Thanks Mike and Hervé!
Somehow, errors in examples that are caused by the state (or absence) of
things on the internet should have a different status in my view than
ones that reflect local state of R and packages - and distinguishing
this could make maintenance of the package corpus & builds
Hi Wolfgang, Mike,
We didn't have a successful build of GenomicFeatures in devel
for many days because of all kinds of problems with the examples
that try to access the Ensembl marts. The latest of which being:
https://support.bioconductor.org/p/105565/
(which also affects GenomicFeatures in
It is important but not completely clear how to address.
I think it has been written that bioc package checking should make minimal
use of the internet, and most
checking concerning manipulation of net-derived objects should use "mocks".
One possible approach is to test with calls to the
Dear Lori,
I have an issue accessing my package called ‘Pi’.
Following the instruction detailed at
http://bioconductor.org/developers/how-to/git/maintain-bioc-only/, I have
submit my SSH public key (shown in red):
$ cat ~/.ssh/id_dsa.pub
ssh-dss
The error TxDbFromBiomart looks like it might be related to a biomaRt
change I made recently to submit queries using httr rather than RCurl.
Others have reported something similar (e.g
https://support.bioconductor.org/p/104502/) and I raised the timeout from
10 to 60 seconds. I guess with the old
Thanks Hervé!
This seems to take a long time to propagate. As of now,
https://bioconductor.org/packages/devel/bioc/html/GenomicFeatures.html
still shows 1.31.3.
( Btw, there's also an error in the build report which seems to come
from a rather excessive-looking example in the