Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop application deadline May 17

2018-06-12 Thread Pijush Das 
Hello Mike,



There is a little mistake in the DESCRIPTION file in my package named
"sigFeature".
In the Description portion inside the DESCRIPTION file, there are
words " Bayesian
T statistic",
it is wrongly placed there. This should be only "t- statistic".

You have given an instruction a month before. According to that instruction
I am trying to solve the problem.
But I have faced another issue which I do not understand.
Please help me to solve that. The Problem is given below.

PC MINGW64 ~/Desktop/BioconductorEdit/sigFeature (master)
$ git push upstream master
fatal: 'upstream' does not appear to be a git repository
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.



Thank you



regards
Pijush





On Fri, May 11, 2018 at 12:12 PM, Mike Smith  wrote:

> Dear Pijush,
>
> Once a package has been accepted to Bioconductor, a copy is made in
> Bioconductor's own git repository and this is the source from which the
> packages are made available to users.  Any change you make in Github won't
> be automatically reflected there, you have to explicitly make the change in
> git.bioconductor.org.
>
> It sounds like you should take a look at https://bioconductor.org/
> developers/how-to/git/new-package-workflow/ to make sure you have access
> to the Bioconductor repository (maybe you've already done this if you've
> added an SSH key) and then https://bioconductor.org/
> developers/how-to/git/push-to-github-bioc/ which describes how to make
> sure you commit changes both to your Github repository and the version at
> Bioconductor.
>
> Regards,
>
> Mike
>
> On 11 May 2018 at 05:48, Pijush Das  wrote:
>
>> Dear Martin Morgan,
>>
>>
>> I have successfully added the SSH key in github account and Bioconductor.
>> After rechecking the package in Bioconductor I have found that there is a
>> mistake
>> in the DESCRIPTION file.
>> In the Description portion inside the DESCRIPTION file, there are
>> words " Bayesian
>> T statistic",
>> it is wrongly placed there. This should be only "t- statistic".
>> I have change it in the github with a version bump.
>>
>> Is that change can be seen in Bioconductor automatically?
>> Or I have to do anything else? Please let me know.
>>
>> Thank you
>>
>>
>> regards
>> Pijush
>>
>>
>>
>>
>>
>>
>>
>>
>> On Wed, May 9, 2018 at 7:15 PM, Martin Morgan <
>> martin.mor...@roswellpark.org
>> > wrote:
>>
>> > The scholarships support up to $500 travel. The scholarship also covers
>> > accommodation and registration.
>> >
>> > A letter inviting you to the conference will be sent separately.
>> >
>> > Martin
>> >
>> > On 05/09/2018 01:13 AM, Pijush Das wrote:
>> >
>> >> Dear Martin Morgan,
>> >>
>> >>
>> >> Thank you Morgan for informing me to join your annual conference BioC
>> >> 2018.
>> >> I am very much interested to attend the BioC 2018 conference.
>> >> Presently I am perusing my PhD from CSIR-Indian Institute of Chemical
>> >> biology.
>> >> So it is not possible to collect all the money to pay all the expenses
>> >> myself.
>> >>
>> >>
>> >> I would like to know if I am selected for the scholarship, they will
>> pay
>> >> for costs such as
>> >> travel, accommodation, and registration ? Or they will pay only $500
>> per
>> >> person?
>> >>
>> >>
>> >> If it is possible please send me an invitation letter for the annual
>> >> conference BioC 2018.
>> >> The invitation letter will help me for grant application to the indian
>> >> funding body such as DBT or CSIR etc.
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> Thank you
>> >>
>> >>
>> >>
>> >> regards
>> >> Pijush
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> On Mon, May 7, 2018 at 2:59 AM, Martin Morgan <
>> >> martin.mor...@roswellpark.org >
>> >> wrote:
>> >>
>> >> Join us for our annual conference BioC 2018: Where Software and
>> >> Biology Connect, at Victoria University on the University of
>> Toronto
>> >> campus
>> >>
>> >> http://bioc2018.bioconductor.org > >
>> >>
>> >> The deadline for poster, talk, scholarship (travel, accommodation,
>> >> and registration), and workshop applications is May 17, see
>> >>
>> >> http://bioc2018.bioconductor.org/call-for-abstracts
>> >> 
>> >> http://bioc2018.bioconductor.org/scholarships
>> >> 
>> >>
>> >> Martin Morgan
>> >> Bioconductor
>> >>
>> >>
>> >> This email message may contain legally privileged
>> >> and/or...{{dropped:2}}
>> >>
>> >> ___
>> >> Bioc-devel@r-project.org  mailing
>> >> list
>> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >> 
>> >>
>> >>
>> >>
>> >
>> > This email message may contain legally privil

