Looking further up the list of error messages, there is a long dependency chain ending with a missing system dependency (see below): * anamiR -> agricolae -> spdep -> sf -> system dependency libgdal-dev
You should be able to fix it with `apt install libgdal-dev` if you're on Debian/Ubuntu. BTW, I figured this out on a Docker+Singularity container and scripts I've been working on to try to make almost all of Bioconductor installable, to make it easier to run release+devel side by side, and to smooth the edges for people who don't feel like learning the million flags Docker has or where their package and home directories go every time they restart :). I'll add libgal-dev. It's early but see https://github.com/waldronlab/bioconductor_devel if you want to try, and I really welcome feedback on documentation or functionality. Dependency error chain: * installing *source* package ‘sf’ ... ** package ‘sf’ successfully unpacked and MD5 sums checked configure: CC: gcc configure: CXX: g++ -std=gnu++11 *checking for gdal-config... no* *no* *configure: error: gdal-config not found or not executable.* *ERROR: configuration failed for package ‘sf’* * removing ‘/usr/local/lib/R/host-site-library/sf’ * installing *source* package ‘minfi’ ... ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (minfi) * installing *source* package ‘klaR’ ... ** package ‘klaR’ successfully unpacked and MD5 sums checked ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (klaR) *ERROR: dependency ‘sf’ is not available for package ‘spdep’* ** removing ‘/usr/local/lib/R/host-site-library/spdep’* * installing *source* package ‘methylumi’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (methylumi) *ERROR: dependency ‘spdep’ is not available for package ‘agricolae’* * removing ‘/usr/local/lib/R/host-site-library/agricolae’ * installing *source* package ‘lumi’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (lumi) ERROR: dependency ‘agricolae’ is not available for package ‘anamiR’ * removing ‘/usr/local/lib/R/host-site-library/anamiR’ The downloaded source packages are in ‘/tmp/RtmpOjPTFv/downloaded_packages’ Warning messages: 1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : installation of package ‘sf’ had non-zero exit status 2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : installation of package ‘spdep’ had non-zero exit status 3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : installation of package ‘agricolae’ had non-zero exit status 4: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : installation of package ‘anamiR’ had non-zero exit status > * On Thu, Feb 21, 2019 at 11:00 PM Dario Strbenac <dstr7...@uni.sydney.edu.au> wrote: > Good day, > > I don't, but your software package imports agricolae which imports spdep. > spdep is available from CRAN, so it's strange that the Bioconductor build > server running Linux has not been able to install it. > > -------------------------------------- > Dario Strbenac > University of Sydney > Camperdown NSW 2050 > Australia > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Levi Waldron http://www.waldronlab.io Associate Professor of Biostatistics CUNY School of Public Health US: +1 646-364-9616 Skype: levi.waldron [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
