Hi,

I am teaching an Advanced Genetics class using R.  There are 45 students working on their own laptops so it is a good test for OS independence.  A subset of students running OS X 10.9-10.10 are having problems.  Students running several different versions of Windows and Ubuntu have no problem.   The students have the same problem using either the annotation or rnaseqGene workflows

>workflowInstall("annotation")
Warning in install.packages :
  cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
  cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
  unable to access index for repository http://bioconductor.org/packages/3.0/workflows/bin/macosx/mavericks/contrib/3.1

   package ‘annotation’ is available as a source package but not as a binary

Warning in install.packages :
  package ‘annotation’ is not available (as a binary package for R version 3.1.3
 

Thanks, Jeff Blanchard

Two options:

1) have them try it again in a fresh R session (I just changed something);

2) have them do:

workflowInstall("annotation", type="source") 

Dan

This worked for me on a OS X machine I had access to.  It also worked for one other student, but 2 students so far get the following error messages when they run

> source("http://bioconductor.org/workflows.R")
> workflowInstall("rnaseqGene", type = "source")

Warning in install.packages :
  installation of package ‘biovizBase’ had non-zero exit status

Warning in install.packages :
  installation of package ‘Gviz’ had non-zero exit status

ERROR: dependencies ‘DESeq2’, ‘Gviz’ are not available for package ‘rnaseqGene’
* removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/rnaseqGene’
Warning in install.packages :
  installation of package ‘rnaseqGene’ had non-zero exit status

Are they missing a set of libraries (e.g. xml2 or libcurl)?  Do they need XCODE installed?

Thanks again, Jeff

Sorry, I misspoke. They should not do workflowInstall with type="source" but simply do 

workflowInstall("rnaseqGene")

I just verified that works for me on a Mavericks machine.