[Bioc-devel] Package failure due to GenomicFeatures update

[Bora.Uyar at mdc-berlin.de]

Thank you Herve! Then, I will pull the code from github to update my code, too. 

Hopefully my package will also go through by 24th :)

Best,
Bora

________________________________________
From: Hervé Pagès [hpages at fredhutch.org]
Sent: Monday, October 23, 2017 6:17 AM
To: Uyar, Bora; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Package failure due to GenomicFeatures update

Hi Bora,

I just fixed this in GenomicFeatures 1.29.15. The error on the build
report won't clear until Tuesday Oct 24 though.

Cheers,
H.


On 10/22/2017 02:59 PM, Bora.Uyar at mdc-berlin.de wrote:
> Hi,
>
> I am the maintainer of the RCAS package. Currently, my package build report shows errors related to the latest commit to GenomicFeatures package (See https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_GenomicFeatures_commit_22b2ea0a81bc064b8554400ce8f7e13e2c833d38&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=e8T4CsJ2raHfOGvsnVFQx06c-caNBkRlC-Wgnb6hL7Q&s=bz4mjLoa7FjycKUx_wCB7Ic1b2nOpTJt0J69fXSaasQ&e=). GenomicFeatures is showing errors because of the same reason.
>
> This is an excerpt from the GenomicFeatures build report:
> "# Creation time: 2017-10-22 00:29:43 -0400 (Sun, 22 Oct 2017)
>
> # GenomicFeatures version at creation time: 1.29.14
> # RSQLite version at creation time: 2.0
> # DBSCHEMAVERSION: 1.2
>>
>> ## Reverse operation:
>> gr2 <- asGFF(txdb)
>>
>> ## Sanity check:
>> stopifnot(identical(as.list(txdb), as.list(makeTxDbFromGRanges(gr2))))
> Error in .get_cds_IDX(type, phase) :
>    when 'gr' contains CDS features, it must have a "phase" metadata column
>    and the phase must be 0, 1, or 2, for all the CDS features
> Calls: stopifnot ... identical -> as.list -> makeTxDbFromGRanges -> .get_cds_IDX
> Execution halted”
>
> The build report for RCAS shows the same error. However, I cannot fix this problem because I can only install GenomicFeatures version 1.29.13, but the bioc-build system is using GenomicFeatures v1.29.14.
>
> Do you know when this will be solved?
>
> Best,
> Bora
>
> _____________
>
> Dr. Bora Uyar
>
> Bioinformatics Scientist
> Scientific Bioinformatics Platform
> The Berlin Institute for Medical Systems Biology (BIMSB)
> Max Delbrueck Center (MDC) for Molecular Medicine
>
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>
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>
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--
Hervé Pagès

Program in Computational Biology
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