Using libgdal-core 3.x fails with: > BiocManager::install(c("sf")) Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable) (2025-02-19 r87757) Installing package(s) 'sf' trying URL 'https://cloud.r-project.org/src/contrib/sf_1.0-20.tar.gz' Content type 'application/x-gzip' length 4492197 bytes (4.3 MB) ================================================== downloaded 4.3 MB
* installing *source* package ‘sf’ ... ** this is package ‘sf’ version ‘1.0-20’ ** package ‘sf’ successfully unpacked and MD5 sums checked ** using staged installation configure: CC: /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 configure: CXX: /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 checking for gdal-config... /home/biocbuild/bioconductor/gdal/.pixi/envs/default/bin/gdal-config checking gdal-config usability... yes configure: GDAL: 3.10.2 checking GDAL version >= 2.0.1... yes checking for gcc... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 accepts -g... yes checking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 option to enable C11 features... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for gdal.h... yes checking GDAL: linking with --libs only... yes checking GDAL: /home/biocbuild/bioconductor/gdal/.pixi/envs/default/share/gdal/pcs.csv readable... no checking GDAL: checking whether PROJ is available for linking:... yes checking GDAL: checking whether PROJ is available for running:... ERROR 1: PROJ: proj_create_from_database: Open of /home/biocbuild/bioconductor/gdal/.pixi/envs/default/share/proj failed ERROR 1: PROJ: proj_create_from_database: Open of /home/biocbuild/bioconductor/gdal/.pixi/envs/default/share/proj failed ERROR 1: PROJ: proj_create: unrecognized format / unknown name ERROR 1: PROJ: proj_create: unrecognized format / unknown name no configure: error: OGRCoordinateTransformation() does not return a coord.trans: PROJ not available? ERROR: configuration failed for package ‘sf’ * removing ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/sf’ gdal 2.x does not provide linux-aarch64 builds, so i cannot try it :-/ Any ideas are welcome ! On Thu, Mar 27, 2025 at 8:52 AM Martin Grigorov <mgrigo...@apache.org> wrote: > Hi, > > The problem is a transitive dependency: > > * installing *source* package ‘sf’ ... > ** this is package ‘sf’ version ‘1.0-20’ > ** package ‘sf’ successfully unpacked and MD5 sums checked > ** using staged installation > configure: CC: > /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc > -std=gnu23 > configure: CXX: > /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ > -std=gnu++17 > checking for gdal-config... no > no > configure: error: gdal-config not found or not executable. > *** Installing this package from source requires the prior > *** installation of external software, see for details > *** https://r-spatial.github.io/sf/#installing > ERROR: configuration failed for package ‘sf’ > * removing ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/sf’ > > There is no such package in the OS repository. > I have tried to install it from conda-forge ( > https://anaconda.org/conda-forge/libgdal-core/files) but it leads to > clashes due to its transitive dependencies ... I will try again ! > > > On Wed, Mar 26, 2025 at 11:37 PM Jing Fu <jing...@brown.edu> wrote: > >> Dear Bioconductor Team, >> >> I am the developer of the package CARDspa, which was recently submitted >> to Bioconductor. While checking the package on the Linux Kunpeng2 platform, >> the build fails with the following error: >> >> ERROR: dependencies ‘concaveman’, ‘sf’ are not available for package >> ‘CARDspa’ >> Perhaps try a variation of: >> install.packages(c('concaveman', 'sf')) >> >> These two packages are listed under Imports in my DESCRIPTION file. I >> understand that both packages rely on system-level libraries or are not yet >> available for ARM-based architectures like Kunpeng2. Is there a preferred >> way to handle such dependencies for ARM platforms? >> >> I look forward to your suggestions. >> >> Best, >> Jing >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel