[Bioc-devel] build cache on bioconductor build system?

Vivek Bhardwaj bh@rdw@j @ending from ie-freiburg@mpg@de
Wed May 30 16:30:24 CEST 2018

The package throwing error is*VariantAnnotation *(coming from function: 
locateVariants). I checked it's build for the dev branch and indeed it's 
broken. **

All right then I would remove version specification from my package and 
I guess I'll wait for**VariantAnnotation to get fixed.


On 05/30/2018 04:04 PM, Martin Morgan wrote:
> There is no cache; like users you get the 'current' version of the 
> package from the relevant repository. If your package used 
> concatenateObjects, then it needs to be updated. If your package is 
> broken through a third package, it needs to be fixed (perhaps it has 
> been but did not propagate, see the build reports for packages in the 
> devel branch http://bioconductor.org/checkResults/ , and look for the 
> stoplight at the right).
> Martin
> On 05/30/2018 09:56 AM, Vivek Bhardwaj wrote:
>> Hi All
>> Is there any build cache on bioc build system? I updated S4Vector and
>> IRanges in my dependencies and triggered a new build of my package, only
>> to find that this broke other dependencies due to renaming of function
>> `concatenateObjects ` to `bindRows` in S4Vector. Now I removed the
>> mentioned versions in my DESCRIPTION, but the build is still broken.
>> Also tried specifying a particular version of these packages and I get
>> the error :
>> ** byte-compile and prepare package for lazy loading Error in
>> loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck =
>> vI[[j]]) : namespace 'IRanges' 2.15.13 is already loaded, but == 2.14.10
>> is required
>> How do I refresh the cache?
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Best Wishes


*Vivek Bhardwaj*
PhD Candidate | International Max Planck Research School
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51, Freiburg
E-mail: bhardwaj using ie-freiburg.mpg.de
Tel: +49-761-5108-472
Website: https://vivekbhr.github.io

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