similar to: methods package: A _R_CHECK_LENGTH_1_LOGIC2_=true error

Thank you. To correct myself, I can indeed reproduce this with R --vanilla too. A reproducible example is: $ R --vanilla R version 3.6.0 Patched (2019-05-31 r76629) -- "Planting of a Tree" ... > Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_" = "true") > loadNamespace("oligo") Error in omittedSig && (signature[omittedSig] != "missing") :

**Maybe this bug needs to be understood further before applying the patch because patch is most likely also wrong** Because, from just looking at the expressions, I think neither the R 3.6.0 version: omittedSig <- omittedSig && (signature[omittedSig] != "missing") nor the patched version (I proposed): omittedSig <- omittedSig & (signature[omittedSig] !=

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?

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)

> 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

>>>>> 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 via R-core >>>>> on Sun, 23 Jun 2019 11:29:58 -0700 writes: > Thank you. > To correct myself, I can indeed reproduce this with R --vanilla too. > A reproducible example is: > $ R --vanilla > R version 3.6.0 Patched (2019-05-31 r76629) -- "Planting of a Tree" > ... >>

This looks obvious enough, so I just committed your fix to R-devel and R-patched. I'm at the wrong machine for thorough testing, but at least it seems to build OK. However, I sense some risk that this could uncover sleeping bugs elsewhere, so watch out. -pd > On 22 Jun 2019, at 18:49 , Henrik Bengtsson <henrik.bengtsson at gmail.com> wrote: > > DISCLAIMER: I can not get this

Argh! Yes you are right, the "fix" doesn't. And I fell into the same "hey it's a vector so && has to be wrong"-trap. So this has to be reverted to something that has at least failed unconspicuously for a decade.... Will do. Thanks to Martin for remaining suspicious! [This code was originally from 2009, by John Chambers. It is not too likely that he'll

>>>>> peter dalgaard >>>>> on Thu, 27 Jun 2019 16:23:14 +0200 writes: > 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

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

>>>>> 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: > >> > >>

>>>>> 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 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 =

promptClass fails to identify methods associated with the class. Here is a fix: Index: promptClass.R =================================================================== --- promptClass.R (revision 41719) +++ promptClass.R (working copy) @@ -165,7 +165,7 @@ if (nmeths > 0) { .meths.body <- " \\describe{" for (i in 1:nmeths) { - .sigmat

Dear Help, After loading the pd.Citrus library and checking the DataFrame, I ran > the R code for: > > 1) 'oligo' > > > > {> library(pd.citrus) > Loading required package: RSQLite > Loading required package: DBI > > data(pmSequence) > > > show(pmSequence) > DataFrame with 341730 rows and 2 columns > fid sequence > <integer>

Full_Name: Fernando Henrique Ferraz Pereira da Rosa Version: 1.8.0 OS: Linux 2.4.21 Submission from: (NULL) (200.206.211.169) After installing R 1.8.0, the R DBI interface stopped working. I tracked it down as a problem in the 'methods' package, that comes in the default installation. Somehow the function '.valueClassTest' which is defined on package 'methods',

Dear all, I've noticed by trying to download gz files from here : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM907811 At the bottom one can download GSM907811.CEL.gz . If I download this manually and try oligo::read.celfiles("GSM907811.CEL.gz") everything works fine. (oligo is a bioConductor package) However, if I download using download.file("

Hi, namespaceImportFrom in base/R/namespace.R has the following: fdef <- methods:::getGeneric(genName, impenv) The definition of getGeneric is in methods/R/RMethodUtils.R starts with: getGeneric <- ## return the definition of the function named f as a generic. ## ## If there is no definition, throws an error or returns ## NULL according to the value of