[Bioc-devel] Missing package 'ggforce' in Mac builds causing ERROR

Dear all, I am the author of NormalyzerDE, and is currently working through some warnings from the package checks. Since previous builds I have included a new dependency 'ggforce'. On the two OS X platforms I get an error for the INSTALL and BUILD: * installing to library

Re: [Bioc-devel] EXTERNAL: Re: SPB inconsistencies

Ah yes, I overwrite the existing resource. I will look into a temporary workaround to downloading the newer GISTIC resource when the cached one is stale. Best, Marcel On 3/4/19 3:50 PM, Martin Morgan wrote: > Thanks Marcel -- when you update this data, do you add a new resource or > over-write

Re: [Bioc-devel] mzR update in the making: any Travis experts ?

Thanks, that got me on track. Yours, Steffen On Mon, 2019-03-04 at 19:55 +, Ramos Perez, Marcel wrote: > Hi Steffen, > > I haven't played with it yet but Travis CI has an Artifacts addon > that > will trigger > in the `after_script` or `after_failure` stages of the build and > upload >

Re: [Bioc-devel] SPB inconsistencies

Thanks Marcel -- when you update this data, do you add a new resource or over-write an existing resource? I think the best practice would be to create a new resource, with updated curateTCGAData package & version bump. Martin On 3/4/19, 2:31 PM, "Bioc-devel on behalf of Ramos Perez, Marcel"

Re: [Bioc-devel] mzR update in the making: any Travis experts ?

Hi Steffen, I haven't played with it yet but Travis CI has an Artifacts addon that will trigger in the `after_script` or `after_failure` stages of the build and upload log files to an AWS bucket. You can see the details here: https://docs.travis-ci.com/user/uploading-artifacts/ Best regards,

Re: [Bioc-devel] failed to access github, how to push updated package to the Github repository

Hi, You seem to be confusing “Github” with Bioconductor’s private git repository. Please note that, git.bioconductor.org is a Bioconductor hosted privately administered git server. Github, is hosted by the company Github.com. Developers of

[Bioc-devel] mzR update in the making: any Travis experts ?

Hi, TL;DR: How can I get to see the *.log files for more information ?! I am working on an upgrade of the C++ code in mzR, which is challenging to build cross-platform, so we use travis to check before pushing/breaking BioC. The Travis config [1] is fairly simple, with main modification that

Re: [Bioc-devel] SPB inconsistencies

Hi Martin, I suspect that this is due to caching because I'm unable to reproduce including after deleting my hub cache. hb <- ExperimentHub::ExperimentHub() #> snapshotDate(): 2019-01-25 unlink( AnnotationHub::hubCache(hb), recursive = TRUE, force = TRUE ) suppressMessages({

Re: [Bioc-devel] failed to access github, how to push updated package to the Github repository

Nitesh, Thank you for the instruction. Yes, I activated my account at https://git.bioconductor.org/BiocCredentials/. Then, I can see the seq2pathway package under the fold "which package you can access to." But I can only do the following four modifications but not the package: Update

Re: [Bioc-devel] failed to access github, how to push updated package to the Github repository

Hi, Firstly, you are not admin on the web app to be able to login with an “admin” account. Please try https://git.bioconductor.org/BiocCredentials/. You have an account under the email, mailto:xya...@uchicago.edu>>. Please try to log in and activate your account first using that email

Re: [Bioc-devel] failed to access github, how to push updated package to the Github repository

Dear Bioconductor developers, I tried to push an update of the existing package seq2pathway to github. However, I did not see the package under my github account. I also tried the following linkage (https://git.bioconductor.org/BiocCredentials/admin/login/?next=/BiocCredentials/admin/)