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Question: VariantAnnotation Installation Failure
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gravatar for andrew.j.skelton73
5 months ago by
United Kingdom
andrew.j.skelton73290 wrote:

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?

ADD COMMENTlink modified 5 months ago by Valerie Obenchain ♦♦ 6.4k • written 5 months ago by andrew.j.skelton73290
2
gravatar for Valerie Obenchain
5 months ago by
Valerie Obenchain ♦♦ 6.4k
United States
Valerie Obenchain ♦♦ 6.4k wrote:

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

ADD COMMENTlink modified 5 months ago • written 5 months ago by Valerie Obenchain ♦♦ 6.4k

Thanks for the insights Valerie. I'd cleared my R session and restarted R several times over about an hour trying to remedy this issue, but it seems this morning it installed no problem. 

I think your latter speculation of `update.packages` makes sense, but would restarting R (within the same RStudio session) not clear the tmp directory?

 

ADD REPLYlink written 5 months ago by andrew.j.skelton73290
1

I'm not an RStudio expert but yes, I would think restarting R within RStudio should delete the tmp/.

If you restarted R and still got the error it sounds like a problem on our end with the caching. I'll look into this further.

Valerie

ADD REPLYlink written 5 months ago by Valerie Obenchain ♦♦ 6.4k
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