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 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 > *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 < > 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 on behalf of Pijush > Das > *Sent:* Tuesday, Jun
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 <mailto:martin.mor...@roswellpark.org>> >> >> wrote: >> >> >> >> Join us for our annual conference BioC 2018: Where Software and >> >> Biology Connect, at
Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop application deadline May 17
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>> >> 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> 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, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop application deadline May 17
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 Morganwrote: > 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 > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Need some help to submit a R package.
Dear Sir, Please inform me the current status of the package named "sigFeature". The package link is given below. https://github.com/Bioconductor/Contributions/issues/713 Thank you regards Pijush On Fri, Apr 27, 2018 at 7:00 PM, Pijush Das <topij...@gmail.com> wrote: > > Now it is opening. It may be some kind of problem is there with the > internet connection. > > > > > On Fri, Apr 27, 2018 at 6:56 PM, Shepherd, Lori < > lori.sheph...@roswellpark.org> wrote: > >> I am still able to open the link: >> >> https://github.com/Bioconductor/Contributions/issues/713 >> >> >> Perhaps there is some firewall or ani-virus program you are running that >> is blocking access? >> >> >> When you try to go to the link, what message is displayed? >> >> >> 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 >> Shepherd, Lori <lori.sheph...@roswellpark.org> >> *Sent:* Friday, April 27, 2018 8:18:23 AM >> *To:* Pijush Das; Morgan, Martin >> *Cc:* bioc-devel@r-project.org >> *Subject:* Re: [Bioc-devel] Need some help to submit a R package. >> >> I am able to open this link. Perhaps it was an intermittent internet >> connection issue? Are you able to open the link now? >> >> >> 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: Friday, April 27, 2018 7:06:07 AM >> To: Morgan, Martin >> Cc: Shepherd, Lori; bioc-devel@r-project.org >> Subject: Re: [Bioc-devel] Need some help to submit a R package. >> >> Dear Sir, >> >> >> I have found some problem in github link given below: >> https://github.com/Bioconductor/Contributions/issues/713 >> The link is not opening. Is there any problem in github repository? >> Please check it. >> >> >> Thank you >> >> >> regards >> Pijush >> >> >> >> >> >> >> >> On Thu, Apr 26, 2018 at 2:32 PM, Martin Morgan < >> martin.mor...@roswellpark.org<mailto:martin.mor...@roswellpark.org>> >> wrote: >> Wait for the reviewer to comment further on your package. >> >> On 04/26/2018 02:20 AM, Pijush Das wrote: >> Dear Sir, >> >> >> I have found that my package sigFeature had passed all the built test >> without errors or warnings >> on all platforms. >> What should I do next ? >> >> >> >> >> >> regards >> Pijush >> >> >> >> >> >> >> >> >> >> >> >> >> On Tue, Apr 24, 2018 at 10:56 PM, Shepherd, Lori < >> lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org> < >> mailto:lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org >> <lori.sheph...@roswellpark.org%3Cmailto:lori.sheph...@roswellpark.org>>>> >> wrote: >> >> It doesn't look like the webhook was ever initialized >> >> >> Please follow the instructions here: >> >> https://github.com/Bioconductor/Contributions/blob/master/ >> CONTRIBUTING.md#adding-a-web-hook >> <https://github.com/Bioconductor/Contributions/blob/master/ >> CONTRIBUTING.md#adding-a-web-hook> >> >> After the webhook is set up you will need to do another version bump >> to trigger the build - Please post further correspondence regarding >> your package submission on the open github issue >> >> >> https://github.com/Bioconductor/Contributions/issues/713 >> <https://github.com/Bioconductor/Contributions/issues/713> >> >> >> Lori Shepherd >> >> Bioconductor Core Team >> >> Roswell Park Cancer Institute >> >> Department of Biostatistics & Bioinformatics >> >> Elm & Carlton Streets >> >> Buffalo, New York 14263 >> >> >> >> *From:* Pijush Das &
Re: [Bioc-devel] Need some help to submit a R package.
