [[alternative HTML version deleted]] > > __ > r-de...@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Gabriel Becker Graduate Student Statistics Department University of California, Davis [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] parsing embedded FASTA data

___ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > >> > > -- > > Hervé Pagès > > > > Program in Computational Biology > > Division of Public Health Sciences > > Fred Hutchinson Cancer Research C

Re: [Bioc-devel] file registry - feedback

> > registerFileType(NewClass, NewPackage, "\\.NewExtension$") > > > > > > Thoughts: > > > > (1) If this sounds generally useful where should it live? rtracklayer, > > GenomicFileViews or other? Alternatively it could be its own lightweight > >

Re: [Bioc-devel] cigarToRleList fails

Method(fun, target.sig)@defined > help(paste0(fun.name, ",", paste(defined.sig, collapse=","), "-method")) > } > > path_to_gff <- "my.gff" > helpwith(import(path_to_gff)) > > helpwith(rbind(DataFrame(mtcars), DataFrame(mtcars))) > > B

Re: [Bioc-devel] cigarToRleList fails

03 PM, Gabriel Becker wrote: > Herve, > > The help is correct (though possibly a bit pedantic), there is no method > for that signature. > > ?import("", "") > > works for me though > > ~G > > > On Thu, Feb 20, 2014 at 4:51 PM, Hervé P

Re: [Bioc-devel] cigarToRleList fails

iterators_1.0.6plyr_1.8 >> >> [13] RSQLite_0.11.4 >> sendmailR_1.1-2 >>stats4_3.1.0 tools_3.1.0 >> >> [17] zlibbioc_1.9.0 >> >> >> ___ >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org >> > >> <mailto:Bioc-devel@r-project.__org >> <mailto:Bioc-devel@r-project.org>> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> <https://stat.ethz.ch/mailman/__listinfo/bioc-devel> >> >> >> <https://stat.ethz.ch/mailman/__listinfo/bioc-devel >> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>> >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> >> >> >> __ >> _ >> Bioc-devel@r-project.org >> <mailto:Bioc-devel@r-project.org> >> <mailto:Bioc-devel@r-project.__org >> <mailto:Bioc-devel@r-project.org>> >> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> <https://stat.ethz.ch/mailman/__listinfo/bioc-devel> >> >> >> <https://stat.ethz.ch/mailman/__listinfo/bioc-devel >> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>> >> >> >> -- >> Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M1-B514 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpa...@fhcrc.org <mailto:hpa...@fhcrc.org> >> <mailto:hpa...@fhcrc.org <mailto:hpa...@fhcrc.org>> >> >> Phone: (206) 667-5791 >> >> Fax: (206) 667-1319 >> >> >> >> >> >> >> >> -- >> Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M1-B514 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpa...@fhcrc.org <mailto:hpa...@fhcrc.org> >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 >> >> >> > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fhcrc.org > Phone: (206) 667-5791 > Fax:(206) 667-1319 > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Gabriel Becker Graduate Student Statistics Department University of California, Davis [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] package citations

> > Many of us would like credit for our work in the form of citations; let us > not make it hard on the user to figure out how to do this. > > Best, > Kasper > > [[alternative HTML version deleted]] > > ___ > Bioc-dev

Re: [Bioc-devel] BiocParallel: Best standards for passing locally assigned variables/functions, e.g. a bpExport()?

But as Ryan has >> noted, a simple sanity check goes a long way. If what he has done could be >> extended to the rest of the search path (people always forget to attach >> packages), I think we've hit the 80% with 20%. Got a 404 on that URL btw. >> >> Michael >>

Re: [Bioc-devel] BiocParallel: Best standards for passing locally assigned variables/functions, e.g. a bpExport()?

tach > packages), I think we've hit the 80% with 20%. Got a 404 on that URL btw. > > Michael > > > On Mon, Nov 4, 2013 at 11:05 AM, Gabriel Becker wrote: > >> Hey guys, >> >> Here is code that I have written which resolves library names into a full >

Re: [Bioc-devel] BiocParallel: Best standards for passing locally assigned variables/functions, e.g. a bpExport()?

solved, a slightly more explicit > > and standardized solution is then: > > > > values <- bplapply(0:9, FUN=function(n, BPGLOBALS=NULL) { > > for (name in names(BPGLOBALS)) assign(name, BPGLOBALS[[name]]) > > fib(n) > > }, BPGLOBALS=list(fib=fib)) >

Re: [Bioc-devel] BiocParallel: Best standards for passing locally assigned variables/functions, e.g. a bpExport()?

nt here, right? As you say, there are necessarily > limitations due to R being a dynamic language, but the goal is to catch > common errors, not stop people from tricking the check. > > I think I'll try to code something up soon. > > -Ryan > > > On 11/3/13, 5:10 PM,

Re: [Bioc-devel] BiocParallel: Best standards for passing locally assigned variables/functions, e.g. a bpExport()?

gt;>> Error in fib(n): could not find function "fib" >>>>> [...] >>>>> >>>>> # Workaround; make fib() aware of itself >>>>> # (this is something the user need to do, and would be very >>>>> # har

Re: [Bioc-devel] Running Perl Scripts from R package

------- > > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Gabriel Becker Graduate Student Statistics Department University of California, Davis [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] A case for specific markup (was BiocStyle for styling ...)

JSS or an organization like Bioconductor could actually enforce/detect violations of package citation rules. Thanks for reading, ~G -- Gabriel Becker Graduate Student Statistics Department University of California, Davis [[alternative HTML versi

Re: [Bioc-devel] finding specific (outdated!) bioc package archives?

r54800 > > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edgeR/ > > > > Dan > > > > > > For more on the topic you bring up, see the thread started by > > https://stat.ethz.ch/pipermail/bioconductor/2013-March/051224.html > &g