Re: [Bioc-devel] Remove from email list

Hi Sara, You can manage your account here: https://stat.ethz.ch/mailman/listinfo/bioc-devel Valerie On 04/24/2018 03:37 PM, Sara Linker wrote: Hi at Bioc-devel, Would it be possible to please remove me from the email list? Best, Sara ___ Bioc-dev

[Bioc-devel] Remove from email list

Hi at Bioc-devel, Would it be possible to please remove me from the email list? Best, Sara ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] " Error in serialize(data, node$con, xdr = FALSE)" during Vignette build (ChIC)

I guess this is ChIC (from the title?) which is clean on today's report: https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ Valerie On 04/24/2018 01:17 PM, Obenchain, Valerie wrote: Carmen, What is the name of your package? Valerie On 04/16/2018 11:42 AM, Carmen M. Livi wrote: H

Re: [Bioc-devel] Bioc 3.7 build failed for GenvisR package

GenVizR looks clean on the build report today: https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ Valerie On 04/20/2018 01:08 PM, Obenchain, Valerie wrote: Hi Zach, The build report for today is not helpful because GenVisR failed on all platforms due to a biomaRt failure. Because

Re: [Bioc-devel] " Error in serialize(data, node$con, xdr = FALSE)" during Vignette build (ChIC)

Carmen, What is the name of your package? Valerie On 04/16/2018 11:42 AM, Carmen M. Livi wrote: Hi all, my package recently got accepted and moved to the Bioconductor repository. Suddenly I get an error during the package build for Linux and OS (the INSTALL is working). The error occurs duri

Re: [Bioc-devel] git push confusion

Wonderful, thank you. It appears to be fixed now. On Mon, Apr 23, 2018 at 8:25 PM, Hervé Pagès wrote: > Hi Karl, > > We don't have an easy way to know when exactly you pushed your changes > to git.bioconductor.org but it seems that you did it only today so you > need to wait about 24h to see thi

Re: [Bioc-devel] Need some help to submit a R package.

It doesn't look like the webhook was ever initialized Please follow the instructions here: https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#adding-a-web-hook After the webhook is set up you will need to do another version bump to trigger the build - Please post furth

Re: [Bioc-devel] biomaRt uswest mirror ERROR

Ok. Thanks Mike. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Mike Smith Sent: Tuesday, April 24, 2018 12:17:58 PM To: Shepherd, Lori Cc:

Re: [Bioc-devel] biomaRt uswest mirror ERROR

Hi Lori, There should be no issue with switching to an alternative mirror with regards to the content. However, in the current release you will also need to set the argument ensemblRedirect = FALSE otherwise it'll end up at the uswest mirror regardless of the host you specify. This is not the ca

[Bioc-devel] biomaRt uswest mirror ERROR

Hello, OrganismDbi is failing. http://bioconductor.org/checkResults/3.7/bioc-LATEST/OrganismDbi/malbec2-checksrc.html It appears that this link is not available for the uswest mirror: http://uswest.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt when specifying the host =

Re: [Bioc-devel] deleting irrelevant legacy objects from git repo?

Ok, please check if everything on the master branch is as expected. I’ve synced it. Best Nitesh > On Apr 24, 2018, at 11:20 AM, Alexander Pico > wrote: > > It’s ready. Thanks! > > - Alex > >> On Apr 24, 2018, at 8:02 AM, Turaga, Nitesh >> wrote: >> >> Hi >> >> Go ahead and clean your

[Bioc-devel] Fwd: Failing package merhr

Begin forwarded message: From: 露崎 弘毅 mailto:k.t.the-ans...@hotmail.co.jp>> Subject: RE: Failing package merhr Date: April 24, 2018 at 11:07:15 AM EDT To: "Turaga, Nitesh" mailto:nitesh.tur...@roswellpark.org>> Cc: "drito...@gmail.com" mailto:drito...@gmail.com>>, "m

Re: [Bioc-devel] Need some help to submit a R package.