Now it is opening. It may be some kind of problem is there with the internet connection. On Fri, Apr 27, 2018 at 6:56 PM, Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > I am still able to open the link: > > https://github.com/Bioconductor/Contributions/issues/713 > > > Perhaps there is some firewall or ani-virus program you are running that > is blocking access? > > > When you try to go to the link, what message is displayed? > > > 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 > Shepherd, Lori <lori.sheph...@roswellpark.org> > *Sent:* Friday, April 27, 2018 8:18:23 AM > *To:* Pijush Das; Morgan, Martin > *Cc:* bioc-devel@r-project.org > *Subject:* Re: [Bioc-devel] Need some help to submit a R package. > > I am able to open this link. Perhaps it was an intermittent internet > connection issue? Are you able to open the link now? > > > 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: Friday, April 27, 2018 7:06:07 AM > To: Morgan, Martin > Cc: Shepherd, Lori; bioc-devel@r-project.org > Subject: Re: [Bioc-devel] Need some help to submit a R package. > > Dear Sir, > > > I have found some problem in github link given below: > https://github.com/Bioconductor/Contributions/issues/713 > The link is not opening. Is there any problem in github repository? > Please check it. > > > Thank you > > > regards > Pijush > > > > > > > > On Thu, Apr 26, 2018 at 2:32 PM, Martin Morgan < > martin.mor...@roswellpark.org<mailto:martin.mor...@roswellpark.org>> > wrote: > Wait for the reviewer to comment further on your package. > > On 04/26/2018 02:20 AM, Pijush Das wrote: > Dear Sir, > > > I have found that my package sigFeature had passed all the built test > without errors or warnings > on all platforms. > What should I do next ? > > > > > > regards > Pijush > > > > > > > > > > > > > On Tue, Apr 24, 2018 at 10:56 PM, Shepherd, Lori < > lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org> < > mailto:lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org > <lori.sheph...@roswellpark.org%3Cmailto:lori.sheph...@roswellpark.org>>>> > wrote: > > It doesn't look like the webhook was ever initialized > > > Please follow the instructions here: > > https://github.com/Bioconductor/Contributions/ > blob/master/CONTRIBUTING.md#adding-a-web-hook > <https://github.com/Bioconductor/Contributions/ > blob/master/CONTRIBUTING.md#adding-a-web-hook> > > After the webhook is set up you will need to do another version bump > to trigger the build - Please post further correspondence regarding > your package submission on the open github issue > > > https://github.com/Bioconductor/Contributions/issues/713 > <https://github.com/Bioconductor/Contributions/issues/713> > > > 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<mailto:topij...@gmail.com> < > mailto:topij...@gmail.com<mailto:topij...@gmail.com > <topij...@gmail.com%3Cmailto:topij...@gmail.com>>>> > *Sent:* Tuesday, April 24, 2018 11:33:14 AM > *To:* Shepherd, Lori > *Cc:* Morgan, Martin; bioc-devel@r-project.org bioc-devel@r-project.org> > <mailto:bioc-devel@r-project.org<mailto:bioc-devel@r-project.org > <bioc-devel@r-project.org%3Cmailto:bioc-devel@r-project.org>>> > > *Subject:* Re: [Bioc-devel] Need some help to submit a R package. > Dear sir, > > > I have uploaded the sigFeature package ( Version: 0.99.1) in the > existing git repository and did a version bump. The link is given > below. > https://github.com/pijush1285/sigFeature > <https://github.com/pijush1285/sigFeature> > But still now I am not getting a
Re: [Bioc-devel] Need some help to submit a R package.