Re: [Bioc-devel] About CMEA package

2018-06-12 Thread Shepherd, Lori 
The issue has been reopened.


Please make sure the webhook is still initialized

https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#adding-a-web-hook


Please also bump the version so that a new build report can be generated.


Your reviewer will get back to you and further correspondence can be on the 
github issue directly:

https://github.com/Bioconductor/Contributions/issues/344




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Isar Nassiri 

Sent: Monday, June 11, 2018 11:53:32 PM
To: Bioconductor/Contributions; Morgan, Martin; bioc-devel@r-project.org
Subject: [Bioc-devel] About CMEA package

Dear Martin,


This is the developer of CMEA package.


You have closed the issue because of my delayed response. As I explained in my 
commented message on Nov 12, 2017, my URMC email was terminated, and I did not 
receive your message on time. I read it on the web page of the package and 
revised the package accordingly. Now the package is ready.


Could you please active the issue?  what is the solution?


Related links:
Bioconductor/Contributions
https://github.com/Bioconductor/Contributions/issues/344
Bioconductor Package Builder - Build History
http://bioconductor.org/spb_reports/CMEA_buildreport_20171117051310.html
GitHub repository of the package
https://github.com/isarnassiri/CMEA


Best regards,

Isar

--
Isar Nassiri, PhD.
Researcher
Department of Oncology
MRC Weatherall Institute of Molecular Medicine
University of Oxford
John Radcliffe Hospital
Headington
Oxford OX3 9DS
United Kingdom
Tel: +44 1865 222569
isar.nass...@oncology.ox.ac.uk
--


[[alternative HTML version deleted]]

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Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop application deadline May 17

2018-06-12 Thread Shepherd, Lori 
What is the results of


git remote -v


Did you add an upstream remote pointing to your package as described in the 
link Mike sent:

https://bioconductor.org/developers/how-to/git/new-package-workflow/






Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Pijush Das 

Sent: Tuesday, June 12, 2018 3:48:04 AM
To: Mike Smith
Cc: bioc-devel
Subject: Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop 
application deadline May 17

Hello Mike,



There is a little mistake in the DESCRIPTION file in my package named
"sigFeature".
In the Description portion inside the DESCRIPTION file, there are
words " Bayesian
T statistic",
it is wrongly placed there. This should be only "t- statistic".

You have given an instruction a month before. According to that instruction
I am trying to solve the problem.
But I have faced another issue which I do not understand.
Please help me to solve that. The Problem is given below.

PC MINGW64 ~/Desktop/BioconductorEdit/sigFeature (master)
$ git push upstream master
fatal: 'upstream' does not appear to be a git repository
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.



Thank you



regards
Pijush





On Fri, May 11, 2018 at 12:12 PM, Mike Smith  wrote:

