Hi Koen,
It seems you have not followed the support documentation to sync the Github and Bioconductor repositories first.
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
If you follow the steps, you?d get this.
/tmp ??? git clone https://github.com/statOmics/stageR
Cloning into 'stageR'...
remote: Counting objects: 783, done.
remote: Compressing objects: 100% (94/94), done.
remote: Total 783 (delta 88), reused 86 (delta 44), pack-reused 645
Receiving objects: 100% (783/783), 1.15 MiB | 204.00 KiB/s, done.
Resolving deltas: 100% (498/498), done.
/tmp ??? cd stageR
1 DESCRIPTION +
/t/stageR ??? git remote add upstream git at git.bioconductor.org:packages/stageR
/t/stageR ??? git fetch --all
Fetching origin
Fetching upstream
remote: Counting objects: 5, done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 5 (delta 3), reused 0 (delta 0)
Unpacking objects: 100% (5/5), done.