[Bioc-devel] failing Bioconductor package DeepBlueR

[Markus List]

Dear all,

Our DeepBlueR package is currently not passing R CMD check in devel because
of a class cache issue:

http://bioconductor.org/checkResults/devel/bioc-LATEST/DeepBlueR/tokay1-checksrc.html

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://stackoverflow.com/questions/44295792/setoldclassxts-causing-problems-in-a-custom-r-package


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
>> > http://felipealbrecht.github.io
>> >
>> > -------- 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):
>> >
>> >
>> http://bioconductor.org/checkResults/3.6/bioc-LATEST/DeepBlueR/malbec1-buildsrc.html
>> >
>> > 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://bioconductor.org/developers/how-to/git/
>> >
>> >
>> >
>> > 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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