Dear admin,
I re-submit my ssh key to the google form.
Maybe I need to wait to get approved.
Actually I do not have access to push updates for bioCancer package.
bioCancer Mezhoud$ git remote -v
originhttps://github.com/Bioconductor-mirror/bioCancer (fetch)
originhttps://github.com/Bioco
Hi Nitesh,
Thanks for looking into it. Unfortunately, I still can't access the
repository since I was using a DSA key which was previously mentioned here
as not supported. I thus generated an RSA key and added it to github. Will
newly added github keys be automatically imported? If not could you p
On 09/11/2017 04:43 AM, Karim Mezhoud wrote:
Dear admin,
I re-submit my ssh key to the google form.
Maybe I need to wait to get approved.
Actually I do not have access to push updates for bioCancer package.
bioCancer Mezhoud$ git remote -v
originhttps://github.com/Bioconductor-mirror/bioCa
On 09/10/2017 08:38 PM, Levi Waldron wrote:
I just dug up this old thread because I realized we still don't have a
coercion method as(sample.ExpressionSet, "SummarizedExperiment"). Since we
try as(sample.ExpressionSet, "RangedSummarizedExperiment"); see
?makeSummarizedExperimentFromExpressionS
Thank You Dr. Morgan,
When I cloned a repository with git clone , it automatically creates a
remote connection called *origin* pointing back to the cloned repository.
I tried to update bioCancer using old scenario 1:
- git clone https://github.com/Bioconductor-mirror/bioCancer
- cd bioCan
On 09/11/2017 07:20 AM, Karim Mezhoud wrote:
Thank You Dr. Morgan,
When I cloned a repository with |git clone| , it automatically creates a
remote connection called *|origin|* pointing back to the cloned repository.
I tried to update bioCancer using old scenario 1:
* git clone https://gi
Thanks Martin! I see the RangedSummarizedExperiment coercion method works
when there are no mappable ranges (for example curatedMetagenomicData
ExpressionSet objects), although the rowRanges is a GRangesList of empty
elements. It might be worth also having a SummarizedExperiment coercion
method it
Dear Bioconductor team,
I cannot push to the master branch of our package (MutationalPatterns).
$ git push origin master
fatal: remote error: FATAL: W any packages/MutationalPatterns nobody DENIED by
fallthru
(or you mis-spelled the reponame)
$ git remote -v
origin https://git.bioconductor.org
You need to use the SSH protocol not HTTPS.
So, your origin needs to be
`g...@git.bioconductor.org:packages/MutationalPatterns.git`.
http://bioconductor.org/developers/how-to/git/maintain-bioc-only/
> On Sep 11, 2017, at 10:26 AM, Janssen-10, R.R.E.
> wrote:
>
> Dear Bioconductor team,
>
>
I have looked through the docs but cannot see where this
is addressed. I would like to use the redland package
from CRAN but it has SystemRequirements:
Mac OSX: redland (>= 1.0.14) ; Linux: librdf0 (>= 1.0.14), librdf0-dev (>=
1.0.14)
is there a particular procedure for requesting such installat
I guess we discussed this with Davide Risso @Bioc2017 in the
MultiAssayExperiment workshop.
> SummarizedExperiment(mouseData)
puts the eSet (rather counterintuitively) into `assays` of
`SummarizedExperiment`, it does not really coerce it to
SummarizedExperiment, eg. `fData` and `pData` are not ac
On Mon, Sep 11, 2017 at 11:56 AM, Ludwig Geistlinger <
ludwig.geistlin...@bio.ifi.lmu.de> wrote:
> I guess we discussed this with Davide Risso @Bioc2017 in the
> MultiAssayExperiment workshop.
>
> > SummarizedExperiment(mouseData)
>
> puts the eSet (rather counterintuitively) into `assays` of
> `S
Hi Vince,
No particular procedure. Asking here is fine. I installed librdf0-dev
on the Linux builders and will install redland on the Mac builders.
Out of curiosity, what is the name of the Bioconductor package that
will depend on CRAN package redland?
Thanks,
H.
On 09/11/2017 07:29 AM, Vincent
Hello,
I am trying to push a new version of my package to git.bioconductor.org. I
was able to do that in the past. But I've recently changed my public key
and not sure whether this causes a problem. However, I can see my new
public key here - https://github.com/wikiselev.keys - and it is the first
Hi Vladimir,
This seems like the same error I was getting. Here is the helpful advice I
got from Sean:
Hi, Simina.
On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
vladimir.yu.kise...@gmail.com> wrote:
> Hello,
>
> I am trying to push a new version of my package to git.bioconductor.org. I
>
It's probably good keeping coercion and construction distinct,
although we have violated that recently with GRanges(). It now
attempts to coerce its first argument to a GRanges. Don't want to
derail the discussion, but it's another data point.
Michael
On Mon, Sep 11, 2017 at 9:26 AM, Levi Waldron
Hi Simina,
Thanks for your quick reply, but it looks like to forgot to paste your
response from Sean (at least I couldn't find it in your email).
Cheers,
Vlad
On Mon, Sep 11, 2017 at 5:58 PM Simina Boca wrote:
> Hi Vladimir,
> This seems like the same error I was getting. Here is the helpful a
Hi, Simina.
Take a look at the FAQ, #3, here:
http://bioconductor.org/developers/how-to/git/faq/
Have you submitted an SSH key somehow?
>
> Am I missing something here? Alternatively, I suppose I can just make the
> changes I want and simply open another issue, although it would be nice to
> h
Thanks Simina,
I think I've done all the steps described there before and was able to push
to upstream. I can't do it anymore and try to figure out why.