> Dear Pijush,
>
> Once a package has been accepted to Bioconductor, a copy is made in
> Bioconductor's own git repository and this is the source from which the
> packages are made available to users.  Any change you make in Github won't
> be automatically reflected there, you have to explicitly make the change in
> git.bioconductor.org.
>
> It sounds like you should take a look at https://bioconductor.org/
> developers/how-to/git/new-package-workflow/ to make sure you have access
> to the Bioconductor repository (maybe you've already done this if you've
> added an SSH key) and then https://bioconductor.org/
> developers/how-to/git/push-to-github-bioc/ which describes how to make
> sure you commit changes both to your Github repository and the version at
> Bioconductor.
>
> Regards,
>
> Mike
>
> On 11 May 2018 at 05:48, Pijush Das  wrote:
>
>> Dear Martin Morgan,
>>
>>
>> I have successfully added the SSH key in github account and Bioconductor.
>> After rechecking the package in Bioconductor I have found that there is a
>> mistake
>> in the DESCRIPTION file.
>> In the Description portion inside the DESCRIPTION file, there are
>> words " Bayesian
>> T statistic",
>> it is wrongly placed there. This should be only "t- statistic".
>> I have change it in the github with a version bump.
>>
>> Is that change can be seen in Bioconductor automatically?
>> Or I have to do anything else? Please let me know.
>>
>> Thank you
>>
>>
>> regards
>> Pijush
>>
>>
>>
>>
>>
>>
>>
>>
>> On Wed, May 9, 2018 at 7:15 PM, Martin Morgan <
>> martin.mor...@roswellpark.org
>> > wrote:
>>
>> > The scholarships support up to $500 travel. The scholarship also covers
>> > accommodation and registration.
>> >
>> > A letter inviting you to the conference will be sent separately.
>> >
>> > Martin
>> >
>> > On 05/09/2018 01:13 AM, Pijush Das wrote:
>> >
>> >> Dear Martin Morgan,
>> >>
>> >>
>> >> Thank you Morgan for informing me to join your annual conference BioC
>> >> 2018.
>> >> I am very much interested to attend the BioC 2018 conference.
>> >> Presently I am perusing my PhD from CSIR-Indian Institute of Chemical
>> >> biology.
>> >> So it is not possible to collect all the money to pay all the expenses
>> >> myself.
>> >>
>> >>
>> >> I would like to know if I am selected for the scholarship, they will
>> pay
>> >> for costs such as
>> >> travel, accommodation, and registration ? Or they will pay only $500
>> per
>> >> person?
>> >>
>> >>
>> >> If it is possible please send me an invitation letter for the annual
>> >> conference BioC 2018.
>> >> The invitation letter will help me for grant application to the indian
>> >> funding body such as DBT or CSIR etc.
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> Thank you
>> >>
>> >>
>> >>
>> >> regards
>> >> Pijush
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> On Mon, May 7, 2018 at 2:59 AM, Martin Morgan <
>> >> martin.mor...@roswellpark.org >
>> >> wrote:
>> >>
>> >> Join us for our annual conference BioC 2018: Where Software and
>> >> Biology Connect, at Victoria University on the University of
>> Toronto
>> >> campus
>> >>
>> >> http://bioc2018.bioconductor.org > >
>> >>
>> >> The deadline for poster, talk, scholarship (travel, accommodation,
>> >> and registration), and workshop applications is May 17, see
>> >>
>> >> http://bioc2018.bioconductor.org/call-for-abstracts
>> >>

Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop application deadline May 17

2018-06-12 Thread Shepherd, Lori 
Please continue to reply all so that the response thread remains on the mailing 
list and that others may help as well.



Are you able to see the results of


ssh -T g...@git.bioconductor.org




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Pijush Das 
Sent: Tuesday, June 12, 2018 8:50:04 AM
To: Shepherd, Lori
Subject: Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop 
application deadline May 17


Dear  Shepherd, Lori


After running the script " git remote -v " the I have found the output given 
below.

PC MINGW64 ~/Desktop/BioconductorEdit/New folder/sigFeature (master)
$ git remote -v
origin  https://github.com/pijush1285/sigFeature (fetch)
origin  https://github.com/pijush1285/sigFeature (push)
upstreamg...@git.bioconductor.org:packages/sigFeature.git (fetch)
upstreamg...@git.bioconductor.org:packages/sigFeature.git (push)



After that I have tried to solve the problem and get a new fatal problem given 
below.

PC MINGW64 ~/Desktop/BioconductorEdit/New folder/sigFeature (master)
$ git push upstream master
ssh: connect to host git.bioconductor.org port 22: 
Connection timed out
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.



