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 g...@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 g...@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.sheph...@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 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 <topij...@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 g...@git.bioconductor.org:packages/sigFeature.git (fetch) > upstream g...@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.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 <bioc-devel-boun...@r-project.org> on behalf of Pijush > Das <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 <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 <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 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 <mailto:martin.mor...@roswellpark.org > <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 <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@r-project.org <mailto:Bioc-devel@r-project.org > <Bioc-devel@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. 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