Please direct further questions to the bioc-devel@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 <hame...@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 g...@git.bioconductor.org:packages/PhenStat (fetch)
origin g...@git.bioconductor.org:packages/PhenStat (push)
Thanks Lori.
Regards,
Hamed,
Hamed Haseli.M
----------------------------------------------------------------------------
| Hamed Haseli.M, PhD (Statistics)
| Data Scientist, Mouse Informatics
| E: hame...@ebi.ac.uk<mailto:hame...@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.sheph...@roswellpark.org<mailto:lori.sheph...@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-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> on
behalf of Hamed Haseli <hame...@ebi.ac.uk<mailto:hame...@ebi.ac.uk>>
Sent: Monday, July 15, 2019 9:17:02 AM
To: bioc-devel@r-project.org<mailto:bioc-devel@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: hame...@ebi.ac.uk<mailto:hame...@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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