No Sir, Still now it is not opening. On Fri, Apr 27, 2018 at 5:48 PM, Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > I am able to open this link. Perhaps it was an intermittent internet > connection issue? Are you able to open the link now? > > > 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:* Friday, April 27, 2018 7:06:07 AM > *To:* Morgan, Martin > *Cc:* Shepherd, Lori; bioc-devel@r-project.org > *Subject:* Re: [Bioc-devel] Need some help to submit a R package. > > Dear Sir, > > > I have found some problem in github link given below: > https://github.com/Bioconductor/Contributions/issues/713 > The link is not opening. Is there any problem in github repository? > Please check it. > > > Thank you > > > regards > Pijush > > > > > > > > On Thu, Apr 26, 2018 at 2:32 PM, Martin Morgan < > martin.mor...@roswellpark.org> wrote: > > Wait for the reviewer to comment further on your package. > > On 04/26/2018 02:20 AM, Pijush Das wrote: > > Dear Sir, > > > I have found that my package sigFeature had passed all the built test > without errors or warnings > on all platforms. > What should I do next ? > > > > > > regards > Pijush > > > > > > > > > > > > > On Tue, Apr 24, 2018 at 10:56 PM, Shepherd, Lori < > lori.sheph...@roswellpark.org <mailto:lori.sheph...@roswellpark.org>> > wrote: > > It doesn't look like the webhook was ever initialized > > > Please follow the instructions here: > > https://github.com/Bioconductor/Contributions/blob/master/CO > NTRIBUTING.md#adding-a-web-hook > <https://github.com/Bioconductor/Contributions/blob/master/C > ONTRIBUTING.md#adding-a-web-hook> > > After the webhook is set up you will need to do another version bump > to trigger the build - Please post further correspondence regarding > your package submission on the open github issue > > > https://github.com/Bioconductor/Contributions/issues/713 > <https://github.com/Bioconductor/Contributions/issues/713> > > > 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 <mailto:topij...@gmail.com>> > *Sent:* Tuesday, April 24, 2018 11:33:14 AM > *To:* Shepherd, Lori > *Cc:* Morgan, Martin; bioc-devel@r-project.org > <mailto:bioc-devel@r-project.org> > > *Subject:* Re: [Bioc-devel] Need some help to submit a R package. > Dear sir, > > > I have uploaded the sigFeature package ( Version: 0.99.1) in the > existing git repository and did a version bump. The link is given > below. > https://github.com/pijush1285/sigFeature > <https://github.com/pijush1285/sigFeature> > But still now I am not getting any response. > Is there required to add the web hook again ? > > Thank you > > regards > Pijush > > > > On Tue, Apr 24, 2018 at 5:34 PM, Shepherd, Lori > <lori.sheph...@roswellpark.org > <mailto:lori.sheph...@roswellpark.org>> wrote: > > We like to keep track of the changes and have the reviews in one > place. If possible it would be better to replace the contents > of existing git repository and do a version bump. > > > 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 > <mailto:bioc-devel-boun...@r-project.org>> on behalf of Pijush > Das <topij...@gmail.com <mailto:topij...@gmail.com>> > *Sent:* Tuesday, April 24, 2018 7:43:04 AM > *To:* Morgan, Martin > *Cc:* bioc-devel@r-project.org <mailto:bioc-devel@r-project.org> > *Subject:* Re: [Bioc-devel] Need some help to submit a R package. > Dear Sir, > >
Re: [Bioc-devel] Need some help to submit a R package.
Dear Sir, I have found some problem in github link given below: https://github.com/Bioconductor/Contributions/issues/713 The link is not opening. Is there any problem in github repository? Please check it. Thank you regards Pijush On Thu, Apr 26, 2018 at 2:32 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > Wait for the reviewer to comment further on your package. > > On 04/26/2018 02:20 AM, Pijush Das wrote: > >> Dear Sir, >> >> >> I have found that my package sigFeature had passed all the built test >> without errors or warnings >> on all platforms. >> What should I do next ? >> >> >> >> >> >> regards >> Pijush >> >> >> >> >> >> >> >> >> >> >> >> >> On Tue, Apr 24, 2018 at 10:56 PM, Shepherd, Lori < >> lori.sheph...@roswellpark.org <mailto:lori.sheph...@roswellpark.org>> >> wrote: >> >> It doesn't look like the webhook was ever initialized >> >> >> Please follow the instructions here: >> >> https://github.com/Bioconductor/Contributions/blob/master/ >> CONTRIBUTING.md#adding-a-web-hook >> <https://github.com/Bioconductor/Contributions/blob/master/ >> CONTRIBUTING.md#adding-a-web-hook> >> >> After the webhook is set up you will need to do another version bump >> to trigger the build - Please post further correspondence regarding >> your package submission on the open github issue >> >> >> https://github.com/Bioconductor/Contributions/issues/713 >> <https://github.com/Bioconductor/Contributions/issues/713> >> >> >> 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 <mailto:topij...