search for: 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? Bonus points for figuring out why it is needed to use numerical indexing in...

**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] != "missing") can be correct. For a starter, 'omittedSig' is a logical vector. We see that '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) trace(methods::conformMethod, at = list(at), tra...

...;>>> 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 for you (and must hit that branch) and tell us what the "signature" and "omittedSig" objects look like at that point? > Bonus points for figuring out why it is needed to use numerical ind...

...elf, 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") : 'length(x) = 4 > 1' in coercion to 'logical(1)' Error: unable to load R code in package ?oligo? /Henrik On Sun, Jun 23, 2019 at 1:54 AM peter dalgaard <pdalgd at gmail.com> wrote: > > This looks obvious e...

...R --vanilla, so it only occurs when some other package is also loaded. I don't have time to find to narrow that down for a reproducible example, but I believe the following error in R 3.6.0: > Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_" = "true") > library(oligo) Error in omittedSig && (signature[omittedSig] != "missing") : 'length(x) = 4 > 1' in coercion to 'logical(1)' Error: unable to load R code in package 'oligo' is because of a '_R_CHECK_LENGTH_1_LOGIC2_=true' mistake in the 'methods' package. Here's th...

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")))...

...code was originally from 2009, by John Chambers. It is not too likely that he'll remember what the intention actually was... The logic does escape me: An omitted signature is only an omitted signature if the signature of the omitted signature is not "missing"? In that case, I think omittedSig[omittedSig] <- (signature[omittedSig] != "missing") might work (omittedSig[omittedSig] == TRUE, so we don't need to &. That is, unless there are NA issues.), but I am not at all sure that is what is wanted! ] -pd > On 25 Jun 2019, at 07:16 , Henrik Bengtsson <henrik.be...

...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 <- omittedSig && (signature[omittedSig] != "missing") >> cc <- 0L >> trace(methods::conformMethod, tracer = quote({ >> cc <<- cc + 1L >> print(cc) >> if (cc == 31) { ## manually identified >> untrace(methods::conformMethod) &g...

...nrik 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 = quote({ > >> cc <<- cc + 1L > >> print(cc) > >> if (cc == 31) { ## manually identified > >> untr...

...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 = quote({ >> >> cc <<- cc + 1L >> >> print(cc) >> >> if (cc == 31) { ## m...

...0 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 = quote({ >>> >> cc <<- cc + 1L >>> >> print(cc) >>> >> i...

...t; 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") : > 'length(x) = 4 > 1' in coercion to 'logical(1)' > Error: unable to load R code in package ?oligo? > /Henrik Thank you Henrik, for the report, etc, but hmm... after loading the oligo package, almo...

...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 = quote({ >>> >> cc <<- cc + 1L >>> >> print(cc) >>> >> i...

...rs when some other package is also loaded. I don't have time to > find to narrow that down for a reproducible example, but I believe the > following error in R 3.6.0: > >> Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_" = "true") >> library(oligo) > Error in omittedSig && (signature[omittedSig] != "missing") : > 'length(x) = 4 > 1' in coercion to 'logical(1)' > Error: unable to load R code in package 'oligo' > > is because of a '_R_CHECK_LENGTH_1_LOGIC2_=true' mistake in the > 'methods'...

>>>>> 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 = quote({ > cc <<- cc + 1L > print(cc) > if (cc == 31) { ## manually identified > untrace(methods::conformMethod) > trace(methods...