Could anyone else please help?
Cheers,
Vlad
On Mon, 11 Sep 2017, 18:03 Simina Boca wrote:
> Hi, Simina.
>
> Take a look at the FAQ, #3, here
"Consider clarifying how 6 object(s) are initialized"
Suppose an object is initialized via data() ... how can I make
this note go away? I don't understand how to clarify the situation.
[[alternative HTML version deleted]]
___
Bioc-devel@r-pro
Hi
Your key will be added in the next run of our script. You can change your
GitHub keys, our script will take in the new one, and you don’t have to
resubmit on the google-form.
It is run manually at the moment at noon EST everyday.
Nitesh
> On Sep 11, 2017, at 1:12 PM, Vladimir Kiselev
> w
Hi,
I added coercion from ExpressionSet to SummarizedExperiment in
SummarizedExperiment 1.7.6.
The current behavior of the SummarizedExperiment() constructor
when called on a ExpressionSet object doesn't make much sense to
me. I'd rather have it consistent with what the coercion does.
Will fix i
Hi Nitesh,
Many thanks, I will check it in a couple of days.
Cheers,
Vlad
On Mon, 11 Sep 2017, 19:01 Turaga, Nitesh
wrote:
> Hi
>
> Your key will be added in the next run of our script. You can change your
> GitHub keys, our script will take in the new one, and you don’t have to
> resubmit on
Thank you again Sean and Lori! I am now past that initial stage. I now have
to resolve merge conflicts, primarily in the DESCRIPTION file. When
following the instructions here http://bioconductor.org/
developers/how-to/git/resolve-conflicts/ however, I ended up getting the
error below:
~\Documents
On Mon, Sep 11, 2017 at 2:02 PM, Hervé Pagès wrote:
> Hi,
>
> I added coercion from ExpressionSet to SummarizedExperiment in
> SummarizedExperiment 1.7.6.
>
Thank you Hervé!
> The current behavior of the SummarizedExperiment() constructor
> when called on a ExpressionSet object doesn't make mu
Concerning 1) Why have some developers chosen to extend eSet instead of
ExpressionSet:
As far as I understand it, ExpressionSet was thought to exclusively
represent a microarray experiment (MIAME = Minimum Information About a
Microarray Experiment).
Thus, back in the days when more and more peopl
An ExpressionSet is an eSet that is guaranteed to have an "exprs" assay.
That makes no sense for example for methylation where we have (say)
Green/Red assays or Meth/Unmeth assays (or transformations of these).
Best,
Kasper
On Mon, Sep 11, 2017 at 3:31 PM, Ludwig Geistlinger <
ludwig.geistlin...@
Hello,
I tried to install my package on a machine and it gives the following warning
which does not make sense.
> source("https://bioconductor.org/biocLite.R";)
Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help
> biocLite("DMCHMM")
BioC_mirror: https://bioconductor.org
Using B
Thanks Ludwig and Kasper. This old presentation from Martin also helped me
a lot:
https://www.bioconductor.org/packages/devel/bioc/vignettes/Biobase/inst/doc/BiobaseDevelopment.pdf
But I still wonder, why provide the coercion for ExpressionSet, if
providing it for eSet would work not only for Exp
I don't know the reasons behind this choice, I didn't implement
these methods. It would make sense to have these coercions defined
for the eSet,SummarizedExperiment and eSet,RangedSummarizedExperiment
signatures if they only access the eSet part of the object.
I'll look into this.
H.
On 09/11/20
I see how an eSet maps to a SummarizedExperiment; one can look at the
assays in the object. I agree with Levi/Herve that this is the natural
(correct) choice. It is less clear how you get the ranges for a
RangedSummarizedExperiment without making assumptions.
On Mon, Sep 11, 2017 at 8:09 PM, Her
The following allowed me to eliminate the duplicated commits in one step
via git merge --squash and then successfully push back to the bioc-git
server. After this I was able to switch to the swap branch approach to
avoid similar problems in the future.
Example here for master branch:
git checkout
It's only available on bioc-devel, not bioc-release. See
http://bioconductor.org/packages/devel/bioc/html/DMCHMM.html and
http://bioconductor.org/developers/how-to/useDevel/
On Mon, Sep 11, 2017 at 7:17 PM, Farhad Shokoohi wrote:
> Hello,
>
> I tried to install my package on a machine and it give
Hi Nima,
The build machines are NOT trying to use version 1.0.0 of the
biotmleData package. They are using the version that is currently
publicly available here:
https://bioconductor.org/packages/3.6/data/experiment/html/biotmleData.html
It's version 1.1.0. The build machines installed it with
Hi all
I have created a branch 'bioanalyse' for the package Prostar in my local
repository and I want to push the changes on the github server.
I ran the following command but it returned an error message :
> git push --set-upstream origin bioanalyse
Counting objects: 17, done.
Delta compressi
Good day,
Although the package seems to build without errors, I can't run the basic
examples of MultiAssayExperiment successfully.
library(MultiAssayExperiment)
> example("ExperimentList")
ExprmL> ## Create an empty ExperimentList instance
ExprmL> ExperimentList()
Error in checkSlotAssignment(o
Hi Hervé ---
Thanks for pointing out all of the information available on the builds to
me. Based on the information you point out, I think I've been able to add
the required data set to the biotmleData package by bumping the versions on
the RELEASE_3_5 and master branches appropriately (and made s
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