@gmail.com>> >> *Sent:* Tuesday, April 24, 2018 11:33:14 AM >> *To:* Shepherd, Lori >> *Cc:* Morgan, Martin; bioc-devel@r-project.org >> <mailto:bioc-devel@r-project.org> >> >> *Subject:* Re: [Bioc-devel] Need some help to submit a R package. >> Dear sir, >> >> >> I have uploaded the sigFeature package ( Version: 0.99.1) in the >> existing git repository and did a version bump. The link is given >> below. >> https://github.com/pijush1285/sigFeature >> <https://github.com/pijush1285/sigFeature> >> But still now I am not getting any response. >> Is there required to add the web hook again ? >> >> Thank you >> >> regards >> Pijush >> >> >> >> On Tue, Apr 24, 2018 at 5:34 PM, Shepherd, Lori >> <lori.sheph...@roswellpark.org >> <mailto:lori.sheph...@roswellpark.org>> wrote: >> >> We like to keep track of the changes and have the reviews in one >> place. If possible it would be better to replace the contents >> of existing git repository and do a version bump. >> >> >> 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 >> <mailto:bioc-devel-boun...@r-project.org>> on behalf of Pijush >> Das <topij...@gmail.com <mailto:topij...@gmail.com>> >> *Sent:* Tuesday, April 24, 2018 7:43:04 AM >> *To:* Morgan, Martin >> *Cc:* bioc-devel@r-project.org <mailto:bioc-devel@r-project.org> >> *Subject:* Re: [Bioc-devel] Need some help to submit a R package. >> Dear Sir, >> >> I have solved most of the issues raised by the reviewers. >> There were significant amount of changes in the original code. >> So should we submit our package (sigFeature) as a new submission >> or replace the contents of existing git repository with version >> increment. >> >> >> regards >> Pijus
Re: [Bioc-devel] Need some help to submit a R package.
Dear Sir, I have found that my package sigFeature had passed all the built test without errors or warnings on all platforms. What should I do next ? regards Pijush On Tue, Apr 24, 2018 at 10:56 PM, Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > It doesn't look like the webhook was ever initialized > > > Please follow the instructions here: > > https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md# > adding-a-web-hook > > After the webhook is set up you will need to do another version bump to > trigger the build - Please post further correspondence regarding your > package submission on the open github issue > > > https://github.com/Bioconductor/Contributions/issues/713 > > > 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, April 24, 2018 11:33:14 AM > *To:* Shepherd, Lori > *Cc:* Morgan, Martin; bioc-devel@r-project.org > > *Subject:* Re: [Bioc-devel] Need some help to submit a R package. > > Dear sir, > > > I have uploaded the sigFeature package ( Version: 0.99.1) in the existing > git repository and did a version bump. The link is given below. > https://github.com/pijush1285/sigFeature > But still now I am not getting any response. > Is there required to add the web hook again ? > > Thank you > > regards > Pijush > > > > On Tue, Apr 24, 2018 at 5:34 PM, Shepherd, Lori < > lori.sheph...@roswellpark.org> wrote: > > We like to keep track of the changes and have the reviews in one place. > If possible it would be better to replace the contents of existing git > repository and do a version bump. > > > 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, April 24, 2018 7:43:04 AM > *To:* Morgan, Martin > *Cc:* bioc-devel@r-project.org > *Subject:* Re: [Bioc-devel] Need some help to submit a R package. > > Dear Sir, > > I have solved most of the issues raised by the reviewers. > There were significant amount of changes in the original code. > So should we submit our package (sigFeature) as a new submission > or replace the contents of existing git repository with version increment. > > > regards > Pijush > > > On Mon, Apr 16, 2018 at 5:01 PM, Martin Morgan < > martin.mor...