Dear sir, I have uploaded the sigFeature package ( Version: 0.99.1) in the existing git repository and did a version bump. The link is given below. https://github.com/pijush1285/sigFeature But still now I am not getting any response. Is there required to add the web hook again ? Thank you rega

Re: [Bioc-devel] deleting irrelevant legacy objects from git repo?

Perfect. Many thanks! - Alex > On Apr 24, 2018, at 8:25 AM, Turaga, Nitesh > wrote: > > Ok, please check if everything on the master branch is as expected. I’ve > synced it. > > Best > > Nitesh >> On Apr 24, 2018, at 11:20 AM, Alexander Pico >> wrote: >> >> It’s ready. Thanks! >> >> -

Re: [Bioc-devel] deleting irrelevant legacy objects from git repo?

Hi Go ahead and clean your repo. Once that is done, I can sync it. Best, Nitesh > On Apr 22, 2018, at 9:07 PM, Alex Pico wrote: > > In an effort to clear a BiocCheck warning and reduce the size of our code > base from 22MB to 7MB, I’d like to sync our recently cleaned git objects > (usi

Re: [Bioc-devel] deleting irrelevant legacy objects from git repo?

It’s ready. Thanks! - Alex > On Apr 24, 2018, at 8:02 AM, Turaga, Nitesh > wrote: > > Hi > > Go ahead and clean your repo. > > Once that is done, I can sync it. > > Best, > > Nitesh > >> On Apr 22, 2018, at 9:07 PM, Alex Pico wrote: >> >> In an effort to clear a BiocCheck warning an

Re: [Bioc-devel] vignette problems

On 04/24/2018 09:42 AM, campos wrote: Hi Martin, thanks for your reply. I do not have vignette warnings, the warnings that I see are: MultivariateGaussianFactory.h:23:9: warning: control reaches end of non-void function [-Wreturn-type] BernoulliFactory.h:27:9: warning: control reaches

Re: [Bioc-devel] vignette problems

Hi Martin, yeah, I have been wondering around the code these days looking for the answer of that, I am the maintainer and not who developed the code... I still couldn't reach the developer and ask about this, for the moment my assumption is that whenever parallel == 0 (Which I also think is mo

Re: [Bioc-devel] vignette problems

I don't see vignette warnings on the build report. You should address the simple namespace issue by adding importFrom("stats", "dnbinom", "kmeans", "optim", "ppois") to your NAMESPACE file. The compiler warnings are from the -Wall flag, which you can set by creating a plain text file ~/.R

Re: [Bioc-devel] vignette problems

Hi Martin, thanks for your reply. I do not have vignette warnings, the warnings that I see are: MultivariateGaussianFactory.h:23:9: warning: control reaches end of non-void function [-Wreturn-type] BernoulliFactory.h:27:9: warning: control reaches end of non-void function [-Wreturn-type]

Re: [Bioc-devel] I could't push My package GMRP to github/master

Please respond following the instructions as Nitesh has suggested - Line by line with output - http://bioconductor.org/developers/how-to/git/maintain-github-bioc/ Please be advised - while he helped you push changes to MBttest - those changes failed to fix the package and still need attenti

Re: [Bioc-devel] Need some help to submit a R package.

We like to keep track of the changes and have the reviews in one place. If possible it would be better to replace the contents of existing git repository and do a version bump. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics

Re: [Bioc-devel] Need some help to submit a R package.

Dear Sir, I have solved most of the issues raised by the reviewers. There were significant amount of changes in the original code. So should we submit our package (sigFeature) as a new submission or replace the contents of existing git repository with version increment. regards Pijush On Mon,

Re: [Bioc-devel] vignette problems

Dear Bio-dev, I have a quick question, for some reason I can reproduce the warnings that are stated in https://bioconductor.org/checkResults/3.7/bioc-LATEST/STAN/malbec2-checksrc.html on my linux machine. The check runs smoothly, any idea why so? Thank you again, Rafael On 11.04.2018 16:5