methods package: A _R_CHECK_LENGTH_1_LOGIC2_=true error
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), tracer = quote({
str(list(signature = signature, mnames = mnames, fnames = fnames))
print(ls())
try(str(list(omittedSig = omittedSig, signature = signature)))
}))
}
}))
loadNamespace("oligo")
gives:
Untracing function "conformMethod" in package "methods"
Tracing function "conformMethod" in package "methods"
Tracing conformMethod(signature, mnames, fnames, f, fdef, definition)
step 12,4,3,2
List of 3
$ signature: Named chr [1:4] "TilingFeatureSet" "ANY" "ANY" "array"
..- attr(*, "names")= chr [1:4] "object" "subset" "target" "value"
..- attr(*, "package")= chr [1:4] "oligoClasses" "methods" "methods" "methods"
$ mnames : chr [1:2] "object" "value"
$ fnames : chr [1:4] "object" "subset" "target" "value"
[1] "f" "fdef" "fnames" "fsig" "imf"
[6] "method" "mnames" "omitted" "omittedSig" "sig0"
[11] "sigNames" "signature"
List of 2
$ omittedSig: logi [1:4] FALSE TRUE TRUE FALSE
$ signature : Named chr [1:4] "TilingFeatureSet" "ANY" "ANY" "array"
..- attr(*, "names")= chr [1:4] "object" "subset" "target" "value"
..- attr(*, "package")= chr [1:4] "oligoClasses" "methods" "methods" "methods"
Error in omittedSig && (signature[omittedSig] != "missing") :
'length(x) = 4 > 1' in coercion to 'logical(1)'
Error: unable to load R code in package 'oligo'
This is with:
sessionInfo()
R version 3.6.0 Patched (2019-06-23 r76734)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS
Matrix products: default
BLAS: /home/hb/software/R-devel/R-3-6-branch/lib/R/lib/libRblas.so
LAPACK: /home/hb/software/R-devel/R-3-6-branch/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 affxparser_1.56.0
[3] XVector_0.24.0 splines_3.6.0
[5] GenomicRanges_1.36.0 BiocGenerics_0.30.0
[7] zlibbioc_1.30.0 IRanges_2.18.1
[9] bit_1.1-14 BiocParallel_1.18.0
[11] lattice_0.20-38 foreach_1.4.4
[13] blob_1.1.1 GenomeInfoDb_1.20.0
[15] tools_3.6.0 SummarizedExperiment_1.14.0
[17] parallel_3.6.0 grid_3.6.0
[19] Biobase_2.44.0 ff_2.2-14
[21] DBI_1.0.0 iterators_1.0.10
[23] oligoClasses_1.46.0 matrixStats_0.54.0
[25] digest_0.6.19 bit64_0.9-7
[27] preprocessCore_1.46.0 affyio_1.54.0
[29] Matrix_1.2-17 GenomeInfoDbData_1.2.1
[31] BiocManager_1.30.4 codetools_0.2-16
[33] S4Vectors_0.22.0 bitops_1.0-6
[35] RCurl_1.95-4.12 memoise_1.1.0
[37] RSQLite_2.1.1 DelayedArray_0.10.0
[39] compiler_3.6.0 Biostrings_2.52.0
[41] stats4_3.6.0
/Henrik
On Thu, Jun 27, 2019 at 8:16 AM Martin Maechler
<maechler at stat.math.ethz.ch> wrote:
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 indexing in
> omittedSig <- seq_along(omittedSig)[omittedSig]
> signature[omittedSig] <- "missing" # logical index will extend signature!
> (I'm sure there is a valid reason, I just don't get it...)
> -pd
I've also have mused over that question... and I had assumed some difference in the case the original omittedSig contains NAs ... but that's NOT true actually, see:
> sign2 <- signatures <- LETTERS
> omittedSig <- LETTERS < "K"
> omittedSig[c(8,18)] <- NA # now have an omittedSig with {T, F, NA}
> iSig <- seq_along(omittedSig)[omittedSig]
> sign2[iSig] <- "missing"
> signatures[omittedSig] <- "missing"
> identical(sign2, signatures)
[1] TRUE
>
so I still don't see the case where it makes a difference. Martin
>> On 25 Jun 2019, at 09:44 , peter dalgaard <pdalgd at gmail.com> wrote:
>>
>> 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 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.bengtsson at gmail.com> wrote:
>>>
>>> **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' is used to subset 'signature'. In other words,
>>> the length of 'signature[omittedSig]' and hence the length of
>>> '(signature[omittedSig] != "missing")' will equal sum(omittedSig),
>>> i.e. the length will be in {0,1,...,length(omittedSig)}.
