[Rd] 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
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Re: [Rd] R-devel (rev 76409) fails 'make check': non-generic function 'isSymmetric' given to findMethods()
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
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Re: [Rd] R-devel (rev 76409) fails 'make check': non-generic function 'isSymmetric' given to findMethods()
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: [Rd] R CMD check does not report redundant '...' argument described in Rd File
Hi,
FWIW I also noticed this problem and reported it on R’s Bugzilla 4 years
ago:
https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16223
I actually had to report it twice because my first report
(https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16153) was closed
after a few days and tagged as NOT REPRODUCIBLE.
Cheers,
H.
On 4/16/19 23:42, Georgi Boshnakov wrote:
> R's checks seem to be failing to notice a redundant '...' argument described
> in the documentation of a function.
>
> Consider a function:
>
> fun_3 <- function(arg1, arg2, arg3) {
> "I am fun_3"
> }
>
> If its documentation describes an argument, say 'dummy', R check reports
> something like:
>
> * checking Rd \usage sections ... WARNING
> Documented arguments not in \usage in documentation object 'fun_3b':
>'dummy'
> ...
>
> But if the non-existent argument is '...' or '\dots' there is no warning. The
> omission seems specific to the 'dots' argument.
>
> Checked under Windows on win-builder on 17 April 2018 with
> R version 3.6.0 beta (2019-04-16 r76403), R version 3.5.3 (2019-03-11) and
> R version 3.4.4 (2018-03-15).
>
> A minimal package illustrating this is at
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GeoBosh_reprexes_tree_master_redundantDots&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=i9g7pqJ1WilGjLfFwtSiajoznNNRWj8CWL0sdNSLKFM&s=8pmMlfLXNctV2CZNAADigKW4C_ZU5phJ5J3EhY7gq7U&e=
>
>
> Georgi Boshnakov
>
> __
> R-devel@r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Ddevel&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=i9g7pqJ1WilGjLfFwtSiajoznNNRWj8CWL0sdNSLKFM&s=VepWHiukhgfnvGnmA3S-5XhITPslNPVKxWwlBeazkEY&e=
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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