[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 at 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 at 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 at 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 at 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 at 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 at git.bioconductor.org:packages/sigFeature.git (fetch) upstream git at 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 at 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 at r-project.org> on behalf of Pijush Das <topijush at 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 at 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 at 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 at 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 at roswellpark.org <mailto:martin.morgan at roswellpark.org
<martin.morgan at roswellpark.org>>>
wrote:
Join us for our annual conference BioC 2018: Where Software and
Biology Connect, at Victoria University on the University of
Toronto
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
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