Re: [Bioc-devel] Accessing updated package through Devel and priming package for next release

Have you pushed your changes to git.bioconductor.org? I see HPAStainR master$ git remote -v origin g...@git.bioconductor.org:packages/HPAStainR (fetch) origin g...@git.bioconductor.org:packages/HPAStainR (push) HPAStainR master$ git pull Already up to date. HPAStainR master$ grep Version DESCRIP

[Bioc-devel] Accessing updated package through Devel and priming package for next release

Hello, I am the maintainer of the package HPAStainR. We are about to respond to reviewer comments on the package's associated paper, and I am trying to have an updated accessible version of the package for the reviewers to use. I currently have the updated version of the package as version 1.1.

[Bioc-devel] Semi-transparency warning in package submitted to Bioconductor

Dear all, I have recently submitted a package to Bioconductor and during the review some issues with semi-transparency in output plots from two functions have been identified. The warning message was: In grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) : semi-transparency is not suppor

Re: [Bioc-devel] ExperimentHub package development - Windows OS specific error

Hey Gavin, This worked perfectly, thanks! However, this did lead to another error where one of the datasets from the metadata file wasn't found in the ExperimentHub dataset. Again this is Windows specific and the dataset in question (alzh_gwas_top100) does exist: > ### ** Examples > > alzh_

Re: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?

My understanding is that we will not permit dependencies outside of Bioc or CRAN. If a repository is created that is at least as rigorous in package admission as CRAN, perhaps it needs to be considered. If there are details known about alternate repositories that we should learn about, please sup

Re: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?

Related: Does Bioconductor support 'Additional_repositories'? From RWE: The ‘Additional_repositories’ field is a comma-separated list of repository URLs where the packages named in the other fields may be found. It is currently used by R CMD check to check that the packages can be found, at least

Re: [Bioc-devel] ExperimentHub package development - Windows OS specific error

Your file seems to be encoded as UTF-8-BOM. When I read it in on my Windows 10 machine the Title column has extra characters at the front ("�..Title"), which is why your function returns "no object found" when checking for the Title column. If I resave your file with UTF-8 format your functio

[Bioc-devel] ExperimentHub package development - Windows OS specific error

Hi all, My apologies, I have emailed before on a related issue but now think I have found a potential cause of the issue I am having but can't seem to find a fix. I am working on an ExperimentHub data package; ewceData, which fails checks on Windows O

Re: [Bioc-devel] Lost Credentials

All sorted now! Thanks a lot Nitesh Sandro On Tue, Mar 2, 2021 at 4:54 PM Nitesh Turaga wrote: > Hi, > > You are not an active user of BiocCredentials. You've never set a password > to reset it. > > You have to first activate your account. > > https://git.bioconductor.org/BiocCredentials/account

Re: [Bioc-devel] Lost Credentials

Hi, You are not an active user of BiocCredentials. You've never set a password to reset it. You have to first activate your account. https://git.bioconductor.org/BiocCredentials/account_activation Best, Nitesh On 3/2/21, 11:06 AM, "Bioc-devel on behalf of Morganella Sandro" wrote:

[Bioc-devel] Lost Credentials

Hi Dev! I have been trying to access my package repository (VegaMC), but I cannot remember my credentials. I have tried to reset my password, with no luck - I haven't received any email (I have checked my spam). Anyone that can help me with this? Thanks, Sandro [[alternative HTML version

Re: [Bioc-devel] Error on BiocCheckGitClone and Windows build

Ah! I didn't bump up the description file. Thank you once again. Regards, Daniel Op di 2 mrt. 2021 om 13:16 schreef Kern, Lori : > Did you follow the instructions for setting up remotes to push to > git.bioconductor.org? > https://bioconductor.org/developers/how-to/git/new-package-workflow/ > >

Re: [Bioc-devel] [Bioc-deve] Check package status / built report

Additionally, Please make sure to do a valid version bump. I took a peak on our git.bioconductor.org server and do see the changes pushed but it does not appear that it included a valid version bump from 1.17.0 to 1.17.1 . Without a valid version bump the most recent version will not propaga

Re: [Bioc-devel] [Bioc-deve] Check package status / built report

Michael is right. Additionally there is some information on the timing of pushing / pulling of the build system on the top of this page: bioconductor.org/developers/how-to/troubleshoot-build-report/ While its possible you made the changes in time for today's report, Most likely the changes will

Re: [Bioc-devel] Error on BiocCheckGitClone and Windows build

Did you follow the instructions for setting up remotes to push to git.bioconductor.org? https://bioconductor.org/developers/how-to/git/new-package-workflow/ And/or set up your git credentials account? https://git.bioconductor.org/BiocCredentials and lastly builds are triggered only by a valid v

Re: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?

thanks for the quick reply Lori! OK, so we will have to submit the package to Bioc ASAP. cheers, jo > On 2 Mar 2021, at 12:51, Kern, Lori wrote: > > Currently the builders do not allow the user of remotes and you would have to > wait for it to be submitted to CRAN or Bioconductor. All Biocon

Re: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?

Currently the builders do not allow the user of remotes and you would have to wait for it to be submitted to CRAN or Bioconductor. All Bioconductor dependencies must be on CRAN or Bioconductor. Get Outlook for iOS From: Bioc-devel on beha

Re: [Bioc-devel] Error on BiocCheckGitClone and Windows build

Hello Lori, Thank you for your insight. I figured out it pays to expressly state that those files not be tracked and committed. I have re-submitted for a new build but I am not getting any notification on the issues page as written out on the Bioconductor website. Is there a reason for this? Reg

[Bioc-devel] Remotes in DESCRIPTION not supported for BioC?

Dear All! in one of the xcms vignettes we are using a R package which is not yet in Bioconductor and I added Remotes: RforMassSpectrometry/MsBackendMgf to the DESCRIPTION thinking that on the BioC build machines the package might get installed (from github). It does apparently not as we ge

Re: [Bioc-devel] [Bioc-deve] Check package status / built report

Hello Ines This is not how the builds of accepted packages work. The builds run once a day, and depending when the builders pull the contents from git.bioconductor.org (see date and time at the top of https://master.bioconductor.org/checkResults/3.13/bioc-LATEST/index.html), your changes may

[Bioc-devel] [Bioc-deve] Check package status / built report

Hello. I updated my package and pushed the changes to bioconductor github Everything went smoothly with no errors, git clone g...@git.bioconductor.org:packages/BaalChIP (changes... add.. rename origin...etc) git push upstream master I thought that by pushing to bioconductor github it would trigge