[Bioc-devel] failing Bioconductor package DeepBlueR

Wed Sep 13 09:55:17 CEST 2017

Dear Hervé,

You are right. I found the issue in rtracklayer and made a pull request
with a fix.
https://github.com/lawremi/rtracklayer/pull/1

Thanks for your help.

Best,
Markus

On Tue, 12 Sep 2017 at 18:01 Hervé Pagès <hpages at fredhutch.org> wrote:

> Hi Markus,
>
> The class cache issue is just a warning here and is distracting.
>
> What seems to break deepblue_liftover() is a recent
> change to rtracklayer::import.chain. Looks like commit
> a3c4308d928290700c6326eabda8dea4a96146e3 from Sep 4 might
> be the culprit.
>
> Cheers,
> H.
>
> On 09/12/2017 06:29 AM, Markus List wrote:
> > Dear all,
> >
> > Our DeepBlueR package is currently not passing R CMD check in devel
> because
> > of a class cache issue:
> >
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_DeepBlueR_tokay1-2Dchecksrc.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sqCu4UFxGa-qRfOicVS9ybuVLjBf9iBoz9K51rrpri8&s=16yr6qe7_7dlWZwyc2Gc-3FYwTUMp05_zrQefmUS5-s&e=
> >
> > Found more than one class "file" in cache; using the first, from
> > namespace 'BiocGenerics'
> > Also defined by ‘filehash’
> > Error in (function (classes, fdef, mtable)  :
> >    unable to find an inherited method for function ‘path’ for signature
> ‘"file"’
> > Calls: deepblue_liftover ... import -> .local -> path.expand -> path
> > -> <Anonymous>
> > Execution halted
> >
> > I suspect this is caused by a conflict between filehashdb and
> BiocGenerics
> > which both use setOldClass with "file" to S4ify it. setOldClass has
> caused
> > trouble for other people, too:
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stackoverflow.com_questions_44295792_setoldclassxts-2Dcausing-2Dproblems-2Din-2Da-2Dcustom-2Dr-2Dpackage&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sqCu4UFxGa-qRfOicVS9ybuVLjBf9iBoz9K51rrpri8&s=zpx_S8s7mXlN0c6p-TWbtP_dye8qcH566wopHfbZq6c&e=
> >
> >
> > Still, don't know is why this suddenly leads to an error in devel and how
> > to fix it.
> >
> > Any ideas?
> >
> > Best,
> >
> > Markus
> >
> > On Mon, 11 Sep 2017 at 11:21 Markus List <markus.list at mpi-inf.mpg.de>
> wrote:
> >
> >> Hi Nitesh,
> >>
> >> Thanks for looking into it. Unfortunately, I still can't access the
> >> repository since I was using a DSA key which was previously mentioned
> here
> >> as not supported. I thus generated an RSA key and added it to github.
> Will
> >> newly added github keys be automatically imported? If not could you
> please
> >> add my new key (github username mlist).
> >>
> >> Best,
> >> Markus
> >>
> >>
> >> On Fri, 8 Sep 2017 at 15:12 Turaga, Nitesh <
> Nitesh.Turaga at roswellpark.org>
> >> wrote:
> >>
> >>> Hi Markus,
> >>>
> >>> Your SSH key has been accepted, but you don’t have access to the
> >>> repository because the SVN system did not know you have access rights
> to
> >>> this package.
> >>>
> >>> I’ll give you access rights to that package.
> >>>
> >>> Best
> >>>
> >>> Nitesh
> >>>
> >>>> On Sep 8, 2017, at 7:34 AM, Shepherd, Lori
> >>> <Lori.Shepherd at RoswellPark.org> wrote:
> >>>>
> >>>>
> >>>>
> >>>> Lori Shepherd
> >>>> Bioconductor Core Team
> >>>> Roswell Park Cancer Institute
> >>>> Department of Biostatistics & Bioinformatics
> >>>> Elm & Carlton Streets
> >>>> Buffalo, New York 14263
> >>>>
> >>>>
> >>>> From: Markus List <markus.list at mpi-inf.mpg.de>
> >>>> Sent: Friday, September 8, 2017 4:31 AM
> >>>> To: Shepherd, Lori; Felipe Albrecht
> >>>> Subject: Re: failing Bioconductor package DeepBlueR
> >>>>
> >>>> Dear Lori,
> >>>>
> >>>> Since Felipe is on vacation I wanted to look into this issue but I can
> >>> not push any changes to the new git repository. I tried to get my SSH
> keys
> >>> accepted twice (August 18 and 22) for this by submitting my github id
> in
> >>> the google form you provide but I have not received any response in .
> Can
> >>> you help me out? My github id is 'mlist'.
> >>>>
> >>>> Best,
> >>>> Markus
> >>>>
> >>>>
> >>>> --
> >>>> Markus List
