Re: [Bioc-devel] Missing knitcitations package on devel for PharmacoGx

2020-11-26 Thread Mike Smith 
Hi Christopher,

It looks like the knitcitations package is no longer on CRAN.  Heading to
https://cran.r-project.org/web/packages/knitcitations/index.html results in:

  Package ‘knitcitations’ was removed from the CRAN repository.

  Formerly available versions can be obtained from the archive.

  Archived on 2020-10-27 as reauired archived package 'RefManageR'.

My guess is the release branch has a copy of knitcitations installed from
before it was removed from CRAN, so you don't see the error, but a fresh R
installation using either release or devel would throw the same problem.

The latest commit message to https://github.com/cboettig/knitcitations is
'prep for release', so it looks likely that the author of knitcitations is
addressing the CRAN issue.  I would hang tight for a while longer and hope
it gets smoothed out there.

Mike

On Thu, 26 Nov 2020 at 04:26, Eeles, Christopher <
christopher.ee...@uhnresearch.ca> wrote:

> Hello Bioc community,
>
> I am the maintainer for PharmacoGx and have noticed that I have an error
> on all platforms of the devel branch related to the knitcitations package.
>
>
> * checking for file ‘PharmacoGx/DESCRIPTION’ ... OK
> * preparing ‘PharmacoGx’:
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... ERROR
> --- re-building ‘CreatingPharmacoSet.Rmd’ using rmarkdown
> Quitting from lines 79-82 (CreatingPharmacoSet.Rmd)
> Error: processing vignette 'CreatingPharmacoSet.Rmd' failed with
> diagnostics:
> there is no package called 'knitcitations'
> --- failed re-building ‘CreatingPharmacoSet.Rmd’
>
> --- re-building ‘PharmacoGx.Rmd’ using rmarkdown
> Quitting from lines 79-82 (PharmacoGx.Rmd)
> Error: processing vignette 'PharmacoGx.Rmd' failed with diagnostics:
> there is no package called 'knitcitations'
> --- failed re-building ‘PharmacoGx.Rmd’
>
> SUMMARY: processing the following files failed:
>   ‘CreatingPharmacoSet.Rmd’ ‘PharmacoGx.Rmd’
>
> Error: Vignette re-building failed.
> Execution halted
>
> The package builds fine on the release branch with the same vignettes and
> knitcitations in the suggests field of the description.
>
> Any advice on how I can fix this? It seems like my suggests aren't being
> installed on the devel branch.
>
> Thanks for your assistance.
>
> Best,
> Christopher Eeles
> Software Developer
> Benjamin Haibe-Kains Lab
> Princess Margaret Cancer Centre
>
> This e-mail may contain confidential and/or privileged i...{{dropped:22}}
>
> ___
> Bioc-devel@r-project.org mailing list
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>

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[Bioc-devel] Solved Bug commiting problem

2020-11-26 Thread Selcen Arı 
  Hi everyone,

I am developer of ceRNAnetsim package (
https://git.bioconductor.org/packages/ceRNAnetsim). We recently saw that it
gave errors in build report (
http://bioconductor.org/checkResults/release/bioc-LATEST/ceRNAnetsim/ ),
and we fixed the errors in the package, in this direction. After making the
local changes, we committed to the master and RELEASE_3_12 branches on the
bioconductor and github repos, following the instructions you can find in
the links (1

and 2
).
The package version in the master branch was higher than RELEASE_3_12.

Is it because the master branch refers to devel?Therefore, I wanted to sync
all versions in these branches to the version in the master. However, in
this case, I encountered the problem like "illegal version bump from 1.2.0
to 1.3.2".

As a result, while the package version is 1.2.1 in RELEASE_3_12 branch, it
is 1.3.2 in the master branch. Will this cause any problems afterwards?

Regards



---
Selcen ARI YUKA
Yildiz Technical University
Faculty of Chemistry and Metallurgical Engineering
Department of Bioengineering
Esenler, Istanbul, Turkey

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Re: [Bioc-devel] Missing knitcitations package on devel for PharmacoGx

2020-11-26 Thread Vincent Carey 
This problem has been recognized:
https://github.com/cboettig/knitcitations/issues/107

In a few days it will likely clear.

