[Bioc-devel] Hook declined on a branch

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

Re: [Bioc-devel] Bioconductor package landing pages

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

Re: [Bioc-devel] Package DMCHMM is not installed

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

Re: [Bioc-devel] Duplicate commit error on and off

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

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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,

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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

[Bioc-devel] Package DMCHMM is not installed

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

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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 <

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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

Re: [Bioc-devel] updating Bioconductor package that is already on Github

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:

Re: [Bioc-devel] Upstream permission denied

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

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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

Re: [Bioc-devel] Upstream permission denied

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

[Bioc-devel] clarifying initialization for BiocCheck

"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]] ___

Re: [Bioc-devel] Upstream permission denied

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

Re: [Bioc-devel] Upstream permission denied

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 >

Re: [Bioc-devel] Upstream permission denied

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

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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

Re: [Bioc-devel] Upstream permission denied

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 >

[Bioc-devel] Upstream permission denied

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

Re: [Bioc-devel] requesting more infrastructure on build/bot system

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,

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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 >

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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

[Bioc-devel] requesting more infrastructure on build/bot system

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

Re: [Bioc-devel] Cannot push to master branch

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: >

[Bioc-devel] Cannot push to master branch

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

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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

Re: [Bioc-devel] denied access to git

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

Re: [Bioc-devel] denied access to git

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

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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

Re: [Bioc-devel] denied access to git

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 origin

Re: [Bioc-devel] failing Bioconductor package DeepBlueR

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

[Bioc-devel] denied access to git

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) origin