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
This is done in GenomicFeatures 1.31.6.
Note that I also made a few changes to makeTxDbFromUCSC() to make it
a little bit faster (about 2x).
@Kasper: moving the makeTxDb* functions to a GenomicFeaturesBuildTools
or GenomicFeaturesForge package is maybe an idea to explore...
H.
On 01/26/2018
26.1.18 14:59, Martin Morgan scripsit:
On 01/24/2018 03:38 PM, Wolfgang Huber wrote:
GenomicFeatures_1.31.3 imports RMySQL.
I'm having great trouble installing RMySQL from source on a recent
MacOS (10.13.3) with homebrew.
The package's homepage says "The 'RMySQL' package contains an old
Yep, moving RMySQL to Suggests makes sense. Will do. Also migrating to
RMariaDB is on the TODO list.
Note that the current problem of RMySQL being hard to install on Mac is
only because CRAN doesn't provide an RMySQL binary for R 3.5 yet:
Moving it to Suggests: would certainly ease installation on clusters and
such.
--t
On Fri, Jan 26, 2018 at 8:59 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:
> On 01/24/2018 03:38 PM, Wolfgang Huber wrote:
>
>> GenomicFeatures_1.31.3 imports RMySQL.
>>
>> I'm having great trouble
On Fri, Jan 26, 2018 at 8:59 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:
> On 01/24/2018 03:38 PM, Wolfgang Huber wrote:
>
>> GenomicFeatures_1.31.3 imports RMySQL.
>>
>> I'm having great trouble installing RMySQL from source on a recent MacOS
>> (10.13.3) with homebrew.
>>
>> The
On 01/24/2018 03:38 PM, Wolfgang Huber wrote:
GenomicFeatures_1.31.3 imports RMySQL.
I'm having great trouble installing RMySQL from source on a recent MacOS
(10.13.3) with homebrew.
The package's homepage says "The 'RMySQL' package contains an old
implementation based on legacy code from
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