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

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

Benjamin Tyner
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

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

Duncan Murdoch-2
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
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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

Benjamin Tyner
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
>

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

Benjamin Tyner
Looks fixed as of revision 76417; thanks Brian!

On 4/21/19 9:02 PM, Benjamin Tyner wrote:

> 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
>>

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