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

[Shepherd, Lori]

The single package builder has not built in the functionality to obey this particular BBSoption but should be active on the builder once officially accepted into Bioconductor.  Your reviewer will be aware of this and be able to proceed with the review.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Vivek Bhardwaj <bhardwaj using ie-freiburg.mpg.de>
Sent: Thursday, May 31, 2018 11:13:52 AM
To: Herv� Pag�s; bioc-devel using r-project.org
Subject: Re: [Bioc-devel] build cache on bioconductor build system?

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).

@Herv� 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.

Best,

Vivek



On 5/30/18 7:31 PM, Herv� Pag�s 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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>>
>


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