[Bioc-devel] Problems with MACPET package

[Martin Morgan]

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 on behalf of 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>>:
    
    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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