On 2018-07-07 17:13, George N. White III wrote:
On Sat, 7 Jul 2018 at 07:52, Göran Broström <goran.brost...@umu.se
<mailto:goran.brost...@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
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