Please help to edit DESCRIPTION file present in Bioconductor repository.


Thank you

regards
Pijush




On Tue, Jun 12, 2018 at 5:09 PM, Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:

What is the results of


git remote -v


Did you add an upstream remote pointing to your package as described in the 
link Mike sent:

https://bioconductor.org/developers/how-to/git/new-package-workflow/






Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Pijush Das mailto:topij...@gmail.com>>
Sent: Tuesday, June 12, 2018 3:48:04 AM
To: Mike Smith
Cc: bioc-devel
Subject: Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop 
application deadline May 17

Hello Mike,



There is a little mistake in the DESCRIPTION file in my package named
"sigFeature".
In the Description portion inside the DESCRIPTION file, there are
words " Bayesian
T statistic",
it is wrongly placed there. This should be only "t- statistic".

You have given an instruction a month before. According to that instruction
I am trying to solve the problem.
But I have faced another issue which I do not understand.
Please help me to solve that. The Problem is given below.

PC MINGW64 ~/Desktop/BioconductorEdit/sigFeature (master)
$ git push upstream master
fatal: 'upstream' does not appear to be a git repository
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.



Thank you



regards
Pijush





On Fri, May 11, 2018 at 12:12 PM, Mike Smith 
mailto:grimbo...@gmail.com>> wrote:

> Dear Pijush,
>
> Once a package has been accepted to Bioconductor, a copy is made in
> Bioconductor's own git repository and this is the source from which the
> packages are made available to users.  Any change you make in Github won't
> be automatically reflected there, you have to explicitly make the change in
> git.bioconductor.org.
>
> It sounds like you should take a look at https://bioconductor.org/
> developers/how-to/git/new-package-workflow/ to make sure you have access
> to the Bioconductor repository (maybe you've already done this if you've
> added an SSH key) and then https://bioconductor.org/
> developers/how-to/git/push-to-github-bioc/ which describes how to make
> sure you commit changes both to your Github repository and the version at
> Bioconductor.
>
> Regards,
>
> Mike
>
> On 11 May 2018 at 05:48, Pijush Das 
> mailto:topij...@gmail.com>> wrote:
>
>> Dear Martin Morgan,
>>
>>
>> I have successfully added the SSH key in github account and Bioconductor.
>> After rechecking the package in Bioconductor I have found that there is a
>> mistake
>> in the DESCRIPTION file.
>> In the Description portion inside the DESCRIPTION file, there are
>> words " Bayesian
>> T statistic",
>> it is wrongly placed there. This should be only "t- statistic".
>> I have change it in the github with a version bump.
>>
>> Is that change can be seen in Bioconductor automatically?
>> Or I have to do anything else? Please let me know.
>>
>> Thank you
>>
>>
>> regards
>> Pijush
>>
>>
>>
>>
>>
>>
>>
>>
>> On Wed, May 9, 2018 at 7:15 PM, Martin Morgan <
>> martin.mor...@roswellpark.org
>> > wrote:
>>
>> > The scholarships support up to $500 travel. The scholarship also covers
>> > accommodation

[Bioc-devel] BiocParallel on Windows Never Ends

2018-06-12 Thread Dario Strbenac 
Good day,

I was interested how the performance of my package is on a 32-bit Windows 
computer because I'm going to give a workshop about it soon and some people 
might bring old laptops. I found that using SnowParam with workers set to more 
than 1 never finishes. The minimal code to cause the issue is:

bplapply(1:10, function(i) LETTERS[i], BPPARAM = SnowParam(workers = 1)) # 
Immediately returns a result.
bplapply(1:10, function(i) LETTERS[i], BPPARAM = SnowParam(workers = 2)) # 
Never completes.

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
LC_MONETARY=English_Australia.1252 LC_NUMERIC=C  
[5] LC_TIME=English_Australia.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base 

other attached packages:
[1] BiocParallel_1.14.1

loaded via a namespace (and not attached):
[1] compiler_3.5.0 snow_0.4-2 parallel_3.5.0

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia

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