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

[peter dalgaard]

> On 6 Jul 2017, at 23:26 , Gabriel Becker <gmbecker at ucdavis.edu> 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]]
> 
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-- 
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