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 >>>>> information. If you are not the intended recipient(s), or the >>>>> employee or >>>>> agent responsible for the delivery of this message to the intended >>>>> recipient(s), you are hereby notified that any disclosure, copying, >>>>> distribution, or use of this email message is prohibited. If you have >>>>> received this message in error, please notify the sender immediately by >>>>> e-mail and delete this email message from your computer. Thank you. >>>>> >>>>> >>>> -- >>>> 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= >>>> >>>> >>> [[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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel