make check-recommended hanging on up-to-date Rdevel from SVN

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make check-recommended hanging on up-to-date Rdevel from SVN

Gabriel Becker
Hi all,

I'm getting an issue with Rdevel where make check-recommended hangs
consistently for me on Mac El Capitan when checking the Matrix package. I
did svn update and tools/rsync_recommended earlier today and it didn't fix
the issue.

Specifically, it is hanging on the

* checking dependencies in R code ...


stage (while checking Matrix, it passes fine for MASS and lattice).
Currently I'm getting the same behavior when I do

tools:::.check_packages("<builddir>/tests/RecPackages/Matrix")


Is this a known issue and if not, do other people see this behavior?

Best,
~G


Various info:

Build script:

#!/bin/bash

export CC="gcc -std=gnu99 -fsanitize=address"
# make -O0 if we want full debugging symbols
export CFLAGS="-fno-omit-frame-pointer -g -O2 -Wall -pedantic -mtune=native"
#export CFLAGS="-fno-omit-frame-pointer -g -O0 -Wall -pedantic
-mtune=native"

export CXX="g++ -fsanitize=address -fno-omit-frame-pointer"
export F77="gfortran -arch x86_64"
export FC="gfortran -arch x86_64"
export MAIN_LDFLAGS=" -fsanitize=address"

../checkedout/Rsource/rawtrunk/configure
--prefix=/Users/beckerg4/local/Rdevel --enable-R-framework
--enable-memory-profiling
make -j3
make install

Svn Info:

beckerg4-T4G3QN:rawtrunk beckerg4$ *svn info*

Path: .

Working Copy Root Path: /Users/beckerg4/gabe/checkedout/Rsource/rawtrunk

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: 72894

Node Kind: directory

Schedule: normal

Last Changed Author: lawrence

Last Changed Rev: 72894

Last Changed Date: 2017-07-06 00:12:06 -0700 (Thu, 06 Jul 2017)



Svn status (no local changes)

beckerg4-T4G3QN:rawtrunk beckerg4$* svn status*

beckerg4-T4G3QN:rawtrunk beckerg4$


Session info after Matrix is attached:

*> library(Matrix)*

*> sessionInfo()*

R Under development (unstable) (2017-07-06 r72894)

Platform: x86_64-apple-darwin15.6.0 (64-bit)

Running under: OS X El Capitan 10.11.6


Matrix products: default

BLAS: /Users/beckerg4/gabe/Rdevelbuild/lib/libRblas.dylib

LAPACK: /Users/beckerg4/gabe/Rdevelbuild/lib/libRlapack.dylib


locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8


attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base


other attached packages:

[1] Matrix_1.2-10


loaded via a namespace (and not attached):

[1] compiler_3.5.0  grid_3.5.0      lattice_0.20-35



--
Gabriel Becker, PhD
Associate Scientist (Bioinformatics)
Genentech Research

        [[alternative HTML version deleted]]

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Re: make check-recommended hanging on up-to-date Rdevel from SVN

Peter Dalgaard-2

> On 6 Jul 2017, at 23:26 , Gabriel Becker <[hidden email]> wrote:
>
> Hi all,
>
> I'm getting an issue with Rdevel where make check-recommended hangs
> consistently for me on Mac El Capitan when checking the Matrix package. I
> did svn update and tools/rsync_recommended earlier today and it didn't fix
> the issue.
>
> Specifically, it is hanging on the
>
> * checking dependencies in R code ...

Not happening for me on Sierra, it seems. However, I have a minimal source install of R-devel, so that

* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘expm’

Packages which this enhances but not available for checking:
  ‘MatrixModels’ ‘graph’ ‘SparseM’ ‘sfsmisc’

... and it is thinkable that the issue is with one of those(?)

-pd

>
>
> stage (while checking Matrix, it passes fine for MASS and lattice).
> Currently I'm getting the same behavior when I do
>
> tools:::.check_packages("<builddir>/tests/RecPackages/Matrix")
>
>
> Is this a known issue and if not, do other people see this behavior?
>
> Best,
> ~G
>
>
> Various info:
>
> Build script:
>
> #!/bin/bash
>
> export CC="gcc -std=gnu99 -fsanitize=address"
> # make -O0 if we want full debugging symbols
> export CFLAGS="-fno-omit-frame-pointer -g -O2 -Wall -pedantic -mtune=native"
> #export CFLAGS="-fno-omit-frame-pointer -g -O0 -Wall -pedantic
> -mtune=native"
>
> export CXX="g++ -fsanitize=address -fno-omit-frame-pointer"
> export F77="gfortran -arch x86_64"
> export FC="gfortran -arch x86_64"
> export MAIN_LDFLAGS=" -fsanitize=address"
>
> ../checkedout/Rsource/rawtrunk/configure
> --prefix=/Users/beckerg4/local/Rdevel --enable-R-framework
> --enable-memory-profiling
> make -j3
> make install
>
> Svn Info:
>
> beckerg4-T4G3QN:rawtrunk beckerg4$ *svn info*
>
> Path: .
>
> Working Copy Root Path: /Users/beckerg4/gabe/checkedout/Rsource/rawtrunk
>
> 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: 72894
>
> Node Kind: directory
>
> Schedule: normal
>
> Last Changed Author: lawrence
>
> Last Changed Rev: 72894
>
> Last Changed Date: 2017-07-06 00:12:06 -0700 (Thu, 06 Jul 2017)
>
>
>
> Svn status (no local changes)
>
> beckerg4-T4G3QN:rawtrunk beckerg4$* svn status*
>
> beckerg4-T4G3QN:rawtrunk beckerg4$
>
>
> Session info after Matrix is attached:
>
> *> library(Matrix)*
>
> *> sessionInfo()*
>
> R Under development (unstable) (2017-07-06 r72894)
>
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>
> Running under: OS X El Capitan 10.11.6
>
>
> Matrix products: default
>
> BLAS: /Users/beckerg4/gabe/Rdevelbuild/lib/libRblas.dylib
>
> LAPACK: /Users/beckerg4/gabe/Rdevelbuild/lib/libRlapack.dylib
>
>
> locale:
>
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
> other attached packages:
>
> [1] Matrix_1.2-10
>
>
> loaded via a namespace (and not attached):
>
> [1] compiler_3.5.0  grid_3.5.0      lattice_0.20-35
>
>
>
> --
> Gabriel Becker, PhD
> Associate Scientist (Bioinformatics)
> Genentech Research
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] 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: [hidden email]  Priv: [hidden email]

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