[Bioc-devel] Failing to get updated version of the package on Bioconductor

[Hamed Haseli]

Sure, thanks.

I will double check the entire process again and update you if the problem
persists.

Many thanks.
Hamed.

On Mon, 15 Jul 2019, 15:45 Shepherd, Lori, <Lori.Shepherd using roswellpark.org>
wrote:

> Please direct further questions to the bioc-devel using r-project.org mailing
> list/ use "reply all" so it remains in the thread....
>
>
> The Bioconductor git repository has been updated and I'm unsure what you
> mean that you do not see the changes when using the R command.
>
>
> When I BiocManager::install("PhenStat")  the version that is installed is 2.21.2
> as expected.
>
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ------------------------------
> *From:* Hamed Haseli <hamedhm using ebi.ac.uk>
> *Sent:* Monday, July 15, 2019 10:23:37 AM
> *To:* Shepherd, Lori
> *Subject:* Re: [Bioc-devel] Failing to get updated version of the package
> on Bioconductor
>
> Sorry for not being specific Lori.
>
> The package is PhenStat. I use PC and a piece of software called
> TortoiseGit for git operations https://tortoisegit.org/
>
> I just noticed that the package is here
> http://bioconductor.org/packages/3.10/bioc/html/PhenStat.html
>
> Still, I cannot see the changes when I use the command below in R:
>
> if (!requireNamespace("BiocManager", quietly = TRUE))
>     install.packages("BiocManager")
>
> # The following initializes usage of Bioc devel
> BiocManager::install(version='devel')
>
> BiocManager::install("PhenStat")
>
> however, I see the changes if I clone rep from
> https://git.bioconductor.org/packages/PhenStat
>
> From the command line I get:
>
>  git remote -v
> origin  git using git.bioconductor.org:packages/PhenStat (fetch)
> origin  git using git.bioconductor.org:packages/PhenStat (push)
>
> Thanks Lori.
>
> Regards,
> Hamed,
>
>
> Hamed Haseli.M
>
>
>
> ----------------------------------------------------------------------------
> | Hamed Haseli.M, PhD (Statistics)
> | Data Scientist, Mouse Informatics
> | E: hamedhm using ebi.ac.uk
> | P:  +44(0) 1223 494 451
> | M: +44(0) 7902 824 097
> | W: hamedhaseli.webs.com
> | European Bioinformatics Institute,
> | Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. CB10 1SD
>
> -------------------------------------------------------------------------------
>
>
> On Mon, 15 Jul 2019 at 14:21, Shepherd, Lori <
> Lori.Shepherd using roswellpark.org> wrote:
>
> We will need more information in order to help you properly.
>
>
> Could you please inform us of the package that you are referring to?
>
>
> When you push make sure you are pushing to the git.bioconductor.org. This
> involves your remotes to be properly set up and that you are pushing to the
> right location.
>
>
> Please also show the results of
>
>
> git remote -v
>
>
> and the actual git push command you use.
>
>
> Thank you.
>
>
>
> 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 using r-project.org> on behalf of Hamed
> Haseli <hamedhm using ebi.ac.uk>
> *Sent:* Monday, July 15, 2019 9:17:02 AM
> *To:* bioc-devel using r-project.org
> *Subject:* [Bioc-devel] Failing to get updated version of the package on
> Bioconductor
>
> Dear All,
>
> I have always problems with updating the R package on Bioconductor and
> installing the updated version of the package fro the repository.
>
> The workflow that I follow is like:
>
>    1. Make changes into the source code
>    2. Increase the subversion x.y.z to x.y.(z+1)
>    3. Push the changes to the repository
>    4. Waiting for a day or more for the package to be compiled by
>    Bioconductor
>
> Doing the workflow above, I do not see the changes when I install the
> package from Bioconductor. Please can you help?
>
>
> Regards,
> Hamed.
>
>
> Hamed Haseli.M
>
>
>
>
> ----------------------------------------------------------------------------
> | Hamed Haseli.M, PhD (Statistics)
> | Data Scientist, Mouse Informatics
> | E: hamedhm using ebi.ac.uk
> | P:  +44(0) 1223 494 451
> | M: +44(0) 7902 824 097
> | W: hamedhaseli.webs.com
> | European Bioinformatics Institute,
> | Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. CB10 1SD
>
>
> -------------------------------------------------------------------------------
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using 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]]