[Bioc-devel] DMRcaller build error

[Hervé Pagès]

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_wJYbW0WYiZvSXAJJKaaPhzWA&m=sC2oO3c16mMorqdk5d8nvHzqg1dL7v228YdPl836xng&s=FzUy1jhF6u2fVJ4oNL_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=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sC2oO3c16mMorqdk5d8nvHzqg1dL7v228YdPl836xng&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=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sC2oO3c16mMorqdk5d8nvHzqg1dL7v228YdPl836xng&s=9d0yj_ILpvoHB0vJLvElIr7feDGWvigQCz4J4bsuCbo&e=>er
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> 
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>     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