[Bioc-devel] Error on BiocCheckGitClone and Windows build

[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/

And/or set up your git credentials account?
https://git.bioconductor.org/BiocCredentials


and lastly builds are triggered only by a valid version bump in the DESCRIPTION.  Please make sure to bump the DESCRIPTION to at least 0.99.5

we encourage further discussion on the issue itself for more specialized assistance.

Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Oluwafemi OLUSOJI <oluwafemi.olusoji using uhasselt.be>
Sent: Tuesday, March 2, 2021 4:47 AM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: 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?

Regards,
Daniel

Op ma 1 mrt. 2021 om 19:51 schreef Kern, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>>:
Please feel free to also comment directly on your issue for your reviewer to assist.

The packages not being available on windows is likely on our end and you can ignore for now.

System files should not be git tracked. They should be remove using git remove and then committed up.
git rm <file>
git commit -a

Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Oluwafemi OLUSOJI <oluwafemi.olusoji using uhasselt.be<mailto:oluwafemi.olusoji using uhasselt.be>>
Sent: Monday, March 1, 2021 12:12 PM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: [Bioc-devel] Error on BiocCheckGitClone and Windows build

Dear All,

I recently submitted a package to Bioconductor and got this error message
as part of the reply email. I am not sure what to do about it.

The two files are git tracked,  but they are also named in .Rbuildignore so
I felt they should have been avoided. This is my first experience with
Bioconductor so any help would be appreciated.

Furthermore, there are errors related to dependencies on the windows build.
Should I worry about these?

Regards,
Olusoji Oluwafemi Daniel

###### Error Related to Windows test build ####

===============================

 R CMD BUILD

===============================

* checking for file 'cyanoFilter/DESCRIPTION' ... OK
* preparing 'cyanoFilter':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
      -----------------------------------
ERROR: dependencies 'flowCore', 'flowDensity' are not available for
package 'cyanoFilter'
* removing 'C:/Users/pkgbuild/AppData/Local/Temp/Rtmp0gaTHW/Rinst8fd05a8549f/cyanoFilter'
      -----------------------------------
ERROR: package installation failed


####### Error related to git tracked files #####

This is BiocCheckGitClone version 1.27.2. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
    * ERROR: System Files found that should not be git tracked:
        .Renviron
        cyanoFilter.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

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