biocbuild@kunpeng2 ~/g/CARDspa (devel)> R CMD build . * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘CARDspa’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added * building ‘CARDspa_0.99.7.tar.gz’
The next build should be fine! On Thu, Mar 27, 2025 at 9:44 AM Martin Grigorov <mgrigo...@apache.org> wrote: > I found a workaround! > > 1) I copied pcs.csv from gdal-2.4.4 ( > https://anaconda.org/conda-forge/gdal/files?page=464) > 2) https://github.com/conda-forge/pyproj-feedstock/issues/130 explained > the problem with PROJ - I had to manually export > PROJ_LIB=/home/biocbuild/bioconductor/gdal/.pixi/envs/default/share/proj > > The 'sf' build is still running! > > On Thu, Mar 27, 2025 at 9:27 AM Martin Grigorov <mgrigo...@apache.org> > wrote: > >> 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
