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

[Vincent Carey]

On Mon, Jan 30, 2017 at 11:14 PM, Martin Morgan <
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> 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" 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"))
>>>   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//RtmpYdXlS
>> Z/repos_https%3A%2F%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 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


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