Code and error:

> source("https://bioconductor.org/biocLite.R")
> biocLite("VariantAnnotation")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘VariantAnnotation’
trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/VariantAnnotation_1.22.0.tar.gz'
Error in download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/VariantAnnotation_1.22.0.tar.gz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/VariantAnnotation_1.22.0.tar.gz': HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘VariantAnnotation’ failed
installation path not writeable, unable to update packages: cairoDevice, colorspace, digest, ggplot2, plyr, proto, Rcpp, reshape2, scales, stringi, stringr,
  evaluate, formatR, htmltools, htmlwidgets, jsonlite, knitr, markdown, R6, rgl, shiny, yaml, foreign

It seems to install no problem on my Mac, but Ubuntu doesn't seem to be fairing as well... 

Session Info:

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8   
 [6] LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.26.0

loaded via a namespace (and not attached):
 [1] compiler_3.4.0   magrittr_1.5     R6_2.1.3         assertthat_0.2.0 formatR_1.4      DBI_0.6-1        tools_3.4.0      dplyr_0.5.0      tibble_1.3.1    
[10] Rcpp_0.12.11     knitr_1.14       rlang_0.1.1  

Any suggestions?

Hi Andrew,

The issue you're seeing is related to a stale PACKAGES file. This file lists package versions - if it's stale then the version will not match that in the repository (e.g., trying to retrieve VariantAnnotation 1.22.0 when the package had moved on to 1.22.1 or greater).

There are a couple of things that may contribute to this. One is the time PACKAGES sits in the cache on the AWS CloudFront edge nodes. We've recently changed this time to refresh every 30 seconds.

Another possibility is the fact that update.packages() that does not refresh PACKAGES in an open R session if the file already exists in a tmp directory. A fix has been committed in R devel to refresh PACKAGES every 24 hours in an open R session but this is not yet ported to R-3-4-patched.

It's probably too late to do more testing with your open R session - PACKAGES will update since it's been >24hours. It would be helpful for us to know if you got the error in a fresh linux session or was it one you had open for some time?

Valerie