> >>>> Postdoc, Computational Biology & Applied Algorithmics
> >>>> Associate Editor, BMC Systems Biology
> >>>> Max-Planck Institute for Informatics
> >>>> Saarland Informatics Campus
> >>>> Building E1.4, Room 516, 66123 Saarbrücken, Germany
> >>>> E-mail: markus.list at mpi-inf.mpg.de
> >>>> Phone: +49 681 93253016 <0681%2093253016> <0681%2093253016>
> >>>> Twitter: @itisalist
> >>>>
> >>>> On Thu, 7 Sep 2017 at 13:15 Shepherd, Lori <
> >>> Lori.Shepherd at roswellpark.org> wrote:
> >>>> Ok. Thank you very much for looking into this.
> >>>>
> >>>> Lori Shepherd
> >>>> Bioconductor Core Team
> >>>> Roswell Park Cancer Institute
> >>>> Department of Biostatistics & Bioinformatics
> >>>> Elm & Carlton Streets
> >>>> Buffalo, New York 14263
> >>>> From: Felipe Albrecht <felipe.albrecht at mpi-inf.mpg.de>
> >>>> Sent: Thursday, September 7, 2017 2:30:10 AM
> >>>> To: Shepherd, Lori; markus.list at mpi-inf.mpg.de
> >>>>
> >>>> Subject: Re: failing Bioconductor package DeepBlueR
> >>>> Hello Lori,
> >>>> Since the problem is only in the devel branch, I will fix this issue
> >>> during next week because I'm out of office right now.
> >>>>
> >>>> Thank you for informing!
> >>>> Felipe Albrecht
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Max Planck Institute for Informatics
> >>>> Computational Biology and Applied Algorithmics Department
> >>>> Campus E 1.4
> >>>> Room 508
> >>>> 66123 Saarbrücken
> >>>> Germany
> >>>> Phone: +49 (681) 9325 3008 <0681%2093253008> <0681%2093253008>
> >>>> Email:  felipe.albrecht at mpi-inf.mpg.de
> >>>>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__felipealbrecht.github.io&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sqCu4UFxGa-qRfOicVS9ybuVLjBf9iBoz9K51rrpri8&s=5PsLbRsqSNF8p-aFTTuQCcBfgwWqTvD3zevglr2b5EE&e=
> >>>>
> >>>> -------- Original message --------
> >>>> From: "Shepherd, Lori" <Lori.Shepherd at RoswellPark.org>
> >>>> Date: 06/09/2017 20:56 (GMT+09:00)
> >>>> To: felipe.albrecht at mpi-inf.mpg.de, markus.list at mpi-inf.mpg.de
> >>>> Subject: failing Bioconductor package DeepBlueR
> >>>>
> >>>> Dear DeepBlueR maintainer,
> >>>>
> >>>> I'd like to bring to your attention that the DeepBlueR package is
> >>> failing to pass 'R CMD build' on all platforms in the devel version of
> >>> Bioconductor (i.e. BioC 3.6):
> >>>>
> >>>>
> >>>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_3.6_bioc-2DLATEST_DeepBlueR_malbec1-2Dbuildsrc.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sqCu4UFxGa-qRfOicVS9ybuVLjBf9iBoz9K51rrpri8&s=HBR9LT3bziKoBkC1YrtJbJJhDmCm56qZ-0P_7faa7A4&e=
> >>>>
> >>>> Would you mind taking a look at this? Don't hesitate to ask on the
> >>> bioc-devel mailing list if you have any question or need help.
> >>>>
> >>>> If no action is taken over the next few weeks we will begin the
> >>> deprecation process for your package.  Thank you for your time and
> effort.
> >>>>
> >>>>
> >>>> Thanks for your contribution to Bioconductor.
> >>>>
> >>>> Pleae be advised that Bioconductor has switched from svn to Git. Some
> >>> helpful
> >>>> links can be found here:
> >>>>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_how-2Dto_git_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sqCu4UFxGa-qRfOicVS9ybuVLjBf9iBoz9K51rrpri8&s=-PxcuWWc9WNLZR5Q0iP67tH5aI29Y2ko8u_PDcIIONk&e=
> >>>>
> >>>>
> >>>>
> >>>> Lori Shepherd
> >>>> Bioconductor Core Team
> >>>> Roswell Park Cancer Institute
> >>>> Department of Biostatistics & Bioinformatics
> >>>> Elm & Carlton Streets
> >>>> Buffalo, New York 14263
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> >>>
> >>>
> >>> This email message may contain legally privileged and/or confidential
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> >>
> >>
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sqCu4UFxGa-qRfOicVS9ybuVLjBf9iBoz9K51rrpri8&s=Iwss_CBq6lciZgUI67nVIHI57fya-eONuTlZ2VrxcNA&e=
> >
>
> --
> 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: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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