On Wed, Nov 25, 2020 at 10:26 PM Eeles, Christopher <
christopher.ee...@uhnresearch.ca> wrote:

> Hello Bioc community,
>
> I am the maintainer for PharmacoGx and have noticed that I have an error
> on all platforms of the devel branch related to the knitcitations package.
>
>
> * checking for file ‘PharmacoGx/DESCRIPTION’ ... OK
> * preparing ‘PharmacoGx’:
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... ERROR
> --- re-building ‘CreatingPharmacoSet.Rmd’ using rmarkdown
> Quitting from lines 79-82 (CreatingPharmacoSet.Rmd)
> Error: processing vignette 'CreatingPharmacoSet.Rmd' failed with
> diagnostics:
> there is no package called 'knitcitations'
> --- failed re-building ‘CreatingPharmacoSet.Rmd’
>
> --- re-building ‘PharmacoGx.Rmd’ using rmarkdown
> Quitting from lines 79-82 (PharmacoGx.Rmd)
> Error: processing vignette 'PharmacoGx.Rmd' failed with diagnostics:
> there is no package called 'knitcitations'
> --- failed re-building ‘PharmacoGx.Rmd’
>
> SUMMARY: processing the following files failed:
>   ‘CreatingPharmacoSet.Rmd’ ‘PharmacoGx.Rmd’
>
> Error: Vignette re-building failed.
> Execution halted
>
> The package builds fine on the release branch with the same vignettes and
> knitcitations in the suggests field of the description.
>
> Any advice on how I can fix this? It seems like my suggests aren't being
> installed on the devel branch.
>
> Thanks for your assistance.
>
> Best,
> Christopher Eeles
> Software Developer
> Benjamin Haibe-Kains Lab
> Princess Margaret Cancer Centre
>
> This e-mail may contain confidential and/or privileged i...{{dropped:22}}
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
The information in this e-mail is intended only for the ...{{dropped:18}}

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Re: [Bioc-devel] Solved Bug commiting problem

2020-11-26 Thread Martin Morgan 
Yes, the 'master' branch in git refers to the 'devel' branch of Bioconductor.

You should not aim to keep the RELEASE_3_12 branch the same as 'devel'.

The RELEASE_3_12 branch is meant to be a snapshot of the 'devel' branch at a 
particular point in time, so that users of the RELEASE_3_12 branch get a stable 
package for doing reproducible research. The one time when a change is 
introduced into the release branch is when it is a bug fix, and then the bug 
fix is usually also added to the devel branch.

The 'devel' branch is meant to allow you to introduce new features, and 
deprecate and remove old features, without disrupting the productive work being 
done by users in the release branch.

So generally there is much more activity in the devel branch, and almost all 
commits in the release branch are also present in the devel branch. Version 
numbers indicate the separate trajectories of the two branches. For version 
x.y.z, 'y' is even in the release branch, and odd (and equal to y + 1 of the 
current release branch) in the devel branch. 'z' is incremented separately in 
the release branch (rarely, bug fixes only) and the devel branch. As an example 
from one of my own packages, AnVIL is 1.2.0 (no bug fixes) in release, and 
1.3.5 (five commits representing new features or non-portable bug fixes) in 
devel.  

The version numbering scheme is discussed at

  https://bioconductor.org/developers/how-to/version-numbering/

Martin

On 11/26/20, 5:49 AM, "Bioc-devel on behalf of Selcen Arı" 
 wrote:

  Hi everyone,

I am developer of ceRNAnetsim package (
https://git.bioconductor.org/packages/ceRNAnetsim). We recently saw that it
gave errors in build report (
http://bioconductor.org/checkResults/release/bioc-LATEST/ceRNAnetsim/ ),
and we fixed the errors in the package, in this direction. After making the
local changes, we committed to the master and RELEASE_3_12 branches on the
bioconductor and github repos, following the instructions you can find in
the links (1

and 2

).
The package version in the master branch was higher than RELEASE_3_12.

Is it because the master branch refers to devel?Therefore, I wanted to sync
all versions in these branches to the version in the master. However, in
this case, I encountered the problem like "illegal version bump from 1.2.0
to 1.3.2".

As a result, while the package version is 1.2.1 in RELEASE_3_12 branch, it
is 1.3.2 in the master branch. Will this cause any problems afterwards?

Regards



---
Selcen ARI YUKA
Yildiz Technical University
Faculty of Chemistry and Metallurgical Engineering
Department of Bioengineering
Esenler, Istanbul, Turkey

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Re: [Bioc-devel] Query on updating version for bioconda-bambu

2020-11-26 Thread Martin Morgan 
bioconda is not maintained by Bioconductor, you should ask through bioconda 
support channels

  https://bioconda.github.io/

maybe as an issue on their github repository?

Martin

On 11/25/20, 8:36 PM, "Bioc-devel on behalf of CHEN Ying" 
 
wrote:

Hello BioC community,

I have recently updated the version of bambu with some small bug fixes. I 
noted that however, the available bionconda-bambu version  is still 1.0.0.

Could you advise on how to update bionconda-bambu to the most recent 
version?

Thank you
Regards,
CHEN Ying

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