Re: [Bioc-devel] Large vignettes
d, cluster labeling silently changed and the text became
> false. We want some kind of flagging
> procedure that will alert us to changes of this sort.
>
> There are technical responses to all of these observations but
> implementing well-engineered solutions will
> require more resources than we currently have. The workshop authoring
> method used in
> https://github.com/seandavi/BuildABiocWorkshop is surely relevant;
> Alex Mahmoud has a work
> in progress called BiocDeployables that is also relevant. Ultimately
> we want to improve communication
> of good analytic methods to the scientific community, and
> monograph-scale resources are definitely
> useful, but smaller-scale resources that don't require the technology
> of package production can also
> be valuable, and BiocDeployables goes in that direction. Maintenance
> and the avoidance of bit/doc rot
> are first-class concerns and really require author commitment.
>
>
>
> Some authors already have books outside bioconductor to have
> extensive examples of their packages.
> They will also benefit from having them with the Bioconductor
> framework and in sync with the packages released to the users.
>
> Best,
>
> Lluís
>
>
> On Wed, 4 Jan 2023 at 21:39, Vincent Carey
> wrote:
>
> I am glad you brought this up here, and I welcome further
> discussion on
> this mailing list. It is important to understand the
> constraints on
> development
> that arise from Bioconductor's package guidelines.
>
> I don't think we want to change the limits on package payload
> size without
> understanding the consequences for users and our build
> system. The split
> approach mentioned by Lambda seems sensible to me, and I hope
> it is
> not too burdensome. Additional commentary and details from
> the community
> are welcome.
>
> On Wed, Jan 4, 2023 at 3:21 PM Lambda Moses
> wrote:
>
> > Hi Adam,
> >
> > I also got this problem, and I would like some input from
> Bioc Core
> > Team. I worked around it by writing a minimal vignette in
> the main
> > branch. Then I made a documentation branch, where I have the
> same code
> > as in main branch, but with more elaborate vignettes used to
> build a
> > pkgdown website. I made a rule for myself that I can only
> merge from the
> > main or devel branch to the documentation branch but not the
> other way
> > round. I would switch branch when I find a bug or want a new
> feature
> > while writing the vignettes. You can see the main branch here:
> > https://github.com/pachterlab/voyager/tree/main The
> documentation branch
> > here: https://github.com/pachterlab/voyager/tree/documentation
> >
> > I kind of wonder if the 5 MB rule is outdated in the age of
> increasing
> > computer power and internet speed. A jpeg photo can easily
> exceed 5 MB.
> > I also wonder if this rule is deliberately kept for good
> reasons, like
> > to make R more inclusive to disadvantaged people with
> limited internet
> > services.
> >
> > Regards,
> >
> > Lambda
> >
> > ___
> > 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}}
>
> ___
> 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 th...{{dropped:15}}
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Large vignettes
d, cluster labeling silently changed and the text became
> false. We want some kind of flagging
> procedure that will alert us to changes of this sort.
>
> There are technical responses to all of these observations but
> implementing well-engineered solutions will
> require more resources than we currently have. The workshop authoring
> method used in
> https://github.com/seandavi/BuildABiocWorkshop is surely relevant;
> Alex Mahmoud has a work
> in progress called BiocDeployables that is also relevant. Ultimately
> we want to improve communication
> of good analytic methods to the scientific community, and
> monograph-scale resources are definitely
> useful, but smaller-scale resources that don't require the technology
> of package production can also
> be valuable, and BiocDeployables goes in that direction. Maintenance
> and the avoidance of bit/doc rot
> are first-class concerns and really require author commitment.
>
>
>
> Some authors already have books outside bioconductor to have
> extensive examples of their packages.
> They will also benefit from having them with the Bioconductor
> framework and in sync with the packages released to the users.