@roswellpark.org> wrote: > > > If you are still having problems understanding warnings, it is probably > > better to use the github issue -- it may take some time to get an answer, > > because the reviewers have many responsibilities. > > > > It looks like your 'webhook' is not correct, and that you are not > changing > > the version of your package (from 0.99.0 to 0.99.1, 0.99.2, ...) when you > > wish to generate another build report. @grimbough indicated in the github > > issue how to address these problems. > > > > Martin > > > > > > On 04/16/2018 03:58 AM, Pijush Das wrote: > > > >> Dear Ruqian, > >> > >> > >> Yes sir, I have opened the build report which is a link to an HTML page > >> with details. > >> But I unable to understand why the WARNING massages are showing. > >> > >> Three days before the other reviewers had made some comments and asked > me > >> to address > >> those issues and also told me to solve the NOTEs produced by BioCheck. > >> > >> Presently I am working on the sigFeature package to address those > issues. > >> I shall communicate soon after solving those issues. > >> > >> > >> Thank you > >> > >> > >> Regards > >> Pijush > >> > >> > >> > >> On Mon, Apr 16, 2018 at 4:06 AM, Ruqian Lyu < > >> ruqi...@student.unimelb.edu.au> > >> wrote: > >> > >> Hi Pijush, > >>> > >>> Did you open the build report which is a link to an HTML page with > >>> details > >>> of the warning? > >>> > >>> > >>> Regards, > >>> Ruqian > >>> > >>> > >>> > >>> On Fri, Apr 13, 2018 at
Re: [Bioc-devel] Need some help to submit a R package.
Dear sir, I have uploaded the sigFeature package ( Version: 0.99.1) in the existing git repository and did a version bump. The link is given below. https://github.com/pijush1285/sigFeature But still now I am not getting any response. Is there required to add the web hook again ? Thank you regards Pijush On Tue, Apr 24, 2018 at 5:34 PM, Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > We like to keep track of the changes and have the reviews in one place. > If possible it would be better to replace the contents of existing git > repository and do a version bump. > > > 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, April 24, 2018 7:43:04 AM > *To:* Morgan, Martin > *Cc:* bioc-devel@r-project.org > *Subject:* Re: [Bioc-devel] Need some help to submit a R package. > > Dear Sir, > > I have solved most of the issues raised by the reviewers. > There were significant amount of changes in the original code. > So should we submit our package (sigFeature) as a new submission > or replace the contents of existing git repository with version increment. > > > regards > Pijush > > > On Mon, Apr 16, 2018 at 5:01 PM, Martin Morgan < > martin.mor...@roswellpark.org> wrote: > > > If you are still having problems understanding warnings, it is probably > > better to use the github issue -- it may take some time to get an answer, > > because the reviewers have many responsibilities. > > > > It looks like your 'webhook' is not correct, and that you are not > changing > > the version of your package (from 0.99.0 to 0.99.1, 0.99.2, ...) when you > > wish to generate another build report. @grimbough indicated in the github > > issue how to address these problems. > > > > Martin > > > > > > On 04/16/2018 03:58 AM, Pijush Das wrote: > > > >> Dear Ruqian, > >> > >> > >> Yes sir, I have opened the build report which is a link to an HTML page > >> with details. > >> But I unable to understand why the WARNING massages are showing. > >> > >> Three days before the other reviewers had made some comments and asked > me > >> to address > >> those issues and also told me to solve the NOTEs produced by BioCheck. > >> > >> Presently I am working on the sigFeature package to address those > issues. > >> I shall communicate soon after solving those issues. > >> > >> > >> Thank you > >> > >> > >> Regards > >> Pijush > >> > >> > >> > >> On Mon, Apr 16, 2018 at 4:06 AM, Ruqian Lyu < > >> ruqi...@student.unimelb.edu.au> > >> wrote: > >> > >> Hi Pijush, > >>> > >>> Did you open the build report which is a link to an HTML page with > >>> details > >>> of the warning? > >>> > >>> > >>> Regards, > >>> Ruqian > >>> > >>> > >>> > >>> On Fri, Apr 13, 2018 at 4:54 PM, Pijush Das <topij...@gmail.com> > wrote: > >>> > >>> Dear Sir, > >>>> > >>>> > >>>> I have submitted an R package named "sigFeature" in Github and also > >>>> Bioconductor 9 days before. > >>>> The reviewers only said that there is some WARNING problem in the > >>>> package > >>>> in different platform. > >>>> > >>>> But after that they are not communicating any thing regarding the > >>>> package. > >>>> I have checked the package > >>>> windows and Ubuntu it is working fine. > >>>> > >>>> I unable to understand what actually the problem is ? > >>>> And the reviewers are not communicating about the problem. Though I am > >>>> getting lots of email from bioc-devel dealing with others package > >>>> problem . > >>>> > >>>> Please suggest me what should I do now ? > >>>> > >>>> > >>>> > >>>> > >>>> Thank you > >>>> > >>>> > >>>> > >>>> Regards > >>>> Pijush > >
Re: [Bioc-devel] Need some help to submit a R package.
