Hi Sam,
I have updated your “master” branch on git.bioconductor.com to reflect what you
have on GitHub, at https://github.com/rafalab/bumphunter. You will not get the
duplicate commit error when you push to the master branch anymore.
However, RELEASE_3_8 still has duplicate commits in the his
Hi Bioconductor,
I received a notification email regarding the building error for our
package 'singscore'.
I pull the RELEASE_3_8 branch and checked/built on my local machine, it was
successful without errors.
The error message was within the vignette which hasn't been updated for
several months
Thanks Val. Indeed, the release version built yesterday, but there still
hasn't been a build on devel since Thursday.
On Sat, Nov 3, 2018 at 10:12 PM Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:
> Hi Levi,
>
> We've had one experimental data build since the release, posted on No
The Bioconductor Team is continuing to identify packages that will be
deprecated in the next release to allow for the Bioconductor community to
respond accordingly. The list will be updated monthly.
The current list of deprecated packages for Bioc 3.9 is as follows:
Maintainer requested depreca
Hi Ruqian,
I think this is a consequence of your internal data.frames have column
names that include the minus sign i.e. "-". The code clearly tries to deal
with this by wrapping them in back-ticks at certain points, but I think it
doesn't do this successfully in projectScoreLandscape()
First, c
Hi Nitesh,
I have fixed the commit history for rafalab/bumphunter RELEASE_3_8
branch, and request synchronization with Bioconductor RELEASE_3_8. We
need this, because bumphunter is not building on RELEASE_3_8, due to an
obsolete URL in one of the tests.
thanks,
- Sam
On 11/5/18 7:56 AM, T
Hi Sam,
I fixed the RELEASE_3_8 branch as well. There was a minor discrepancy in the
commit history for RELEASE_3_8 though, (which I fixed in
git.bioconductor.org/packages/bumphunter) so you should resync RELEASE_3_8 in
rafalab/bumphunter.
The commit history on rafalab/bumphunter:RELEASE_3_8
Further to this it is helpful to ensure that you are using the correct version
of Bioconductor and that your packages are up-to-date
BiocManager::version() == "3.8"
BiocManager::valid()
Martin
On 11/5/18, 12:11 PM, "Bioc-devel on behalf of Mike Smith"
wrote:
Hi Ruqian,
I th
Hi bioc-devel,
recount is getting a warning on Bioc 3.9 (devel) on macOS:
* checking whether package ‘recount’ can be installed ... WARNING
Found the following significant warnings:
Warning: S3 method ‘xts::as.xts.data.table’ was declared in
NAMESPACE but not found
I'm not sure how to trace th
This is a continuation of the discussion at
https://support.bioconductor.org/p/114814/#114824
Where Wolfgang asks about "creating a corner in the Bioconductor package
ecosystem for packages that are only ever supposed to build and check with a
single release"
I think this would be quite chall
Thanks for fixing this Nitesh and Sam!
I wrote that R check and forgot that it depended on the Gencode url. I
had to fix this too for recount
https://github.com/leekgroup/recount/commit/056e81c326143e3748b452988ac15a6bed3b035e.
Best,
Leo
On Mon, Nov 5, 2018 at 3:14 PM Turaga, Nitesh
wrote:
>
>
On 11/5/18, 5:11 PM, "Bioc-devel on behalf of Leonardo Collado Torres"
wrote:
Hi bioc-devel,
recount is getting a warning on Bioc 3.9 (devel) on macOS:
* checking whether package ‘recount’ can be installed ... WARNING
Found the following significant warnings:
W
For the general problem of understanding your package dependency structure,
see http://bioconductor.org/packages/release/bioc/html/pkgDepTools.html.
On Mon, Nov 5, 2018 at 3:44 PM Martin Morgan
wrote:
>
>
> On 11/5/18, 5:11 PM, "Bioc-devel on behalf of Leonardo Collado Torres" <
> bioc-devel-bo
That's interesting, thank you for testing it. :)
Regards,
Ruqian
On Tue, Nov 6, 2018 at 5:01 AM Martin Morgan
wrote:
> Further to this it is helpful to ensure that you are using the correct
> version of Bioconductor and that your packages are up-to-date
>
> BiocManager::version() == "3.8"
>
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