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

[Hervé Pagès]

Hi Vivek,

Are you submitting a package and bumped its version in order to trigger
a new build? The build system used for the submission is the "Single
Package Builder" (SPB) and is not the same as the main builder used
for the daily builds (BBS). It would help if you could provide the link
to the build report where you see the error or at least the name of
your package.

On 05/30/2018 07:30 AM, Vivek Bhardwaj wrote:
> 
> 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.

FWIW the latest version of VariantAnnotation in devel is 1.27.1:

   https://bioconductor.org/packages/3.8/bioc/html/VariantAnnotation.html

and it passes BUILD and CHECK today on all platforms today.

The SPB sometimes needs to install dependencies that in some rare
occasion can get stale a few days later. So in a sense yes it can
cache packages. Lori, our SPB expert, will be able to help you with
this if you provide the name of your package. Thanks!

H.

> 
> Best,
> Vivek
> 
> 
> 
> 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=XilqVN5SNnjEa4_siRsVQPa3EsNEK53OKM7n156DDnc&s=nghjJ8CDqIvM9dcgTCxhGrxP3XlnGhurWc5aREDAIyk&e= , 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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> 
> 

-- 
Hervé Pagès

Program in Computational Biology
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