[Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

[Martin Morgan]

On 01/31/2017 11:41 AM, Vincent Carey wrote:
>
>
> On Mon, Jan 30, 2017 at 11:14 PM, Martin Morgan
> <martin.morgan at roswellpark.org <mailto:martin.morgan at roswellpark.org>>
> wrote:
>
>     On 01/30/2017 09:52 AM, Levi Waldron wrote:
>
>         On Mon, Jan 30, 2017 at 12:23 AM, Martin Morgan
>         <martin.morgan at roswellpark.org
>         <mailto:martin.morgan at roswellpark.org>> wrote:
>
>             It seems like this is a local cache of the rstudio file that
>             describes the
>             mac repository. Maybe your vanilla execution of
>             install.packages() does not
>             use the repository that BiocInstaller does. So maybe
>
>                 install.packages("lazyeval", repos=biocinstallRepos())
>
>             fails (maybe if repeated a second time)?
>
>
>         Yes, you're right, it fails.
>
>
>     so it seems like you can make this fail with pure R commands,
>     repos="https://cran.r-project.org <https://cran.r-project.org>" or
>     maybe a vector of two repositories?
>
>     artin
>
>             This would sound like an RStudio
>             problem. Is a work-around possible with
>
>               options(repos=c(CRAN="https://cran.r-project.org
>             <https://cran.r-project.org>"))
>               biocinstallRepos()                   # should pick up new
>             repository
>               biocLite("lazyeval")
>
>
>         This works for one install, then subsequently produces the same
>         error:
>
>         Browse[1]> file
>
>         [1]
>         "/var/folders/6n/cj15_ryn3ls0jtvfhtxztq080000gn/T//RtmpYdXlSZ/repos_https%3A%2F%2Fcran.r-project.org
>         <http://2Fcran.r-project.org>%2Fbin%2Fmacosx%2Fmavericks%2Fcontrib%2F3.4.rds"
>
>
> we triggered the problem on a new Rstudio under Sierra ... the offending
> RDS file from cran.rstudio.org <http://cran.rstudio.org> is still present.
>
> we wanted to install ldblock in the devel branch, and succeeded with
>
> install.packages("ldblock", repos="https://bioconductor.org/3.5/bioc")
>
> and this succeeded repetitively
>
> there is something wrong with the process in biocLite that creates the file
>
> /var/folders/6n/cj15_ryn3ls0jtvfhtxztq080000gn/T//Rtmpvc0v9g/repos_https%3A%2F%2Fcran.rstudio.com
> <http://2fcran.rstudio.com/>%2Fbin%2Fmacosx%2Fmavericks%2Fcontrib%2F3.4.rds
>
> can't track any further at this time

Levi triggered the problem with install.packages("lazyeval", 
repos=biocinstallRepos(), which is an R-only command. Also, there have 
not been any changes to the logic of biocLite() in this regard, so the 
problem is likely to be in R (devel) per se. I'll try to get access to a 
Mac and investigate.

Martin

>
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