Re: [Bioc-devel] failing Bioconductor package DeepBlueR

[Markus List]

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  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=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=sqCu4UFxGa-qRfOicVS9ybuVLjBf9iBoz9K51rrpri8=16yr6qe7_7dlWZwyc2Gc-3FYwTUMp05_zrQefmUS5-s=
> >
> > 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
> > -> 
> > 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=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=sqCu4UFxGa-qRfOicVS9ybuVLjBf9iBoz9K51rrpri8=zpx_S8s7mXlN0c6p-TWbtP_dye8qcH566wopHfbZq6c=
> >
> >
> > 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 
> 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.tur...@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
> >>>  wrote:
> 
> 
> 
>  Lori Shepherd
>  Bioconductor Core Team
>  Roswell Park Cancer Institute
>  Department of Biostatistics & Bioinformatics
>  Elm & Carlton Streets
>  Buffalo, New York 14263
> 
> 
>  From: Markus List 
>  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.l...@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.sheph...@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 
>  Sent: Thursday, September 7, 2017 2:30:10 AM
>  To: Shepherd, Lori; markus.l...@mpi-inf.mpg.de
> 
>  Subject: Re: failing Bioconductor package DeepBlueR
>  Hello Lori,
> 

Re: [Bioc-devel] failing Bioconductor package DeepBlueR

[Hervé Pagès]

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=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=sqCu4UFxGa-qRfOicVS9ybuVLjBf9iBoz9K51rrpri8=16yr6qe7_7dlWZwyc2Gc-3FYwTUMp05_zrQefmUS5-s=

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
-> 
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=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=sqCu4UFxGa-qRfOicVS9ybuVLjBf9iBoz9K51rrpri8=zpx_S8s7mXlN0c6p-TWbtP_dye8qcH566wopHfbZq6c=


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  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 
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

 wrote:




Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263


From: Markus List 
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.l...@mpi-inf.mpg.de
Phone: +49 681 93253016 <0681%2093253016>
Twitter: @itisalist

On Thu, 7 Sep 2017 at 13:15 Shepherd, Lori <

lori.sheph...@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 
Sent: Thursday, September 7, 2017 2:30:10 AM
To: Shepherd, Lori; markus.l...@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.albre...@mpi-inf.mpg.de
https://urldefense.proofpoint.com/v2/url?u=http-3A__felipealbrecht.github.io=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=sqCu4UFxGa-qRfOicVS9ybuVLjBf9iBoz9K51rrpri8=5PsLbRsqSNF8p-aFTTuQCcBfgwWqTvD3zevglr2b5EE=

 Original message 
From: "Shepherd, Lori" 
Date: 06/09/2017 20:56 (GMT+09:00)
To: felipe.albre...@mpi-inf.mpg.de, markus.l...@mpi-inf.mpg.de
Subject: failing Bioconductor package DeepBlueR

Dear DeepBlueR maintainer,

I'd like to bring to your attention that the 

Re: [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
-> 
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  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 
> 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
>>  wrote:
>> >
>> >
>> >
>> > Lori Shepherd
>> > Bioconductor Core Team
>> > Roswell Park Cancer Institute
>> > Department of Biostatistics & Bioinformatics
>> > Elm & Carlton Streets
>> > Buffalo, New York 14263
>> >
>> >
>> > From: Markus List 
>> > 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.l...@mpi-inf.mpg.de
>> > Phone: +49 681 93253016 <0681%2093253016>
>> > Twitter: @itisalist
>> >
>> > On Thu, 7 Sep 2017 at 13:15 Shepherd, Lori <
>> lori.sheph...@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 
>> > Sent: Thursday, September 7, 2017 2:30:10 AM
>> > To: Shepherd, Lori; markus.l...@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.albre...@mpi-inf.mpg.de
>> > http://felipealbrecht.github.io
>> >
>> >  Original message 
>> > From: "Shepherd, Lori" 
>> > Date: 06/09/2017 20:56 (GMT+09:00)
>> > To: felipe.albre...@mpi-inf.mpg.de, markus.l...@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.
>> >
>> 

Re: [Bioc-devel] failing Bioconductor package DeepBlueR

[Markus List]

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 
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 
> wrote:
> >
> >
> >
> > Lori Shepherd
> > Bioconductor Core Team
> > Roswell Park Cancer Institute
> > Department of Biostatistics & Bioinformatics
> > Elm & Carlton Streets
> > Buffalo, New York 14263
> >
> >
> > From: Markus List 
> > 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.l...@mpi-inf.mpg.de
> > Phone: +49 681 93253016 <0681%2093253016>
> > Twitter: @itisalist
> >
> > On Thu, 7 Sep 2017 at 13:15 Shepherd, Lori <
> lori.sheph...@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 
> > Sent: Thursday, September 7, 2017 2:30:10 AM
> > To: Shepherd, Lori; markus.l...@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.albre...@mpi-inf.mpg.de
> > http://felipealbrecht.github.io
> >
> >  Original message 
> > From: "Shepherd, Lori" 
> > Date: 06/09/2017 20:56 (GMT+09:00)
> > To: felipe.albre...@mpi-inf.mpg.de, markus.l...@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
> > 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.
>
>
>
> 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 

Re: [Bioc-devel] failing Bioconductor package DeepBlueR

[Turaga, Nitesh]

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  
> wrote:
> 
> 
> 
> Lori Shepherd
> Bioconductor Core Team
> Roswell Park Cancer Institute
> Department of Biostatistics & Bioinformatics
> Elm & Carlton Streets
> Buffalo, New York 14263
> 
> 
> From: Markus List 
> 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.l...@mpi-inf.mpg.de
> Phone: +49 681 93253016
> Twitter: @itisalist
> 
> On Thu, 7 Sep 2017 at 13:15 Shepherd, Lori  
> 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 
> Sent: Thursday, September 7, 2017 2:30:10 AM
> To: Shepherd, Lori; markus.l...@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
> Email:  felipe.albre...@mpi-inf.mpg.de
> http://felipealbrecht.github.io
> 
>  Original message 
> From: "Shepherd, Lori"  
> Date: 06/09/2017 20:56 (GMT+09:00)
> To: felipe.albre...@mpi-inf.mpg.de, markus.l...@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
> 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.



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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel