search for: biocgenerics

...it > wouldn't help (as it shouldn't) if the two generics didn't agree on > signature or both carried methods for the same class signature. > > ~G > > > On Wed, Mar 26, 2014 at 4:38 AM, Michael Lawrence < > lawrence.michael@gene.com> wrote: > >> The BiocGenerics package was designed to solve this issue within >> Bioconductor. It wouldn't be the worst thing in the world to depend on the >> simple BiocGenerics package for now, but ideally the base generics would >> be >> defined higher up, perhaps in the methods package itself. Ma...

...N packages I am maintaining ('apcluster'). I started with using setMethod("sort", ...) in my package, which worked fine. Since many users of my package are from the bioinformatics field, I want to ensure that my package works smoothly with Bioconductor. The problem is that the BiocGenerics package also redefines 'sort' as an S4 generic. If I load BiocGenerics before my package, everything is fine. If I load BiocGeneric after I have loaded my package, my setMethod("sort", ...) is overridden by BiocGenerics and does not work anymore. A simple solution would be to...

...I do not really feel in the position to demand such a > fundamental change. > > 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 the problem open, mentioning in the documentation that users > who want to use apcluster in conjunction with Bioconductor should load > BiocGenerics first 4) define an S3 method, as mentioned in my previous post H. > > As far as I got it, there seems to be no other cl...

...being an R core team member, I do not really feel in the position to demand such a fundamental change. 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 the problem open, mentioning in the documentation that users who want to use apcluster in conjunction with Bioconductor should load BiocGenerics first As far as I got it, there seems to be no other clean way to get rid of the problem, right? Best regards, Ulrich On 03/26/2014 02:4...

...ificial dependencies on stats4, the latter allows for several independently defined S4 generics on plot. Neither is satisfactory. Dozens of Bioconductor packages importFrom(graphics, plot) and exportMethods(plot), in addition to other common functions. Our solution has been to create a package BiocGenerics whose purpose is to create and document otherwise implicit generics of base packages (see ?BiocGenerics for a list of generics). Packages then Import: BiocGenerics and importFrom(BiocGenerics, plot). This kind of approach, whatever limitations of current implementation, seems much better, provi...

...silent = mc.silent)) res <- mccollect(jobs) On 10/24/2012 05:07 PM, Cook, Malcolm wrote: > On 10/24/12 12:44 AM, "Michael Lawrence" <lawrence.michael at gene.com> wrote: > >> I agree that it would fruitful to have parLapply in BiocGenerics. It looks >> to be a flexible abstraction and its presence in the parallel package >> makes >> it ubiquitous. If it hasn't been done already, mclapply (and mcmapply) >> would be good candidates, as well. The fork-based parallelism is >> substantively different in t...

...9;, 'gWidgetstcltk', 'HH', 'Hmisc', 'httr', 'igraph',   'igraph0', 'inline', 'ipred', 'isa2', 'JavaGD', 'JGR', 'kernlab', 'KernSmoot [... truncated] > library(KEGGSOAP) Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following object(s) are masked from ‘package:stats’:     xtabs The following object(s) are masked from ‘package:base’:     anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste,     pmax, pm...

...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 the problem open, mentioning in the documentation that users >> who want to use apcluster in conjunction with Bioconductor should load >> BiocGenerics first > > 4) define an S3 method, as mentioned in my previous post > > H. > After a while, I came bac...

....121856 10 Dispatch seems to be especially slow when packages are involved, e.g., with the Bioconductor IRanges package (http://bioconductor.org/packages/release/bioc/html/IRanges.html) removeGeneric("paste") library(IRanges) showMethods(paste) ## Function: paste (package BiocGenerics) ## ...="ANY" ## ...="Rle" selectMethod(paste, "ANY") ## Method Definition (Class "derivedDefaultMethod"): ## ## function (..., sep = " ", collapse = NULL) ## .Internal(paste(list(...), sep, collapse)) ## <environment: nam...

...?, ?elementMetadata?, ?ifelse?, ?queryHits?, ?Rle?, ?subjectHits?, ?t? when loading ?bumphunter? Error: package or namespace load failed for ?methyAnalysis?: objects ?.__T__split:base?, ?split? are not exported by 'namespace:IRanges' In addition: Warning message: replacing previous import ?BiocGenerics::image? by ?graphics::image? when loading ?methylumi? I also try to install the package after downloading the source package from Bioconductor but the method is useless. Please help me to install the package named "methyAnalysis". Thanking you regards Pijush [[alternative HTML ver...

