[Bioc-devel] failing Bioconductor package DeepBlueR

Wed, Sep 13, 2017 12:55 AM

Dear Herv?,

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 Herv? Pag?s <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 Saarbr?cken, 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 Saarbr?cken
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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[Bioc-devel] failing Bioconductor package DeepBlueR

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