[Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?
Wolfgang Huber
wolfgang.huber at embl.de
Fri Feb 2 15:16:40 CET 2018
Thanks Mike and Hervé!
Somehow, errors in examples that are caused by the state (or absence) of
things on the internet should have a different status in my view than
ones that reflect local state of R and packages - and distinguishing
this could make maintenance of the package corpus & builds more modular.
But I'm not entirely confident whether this view is coherent or
practicable, what do others think?
Wolfgang
2.2.18 12:19, Hervé Pagès scripsit:
> Hi Wolfgang, Mike,
>
> We didn't have a successful build of GenomicFeatures in devel
> for many days because of all kinds of problems with the examples
> that try to access the Ensembl marts. The latest of which being:
>
> https://support.bioconductor.org/p/105565/
>
> (which also affects GenomicFeatures in release).
>
> Thanks Mike for looking at the timeout issue (FWIW I can reproduce
> it). I thought this timeout was a new setting on the Ensembl mart
> server side :-)
>
> In GenomicFeatures 1.31.7 I replaced RMySQL with RMariaDB:
>
>
> https://github.com/Bioconductor/GenomicFeatures/commit/08dd24296d94ef31b5f5685240b871c79a160e91
>
>
> I also made another small speed improvement to makeTxDbFromUCSC().
>
> H.
>
>
> On 02/02/2018 02:33 AM, Mike Smith wrote:
>> The error TxDbFromBiomart looks like it might be related to a biomaRt
>> change I made recently to submit queries using httr rather than RCurl.
>> Others have reported something similar (e.g
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_104502_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=nTaIFim9PZDsGaU0xtK3D4cw4UKBrPzen-jCDV-ppDE&s=k3wnoKsf0v7Biv9DKASzF3hSAzhO02fR9UMIiznM2EA&e=)
>> and I raised the timeout from
>> 10 to 60 seconds. I guess with the old version it was even longer than
>> that.
>>
>> I haven't been able to recreate the problem at my end, I think the time
>> taken is related as much to the internet connection as to the query, but
>> I'll take a look at the failing example to see if I can shed any more
>> light
>> on it.
>>
>> Mike
>>
>> On 2 February 2018 at 10:41, Wolfgang Huber <wolfgang.huber at embl.de>
>> wrote:
>>
>>> Thanks Hervé!
>>>
>>> This seems to take a long time to propagate. As of now,
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_devel_bioc_html_GenomicFeatures.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=nTaIFim9PZDsGaU0xtK3D4cw4UKBrPzen-jCDV-ppDE&s=09LGf-6SKIrEdIR2hwC4Vq1YOBj-3PrsuCanwxv9AMs&e=
>>>
>>> still shows 1.31.3.
>>>
>>> ( Btw, there's also an error in the build report which seems to come
>>> from
>>> a rather excessive-looking example in the makeTxDbFromBiomart man page -
>>> that maybe could better live in a vignette, not least for reducing
>>> brittleness? )
>>>
>>> Best wishes
>>> Wolfgang
>>>
>>> 30.1.18 19:00, Hervé Pagès scripsit:
>>>
>>> This is done in GenomicFeatures 1.31.6.
>>>>
>>>> Note that I also made a few changes to makeTxDbFromUCSC() to make it
>>>> a little bit faster (about 2x).
>>>>
>>>> @Kasper: moving the makeTxDb* functions to a GenomicFeaturesBuildTools
>>>> or GenomicFeaturesForge package is maybe an idea to explore...
>>>>
>>>> H.
>>>>
>>>> On 01/26/2018 06:09 PM, Kasper Daniel Hansen wrote:
>>>>
>>>>> As an alternative to Suggests, perhaps make a
>>>>> GenomicFeaturesBuildTools.
>>>>> Not sure if it is better or worse, just different
>>>>>
>>>>> On Fri, Jan 26, 2018 at 2:39 PM, Wolfgang Huber
>>>>> <wolfgang.huber at embl.de>
>>>>> wrote:
>>>>>
>>>>>
>>>>>>
>>>>>> 26.1.18 14:59, Martin Morgan scripsit:
>>>>>>
>>>>>> On 01/24/2018 03:38 PM, Wolfgang Huber wrote:
>>>>>>>
>>>>>>> GenomicFeatures_1.31.3 imports RMySQL.
>>>>>>>>
>>>>>>>> I'm having great trouble installing RMySQL from source on a recent
>>>>>>>> MacOS
>>>>>>>> (10.13.3) with homebrew.