...;> ?subjectHits?, ?t? when loading ?bumphunter? >> Error: package or namespace load failed for ?methyAnalysis?: >> objects ?.__T__split:base?, ?split? are not exported by >> 'namespace:IRanges' >> In addition: Warning message: >> replacing previous import ?BiocGenerics::image? by ?graphics::image? when >> loading ?methylumi? >> >> I also try to install the package after downloading the source package >> from >> Bioconductor but the method is useless. >> >> Please help me to install the package named "methyAnalysis&qu...

...e fails; I've tried re-installing R and BioC from scratch, including all new packages etc, to no avail. Any ideas? > require("hugene10sttranscriptcluster.db") Loading required package: hugene10sttranscriptcluster.db Loading required package: AnnotationDbi Loading required package: BiocGenerics Attaching package: ?BiocGenerics? The following object(s) are masked from ?package:stats?: xtabs The following object(s) are masked from ?package:base?: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pm...

This is about the new note Depends: includes the non-default packages: ‘BiocGenerics’ ‘Biobase’ ‘lattice’ ‘reshape’ ‘GenomicRanges’ ‘Biostrings’ ‘bumphunter’ Adding so many packages to the search path is excessive and importing selectively is preferable. Let us say my package A either uses a class B (by producing an object that has B embedded as a slot) from another package or p...

Hi, The acrobatics that as.data.frame.factor() is going thru in order to recognize a direct call don't play nice if as.data.frame() is an S4 generic: ??? df <- as.data.frame(factor(11:12)) ??? suppressPackageStartupMessages(library(BiocGenerics)) ??? isGeneric("as.data.frame") ??? # [1] TRUE ??? df <- as.data.frame(factor(11:12)) ??? # Warning message: ??? # In as.data.frame.factor(factor(11:12)) : ??? # ? Direct call of 'as.data.frame.factor()' is deprecated. Use 'as.data.frame.vector()' or 'as.da...

...lse?, ?queryHits?, ?Rle?, > ?subjectHits?, ?t? when loading ?bumphunter? > Error: package or namespace load failed for ?methyAnalysis?: > objects ?.__T__split:base?, ?split? are not exported by 'namespace:IRanges' > In addition: Warning message: > replacing previous import ?BiocGenerics::image? by ?graphics::image? when > loading ?methylumi? > > I also try to install the package after downloading the source package from > Bioconductor but the method is useless. > > Please help me to install the package named "methyAnalysis". > > Thanking you &g...

...default method, it's good to see: Method Definition (Class "derivedDefaultMethod"): function (x, table, nomatch = NA_integer_, incomparables = NULL, ...) base::match(x, table, nomatch = nomatch, incomparables = incomparables, ...) <environment: namespace:BiocGenerics> Signatures: x table target "DataFrame" "ANY" defined "ANY" "ANY" rather than some obscure/uninformative body. I hope we can keep that. > >> The implementation of these functions is almost simpler in C than...

...t gmail.com> ?????: > The acrobatics that as.data.frame.factor() is going thru in order to > recognize a direct call don't play nice if as.data.frame() is an S4 > generic: > > ??? df <- as.data.frame(factor(11:12)) > > ??? suppressPackageStartupMessages(library(BiocGenerics)) > ??? isGeneric("as.data.frame") > ??? # [1] TRUE > > ??? df <- as.data.frame(factor(11:12)) > ??? # Warning message: > ??? # In as.data.frame.factor(factor(11:12)) : > ??? # ? Direct call of 'as.data.frame.factor()' is deprecated. How about somet...

...of this attribute causes the entire application to exit with an error (with no stack trace available). For example, within a shiny context: > foo <- try(nrow(my_reactive())) > attr(foo,"condition") <shiny.silent.error: > Where the S4 generic returns: > bar <- try(BiocGenerics::nrow(my_reactive())) > attr(bar,"condition") <simpleError in (function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = ""), class = c("shiny.silent.error", "validation", "error", "condition"), stack.tr...

...date.packages(oldPkgs="AnnotationDbi") AnnotationDbi : Version 1.0 installed in /Library/Frameworks/R.framework.develMav/Versions/3.2/Resources/library Version 1.29.17 available at http://bioconductor.org/packages/3.1/bioc Update (y/N/c)? y also installing the dependencies ?IRanges?, ?BiocGenerics?, ?Biobase?, ?GenomeInfoDb?, ?DBI?, ?RSQLite?, ?S4Vectors? trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/IRanges_2.1.35.tgz' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'http://bioconductor.org/packages/3.1/bioc/src...

...n reg-tests-1e.R and with make check-all > and commit later today, > thanking you, Ivan! This has been committed to R-devel svn rev 86139 now. So these spurious warnings in situations where as.data.frame() is an S4 generic --- notably for the many Bioconductor package depending on {BiocGenerics} --- should disappear within 24 hours or less. Martin