cted the issue but if you still do not see the package
> propagating next week please reach back out.
>
>
> Lori Shepherd
> Bioconductor Core Team
> Roswell Park Cancer Institute
> Department of Biostatistics & Bioinformatics
> Elm & Carlton Streets
> Buffalo, New
Dear Bioc-Team,
it seem like our MyEndToEnd workflow has somehow
been dropped from the build system, the last build is
from Aug 8th:
http://bioconductor.org/checkResults/3.8/workflows-LATEST/maEndToEnd/
at version 1.99.1
However, the current version is 1.99.4, the last commit is
135704a by L
Dear all,
we recently observed a similar behavior due to a bug
in the remotes package which has been fixed in the github
version of the package:
https://github.com/r-lib/remotes/commit/d3a6766c0bcb456b82a0b06608f6149
fe4f5d83e
essentially, internally, somewhere, it would do something like:
Cheers,
>
> Lori Shepherd
> Bioconductor Core Team
> Roswell Park Cancer Institute
> Department of Biostatistics & Bioinformatics
> Elm & Carlton Streets
> Buffalo, New York 14263
> From: Bernd Klaus
> Sent: Tuesday, June 5, 2018 2:53:41 AM
> To: Shepherd, Lori; bioc-deve
gleCell.
html
?
Thanks and best wishes,
Bernd
On Do, 2018-05-03 at 18:41 +0200, Bernd Klaus wrote:
> Hello Lori,
>
> thanks a lot for your prompt and your constructive feedback!
>
> We will revise the workflow accordingly and then submit it
> to the submission tracker.
>
>
could reproduce your
> work.
>
> We look forward to getting this workflow active again and on the
> builder.
>
> Cheers,
>
> Lori Shepherd
> Bioconductor Core Team
> Roswell Park Cancer Institute
> Department of Biostatistics & Bioinformatics
> Elm & Carl
Dear Bioc Team,
I submitted a Microarray workflow some time ago (using SVN / Jenkins)
to Bioconductor, but I never published it at the (now retired) workflow
page.
Upon a recent request by the Bioc Team, I changed into a package, which
is now at:
packages/maEndToEnd
on the Bioconductor git s
t;
> http://docbuilder.bioconductor.org:8080/job/maEndToEnd/8/
>
> Dan
>
>
> - Original Message -
> > From: "Bernd Klaus"
> > To: "bioc-devel"
> > Sent: Monday, May 23, 2016 3:33:24 AM
> > Subject: [Bioc-devel] workflow builds on
Dear all,
I recently took up developing a workflow again (matEndToEnd).
http://docbuilder.bioconductor.org:8080/job/maEndToEnd/
While it builds fine on windows (winbuilder1) I get error message on
linux (master) and mac (vagrantmac) that I cannot really trace down.
1.) On vagrantmac, it gives
Hi Stefano,
developers are not supposed to change the package fundamentally in the
release branch, however small fixes are allowed to be back-ported and
marked by a bump of the last digit:
http://bioconductor.org/developers/how-to/version-numbering/
(E.g. fixing typos in the vignette or updating
lot again for your help and input!
Bernd
On Mo, 2015-12-07 at 11:00 +0100, Bernd Klaus wrote:
> Hi Dan,
>
> wow, thanks a lot for identifying the problem! This is great
> and gives me a hint on what to look into.
>
> Thanks again,
>
> Bernd
>
> On Fr, 2015-12-04
Hi Dan,
wow, thanks a lot for identifying the problem! This is great
and gives me a hint on what to look into.
Thanks again,
Bernd
On Fr, 2015-12-04 at 10:55 -0800, Dan Tenenbaum wrote:
>
> - Original Message -
> > From: "Bernd Klaus"
> > To: &quo
Dear all,
I am currently developing an end-to-end workflow for Microarray
analysis.
In this workflow I download some clinical microarray
data from arrayExpress (CEL files),
import it with oligo, annotate it using the
appropriate ChipDB and then obtain
results with limma. This gives me a data.f
mns
> Quitting from lines 229-264 (dummy-Workflow.Rmd)
> Error: processing vignette 'dummy-Workflow.Rmd' failed with
> diagnostics:
> invalid genes selected
> Execution halted
> Build step 'Execute shell' marked build as failure
>
>
>
> Hope this
Dear all,
unfortunately, winbuilder1 is offline since a day or so,
so that new submissions to the svn are cannot be build in
the Jenkins system for the workflows.
Does anyone know when he will (most likely) be back up?
Thanks and best wishes,
Bernd
_
Hi Dario,
side note: if you want to find a bug and load the updated package over and
over again
it is much easier to use use devtools::load_all()!
It directly loads the updated version
using the source package directory without the need to detach / recompile /
reinstall.
So you can e.g. do:
1
thanks a lot to Dan for the prompt response and Hervê for
the fix!
Bernd
On Di, 2015-10-20 at 08:45 -0700, Dan Tenenbaum wrote:
>
> - Original Message -
> > From: "Bernd Klaus"
> > To: "bioc-devel"
> > Sent: Tuesday, October 20, 2015 4:32:48
Hi Kasper,
I also installed a clean devel version today and had no such problems,
also
https://www.bioconductor.org/developers/how-to/useDevel/
works for me and says that using an R-devel version is necessary
to use Bioc-devel. I also get the correct BiocInstaller version:
> biocLite()
> BioC
Dear all,
unfortunately it seems that IRanges fails the check at moment
in the devel version:
http://bioconductor.org/checkResults/3.3/bioc-LATEST/IRanges/
So that it can not be installed in a current R-devel. Additionally, the
landing page cannot be accessed.
http://bioconductor.org/packages/
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