similar to: changes in recent R-devel revisions?

> On 28 Jun 2019, at 16:03 , Martin Maechler <maechler at stat.math.ethz.ch> wrote: > >>>>>> Henrik Bengtsson >>>>>> on Thu, 27 Jun 2019 16:00:39 -0700 writes: > >> Using: >> >> untrace(methods::conformMethod) >> at <- c(12,4,3,2) >> str(body(methods::conformMethod)[[at]]) >> ## language omittedSig

Using: untrace(methods::conformMethod) at <- c(12,4,3,2) str(body(methods::conformMethod)[[at]]) ## language omittedSig <- omittedSig && (signature[omittedSig] != "missing") cc <- 0L trace(methods::conformMethod, tracer = quote({ cc <<- cc + 1L print(cc) if (cc == 31) { ## manually identified untrace(methods::conformMethod)

Hi, There seems to be a problem with setGroupGeneric() from package 'methods'. The symptoms are somewhat erratic, in the sense that small changes may lead to any of the following behaviours. 1.Package works without problems on Windows and installs on Linux but gives error when loaded with library(). 2.Package installs on both systems and gives error when loaded on any of them. 3.

Hi, I am a Ph.D. student from Québec, Canada. I’m a beginner with R and Bioconductor. Until now the only experience I have is in analyzing microarray data using affy and limma packages. Now I am trying to analyze Rat Gene 10 st arrays and I would like to run RMA analysis and Smyth moderated t test on those arrays. Since no cdf official package is available for those arrays, after reading many

Hi, ExonFeatureSet I have an object of the above class. The following document mentioned it. http://www.bioconductor.org/packages/2.5/bioc/vignettes/oligo/inst/doc/ClassesUsedInOligo.pdf But I would like to see its defintion. I'm wondering if there is a way in R to give me the definition of any class? Regards, Peng

Hello, I'm wondering how I can merge two featuresets into one. My dataset is two sets of microarray data and it looks like followings: > rawData $v1 TilingFeatureSet (storageMode: lockedEnvironment) assayData: 2197815 features, 59 samples element names: channel1, channel2 protocolData rowNames: LT290677RU_D1_2011-02-16 LT286300LU_D1_2010-07-24 ... LT003990RU_D1_2010-11-04 (59

>>>>> Martin Maechler >>>>> on Sat, 29 Jun 2019 10:33:10 +0200 writes: >>>>> peter dalgaard >>>>> on Fri, 28 Jun 2019 16:20:03 +0200 writes: >> > On 28 Jun 2019, at 16:03 , Martin Maechler <maechler at stat.math.ethz.ch> wrote: >> > >> >>>>>> Henrik Bengtsson

I run checks with R-devel rev. 76756 on several of my packages which use S4, with no ill effects. With the risk of not adding much, it seems that Martin's example, which I repeat below, suggests a crossover between several "signatures" involved here - the signature of the generic, the signature of the method (the argument for setMethod()), and the signature of the function object

>>>>> Henrik Bengtsson >>>>> on Thu, 27 Jun 2019 16:00:39 -0700 writes: > Using: > > untrace(methods::conformMethod) > at <- c(12,4,3,2) > str(body(methods::conformMethod)[[at]]) > ## language omittedSig <- omittedSig && (signature[omittedSig] != "missing") > cc <- 0L > trace(methods::conformMethod, tracer =

Dear all, Consider this code: >library("data.table") >unloadNamespace('data.table') It produces some warnings Warning in FUN(X[[1L]], ...) : Created a package name, ‘2013-10-29 17:05:51’, when none found Warning in FUN(X[[1L]], ...) : Created a package name, ‘2013-10-29 17:05:51’, when none found ... The warning is produced by the getPackageName() function. e.g.

>>>>> peter dalgaard >>>>> on Fri, 28 Jun 2019 16:20:03 +0200 writes: > > On 28 Jun 2019, at 16:03 , Martin Maechler <maechler at stat.math.ethz.ch> wrote: > > > >>>>>> Henrik Bengtsson > >>>>>> on Thu, 27 Jun 2019 16:00:39 -0700 writes: > > > >> Using: > >> > >>

In 'conformMethod', there is another instance of omittedSig & <something about signature[omittedSig]> . It just affects error message. Original: ? ? if(any(is.na(match(signature[omittedSig], c("ANY", "missing"))))) { ? ? ? ? bad <- omittedSig & is.na(match(signature[omittedSig], c("ANY", "missing"))) After r76756: ? ? if(any(iiN

>>>>> Martin Maechler >>>>> on Sat, 29 Jun 2019 12:05:49 +0200 writes: >>>>> Martin Maechler >>>>> on Sat, 29 Jun 2019 10:33:10 +0200 writes: >>>>> peter dalgaard >>>>> on Fri, 28 Jun 2019 16:20:03 +0200 writes: >>> > On 28 Jun 2019, at 16:03 , Martin Maechler <maechler at

Henrik, If a minimal reprex is hard to construct, could you perhaps instrument your version of R to include a browser() call at the start of the else if(!all(signature[omittedSig] == "missing")) { branch, run the code that triggers the issue for you (and must hit that branch) and tell us what the "signature" and "omittedSig" objects look like at that point?

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is

Hi everybody, I've been looking for information on "how to create administrative shares", but I didn't find... Can you help me on this matter? Regards, -- Benilton Carvalho DE / IMECC / UNICAMP Red Hat Linux i18n Team

Hi Everyone, After searching the subject and not being successful, I was wondering if any you could explain me the idea behind the following fact: all(NULL == 2) ## TRUE any(NULL == 2) ## FALSE Thanks a lot, Benilton -- Benilton Carvalho PhD Candidate Department of Biostatistics Johns Hopkins University

Hi everyone, sorry if this was discussed before (and in this situation, could you please point me to the discussion in the archive? My search didn't seem to be effective). Is there a way of getting the names of objects in a .rda file without having to load it? Thank you very much, benilton -- PhD Candidate Department of Biostatistics Bloomberg School of Public Health Johns Hopkins

I need to read in csv files, created by 3rd party, with fields containing single quotes (as shown below). "header1","header2","header3","header4" "field1r1","field2r1","field3r1","field4r1" "field1r2","field2r2","field3r2PartA), field3r2PartB Very" Long","field4r2"

Hi Everyone, Given the scenario I have, I was wondering if anyone would be able to give me a hind on how to get the results from hubers() in a more efficient way. I have an outcome on an array [N x S x D]. I also have a factor (levels 1,2,3) stored on a matrix N x S. My objective is to get "mu" and "sigma" for each of the N rows (outcome) stratified by the factor