It should also be pointed out that reference classes classes are rarely
needed and can easily be used for the wrong reasons (e.g. performance?).
The pass-by-reference semantic they provide can fire back. Most of the
time objects don't need and should not have pass-by-reference semantic,
only *some
If Biocondutor integration is important, then reference classes
(setRefClass) are preferable, since they fully integrate with the rest of
S4, including class hierarchies and method dispatch. It's important not to
be confused by the R6 branding. It's (sort of) an alternative to S4, not an
evolution
Good day,
If I have a FASTA file that contains
>sp|Q9NYW0|T2R10_HUMAN Taste receptor type 2 member 10 OS=Homo sapiens
>GN=TAS2R10 PE=1 SV=3
MLRVVEGIFIFVVVSESVFGVLGNGFIGLVNCIDCAKNKLSTIGFILTGLAISRIFLIWI
IITDGFIQIFSPNIYASGNLIEYISYFWVIGNQSSMWFATSLSIFYFLKIANFSNYIFLW
LKSRTNMVLPFMIVFLLISSLLNFAYIAKILNDY
Dear Bioconductor maintainers,
I'm the co-maintainer of the Rsubread package. When we're preparing Rsubread
for the new release, I found that I don't have the access to the "devel" Git
Repository (g...@git.bioconductor.org:packages/Rsubread).
My SVN account is "y.liao", and my GitHub account
Yes, if all is green on the build report you can ignore it.
Thanks.
Valerie
On 10/17/2017 11:46 AM, Samuel E Zimmerman wrote:
Hi all,
The below email was sent to me regarding an error in my package attract. I
haven't updated the package in several months but this is the first time I am
seeing
I found it a very congenial presentation.
One related issue -- perhaps -- a new HDF5 interface package, that is
based on R6!
https://github.com/hhoeflin/hdf5r
Core class consciousness is surely worthy of promotion. But what about OOP
methodology? I personally am happy with S4. I believe there
Good day,
I developed ClassifyR, which is a classification framework, based on
ExpressionSet. Now that we're getting enquiries about inputting multiple
datasets derived from the same patients, we plan to completely refactor the
software to use MultiAssayExperiment as a foundation class.
--
I'm putting together a presentation with a demo on why Bioconductor
developers should re-use and extend core classes whenever possible. It
includes a demo of some real-life consequences from two packages I use a
lot, metagenomeSeq and phyloseq. These are far from the only examples, many
Bioconducto
Hi bioc-devel
I have for a couple of days tried pushing the last updates of my package
IsoformSwitchAnalyzeR to git.bioconducor.org so they could be part of the
stable release - but unfortunately without luck.
I have followed instructions in the developer section and I have submitted
my
public ke
Hi Kylie,
I will take a look at your package and get back to you. Avoid making any
changes till I give you further notice.
Best,
Nitesh
> On Oct 17, 2017, at 1:13 PM, Bemis, Kylie wrote:
>
> Hi all,
>
> I have a problem with duplicate commits in my package “Cardinal”. So far I
> have avo
Dear Turaga,
Thank you for your comments.
Regarding 'COMMIT_EDITMSG' I have just found a link, which explains the
contents of the '.git' directory:
http://gitready.com/advanced/2009/03/23/whats-inside-your-git-directory.html
Meanwhile, my changes to 'xps' were finally uploaded to:
http://bi
Hi all,
The below email was sent to me regarding an error in my package attract. I
haven't updated the package in several months but this is the first time I am
seeing an error reported. I also went to the link below to check the build
report and everything returns OK. Should I ignore this erro
Hi,
In one hour, at approx 3:30pm EST, we will stop commits to the current release
branch, BioC 3.5. We will run the 3.5 builds once more to incorporate changes
committed since the last build. If all goes as expected, tomorrow's report will
serve as the final build report for BioC 3.5.
Please
Hi all,
I have a problem with duplicate commits in my package “Cardinal”. So far I have
avoided making more commits to my other package “matter” until I am sure how to
avoid this again.
Soon after the git transition, I made a few small commits to the Bioconductor
git repo, which I notice now i
If you have further trouble, I think you should submit your key again to the
google form. And wait for the new key to be added.
It might also help to read the instructions here again,
bioconductor.org/developers/how-to/git/.
> On Oct 17, 2017, at 11:39 AM, Zhao, Shilin
> wrote:
>
> See be
Hi,
Explicitly specifying the citation worked, just like in
https://github.com/leekgroup/derfinderHelper/commit/b63f8c4119686630a5b3cf71c36b16e3e719cf89.
Here are the citations I ended up using:
S4Vectors = RefManageR::BibEntry(bibtype = 'manual', key = 'S4Vectors',
author = 'Hervé Pagès and
Hi Christian,
Please see my inline comments for all your questions.
> On Oct 16, 2017, at 5:46 PM, cstrato wrote:
>
> Dear Turaga,
>
> Thank you for your reply.
>
> This is exactly the problem which I do not understand.
>
> I did NOT add "rabbitus@lumimacs-iMac.local” as my email.
>
Th
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