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bio-arm / bio-arm.github.io

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Provide gdal-devel #8

Closed martin-g closed 1 year ago

martin-g commented 1 year ago

openEuler OS does not provide gdal-devel package. It is needed by Bioconductor apt-cran.txt - https://github.com/Bioconductor/BBS/blob/f87de6f9b752c653e2b52914635cca4c4deb78c9/Ubuntu-files/22.04/apt_cran.txt#L19

Currently we build it from source but it is slow to build and Github Actions often times out during the execution of setup-gdal.sh. It would be good to create a .rpm for it soon!

Yikun commented 1 year ago

Please address this issue with high priority: @XingYuuuuu

Yikun commented 1 year ago

https://src.fedoraproject.org/rpms/gdal and https://github.com/bio-arm/dockerfiles/blob/main/scripts/setup-gdal.sh might a good reference

martin-g commented 1 year ago

The Github Actions workflow often fails during the build of GDAL with errors like:

But you can build the Docker image locally as a workaround: docker build -t bioc-oe .

Yikun commented 1 year ago

@martin-g Could you also push the image to ghcr or dockerhub, this might also help!

martin-g commented 1 year ago

There is some problem with the aarch64 version of docker.io/openeuler/openeuler:22.03-lts-sp1 I can't use sudo in it. First it failed with Permissions denied because its permissions were ---s--x--x instead of -rwsr-xr-x. I manually set the correct ones but now it fails with sudo: effective uid is not 0, is /usr/bin/sudo on a file system with the 'nosuid' option set or an NFS file system without root privileges? It seems I will need to push an x86_64 from my dev machine and an aarch64 from a VM ...

Yikun commented 1 year ago

Is the x86 version of docker.io/openeuler/openeuler:22.03-lts-sp1 ok?

martin-g commented 1 year ago

Yes, it seems so! I was able to upload a x86_64 image at https://github.com/users/martin-g/packages/container/package/bioc-openeuler-22.03 But the build on my ARM64 VM failed with other kind of problems... I will investigate it now!

martin-g commented 1 year ago

gdal rpm is available at https://eur.openeuler.openatom.cn/coprs/yikun/bioconductor/

martin-g commented 1 year ago

The latest Github CI build passed in building the packages which still don't have rpms but failed with no space left on device: https://github.com/bio-arm/dockerfiles/actions/runs/5376109096/jobs/9752817614