[Bioc-devel] BioC 2018 poster / talk / scholarship / workshop application deadline May 17
Pijush Das
topiju@h @ending from gm@il@com
Thu Jun 14 09:43:49 CEST 2018
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 (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,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> 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
>
>
>
>
> 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:* 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 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> 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> on behalf of Pijush
> Das <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> 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 <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
> >> > 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
> <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
> <Bioc-devel using r-project.org>> mailing
> >> >> list
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> >> >>
> >> >>
> >> >>
> >> >
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> >> or
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