Dear Sir, I have solved most of the issues raised by the reviewers. There were significant amount of changes in the original code. So should we submit our package (sigFeature) as a new submission or replace the contents of existing git repository with version increment. regards Pijush On Mon, Apr 16, 2018 at 5:01 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > If you are still having problems understanding warnings, it is probably > better to use the github issue -- it may take some time to get an answer, > because the reviewers have many responsibilities. > > It looks like your 'webhook' is not correct, and that you are not changing > the version of your package (from 0.99.0 to 0.99.1, 0.99.2, ...) when you > wish to generate another build report. @grimbough indicated in the github > issue how to address these problems. > > Martin > > > On 04/16/2018 03:58 AM, Pijush Das wrote: > >> Dear Ruqian, >> >> >> Yes sir, I have opened the build report which is a link to an HTML page >> with details. >> But I unable to understand why the WARNING massages are showing. >> >> Three days before the other reviewers had made some comments and asked me >> to address >> those issues and also told me to solve the NOTEs produced by BioCheck. >> >> Presently I am working on the sigFeature package to address those issues. >> I shall communicate soon after solving those issues. >> >> >> Thank you >> >> >> Regards >> Pijush >> >> >> >> On Mon, Apr 16, 2018 at 4:06 AM, Ruqian Lyu < >> ruqi...@student.unimelb.edu.au> >> wrote: >> >> Hi Pijush, >>> >>> Did you open the build report which is a link to an HTML page with >>> details >>> of the warning? >>> >>> >>> Regards, >>> Ruqian >>> >>> >>> >>> On Fri, Apr 13, 2018 at 4:54 PM, Pijush Das <topij...@gmail.com> wrote: >>> >>> Dear Sir, >>>> >>>> >>>> I have submitted an R package named "sigFeature" in Github and also >>>> Bioconductor 9 days before. >>>> The reviewers only said that there is some WARNING problem in the >>>> package >>>> in different platform. >>>> >>>> But after that they are not communicating any thing regarding the >>>> package. >>>> I have checked the package >>>> windows and Ubuntu it is working fine. >>>> >>>> I unable to understand what actually the problem is ? >>>> And the reviewers are not communicating about the problem. Though I am >>>> getting lots of email from bioc-devel dealing with others package >>>> problem . >>>> >>>> Please suggest me what should I do now ? >>>> >>>> >>>> >>>> >>>> Thank you >>>> >>>> >>>> >>>> Regards >>>> Pijush >>>> >>>> >>>> >>>> >>>> On Mon, Apr 2, 2018 at 4:26 PM, Turaga, Nitesh < >>>> nitesh.tur...@roswellpark.org> wrote: >>>> >>>> Hi, >>>>> >>>>> Please read through this documentation. >>>>> >>>>> http://bioconductor.org/developers/package-submission/ >>>>> >>>>> >>>>> Nitesh >>>>> >>>>> On Apr 2, 2018, at 2:00 AM, Pijush Das <topij...@gmail.com> wrote: >>>>>> >>>>>> Dear Sir, >>>>>> >>>>>> >>>>>> >>>>>> I have developed an R package. I want to submit this package in >>>>>> Bioconductor. >>>>>> Please help me to submit the R package. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> regards >>>>>> Pijush Das >>>>>> >>>>>>[[alternative HTML version deleted]] >>>>>> >>>>>> ___ >>>>>> Bioc-devel@r-project.org mailing list >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>>> >>>>> >>>>> >>>>> >>>>> This email message may contain legally privileged
Re: [Bioc-devel] Need some help to submit a R package.
