[Bioc-devel] Behavior of BiocManager::install() with github repos on Mac

[Martin Morgan]

BiocManager delegates to remotes::install_github() for github installations.

I think the warning-as-error comes from

https://github.com/r-lib/remotes/blob/a0d6cd5d52062fcaedac7dd19b03f9211f578791/R/install.R#L61-L71

with warning-only behavior recovered with

  Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS, FALSE)

BiocManager could set this before calling remotes::install_github(), but this seems like a non-productive battle over this behavior.

There are additional issues with using remotes::install_github(), e.g., offering to update the Bioconductor version of BiocPkgTools with the more recent github version.

  > BiocManager::install("seandavi/BiocWorkshopMaterialTest")
  Bioconductor version 3.9 (BiocManager 1.30.4), R Under development (unstable)
    (2019-01-14 r75991)
  Installing github package(s) 'seandavi/BiocWorkshopMaterialTest'
  Downloading GitHub repo seandavi/BiocWorkshopMaterialTest using master
  These packages have more recent versions available.
  Which would you like to update?

  1:   BiocPkgTools (1.1.3 -> d676b5fc7...) [GitHub]

  Enter one or more numbers separated by spaces, or an empty line to cancel 
  1: 

This seems to undermine the goal of BiocManager, which is to provide a consistent and tested installation.

I opened two issues on BiocManager's github

https://github.com/Bioconductor/BiocManager/issues/37
https://github.com/Bioconductor/BiocManager/issues/38 

Martin

On 1/19/19, 11:42 AM, "Bioc-devel on behalf of Sean Davis" <bioc-devel-bounces using r-project.org on behalf of seandavi using gmail.com> wrote:

    I have been working a bit on a small test package to learn a bit about
    "Remotes" in the DESCRIPTION file. In doing so, there appears to be a bit
    of a discordance between how github-based installation and non-github-based
    installation works with respect to installing dependencies. The former
    generates an error right now because of lack of Mac binary packages; the
    latter generates warnings only. See below for details. Is the error in the
    first case necessary, or could we get away with warnings?
    
    Thanks,
    Sean
    
    > BiocManager::version()
    [1] ‘3.9’
    > # missing GEOquery as a dependency, for example
    > BiocManager::install("seandavi/BiocWorkshopMaterialTest")
    Bioconductor version 3.9 (BiocManager 1.30.4), R Under development
    (unstable) (2019-01-14 r75992)
    Installing github package(s) 'seandavi/BiocWorkshopMaterialTest'
    Downloading GitHub repo seandavi/BiocWorkshopMaterialTest using master
    Installing 1 packages: GEOquery
    Error: (converted from warning) unable to access index for repository
    https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6:
      cannot open URL '
    https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/PACKAGES'
    > BiocManager::install("GEOquery")
    Bioconductor version 3.9 (BiocManager 1.30.4), R Under development
    (unstable) (2019-01-14 r75992)
    Installing package(s) 'GEOquery'
    Warning in download.file(url = paste0(repos, "/PACKAGES.rds"), destfile =
    dest,  :
      cannot open URL '
    https://bioconductor.org/packages/3.9/data/experiment/bin/macosx/el-capitan/contrib/3.6/PACKAGES.rds':
    HTTP status was '404 Not Found'
    Warning in download.file(url = paste0(repos, "/PACKAGES.rds"), destfile =
    dest,  :
      cannot open URL '
    https://bioconductor.org/packages/3.9/workflows/bin/macosx/el-capitan/contrib/3.6/PACKAGES.rds':
    HTTP status was '404 Not Found'
    Warning in download.file(url = paste0(repos, "/PACKAGES.rds"), destfile =
    dest,  :
      cannot open URL '
    https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/PACKAGES.rds':
    HTTP status was '404 Not Found'
    Warning in download.file(url = paste0(repos, "/PACKAGES.gz"), destfile =
    tmpf,  :
      cannot open URL '
    https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/PACKAGES.gz':
    HTTP status was '404 Not Found'
    Warning in download.file(url = paste0(repos, "/PACKAGES"), destfile =
    tmpf,  :
      cannot open URL '
    https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/PACKAGES': HTTP
    status was '404 Not Found'
    Warning: unable to access index for repository
    https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6:
      cannot open URL '
    https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/PACKAGES'
    trying URL '
    https://bioconductor.org/packages/3.9/bioc/bin/macosx/el-capitan/contrib/3.6/GEOquery_2.51.5.tgz
    '
    Content type 'application/x-gzip' length 13828923 bytes (13.2 MB)
    ==================================================
    downloaded 13.2 MB
    
    
    -- 
    Sean Davis, MD, PhD
    Center for Cancer Research
    National Cancer Institute
    National Institutes of Health
    Bethesda, MD 20892
    https://seandavi.github.io/
    https://twitter.com/seandavis12
    
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