On 2018-07-07 06:27, Dirk Eddelbuettel wrote:> > On 7 July 2018 at 00:51, G?ran Brostr?m 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() 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! G?ran> > Additional package repos then build on top of this one and give you several > _thousand_ r-cran-* binary packages prebuilt. > > Dirk >
On Sat, 7 Jul 2018 at 07:52, G?ran Brostr?m <goran.brostrom at umu.se> wrote:> > > On 2018-07-07 06:27, Dirk Eddelbuettel wrote: > > > > On 7 July 2018 at 00:51, G?ran Brostr?m 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: deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ and didn't get segfaults (eha even installed without issues). G?ran -- 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?> [...] >-- George N. White III [[alternative HTML version deleted]]
On 2018-07-07 17:13, George N. White III wrote:> On Sat, 7 Jul 2018 at 07:52, G?ran Brostr?m <goran.brostrom at umu.se > <mailto:goran.brostrom at umu.se>> wrote: > > > > On 2018-07-07 06:27, Dirk Eddelbuettel wrote: > > > > On 7 July 2018 at 00:51, G?ran Brostr?m 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). > G?ran?-- 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. G?ran> -- > George N. White III >