[R-sig-Debian] Segfault on ubuntu 18.04

[Göran Broström]

On 2018-07-07 17:13, George N. White III wrote:
> On Sat, 7 Jul 2018 at 07:52, Göran Broström <goran.brostrom using umu.se 
> <mailto:goran.brostrom using umu.se>> wrote:
> 
> 
> 
>     On 2018-07-07 06:27, Dirk Eddelbuettel wrote:
>      >
>      > On 7 July 2018 at 00:51, Göran Broström wrote:
>      > | My repo is
>      > |
>      > | deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/
>      > |
>      > | Is that wrong?
>      >
>      > That repo will give you R and key R packages like Matrix lme4. 
>     (And you
>      > chose to ignore this repo by compiling R yourself ...).
> 
>     Not really: I installed r-base and r-base-dev from "My repo", but
>     ignored
> 
>     deb http://ppa.launchpad.net/marutter/c2d4u3.5/ubuntu bionic main
>     # deb-src http://ppa.launchpad.net/marutter/c2d4u3.5/ubuntu bionic main
> 
>     because I thought it was easier to handle the rest via
>     install.packages()
> 
> 
> There can be benefits to using "install.packages()" when distro packages
> for supporting libraries can't be used (too old or built without some needed
> configuration option for some other software you need).
> 
> 
>     I was wrong. After reinstalling all extra packages via apt and
>     "c2d4u3.5", all my problems have vanished (or been swept under the
>     carpet;), no segfaults. Many thanks!
> 
> 
> This issue caught my interest because I often have to deal with conflicts
> encountered by people using multiple "big" packages that rely on upstream
> libraries such as libcurl, gdal, hdfN, netcdf, etc. with R and other 
> "mission
> critical" apps supplied by ESA and NASA.   Ubuntu 18.04 has been
> problematic, so I tried to reproduce your problem (using the WSL version of
> Ubuntu 18.04) and failed to see the problem.
> 
> I installed the R curl package from source using the base packages from:
> 
>     debhttps://cloud.r-project.org/bin/linux/ubuntubionic-cran35/ 
> 
> 
> and didn't get segfaults (eha even installed without issues).
> Göran -- I'm glad you have been able to get R working, but it could be
> useful to understand what was broken.  The original missing symbol error
> was for something that should have been defined in the header
> files from the libcurl dev package.   Is there anything non-standard about
> your libcurl and the associated header files?
> 
>     [...]

I think that my problems started when I moved ...eha/src/Makevars, 
containing

PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

to ~/.R/Makevars

following the previous discussion here. This worked well for building 
and installing eha, but not for other builds from source, particularly 
R  itself. So I decided to keep Makevars (with that single line) in 
eha/src, and simply ignore the warnings about nonstandard CFLAGS when 
checking the build. I can live with those. Everything else seems to be 
OK now.

Göran

> -- 
> George N. White III
>