[Bioc-devel] failing Bioconductor package DeepBlueR

Tue Sep 12 18:01:19 CEST 2017

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>
>>>> 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>
>>>> 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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>>
>>
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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