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

Vivek Bhardwaj bh@rdw@j @ending from ie-freiburg@mpg@de
Thu May 31 17:13:52 CEST 2018

The name of my package is icetea. Here's the link 
<https://github.com/Bioconductor/Contributions/issues/719> to the 
submission. I checked today and VariantAnnotation build was passing now, 
so simply re-pushed with bumped version and it worked! (well not 
exactly, I still have the RSubread issue with windows that I mentioned 
last week, but at least VariantAnnotation is not throwing errors).

@Hervé Regarding the issue with RSubread, I tried adding the .BBSoptions 
file in the package source dir. Although I added this file under 
.Rbuildignore as well to avoid R CMD check complaining about 
non-standard dir. It didn't work.

Thanks for the input everyone.



On 5/30/18 7:31 PM, Hervé Pagès wrote:
> 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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