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
>>>
>>
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