[Bioc-devel] DMRcaller build error

[Radu Zabet]

Thanks for the feedback!

I've just done that!

Radu

On Fri, Apr 27, 2018 at 8:40 PM, Hervé Pagès <hpages at fredhutch.org> wrote:

> On 04/27/2018 12:31 PM, Radu Zabet wrote:
>
>> Thank you for that Herve!
>>
>> I managed to figure out what the problem was.
>>
>> I was using a GRangesList constructor and,  when validating the argument
>> passed to the function, I was checking if the class was GRangesList instead
>> of CompressedGRangesList.
>>
>
> CompressedGRangesList is a subclass of virtual class GRangesList that
> uses a particular internal representation to store the list in an
> efficient manner.
>
> Note that it's alway better to use is(x, "GRangesList") for this kind
> of checks. The exact class of 'x' does not matter as long as 'x' derives
> from GRangesList. Doing class(x) == "CompressedGRangesList" will be
> FALSE if 'x' is another GRangesList derivative and that is probably not
> what you want.
>
> Cheers,
> H.
>
>
>> Radu
>>
>> On Fri, Apr 27, 2018 at 8:11 PM, Hervé Pagès <hpages at fredhutch.org
>> <mailto:hpages at fredhutch.org>> wrote:
>>
>>     Hi Radu,
>>
>>     DMRcaller is all green on today's report:
>>
>>     https://bioconductor.org/checkResults/3.7/bioc-LATEST/DMRcaller/
>>     <https://urldefense.proofpoint.com/v2/url?u=https-3A__
>> bioconductor.org_checkResults_3.7_bioc-2DLATEST_DMRcaller_&d=DwMFaQ&c=
>> eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJ
>> KaaPhzWA&m=sC2oO3c16mMorqdk5d8nvHzqg1dL7v228YdPl836xng&s=FzU
>> y1jhF6u2fVJ4oNL_dP1E2-djzZldXsth0bOXXfEg&e=>
>>
>>     Remember that after you update (and push to git.bioconductor.org
>>     <https://urldefense.proofpoint.com/v2/url?u=http-3A__git.
>> bioconductor.org&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3Xe
>> AvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sC2oO3c16mMorqdk5d8nv
>> Hzqg1dL7v228YdPl836xng&s=XmaKhXkb20E2q6udR5bDulIMCnvWq3qxtVUhHLOTZiQ&e=>)
>>     you
>>     need to wait at least 18h before the update is visible on the build
>>     report. 18h is if you pushed right before the builds start (the
>> software
>>     builds start every day at 4:45 pm EST). If you push right after the
>>     builds start then you will need to wait 42h!
>>
>>     Cheers,
>>     H.
>>
>>     On 04/20/2018 07:47 AM, Radu Zabet wrote:
>>
>>         Hi everyone,
>>
>>         I am the maintainer of DMRcaller. I did an update yesterday and
>>         on the
>>         build report today, the package failed with the error.
>>
>>         Error: processing vignette 'DMRcaller.Rnw' failed with
>> diagnostics:
>>            methylationProfile needs to be a GRangesList
>>         Execution halted
>>
>>
>>         On my machine (MacOS with R 3.4.4) it works
>>
>>         * creating vignettes ... OK
>>
>>         Any suggestion of why this might happen? Is there something I am
>>         missing?
>>
>>         Radu
>>
>>
>>
>>     --     Hervé Pagès
>>
>>     Program in Computational Biology
>>     Division of Public Health Sciences
>>     Fred Hutchinson Canc
>>     <https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.
>> google.com_-3Fq-3DFred-2BHutchinson-2BCanc-26entry-
>> 3Dgmail-26source-3Dg&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7
>> q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sC2oO3c16mMorqdk5
>> d8nvHzqg1dL7v228YdPl836xng&s=9d0yj_ILpvoHB0vJLvElIr7feDGWvi
>> gQCz4J4bsuCbo&e=>er
>>     Research Center
>>     1100 Fairview Ave. N, M1-B514
>>     P.O. Box 19024
>>     Seattle, WA 98109-1024
>>
>>     E-mail: hpages at fredhutch.org <mailto:hpages at fredhutch.org>
>>     Phone:  (206) 667-5791
>>     Fax:    (206) 667-1319
>>
>>
>>
>>
>> --
>> Best regards,
>>
>> Dr Nicolae Radu Zabet
>> Lecturer in Computational Biology,
>> School of Biological Sciences, University of Essex,
>> Colchester, CO4 3SQ, United Kingdom
>> T: +44(0)1206872630
>> E: nzabet at essex.ac.uk <mailto:nzabet at essex.ac.uk>
>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>



-- 
Best regards,

Dr Nicolae Radu Zabet
Lecturer in Computational Biology,
School of Biological Sciences, University of Essex,
Colchester, CO4 3SQ, United Kingdom
T: +44(0)1206872630
E: nzabet at essex.ac.uk

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