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

[Martin Grigorov]

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
>
>
>
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>
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