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://support.bioconductor.org/p/104502/) 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.hu...@embl.de> wrote:

> Thanks Hervé!
>
> This seems to take a long time to propagate. As of now,
> https://bioconductor.org/packages/devel/bioc/html/GenomicFeatures.html
> 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.hu...@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__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.hu...@embl.de
>>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.hube
>>>>>> r.embl.de&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWd
>>>>>> GbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=jUD3XGyxapAK8nfWvxbR_9Rz7RBx
>>>>>> P592NO0nWz_wyr0&s=Vp0j7sKJXiZSWHn3LVWSECRS-f-AFZZSSh0mq5rvJ-0&e=
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel@r-project.org mailing list
>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>>>>>> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt
>>>>>> 84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=jU
>>>>>> D3XGyxapAK8nfWvxbR_9Rz7RBxP592NO0nWz_wyr0&s=0h8ajRHX9SrbTr3P
>>>>>> P9GKMvt8hoBxj6c4Op-wxmvtyLA&e=
>>>>>>
>>>>>>
>>>>>
>>>>> This email message may contain legally privileged and/or confidential
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>>>>>
>>>> --
>>>> With thanks in advance-
>>>> Wolfgang
>>>>
>>>> -------
>>>> Wolfgang Huber
>>>> Principal Investigator, EMBL Senior Scientist
>>>> European Molecular Biology Laboratory (EMBL)
>>>> Heidelberg, Germany
>>>>
>>>> wolfgang.hu...@embl.de
>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.hube
>>>> r.embl.de&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWd
>>>> GbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=jUD3XGyxapAK8nfWvxbR_9Rz7RBx
>>>> P592NO0nWz_wyr0&s=Vp0j7sKJXiZSWHn3LVWSECRS-f-AFZZSSh0mq5rvJ-0&e=
>>>>
>>>> _______________________________________________
>>>> Bioc-devel@r-project.org mailing list
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>>>> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt
>>>> 84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=jU
>>>> D3XGyxapAK8nfWvxbR_9Rz7RBxP592NO0nWz_wyr0&s=0h8ajRHX9SrbTr3P
>>>> P9GKMvt8hoBxj6c4Op-wxmvtyLA&e=
>>>>
>>>>
>>>     [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel@r-project.org mailing list
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>>> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt
>>> 84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=jU
>>> D3XGyxapAK8nfWvxbR_9Rz7RBxP592NO0nWz_wyr0&s=0h8ajRHX9SrbTr3P
>>> P9GKMvt8hoBxj6c4Op-wxmvtyLA&e=
>>>
>>>
>>
> --
> With thanks in advance-
> Wolfgang
>
> -------
> Wolfgang Huber
> Principal Investigator, EMBL Senior Scientist
> European Molecular Biology Laboratory (EMBL)
> Heidelberg, Germany
>
> wolfgang.hu...@embl.de
> http://www.huber.embl.de
>
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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