Re: [Bioc-devel] transfer maintainer status of gCrisprTools
Great, thanks! -R On Tue, Nov 26, 2019 at 1:07 PM Turaga, Nitesh < nitesh.tur...@roswellpark.org> wrote: > Hi, > > You should be able to access your package once you activate your > BiocCredentials account and activate it. > > Best > > Nitesh > > > On Nov 26, 2019, at 3:54 PM, Russell Bainer > wrote: > > > > Hello Nitesh, > > > > Please associate it with russ.bai...@gmail.com. > > > > Thanks very much. I think that I will also need to associate my github > account (RussBainer), but i see that there is a FAQ about that and will > contact you in due course if I'm not able to access it. > > > > Best Regards, > > > > -Russ > > > > On Tue, Nov 26, 2019 at 12:09 PM Turaga, Nitesh < > nitesh.tur...@roswellpark.org> wrote: > > Hi, > > > > Which email would Russ like to use as his email account with > BiocCredentials? > > > > Best, > > > > Nitesh > > > > > On Nov 22, 2019, at 5:11 PM, Peter Haverty < > peterhave...@ucdavis-alumni.com> wrote: > > > > > > I'd like to transfer gCrisprTools to Russ Bainer ( > russ.bai...@gmail.com, > > > rbai...@mazetx.com). How do I do that? > > > > > > [[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. > > > > 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] transfer maintainer status of gCrisprTools
Hello Nitesh, Please associate it with russ.bai...@gmail.com. Thanks very much. I think that I will also need to associate my github account (RussBainer), but i see that there is a FAQ about that and will contact you in due course if I'm not able to access it. Best Regards, -Russ On Tue, Nov 26, 2019 at 12:09 PM Turaga, Nitesh < nitesh.tur...@roswellpark.org> wrote: > Hi, > > Which email would Russ like to use as his email account with > BiocCredentials? > > Best, > > Nitesh > > > On Nov 22, 2019, at 5:11 PM, Peter Haverty < > peterhave...@ucdavis-alumni.com> wrote: > > > > I'd like to transfer gCrisprTools to Russ Bainer (russ.bai...@gmail.com, > > rbai...@mazetx.com). How do I do that? > > > > [[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
Re: [Bioc-devel] CRAN packages depending on broken Bioc 3.11 packages may be archived
Hi Lori, Let me know if you don't hear from Benilton. It shouldn't be much work to fix oligo - we could convert to using Gviz for the graphic that is currently using GenomeGraphs. I can make the change next week if necessary. Best, Jim On Tue, Nov 26, 2019 at 12:57 PM Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > typo - heatplus and topGO have responded directly. > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > > From: Bioc-devel on behalf of > Shepherd, Lori > Sent: Tuesday, November 26, 2019 12:54 PM > To: Henrik Bengtsson ; > bioc-devel@r-project.org > Subject: Re: [Bioc-devel] CRAN packages depending on broken Bioc 3.11 > packages may be archived > > All of these package have been notified from the Bioconductor side as > well. We hope the maintainers will respond shortly. > heatmap and topGO have responded directly and are working on fixes. I > hope the others are too. > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > > From: Bioc-devel on behalf of Henrik > Bengtsson > Sent: Tuesday, November 26, 2019 12:47 PM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] CRAN packages depending on broken Bioc 3.11 packages > may be archived > > In case it's not known, paraphrasing from CRAN notification email, > CRAN [sic!] packages: > > TROM, demi, diffMeanVar, maGUI, metaboGSE > > risk being archived on December 7 because broken Bioconductor dependencies: > > Heatplus, missMethyl, oligo, oligoClasses, topGO > > prevent pdInfoBuilder from being installed. > > I don't maintain any of the above - I'm just the messenger. > > /Henrik > > ___ > 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 > > > 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 > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] transfer maintainer status of gCrisprTools
Hi, Which email would Russ like to use as his email account with BiocCredentials? Best, Nitesh > On Nov 22, 2019, at 5:11 PM, Peter Haverty > wrote: > > I'd like to transfer gCrisprTools to Russ Bainer (russ.bai...@gmail.com, > rbai...@mazetx.com). How do I do that? > > [[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. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] CRAN packages depending on broken Bioc 3.11 packages may be archived
typo - heatplus and topGO have responded directly. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Shepherd, Lori Sent: Tuesday, November 26, 2019 12:54 PM To: Henrik Bengtsson ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] CRAN packages depending on broken Bioc 3.11 packages may be archived All of these package have been notified from the Bioconductor side as well. We hope the maintainers will respond shortly. heatmap and topGO have responded directly and are working on fixes. I hope the others are too. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Henrik Bengtsson Sent: Tuesday, November 26, 2019 12:47 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] CRAN packages depending on broken Bioc 3.11 packages may be archived In case it's not known, paraphrasing from CRAN notification email, CRAN [sic!] packages: TROM, demi, diffMeanVar, maGUI, metaboGSE risk being archived on December 7 because broken Bioconductor dependencies: Heatplus, missMethyl, oligo, oligoClasses, topGO prevent pdInfoBuilder from being installed. I don't maintain any of the above - I'm just the messenger. /Henrik ___ 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 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] CRAN packages depending on broken Bioc 3.11 packages may be archived
All of these package have been notified from the Bioconductor side as well. We hope the maintainers will respond shortly. heatmap and topGO have responded directly and are working on fixes. I hope the others are too. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Henrik Bengtsson Sent: Tuesday, November 26, 2019 12:47 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] CRAN packages depending on broken Bioc 3.11 packages may be archived In case it's not known, paraphrasing from CRAN notification email, CRAN [sic!] packages: TROM, demi, diffMeanVar, maGUI, metaboGSE risk being archived on December 7 because broken Bioconductor dependencies: Heatplus, missMethyl, oligo, oligoClasses, topGO prevent pdInfoBuilder from being installed. I don't maintain any of the above - I'm just the messenger. /Henrik ___ 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] CRAN packages depending on broken Bioc 3.11 packages may be archived