>
> Best,
>
> Lluís
>
>
> On Wed, 4 Jan 2023 at 21:39, Vincent Carey
> wrote:
>
> I am glad you brought this up here, and I welcome further
> discussion on
> this mailing list. It is important to understand the
> constraints on
> development
> that arise from Bioconductor's package guidelines.
>
> I don't think we want to change the limits on package payload
> size without
> understanding the consequences for users and our build
> system. The split
> approach mentioned by Lambda seems sensible to me, and I hope
> it is
> not too burdensome. Additional commentary and details from
> the community
> are welcome.
>
> On Wed, Jan 4, 2023 at 3:21 PM Lambda Moses
> wrote:
>
> > Hi Adam,
> >
> > I also got this problem, and I would like some input from
> Bioc Core
> > Team. I worked around it by writing a minimal vignette in
> the main
> > branch. Then I made a documentation branch, where I have the
> same code
> > as in main branch, but with more elaborate vignettes used to
> build a
> > pkgdown website. I made a rule for myself that I can only
> merge from the
> > main or devel branch to the documentation branch but not the
> other way
> > round. I would switch branch when I find a bug or want a new
> feature
> > while writing the vignettes. You can see the main branch here:
> > https://github.com/pachterlab/voyager/tree/main The
> documentation branch
> > here: https://github.com/pachterlab/voyager/tree/documentation
> >
> > I kind of wonder if the 5 MB rule is outdated in the age of
> increasing
> > computer power and internet speed. A jpeg photo can easily
> exceed 5 MB.
> > I also wonder if this rule is deliberately kept for good
> reasons, like
> > to make R more inclusive to disadvantaged people with
> limited internet
> > services.
> >
> > Regards,
> >
> > Lambda
> >
> > ___
> > 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}}
>
> ___
> 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 th...{{dropped:15}}
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Large vignettes
Hi Adam, I also got this problem, and I would like some input from Bioc Core Team. I worked around it by writing a minimal vignette in the main branch. Then I made a documentation branch, where I have the same code as in main branch, but with more elaborate vignettes used to build a pkgdown website. I made a rule for myself that I can only merge from the main or devel branch to the documentation branch but not the other way round. I would switch branch when I find a bug or want a new feature while writing the vignettes. You can see the main branch here: https://github.com/pachterlab/voyager/tree/main The documentation branch here: https://github.com/pachterlab/voyager/tree/documentation I kind of wonder if the 5 MB rule is outdated in the age of increasing computer power and internet speed. A jpeg photo can easily exceed 5 MB. I also wonder if this rule is deliberately kept for good reasons, like to make R more inclusive to disadvantaged people with limited internet services. Regards, Lambda ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Bioc-devel Digest, Vol 226, Issue 3
Hi Adam, I also got this problem, and I would like some input from Bioc Core Team. I worked around it by writing a minimal vignette in the main branch. Then I made a documentation branch, where I have the same code as in main branch, but with more elaborate vignettes used to build a pkgdown website. I made a rule for myself that I can only merge from the main or devel branch to the documentation branch but not the other way round. I would switch branch when I find a bug or want a new feature while writing the vignettes. You can see the main branch here: https://github.com/pachterlab/voyager/tree/main The documentation branch here: https://github.com/pachterlab/voyager/tree/documentation I kind of wonder if the 5 MB rule is outdated in the age of increasing computer power and internet speed. A jpeg photo can easily exceed 5 MB. I also wonder if this rule is deliberately kept for good reasons, like to make R more inclusive to disadvantaged people with limited internet services. Regards, Lambda ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Give commit access to new author
Hi, I would like to add a new author to the packages Voyager and SFEData, of which I'm an original author, and give her git commit access to the repos on Bioconductor. Her email is kayla...@caltech.edu Thanks, Lambda ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Give commit access to new author
Hi, I would like to add a new author to the packages Voyager and SFEData, of which I'm an original author, and give her git commit access to the repos on Bioconductor. Her email is kayla...@caltech.edu Thanks, Lambda ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
