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

[Shepherd, Lori]

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<mailto:hamedhm using ebi.ac.uk>
| P:  +44(0) 1223 494 451
| M: +44(0) 7902 824 097
| W: hamedhaseli.webs.com<http://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<mailto: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<http://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<mailto:bioc-devel-bounces using r-project.org>> on behalf of Hamed Haseli <hamedhm using ebi.ac.uk<mailto:hamedhm using ebi.ac.uk>>
Sent: Monday, July 15, 2019 9:17:02 AM
To: bioc-devel using r-project.org<mailto: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<mailto:hamedhm using ebi.ac.uk>
| P:  +44(0) 1223 494 451
| M: +44(0) 7902 824 097
| W: hamedhaseli.webs.com<http://hamedhaseli.webs.com>
| European Bioinformatics Institute,
| Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. CB10 1SD

-------------------------------------------------------------------------------

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