>>>
>>> The R 3.6.0 version with '&&' is not correct because '&&' requires
>>> length(omittedSig) == 1L and sum(omittedSig) == 1L, which is unlikely
>>> to be the original intention.
>>>
>>> The patched version with '&' is most likely not correct either because
>>> 'LHS & RHS' assume length(LHS) == length(RHS), unless it relies on the
>>> auto-expansion of either vector. So, for the '&' version to be
>>> correct, it basically requires that length(omittedSig) = length(LHS) =
>>> length(RHS) = sum(omittedSig), which also sounds unlikely to be the
>>> original intention.
>>>
>>> Disclaimer: Please note that I have not at all studied the rest of the
>>> function, so the above is just based on that single line plus
>>> debugging that 'omittedSig' is a logical vector.
>>>
>>> Martin, I don't have the time to dive into this further. Though I did
>>> try to see if it happened when one of oligo's dependencies were
>>> loaded, but that was not the case. It kicks in when oligo is loaded.
>>> FYI, I can also replicate your non-replicatation on another R 3.6.0
>>> version. I'll see if I can narrow down what's different, e.g.
>>> comparing sessionInfo():s, etc. However, I want to reply with
>>> findings above asap due to the R 3.6.1 release and you might roll back
>>> the patch (since it might introduce other bugs as Peter mentioned).
>>>
>>> /Henrik
>>>
>>>
>>> On Mon, Jun 24, 2019 at 3:05 AM Martin Maechler
>>> <maechler at stat.math.ethz.ch> wrote:
>>>>
>>>>>>>>> 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"
>>>>> ...
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, almost 40 (non
>>>> base+Recommended) packages have been loaded as well, which hence
>>>> need to have been installed before, too ..
>>>> which is not quite a "vanilla repr.ex." in my view
>>>>
>>>> Worse, I cannot reproduce :
>>>>
>>>>> Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_" = "true")
>>>>> Sys.getenv("_R_CHECK_LENGTH_1_LOGIC2_")
>>>> [1] "true"
>>>>> debugonce(conformMethod)
>>>>> loadNamespace("oligo")
>>>> <environment: namespace:oligo>
>>>> Warning messages:
>>>> 1: multiple methods tables found for ?rowSums?
>>>> 2: multiple methods tables found for ?colSums?
>>>> 3: multiple methods tables found for ?rowMeans?
>>>> 4: multiple methods tables found for ?colMeans?
>>>>> sessionInfo()
>>>> R Under development (unstable) (2019-06-20 r76729)
>>>>
>>>> (similarly with other versions of R >= 3.6.0).
>>>>
>>>> So, even though R core has fixed this now in the sources, it
>>>> would be nice to have an "as simple as possible" repr.ex. for this.
>>>>
>>>> Martin
>>>>
>>>>
>>>>
>>>>> On Sun, Jun 23, 2019 at 1:54 AM peter dalgaard <pdalgd at gmail.com> wrote: 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 error with 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 the patch:
>>>>>>>
>>>>>>> $ svn diff src/library/methods/R/RMethodUtils.R &
>>>>>>> [1] 1062
>>>>>>> Index: src/library/methods/R/RMethodUtils.R
>>>>>>> ===================================================================
>>>>>>> --- src/library/methods/R/RMethodUtils.R (revision 76731)
>>>>>>> +++ src/library/methods/R/RMethodUtils.R (working copy)
>>>>>>> @@ -343,7 +343,7 @@
>>>>>>> call. = TRUE, domain = NA)
>>>>>>> }
>>>>>>> else if(!all(signature[omittedSig] == "missing")) {
>>>>>>> - omittedSig <- omittedSig && (signature[omittedSig] != "missing")
>>>>>>> + omittedSig <- omittedSig & (signature[omittedSig] != "missing")
>>>>>>> .message("Note: ", .renderSignature(f, sig0),
>>>>>>> gettextf("expanding the signature to include omitted
>>>>>>> arguments in definition: %s",
>>>>>>> paste(sigNames[omittedSig], "=
>>>>>>> \"missing\"",collapse = ", ")))
>>>>>>> [1]+ Done svn diff src/library/methods/R/RMethodUtils.R
>>>>>>>
>>>>>>> Maybe still in time for R 3.6.1?
>>>>>>>
>>>>>>> /Henrik
>>>>>>>
>>>>>>> ______________________________________________
>>>>>>> R-devel at r-project.org mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
-- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
>>>>
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>> --
>> Peter Dalgaard, Professor,
>> Center for Statistics, Copenhagen Business School
>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> Phone: (+45)38153501
>> Office: A 4.23
>> Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
>>
>>
>>
>>
>>
>>
>>
>>
>>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
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