In case it's not known, paraphrasing from CRAN notification email, CRAN [sic!] packages: TROM, demi, diffMeanVar, maGUI, metaboGSE risk being archived on December 7 because broken Bioconductor dependencies: Heatplus, missMethyl, oligo, oligoClasses, topGO prevent pdInfoBuilder from being installed. I don't maintain any of the above - I'm just the messenger. /Henrik ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Submitting a package with heavy data and vignette
rather than aiming for an a large ExperimentData package it might make more sense to create an ExperimentHub package, with the data hosted in the cloud for download-on-demand. It is cached locally so the download cost is only paid once. This is especially useful if your data consist of several sets, and only one is needed for the purposes of the vignette. In general it seems like a better strategy, since it makes it easier on mirrors (and our git server) to host the package. http://bioconductor.org/packages/devel/bioc/vignettes/ExperimentHub/inst/doc/CreateAnExperimentHubPackage.html I wanted to mention though that *many* authors have said 'my data is too big and I can't do a realistic vignette', only to in the long run come up with a real-enough example that exercises their package. This is tremendously valuable to the user, who can walk through tough areas of package functionality illustrated in the vignette, without having to invest excessive compute time. Martin On 11/26/19, 8:54 AM, "Bioc-devel on behalf of Turaga, Nitesh" wrote: Hi, I think this is a good path forward. Please take a look at the link below which will provide further guidelines for you, http://bioconductor.org/developers/package-guidelines/#data https://bioconductor.org/developers/package-submission/#experPackage https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#submitting-related-packages Best regards, Nitesh On 11/26/19, 8:25 AM, "Bioc-devel on behalf of Joris Meys" wrote: Dear, we're planning on submitting a new package to Bioconductor. Due to the fact that this package revolves around simulation methods for massive datasets, the vignette necessarily need about 10 Mb of data and way more than 5 minutes to build. We were wondering how we would proceed best to submit this package. Downsizing the data and build time is alas not possible, as it would make the example in the vignette totally irrelevant. I was thinking about the following construct: - a main software package with the actual simulation functionality - a "data" package depending on the main software package with only the example data and vignette. We would love to hear your view on this, as we'd like to limit the amount of issues for both you and us once we submit the package(s). Other suggestions are more than welcome too. Thank you in advance Joris -- Joris Meys Statistical consultant Department of Data Analysis and Mathematical Modelling Ghent University Coupure Links 653, B-9000 Gent (Belgium) -- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php [[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. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Submitting a package with heavy data and vignette
Hi, I think this is a good path forward. Please take a look at the link below which will provide further guidelines for you, http://bioconductor.org/developers/package-guidelines/#data https://bioconductor.org/developers/package-submission/#experPackage https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#submitting-related-packages Best regards, Nitesh On 11/26/19, 8:25 AM, "Bioc-devel on behalf of Joris Meys" wrote: Dear, we're planning on submitting a new package to Bioconductor. Due to the fact that this package revolves around simulation methods for massive datasets, the vignette necessarily need about 10 Mb of data and way more than 5 minutes to build. We were wondering how we would proceed best to submit this package. Downsizing the data and build time is alas not possible, as it would make the example in the vignette totally irrelevant. I was thinking about the following construct: - a main software package with the actual simulation functionality - a "data" package depending on the main software package with only the example data and vignette. We would love to hear your view on this, as we'd like to limit the amount of issues for both you and us once we submit the package(s). Other suggestions are more than welcome too. Thank you in advance Joris -- Joris Meys Statistical consultant Department of Data Analysis and Mathematical Modelling Ghent University Coupure Links 653, B-9000 Gent (Belgium) -- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php [[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. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Submitting a package with heavy data and vignette
Dear, we're planning on submitting a new package to Bioconductor. Due to the fact that this package revolves around simulation methods for massive datasets, the vignette necessarily need about 10 Mb of data and way more than 5 minutes to build. We were wondering how we would proceed best to submit this package. Downsizing the data and build time is alas not possible, as it would make the example in the vignette totally irrelevant. I was thinking about the following construct: - a main software package with the actual simulation functionality - a "data" package depending on the main software package with only the example data and vignette. We would love to hear your view on this, as we'd like to limit the amount of issues for both you and us once we submit the package(s). Other suggestions are more than welcome too. Thank you in advance Joris -- Joris Meys Statistical consultant Department of Data Analysis and Mathematical Modelling Ghent University Coupure Links 653, B-9000 Gent (Belgium) -- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
