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

[Sean Davis]

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

	[[alternative HTML version deleted]]