Dear Ruqian, Yes sir, I have opened the build report which is a link to an HTML page with details. But I unable to understand why the WARNING massages are showing. Three days before the other reviewers had made some comments and asked me to address those issues and also told me to solve the NOTEs produced by BioCheck. Presently I am working on the sigFeature package to address those issues. I shall communicate soon after solving those issues. Thank you Regards Pijush On Mon, Apr 16, 2018 at 4:06 AM, Ruqian Lyu <ruqi...@student.unimelb.edu.au> wrote: > Hi Pijush, > > Did you open the build report which is a link to an HTML page with details > of the warning? > > > Regards, > Ruqian > > > > On Fri, Apr 13, 2018 at 4:54 PM, Pijush Das <topij...@gmail.com> wrote: > >> Dear Sir, >> >> >> I have submitted an R package named "sigFeature" in Github and also >> Bioconductor 9 days before. >> The reviewers only said that there is some WARNING problem in the package >> in different platform. >> >> But after that they are not communicating any thing regarding the package. >> I have checked the package >> windows and Ubuntu it is working fine. >> >> I unable to understand what actually the problem is ? >> And the reviewers are not communicating about the problem. Though I am >> getting lots of email from bioc-devel dealing with others package >> problem . >> >> Please suggest me what should I do now ? >> >> >> >> >> Thank you >> >> >> >> Regards >> Pijush >> >> >> >> >> On Mon, Apr 2, 2018 at 4:26 PM, Turaga, Nitesh < >> nitesh.tur...@roswellpark.org> wrote: >> >> > Hi, >> > >> > Please read through this documentation. >> > >> > http://bioconductor.org/developers/package-submission/ >> > >> > >> > Nitesh >> > >> > > On Apr 2, 2018, at 2:00 AM, Pijush Das <topij...@gmail.com> wrote: >> > > >> > > Dear Sir, >> > > >> > > >> > > >> > > I have developed an R package. I want to submit this package in >> > > Bioconductor. >> > > Please help me to submit the R package. >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > >> > > regards >> > > Pijush Das >> > > >> > > [[alternative HTML version deleted]] >> > > >> > > ___ >> > > Bioc-devel@r-project.org mailing list >> > > 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, >> > distribution, or use of this email message is prohibited. If you have >> > received this message in error, please notify the sender immediately by >> > e-mail and delete this email message from your computer. Thank you. >> > >> >> [[alternative HTML version deleted]] >> >> ___ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Need some help to submit a R package.
Dear Sir, I have submitted an R package named "sigFeature" in Github and also Bioconductor 9 days before. The reviewers only said that there is some WARNING problem in the package in different platform. But after that they are not communicating any thing regarding the package. I have checked the package windows and Ubuntu it is working fine. I unable to understand what actually the problem is ? And the reviewers are not communicating about the problem. Though I am getting lots of email from bioc-devel dealing with others package problem . Please suggest me what should I do now ? Thank you Regards Pijush On Mon, Apr 2, 2018 at 4:26 PM, Turaga, Nitesh < nitesh.tur...@roswellpark.org> wrote: > Hi, > > Please read through this documentation. > > http://bioconductor.org/developers/package-submission/ > > > Nitesh > > > On Apr 2, 2018, at 2:00 AM, Pijush Das <topij...@gmail.com> wrote: > > > > Dear Sir, > > > > > > > > I have developed an R package. I want to submit this package in > > Bioconductor. > > Please help me to submit the R package. > > > > > > > > > > > > > > > > > > > > regards > > Pijush Das > > > > [[alternative HTML version deleted]] > > > > ___ > > Bioc-devel@r-project.org mailing list > > 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, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Need some help to submit a R package.
Dear Sir, I have developed an R package. I want to submit this package in Bioconductor. Please help me to submit the R package. regards Pijush Das [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel