[Bioc-devel] Problems with MACPET package

[Shepherd, Lori]

Your package is building clean on the RELEASE_3_9 branch.  What are you updating?

This is clean:

http://bioconductor.org/checkResults/release/bioc-LATEST/MACPET/



The branch that is failing and that needs to be updated is the current Bioconductor devel (3.10) branch.  That branch is the "master" branch on git.bioconductor.org

http://bioconductor.org/checkResults/devel/bioc-LATEST/MACPET/



You would follow the steps provided here:

http://bioconductor.org/developers/how-to/git/push-to-github-bioc/


Please check that the remotes are set up correctly and show the results of  (Step 2)


git remote -v



Assuming you have your remotes set up correctly and you have merged with Bioconductor Please then try (Step 6)


git push upstream master



Please show any ERRORs or outputs you receive so we can better assist.


I see you made at least one push to the master branch on Jun 25.

Bioconductor will only recognize and propagate the package if there has been a valid version bump.  For devel,  Please make sure you commit any changes with an increase from 1.5.0  (current) to 1.5.1 or the Bioconductor package/pages will not be updated.


Thank you,

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Ioannis Vardaxis <ioannis.vardaxis using ntnu.no>
Sent: Monday, July 29, 2019 10:56:23 AM
To: Martin Morgan <mtmorgan.bioc using gmail.com>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Problems with MACPET package

I have been trying to push the updates on RELEASE_3_9, but they don’t seem to get updated. They are only updated on GitHub.

Best,
Ioannis

17. jul. 2019 kl. 12:50 skrev Martin Morgan <mtmorgan.bioc using gmail.com<mailto:mtmorgan.bioc using gmail.com>>:

Bioc devel prepares for the next release of bioc, using the version of R that will be closest to that in use at the time of the release.

The version of R that will be in use at the time of the next bioc release will be R-3.6.*.

You should be using R-3.6 for bioc-devel.

This is summarized at http://bioconductor.org/developers/how-to/useDevel/ ; if there are improvments to the wording there please feel free to provide a pull request on https://github.com/Bioconductor/bioconductor.org/blob/master/content/developers/how-to/useDevel.md

'RELEASE_3_10' as a branch does not exist because there has not yet been a release 3.10; the 'master' branch is the location where devel builds from.

Martin

On 7/17/19, 5:46 AM, "Bioc-devel on behalf of Ioannis Vardaxis" <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org> on behalf of ioannis.vardaxis using ntnu.no<mailto:ioannis.vardaxis using ntnu.no>> wrote:

   My seesionInfo:
   sessionInfo()
   R Under development (unstable) (2019-07-11 r76823)
   Platform: x86_64-apple-darwin15.6.0 (64-bit)
   Running under: macOS Mojave 10.14.5

   And
   BiocManager::install("stringdist")
   Bioconductor version 3.10 (BiocManager 1.30.4), R Under development (unstable) (2019-07-11 r76823)
   Installing package(s) 'stringdist'
   Warning: unable to access index for repository https://bioconductor.org/packages/3.10/data/annotation/bin/macosx/el-capitan/contrib/3.7:
    cannot open URL 'https://bioconductor.org/packages/3.10/data/annotation/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
   Warning: unable to access index for repository https://bioconductor.org/packages/3.10/data/experiment/bin/macosx/el-capitan/contrib/3.7:
    cannot open URL 'https://bioconductor.org/packages/3.10/data/experiment/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
   Warning: unable to access index for repository https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.7:
    cannot open URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
   Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘stringdist’
   Do you want to attempt to install these from sources? (Yes/no/cancel) Yes


   Also, I cannot push to RELEASE_3_10 because I get error:

   $git checkout RELEASE_3_10
   error: pathspec 'RELEASE_3_10' did not match any file(s) known to git


   Shouldn’t I use the R devel version?

   Best,
   Ioannis


   15. jul. 2019 kl. 09:53 skrev Ioannis Vardaxis <ioannis.vardaxis using ntnu.no<mailto:ioannis.vardaxis using ntnu.no><mailto:ioannis.vardaxis using ntnu.no>>:

   My seesionInfo:
   sessionInfo()
   R Under development (unstable) (2019-07-11 r76823)
   Platform: x86_64-apple-darwin15.6.0 (64-bit)
   Running under: macOS Mojave 10.14.5

   And
   BiocManager::install("stringdist")
   Bioconductor version 3.10 (BiocManager 1.30.4), R Under development (unstable) (2019-07-11 r76823)
   Installing package(s) 'stringdist'
   Warning: unable to access index for repository https://bioconductor.org/packages/3.10/data/annotation/bin/macosx/el-capitan/contrib/3.7:
    cannot open URL 'https://bioconductor.org/packages/3.10/data/annotation/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
   Warning: unable to access index for repository https://bioconductor.org/packages/3.10/data/experiment/bin/macosx/el-capitan/contrib/3.7:
    cannot open URL 'https://bioconductor.org/packages/3.10/data/experiment/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
   Warning: unable to access index for repository https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.7:
    cannot open URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.7/PACKAGES'
   Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘stringdist’
   Do you want to attempt to install these from sources? (Yes/no/cancel) Yes


   Also, I cannot such to RELEASE_3_10 because I get error:

   $git checkout RELEASE_3_10
   error: pathspec 'RELEASE_3_10' did not match any file(s) known to git



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