[Bioc-devel] Excluding internal functions from package manual

2025-02-13 Thread Burak Ogan Mancarci
I maintain gemma.R in bioconductor, a package with quite a few internal functions with documentation. In CRAN, functions that are not exported are not included in the reference pdf that is generated, however in Bioconductor, we seem to have all documented functions included. I have been trying to s

[Bioc-devel] Fixed error on gemma.R

2024-04-26 Thread Ogan Mancarci
Hi, I am the maintainer of gemma.R package. The latest test came up with an error due to a sporadic server issue. I have included a fix in a last push to try to addre

[Bioc-devel] Errors on package post 3.18 deadline

2023-10-20 Thread Burak Ogan Mancarci
Hi, I am a developer working on the bioconductor package gemma.R . This is a API package that interacts with our servers and we had an unfortunate case of updating our databases when the tests were running. I was wondering h

[Bioc-devel] Check error after deadline

2022-10-28 Thread Burak Ogan Mancarci
Hi, On the release schedule ( https://bioconductor.org/developers/release-schedule/) it was stated that the last day to pass without errors was 28th. In the latest build of gemma.R triggered by changes to documentation, we got a connection timeout error when communicating with the API that the pac

Re: [Bioc-devel] Package Classifications via BiocViews

2022-09-28 Thread Burak Ogan Mancarci
new terms from the Software ontology! > > Thanks, > > H. > > > > > 3. Bump the package version (only the z part in x.y.z), and push your > > changes to git.bioconductor.org. > > > > 4. Let us know when you're done. We'll make the required adjustmen

Re: [Bioc-devel] Package Classifications via BiocViews

2022-09-28 Thread Burak Ogan Mancarci
t; > Elm & Carlton Streets > > Buffalo, New York 14263 > -- > *From:* Bioc-devel on behalf of Burak > Ogan Mancarci > *Sent:* Wednesday, September 28, 2022 9:17 AM > *To:* bioc-devel@r-project.org > *Subject:* [Bioc-devel] Package Classifications v

[Bioc-devel] Package Classifications via BiocViews

2022-09-28 Thread Burak Ogan Mancarci
Hi, I am a developer working on the bioconductor package gemma.R . On publication we have used the ExperimentData biocview to classify the package but we believe this was not the correct decision since the package's function

Re: [Bioc-devel] Nightly builds for Gemma.R

2022-08-16 Thread Burak Ogan Mancarci
ages/devel/data/experiment/html/gemma.R.html. > > On Wed, 17 Aug 2022 at 06:55, Burak Ogan Mancarci > wrote: > > > > Hi, > > > > I have been maintaining the Gemma.R package which was recently accepted > to > > bioconductor. As per this > > < &

[Bioc-devel] Nightly builds for Gemma.R

2022-08-16 Thread Burak Ogan Mancarci
Hi, I have been maintaining the Gemma.R package which was recently accepted to bioconductor. As per this comment, it was supposed to be accessible at https://bioconductor.org/packages/gemma.R but it currently redir