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
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
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
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