R devel - Jun 2019 - methods package: A _R_CHECK_LENGTH_1_LOGIC2_=true error

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

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

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

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
>
>
>
>
>
>
>
>
>