Re: [Bioc-devel] DMRcaller build error

2018-04-27 Thread Radu Zabet 
Thanks for the feedback!

I've just done that!

Radu

On Fri, Apr 27, 2018 at 8:40 PM, Hervé Pagès  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 > > wrote:
>>
>> Hi Radu,
>>
>> DMRcaller is all green on today's report:
>>
>> https://bioconductor.org/checkResults/3.7/bioc-LATEST/DMRcaller/
>> > 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
>> > 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
>> > 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: hpa...@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: nza...@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: hpa...@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: nza...@essex.ac.uk

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Re: [Bioc-devel] DMRcaller build error

2018-04-27 Thread 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 > wrote:


Hi Radu,

DMRcaller is all green on today's report:

https://bioconductor.org/checkResults/3.7/bioc-LATEST/DMRcaller/



Remember that after you update (and push to git.bioconductor.org

)
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

er
Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@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: nza...@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: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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Re: [Bioc-devel] DMRcaller build error

2018-04-27 Thread Radu Zabet 
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.

Radu

On Fri, Apr 27, 2018 at 8:11 PM, Hervé Pagès  wrote:

> Hi Radu,
>
> DMRcaller is all green on today's report:
>
>   https://bioconductor.org/checkResults/3.7/bioc-LATEST/DMRcaller/
>
> Remember that after you update (and push to git.bioconductor.org) 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
> er
> Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@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: nza...@essex.ac.uk

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Re: [Bioc-devel] DMRcaller build error

2018-04-27 Thread Hervé Pagès 

Hi Radu,

DMRcaller is all green on today's report:

  https://bioconductor.org/checkResults/3.7/bioc-LATEST/DMRcaller/

Remember that after you update (and push to git.bioconductor.org) 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 Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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[Bioc-devel] DMRcaller build error

2018-04-20 Thread Radu Zabet 
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


-- 
Best regards,

Dr Nicolae Radu Zabet
Lecturer in Computational Biology,
School of Biological Sciences,
University of Essex,
Colchester, CO4 3SQ,
United Kingdom

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