Hi guys,
the problem was that `rgdal` was installed using its binary - which causes
problems due to a wrong link to `libgdal.dylib`. When testing on OSX on travis
and using `sudo: required`, all dependencies are installed using binaries (see
https://docs.travis-ci.com/user/languages/r/).
My workaround was to reinstall `rgdal` after installation of all dependencies
using `R -e "install.packages('rgdal', type = 'source’)”`.
I also opened an issue on travis-ci on how to deal with that specific rgdal
issue in the future: https://github.com/travis-ci/travis-ci/issues/7675
Thanks again to Jonathan Love for tracking down the issue. Very much
appreciated!
Cheers, Patrick
PhD Student at Department of Geography - GIScience group
Friedrich-Schiller-University Jena, Germany
Tel.: +49-3641-9-48973
Web: https://pat-s.github.io
On 29. Apr 2017, 15:34 +0200, Patrick Schratz <patrick.schr...@gmail.com>,
wrote:
> Hi guys,
>
> @ Alexandre
> Thanks for suggesting to compile from source. I normally try to use this as
> the last option because this will usually take a while for gdal. However, it
> may install to other locations as the brew installation does so I just tried
> it and faced some permission problems during copying:
>
> /Users/travis/build/jannes-m/RQGIS/gdal-2.1.3/install-sh -c
> /Users/travis/build/jannes-m/RQGIS/gdal-2.1.3/libgdal.dylib
> /usr/lib/libgdal.dylib.2.1.3
> cp: /usr/lib/#inst.15842#: Operation not permitted
> make: *** [install-lib] Error 1
>
> Log: https://travis-ci.org/jannes-m/RQGIS/jobs/227128054
>
> I am somewhat hesitate to “go back” and solve this gdal2 installation/make
> issue when I already have a working gdal2 installation via homebrew which
> “just” seems to miss some correct linking to libgdal.dylib.
> On Linux I use the ubuntugis PPA to install gdal 2.1.0 which is way faster
> than compiling from source (I did that in the past). So maybe this would be
> even an option for you to speed up your travis builds?
> Thanks for your reply, much appreciated!
>
> @ Jonathan
> A walk through of your suggested option would be awesome! We could do so in
> our Slack group if this is better suited than mailing for this case? Just
> write me whatever you prefer.
>
> Cheers, Patrick
>
>
> PhD Student at Department of Geography - GIScience group
> Friedrich-Schiller-University Jena, Germany
> Tel.: +49-3641-9-48973
> Web: https://pat-s.github.io
>
> On 29. Apr 2017, 15:22 +0200, Jonathon Love <j...@thon.cc>, wrote:
> > hi,
> >
> > On 29/4/17 21:29, Patrick Schratz wrote:
> > > Nope, still an open issue. I also do not have any ideas left what I could
> > > try next.
> > >
> > > Tried the export hints (e.g. bash profile) given in 'brew info gdal2' and
> > > checked with my local configuration but I do not see what the possible
> > > issue could be here.
> > >
> > > On 29. Apr 2017, 13:24 +0200, Alexandre Courtiol
> > > <alexandre.court...@gmail.com>, wrote:
> > > > Did you already sort out your issue?
> > > >
> > > > On 28 April 2017 at 17:19, Patrick Schratz <patrick.schr...@gmail.com
> > > > (mailto:patrick.schr...@gmail.com)> wrote:
> > > > > Hi everyone,
> > > > >
> > > > > the following error gives me headaches. When building my package on
> > > > > Travis CI (OS X build), I get the following error:
> > > > >
> > > > > Building with: R CMD build
> > > > > 4.64s$ R CMD build .
> > > > > * checking for file ‘./DESCRIPTION’ ... OK
> > > > > * preparing ‘RQGIS’:
> > > > > * checking DESCRIPTION meta-information ... OK
> > > > > * installing the package to build vignettes
> > > > > -----------------------------------
> > > > > * installing *source* package ‘RQGIS’ ...
> > > > > ** R
> > > > > ** data
> > > > > *** moving datasets to lazyload DB
> > > > > ** inst
> > > > > ** byte-compile and prepare package for lazy loading
> > > > > Error in dyn.load(file, DLLpath = DLLpath, ...) :
> > > > > unable to load shared object
> > > > > '/Users/travis/R/Library/rgdal/libs/rgdal.so':
> > > > > dlopen(/Users/travis/R/Library/rgdal/libs/rgdal.so, 6): Library not
> > > > > loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
> > > > > Referenced from: /Users/travis/R/Library/rgdal/libs/rgdal.so
> > > > > Reason: image not found
> >
> > it looks to me that rgdal.so is looking for libgdal.dylib in
> > /Builds/unix/recipes/build/build/gdal02.1.3-obj
> >
> > you can confirm this with the command:
> >
> > otool -L /Users/travis/R/Library/rgdal/libs/rgdal.so
> >
> > it will list where it's expecting to find libgdal.dylib
> >
> > my guess is that the root of the issue is that the libgdal.dylib that
> > rgdal.so linked against, thinks that it lives at
> > /Builds/unix/recipes/build/build/gdal02.1.3-obj
> >
> > you can confirm this with:
> >
> > otool -L /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
> >
> > you can change where .so's and .dylibs think they live, and where they
> > think their dependencies live with the install_name_tool tool.
> >
> > i can walk you through this off-list if you need.
> >
> > cheers
> >
> > jonathon
> >
> > ______________________________________________
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
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