From gmbecker at ucdavis.edu  Thu Jul  6 23:26:39 2017
From: gmbecker at ucdavis.edu (Gabriel Becker)
Date: Thu, 6 Jul 2017 14:26:39 -0700
Subject: [Rd] make check-recommended hanging on up-to-date Rdevel from SVN
Message-ID: <CADwqtCM4Nse-nUrHnaxACa9CYBHg4iq4yMLQT89tSnnBH3mNQQ@mail.gmail.com>

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

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