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

Thu Jun 14 13:03:14 CEST 2018

It can take up to 24 hours to appear on the landing page for the package. We do a daily build and depending on when you pushed changes to the package will determine if the change is picked up in todays build or tomorrows build.

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Pijush Das <topijush using gmail.com>
Sent: Thursday, June 14, 2018 3:43:49 AM
To: Shepherd, Lori
Cc: bioc-devel using r-project.org
Subject: Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop application deadline May 17

Dear Shepherd, Lori ,

The DESCRIPTION file is already edited before in github repository but that time I unable to make the
same changes in Bioconductor repository.

After following your instruction what I have done is given below.

The SSH key is already set in github and Bioconductor repository before. I hope it will helpful for other.
May be some step are not necessary for such kind of changes, I do not know.
It is just my experiment.

Firstly what I have done that I have downloaded the all content from github repository by using the command below

$ git clone git using github.com:pijush1285/sigFeature.git

After that I add the description file and commit by using the following command. This downloading and committing is not
required for this case because I have done the changes in github repository previously manually. Though I have done it

$ git add DESCRIPTION
$ git commit -m "commit DSCRIPTION"

After that I have puss the Description file in github repository. Some kind of warning is showing.

$ git push origin master
Warning: Permanently added the RSA host key for IP address '192.30.253.112' to the list of known hosts.
Everything up-to-date

After that I Configure the �remotes� of my local git repository by using the command given below.

$ git remote add upstream git using git.bioconductor.org:packages/sigFeature.git

After that I try to puss upstream master by using the command below.

$ git push upstream master
The authenticity of host 'git.bioconductor.org<http://git.bioconductor.org> (34.192.48.227)' can't be established.
ECDSA key fingerprint is SHA256:nXILc5fVCnDfOID8HgPi+mSufGtr2JMYgnRa1JAQj/Q.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 'git.bioconductor.org<http://git.bioconductor.org>,34.192.48.227' (ECDSA) to the list of known hosts.
Counting objects: 3, done.
Delta compression using up to 2 threads.
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 721 bytes | 721.00 KiB/s, done.
Total 3 (delta 2), reused 1 (delta 0)
To git.bioconductor.org:packages/sigFeature.git
   727af94..8d24bbb  master -> master

But the change is not showing in Bioconductor repository. Will it take time ?

Please inform me if I have taken some wrong step in updating/editing  the DESCRIPTION
file in Biocnductor repository.

Thank you

regards
Pijush

On Tue, Jun 12, 2018 at 7:38 PM, Shepherd, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> wrote:

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 git using git.bioconductor.org<mailto:git using 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 <topijush using gmail.com<mailto:topijush using gmail.com>>
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)
upstream        git using git.bioconductor.org:packages/sigFeature.git (fetch)
upstream        git using 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<http://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 <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using 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 <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Pijush Das <topijush using gmail.com<mailto:topijush using 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 <grimbough using gmail.com<mailto:grimbough using 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<http://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 <topijush using gmail.com<mailto:topijush using 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.morgan using roswellpark.org<mailto:martin.morgan using 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.morgan using roswellpark.org<mailto:martin.morgan using roswellpark.org> <mailto:martin.morgan using 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 <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/call-for-abstracts>
>> >>     http://bioc2018.bioconductor.org/scholarships
>> >>     <http://bioc2018.bioconductor.org/scholarships>
>> >>
>> >>     Martin Morgan
>> >>     Bioconductor
>> >>
>> >>
>> >>     This email message may contain legally privileged
>> >> and/or...{{dropped:2}}
>> >>
>> >>     _______________________________________________
>> >>     Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> <mailto:Bioc-devel using r-project.org> mailing
>> >> list
>> >>     https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >>     <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>> >>
>> >>
>> >>
>> >
>> > 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,
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>>
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