R devel - Apr 2019 - R-devel (rev 76409) fails 'make check': non-generic function 'isSymmetric' given to findMethods()

Hello,

Most likely I'm doing something wrong, but am at a loss as to what the 
issue is. I have a clean checkout of trunk here:

 ?? ~/svn/r-devel/R$ svn info
 ?? Path: .
 ?? Working Copy Root Path: /home/btyner/svn/r-devel/R
 ?? URL: https://svn.r-project.org/R/trunk
 ?? Relative URL: ^/trunk
 ?? Repository Root: https://svn.r-project.org/R
 ?? Repository UUID: 00db46b3-68df-0310-9c12-caf00c1e9a41
 ?? Revision: 76409
 ?? Node Kind: directory
 ?? Schedule: normal
 ?? Last Changed Author: ripley
 ?? Last Changed Rev: 76409
 ?? Last Changed Date: 2019-04-21 06:32:24 -0400 (Sun, 21 Apr 2019)

I then ran:

 ?? mkdir ~/svn/R-devel-build
 ?? cd ~/svn/R-devel-build
 ?? ../r-devel/R/configure --prefix=/home/btyner/R-76409 
--enable-R-shlib --with-blas --with-lapack --with-readline 
--without-recommended-packages
 ?? make
 ?? make check

which fails at reg-tests-1d.R; the failure being:

 ?? > ## str() now even works with invalid objects:
 ?? > moS <- mo <- findMethods("isSymmetric")
 ?? Error in findMethods("isSymmetric") :
 ? ?? (converted from warning) non-generic function 'isSymmetric' given 
to findMethods()
 ?? Execution halted

I am able to build revision 76407 from source just fine (using 
https://cran.r-project.org/src/base-prerelease/R-devel_2019-04-20_r76407.tar.gz)
and all make check tests are successful.

Any ideas? Here is my sessionInfo() from the revision 76407 build:

    R Under development (unstable) (2019-04-20 r76407)
    Platform: x86_64-pc-linux-gnu (64-bit)
    Running under: Ubuntu 18.04.2 LTS

    Matrix products: default
    BLAS: /home/btyner/R-devel_2019-04-20_r76407/lib64/R/lib/libRblas.so
    LAPACK: /home/btyner/R-devel_2019-04-20_r76407/lib64/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] compiler_3.7.0

Regards,

Ben

On 21/04/2019 4:56 p.m., Benjamin Tyner wrote:
> Hello,
> 
> Most likely I'm doing something wrong, but am at a loss as to what the
> issue is. I have a clean checkout of trunk here: >
>   ?? ~/svn/r-devel/R$ svn info
>   ?? Path: .
>   ?? Working Copy Root Path: /home/btyner/svn/r-devel/R
>   ?? URL: https://svn.r-project.org/R/trunk
>   ?? Relative URL: ^/trunk
>   ?? Repository Root: https://svn.r-project.org/R
>   ?? Repository UUID: 00db46b3-68df-0310-9c12-caf00c1e9a41
>   ?? Revision: 76409
>   ?? Node Kind: directory
>   ?? Schedule: normal
>   ?? Last Changed Author: ripley
>   ?? Last Changed Rev: 76409
>   ?? Last Changed Date: 2019-04-21 06:32:24 -0400 (Sun, 21 Apr 2019)
> 
> I then ran:
> 
>   ?? mkdir ~/svn/R-devel-build
>   ?? cd ~/svn/R-devel-build
>   ?? ../r-devel/R/configure --prefix=/home/btyner/R-76409
> --enable-R-shlib --with-blas --with-lapack --with-readline
> --without-recommended-packages
>   ?? make
>   ?? make check
> 
> which fails at reg-tests-1d.R; the failure being:
> 
>   ?? > ## str() now even works with invalid objects:
>   ?? > moS <- mo <- findMethods("isSymmetric")
>   ?? Error in findMethods("isSymmetric") :
>   ? ?? (converted from warning) non-generic function 'isSymmetric'
given
> to findMethods()
>   ?? Execution halted
Likely the problem is that you don't have the recommended packages 
loaded.  When I was running tests regularly, they were required.  Later, 
I think they became optional.  Perhaps a new test has been added that 
once again assumes the required packages are installed.

Duncan Murdoch
> 
> I am able to build revision 76407 from source just fine (using
>
https://cran.r-project.org/src/base-prerelease/R-devel_2019-04-20_r76407.tar.gz)
> and all make check tests are successful.
> 
> Any ideas? Here is my sessionInfo() from the revision 76407 build:
> 
>      R Under development (unstable) (2019-04-20 r76407)
>      Platform: x86_64-pc-linux-gnu (64-bit)
>      Running under: Ubuntu 18.04.2 LTS
> 
>      Matrix products: default
>      BLAS: /home/btyner/R-devel_2019-04-20_r76407/lib64/R/lib/libRblas.so
>      LAPACK:
/home/btyner/R-devel_2019-04-20_r76407/lib64/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] compiler_3.7.0
> 
> Regards,
> 
> Ben
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

Duncan that does indeed look to be the case. Many thanks!

In particular, tests/reg-tests-1d.R optionally loads the Matrix 
namespace which allows the test to succeed. Compare:

    ~/R-rc_2019-04-21_r76409/bin/Rscript -e "options(warn=2);
    library(Matrix); res <- findMethods('isSymmetric');
print('success')"
    [1] "success"

versus

    ~/R-rc_2019-04-21_r76409/bin/Rscript -e "options(warn=2); res <-
    findMethods('isSymmetric'); print('success')"
    Error in findMethods("isSymmetric") :
     ? (converted from warning) non-generic function 'isSymmetric' given
    to findMethods()
    Execution halted


On 4/21/19 7:47 PM, Duncan Murdoch wrote:
>
> Likely the problem is that you don't have the recommended packages 
> loaded.? When I was running tests regularly, they were required. 
> Later, I think they became optional.? Perhaps a new test has been 
> added that once again assumes the required packages are installed.
>
> Duncan Murdoch
>