Re: [Bioc-devel] Large vignettes
ction in an upstream package was > modified, 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
ction in an upstream package was > modified, 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