Re: [Bioc-devel] Using https to maintain a package
Thanks for the info, both. Cheers, Monther On Tue, May 8, 2018 at 9:42 PM Turaga, Nitesh <nitesh.tur...@roswellpark.org> wrote: > Hi, > > Sean is correct. There is only read-only access available through HTTP. > You would need SSH access for read-write privileges at the moment. > > We show this in the package landing pages. As you scroll to “Package > Archives”, you will notice 'Source repository’, and 'Source Repository > (Developer Access)' > > Take the package “BiocParallel” for example: > > > https://bioconductor.org/packages/release/bioc/html/BiocParallel.html > > > Source Repository: git clone > https://git.bioconductor.org/packages/BiocParallel > Source Repository (Developer Access): git clone > g...@git.bioconductor.org:packages/BiocParallel > > Best, > > Nitesh > > > On May 8, 2018, at 6:17 AM, Sean Davis <seand...@gmail.com> wrote: > > > > On Tue, May 8, 2018 at 12:34 AM Monther Alhamdoosh <m.hamdo...@gmail.com > > > > wrote: > > > >> Hi, > >> > >> Is there a way to access Bioconductor git repository via https instead > of > >> ssh? > >> > > > > Just for read-only access. Write access requires ssh. > > > > Sean > > > > > >> > >> Thanks, > >> Monther > >> > >>[[alternative HTML version deleted]] > >> > >> ___ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > > > > > > -- > > Sean Davis, MD, PhD > > Center for Cancer Research > > National Cancer Institute > > National Institutes of Health > > Bethesda, MD 20892 > > https://seandavi.github.io/ > > https://twitter.com/seandavis12 > > > > [[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] Using https to maintain a package
Hi, Is there a way to access Bioconductor git repository via https instead of ssh? Thanks, Monther [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Citation of an accompanying paper
Hi Alina,
I think you need to add a file named CITATION in your package (usually
under the inst folder) and use bibentry as follows
bibentry(bibtype = "Article",
title = "Combining multiple tools outperforms individual methods
in gene set enrichment analyses",
author = c(person("Monther", "Alhamdoosh"),
person("Milica", "Ng"),
person("Nicholas", "Wilson"),
person("Julie", "Sheridan"),
person("Huy", "Huynh"),
person("Michael", "Wilson"),
person("Matthew", "Ritchie")),
journal = "Bioinformatics",
page = "414-424",
volume = 33,
number = 3,
year = 2017,
doi = "10.1093/bioinformatics/btw623")
Cheers,
Monther
On Wed, Mar 22, 2017 at 8:11 AM, Alina Selega <alina.sel...@gmail.com>
wrote:
> Hi,
>
> My methods paper (doi:10.1038/nmeth.4068) associated with my package BUMHMM
> was accepted before I submitted the package for revision at Bioconductor. I
> would like the package page to also hold the citation to the paper. What is
> the best way to add this paper citation? (I cite it in the vignette, but it
> would be nice to also have it on the main page.)
>
> Thank you,
> Alina Selega
>
> [[alternative HTML version deleted]]
>
> ___
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>
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Re: [Bioc-devel] Updating author/maintainer info
Did you add --username xxx --password to the svn co command? On Thu, Sep 22, 2016 at 1:42 PM, Bemis, Kylie <k.be...@northeastern.edu> wrote: > Thanks, but when I follow the directions, it doesn’t work: > > svn: E175013: Commit failed (details follow): > svn: E175013: Unable to connect to a repository at URL ' > https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/ > pkgs/CardinalWorkflows' > svn: E175013: Access to 'https://hedgehog.fhcrc.org/ > bioc-data/trunk/experiment/pkgs/CardinalWorkflows' forbidden > > Kylie > > ~~~ > Kylie Ariel Bemis > Future Faculty Fellow > College of Computer and Information Science > Northeastern University > > > > > > On Sep 21, 2016, at 10:37 PM, Monther Alhamdoosh <m.hamdo...@gmail.com > <mailto:m.hamdo...@gmail.com>> wrote: > > Hi Kyle, > > See the Experiment Data Packages section here > > https://bioconductor.org/developers/how-to/source-control/ > > Cheers, > Monther > > > On Thu, Sep 22, 2016 at 12:16 PM, Kyle Dwayne Bemis <kbe...@purdue.edu > <mailto:kbe...@purdue.edu>> wrote: > Hello, > > My personal information has changed and I need to update my > author/maintainer name and email address on my packages. > > For Cardinal, this is easy, but CardinalWorkflows is a data package, so I > cannot update it myself. How can I update the data package info? > > Besides subscribing to the mailing list on my new institution's email > address, is there anything else I need to do? > > Thank you, > Kylie > > ~~~ > Kylie Ariel Bemis > Future Faculty Fellow > College of Computer and Information Science > Northeastern University > > ___ > Bioc-devel@r-project.org<mailto: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 > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Build reports not updated
Hi Chen, You may check now. My package was built last night. Cheers, Monther On Fri, Jul 8, 2016 at 3:43 PM, Chen Hao <chen_...@immunol.a-star.edu.sg> wrote: > Dear Monther, > > There seems no building yesterday. Do you have any good news for the next > building? > I have a package(cytofkit) with important updating need to replaced the > old one. > > Best Regards, > Chen Hao > > > On 7 Jul 2016, at 8:57 AM, Hervé Pagès <hpa...@fredhutch.org> wrote: > > > > Hi Monther, > > > > On 07/06/2016 05:05 PM, Monther Alhamdoosh wrote: > >> I just noticed that the latest snapshot of the build reports was based > on > >> Sunday 3rd. Has been any change to the building cycle of software > packages? > > > > No changes to the build schedule. We're still trying to run the software > > builds every day but have had many fatal build system failures in the > > last 3 weeks or so. As a result, we've had many days without an updated > > build report. The situation is particularly serious on Windows > > (moscato1) where we haven't been able to complete a full build run > > for at least 3 weeks. We're actively working on this. > > > > Hopefully we'll have an updated build report tomorrow (Jul 7). If we > > are lucky, it might even contain results for Windows. Fingers crossed... > > > > H. > > > >> > >> Cheers, > >> Monther > >> > >> [[alternative HTML version deleted]] > >> > >> ___ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > > > > -- > > Hervé Pagès > > > > Program in Computational Biology > > Division of Public Health Sciences > > Fred Hutchinson Cancer Research Center > > 1100 Fairview Ave. N, M1-B514 > > P.O. Box 19024 > > Seattle, WA 98109-1024 > > > > E-mail: hpa...@fredhutch.org > > Phone: (206) 667-5791 > > Fax:(206) 667-1319 > > > > ___ > > 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
[Bioc-devel] Build reports not updated
I just noticed that the latest snapshot of the build reports was based on Sunday 3rd. Has been any change to the building cycle of software packages? Cheers, Monther [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] gage fails to build on Windows in devel
Hi developers, It seems the gage package failed to build on Windows with this error inst ** preparing package for lazy loading Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : there is no package called 'zlibbioc' Any clue? I recently submitted a package, named EGSEA, which depends on gage. Cheers, Monther -- Dr Monther Alhamdoosh, PhD Research Scientist -sent from phone [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] No report from automated single package builder
Hi, I submitted a modified version of my package to the issue tracker yesterday and haven't received the automated builder report so far. Any clue on this? Do I have to resubmit it? Cheers, Monther [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
