Hello;

I’ve been unable to install the package Biostrings on my desktop (Dell, Windows),despite numerous attempts.  It appears that only a portion of the zipfile is being downloaded.  I am downloading onto a US federal computer;  so perhaps there is a firewall problem. I was able to install on my laptop as long as I was using public wifi, which suggests my suspicions are correct.  I’m hoping someone can give some advice.

I’m trying to install the package from the latest Bioconductor release (3.3).  The version of R installed on my computer is 3.3.1. 

Here are the initial commands, the sessioninfo, and the traceback:

> ## try http:// if https:// URLs are not supported
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
> biocLite("Biostrings")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘Biostrings’
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/Biostrings_2.40.2.zip'
Content type 'application/zip' length 27165761 bytes (25.9 MB)
downloaded 2.2 MB

Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open the connection
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 2301952 != reported length 27165761
2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open compressed file 'Biostrings/DESCRIPTION', probable reason 'No such file or directory'
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252  
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                         
[5] LC_TIME=English_United States.1252   

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

other attached packages:
[1] BiocInstaller_1.22.3

loaded via a namespace (and not attached):
[1] tools_3.3.1
> traceback()
7: read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type"))
6: unpackPkgZip(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib, libs_only,
       lock)
5: .install.winbinary(pkgs = bins, lib = lib, contriburl = contrib.url(repos,
       type2), method = method, available = av2, destdir = destdir,
       dependencies = NULL, libs_only = libs_only, quiet = quiet,
       ...)
4: install.packages(pkgs = doing, lib = lib, ...)
3: .reposInstall(todo, lib = lib, ...)
2: .biocLiteInstall(pkgs, ask = ask, siteRepos = siteRepos, suppressUpdates = suppressUpdates,
       ...)
1: biocLite("Biostrings")
>  

You might try different download methods, as described in

> ?options

and looking for 'download.file.method', e.g.,

> options(download.file.method="auto")

Set this option before running biocLite("Biostrings"). For trouble-shooting, it might be helpful to avoid using https

> options(useHTTPS=FALSE)

because not all download methods fully support https://. You might also consult with your local system administrator to see what sorts of restrictions are placed on file downloads. And while not generally recommended or needed, you might try an alternative mirror, in particular at NIH.

> options(BioC_mirror="http://watson.nci.nih.gov/bioc_mirror/")

(reset to default with options(BioC_mirror=NULL)).