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

[Martin Morgan]

On 01/29/2017 11:57 PM, Levi Waldron wrote:
> On Sun, Jan 29, 2017 at 11:36 PM, Martin Morgan
> <martin.morgan at roswellpark.org> wrote:
>>
>>
>> can you try to find out what file it is trying to read and what function call, e.g.,
>>
>>   options(error=recover)
>>   biocLite("lazyeval")
>>
>> That should get the call stack; choose readRDS and look for the 'file' variable for the exact file.
>>
>> Martin
>
>
> It is:
>
> /var/folders/6n/cj15_ryn3ls0jtvfhtxztq080000gn/T//Rtmpvc0v9g/repos_https%3A%2F%2Fcran.rstudio.com%2Fbin%2Fmacosx%2Fmavericks%2Fcontrib%2F3.4.rds
>
>
> Lewis-MacBook-Air:~ lw391$ ls -l
> /var/folders/6n/cj15_ryn3ls0jtvfhtxztq080000gn/T//Rtmpvc0v9g/repos_https%3A%2F%2Fcran.rstudio.com%2Fbin%2Fmacosx%2Fmavericks%2Fcontrib%2F3.4.rds
>

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)? This would sound like an 
RStudio  problem. Is a work-around possible with

   options(repos=c(CRAN="https://cran.r-project.org"))
   biocinstallRepos()                   # should pick up new repository
   biocLite("lazyeval")

?

> -rw-r--r--  1 lw391  staff  0 Jan 29 23:49
> /var/folders/6n/cj15_ryn3ls0jtvfhtxztq080000gn/T//Rtmpvc0v9g/repos_https%3A%2F%2Fcran.rstudio.com%2Fbin%2Fmacosx%2Fmavericks%2Fcontrib%2F3.4.rds
>
> I removed this file, then I could call biocLite once, but the second
> time got the same error and the same file:
>
> /var/folders/6n/cj15_ryn3ls0jtvfhtxztq080000gn/T//Rtmpvc0v9g/repos_https%3A%2F%2Fcran.rstudio.com%2Fbin%2Fmacosx%2Fmavericks%2Fcontrib%2F3.4.rds
>


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