[Bioc-devel] Package Installation Fails on Linux Kunpeng2 Due to ‘concaveman’ and ‘sf’ Dependencies

[Martin Grigorov]

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 <mgrigorov using 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_fu using 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 using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>

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