>>>>>>>>
>>>>>>>> The package's homepage says "The 'RMySQL' package contains an old
>>>>>>>> implementation based on legacy code from S-PLUS which being phased
>>>>>>>> out. A
>>>>>>>> modern 'MySQL' client based on 'Rcpp' is available from the
>>>>>>>> 'RMariaDB'
>>>>>>>> package"
>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-
>>>>>>>> 2Dproject.org_web_packages_RMySQL_index.html&d=DwICAg&c=eRAM
>>>>>>>> FD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaP
>>>>>>>> hzWA&m=jUD3XGyxapAK8nfWvxbR_9Rz7RBxP592NO0nWz_wyr0&s=0neTB2B
>>>>>>>> Jghm4wF-LnEZ9V9sV_AbF1botcOeTb_bWk-w&e=
>>>>>>>>
>>>>>>>> So is it time to heed that advice and migrate GenomicFeatures to
>>>>>>>> RMariaDB ?
>>>>>>>>
>>>>>>>>
>>>>>>> Out of curiosity, is MariaDB easier to install on your system? Its
>>>>>>> system
>>>>>>> dependencies are described at
>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__urldefense.proofpoint&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=nTaIFim9PZDsGaU0xtK3D4cw4UKBrPzen-jCDV-ppDE&s=t1JSruTyZxTGystW_bcaK5XfEnAVD0dTfxdLOO3boT4&e=.
>>>>>>>
>>>>>>> com/v2/url?u=https-3A__CRAN.R-2Dproject.org_package-3DRMaria
>>>>>>> DB&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJ
>>>>>>> YbW0WYiZvSXAJJKaaPhzWA&m=jUD3XGyxapAK8nfWvxbR_9Rz7RBxP592NO0
>>>>>>> nWz_wyr0&s=55tLfrRpaigMug-pW7L1AhpsD1A830xw1f9d1FZEANo&e=
>>>>>>>
>>>>>>>
>>>>>> I have no problems installing RMariaDB on MacOS (10.13.3) on an
>>>>>> R-devel
>>>>>> from source, after installing mariadb-connector-c with homebrew.
>>>>>>
>>>>>> OTOH, I have not figured out a way to install RMySQL neither on my
>>>>>> R-devel
>>>>>> from source (various complaints about missing .h files) nor on a
>>>>>> binary
>>>>>> R
>>>>>> 3.4.2 with the binary package download (complaints about missing
>>>>>> system
>>>>>> libraries / wrong versions).
>>>>>>
>>>>>> Thanks and kind regards
>>>>>> Wolfgang
>>>>>>
>>>>>> FWIW MySQL is a relatively recent addition as a dependency to
>>>>>>
>>>>>>> GenomicFeatures; it enables `makeTxDbFromEnsembl()`, which is
>>>>>>> probably
>>>>>>> a
>>>>>>> much more stable solution than `makeTxDbFromBiomart()`. On the other
>>>>>>> had
>>>>>>> Johannes does an excellent job on the ensembldb packages, so perhaps
>>>>>>> this
>>>>>>> code could really be conditional with the RMySQL dependency moved to
>>>>>>> Suggests:
>>>>>>>
>>>>>>> Martin
>>>>>>>
>>>>>>>
>>>>>>> With thanks in advance-
>>>>>>>> Wolfgang
>>>>>>>>
>>>>>>>> -------
>>>>>>>> Wolfgang Huber
>>>>>>>> Principal Investigator, EMBL Senior Scientist
>>>>>>>> European Molecular Biology Laboratory (EMBL)
>>>>>>>> Heidelberg, Germany
>>>>>>>>
>>>>>>>> wolfgang.huber at embl.de
>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.hube
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>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>>
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>>>>>> --
>>>>>> With thanks in advance-
>>>>>> Wolfgang
>>>>>>
>>>>>> -------
>>>>>> Wolfgang Huber
>>>>>> Principal Investigator, EMBL Senior Scientist
>>>>>> European Molecular Biology Laboratory (EMBL)
>>>>>> Heidelberg, Germany
>>>>>>
>>>>>> wolfgang.huber at embl.de
>>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.hube
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>>>>> [[alternative HTML version deleted]]
>>>>>
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>>>>>
>>>>>
>>>>
>>> --
>>> With thanks in advance-
>>> Wolfgang
>>>
>>> -------
>>> Wolfgang Huber
>>> Principal Investigator, EMBL Senior Scientist
>>> European Molecular Biology Laboratory (EMBL)
>>> Heidelberg, Germany
>>>
>>> wolfgang.huber at embl.de
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.huber.embl.de&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=nTaIFim9PZDsGaU0xtK3D4cw4UKBrPzen-jCDV-ppDE&s=y0PiNkZtZmjkVXUcY4uOoz6Dism0uJaGHU8tDbtbqXU&e=
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>>>
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>>
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>
--
With thanks in advance-
Wolfgang
-------
Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany
wolfgang.huber at embl.de
http://www.huber.embl.de
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