Re: [Bioc-devel] Compatibility of Bioconductor with tidyverse S3 classes/methods

Would this scenario satisfy " make the package _directly_ compatible with standard Bioconductor data structures" If an input is SummarizedExperiment return SummarizedExperiment, if the input is a tbl_df or ttBulk, return ttBulk (?) Best wishes. *Stefano * Stefano Mangiola | Postdoctoral

Re: [Bioc-devel] Compatibility of Bioconductor with tidyverse S3 classes/methods

I would urge you to make the package _directly_ compatible with standard Bioconductor data structures; no explicit conversion. But you can create wrapper methods (even on an S3 generic) that perform the conversion automatically. You'll probably want two separate APIs though (in different styles),

Re: [Bioc-devel] Compatibility of Bioconductor with tidyverse S3 classes/methods

Thanks Michael, yes in a sense, ttBulk and SummariseExperiment can be considere as two interfaces. Would be fair enough to create a function that convert from one to the other, although the default would be ttBulk? *> I'm not sure the tidyverse is a great answer to the user interface, because it

Re: [Bioc-devel] Compatibility of Bioconductor with tidyverse S3 classes/methods

There's a difference between implementing software, where one wants formal data structures, and providing a convenient user interface. Software needs to interface with other software, so a package could provide both types of interfaces, one based on rich (S4) data structures, another on simpler

Re: [Bioc-devel] Compatibility of Bioconductor with tidyverse S3 classes/methods

Thanks a lot for your comment Martin and Michael, Here I reply to Marti's comment. Michael I will try to implement your solution! I think a key point from https://github.com/Bioconductor/Contributions/issues/1355#issuecomment-580977106 (that I was under-looking) is *>> "So to sum up: if you

Re: [Bioc-devel] Compatibility of Bioconductor with tidyverse S3 classes/methods

Martin's comments are great. I'll just give some technical help. The "tbl_df" S4 class is already defined by dplyr (and more properly), so omit the call to setOldClass(). Then, things work a bit better. > my %>% nest(-b) # had to fix this from your example [some ugly result] Warning messages: 1:

Re: [Bioc-devel] Compatibility of Bioconductor with tidyverse S3 classes/methods

The idea isn't to use S4 at any cost, but to 'play well' with the Bioconductor ecosystem, including writing robust and maintainable code. This comment https://github.com/Bioconductor/Contributions/issues/1355#issuecomment-580977106 provides some motivation; there was also an interesting

[Bioc-devel] Compatibility of Bioconductor with tidyverse S3 classes/methods

Hello, I have a package (ttBulk) under review. I have been told to replace the S3 system to S4. My package is based on the class tbl_df and must be fully compatible with tidyverse methods (inheritance). After some tests and research I understood that tidyverse ecosystem is not compatible with S4

Re: [Bioc-devel] how to trace 'Matrix' as package dependency for 'GenomicScores'

true, i was just searching for the shortest path, we can search for all simple (i.e., without repeating "vertices") paths and there are up to five routes from "GenomicScores" to "Matrix" igraph::all_simple_paths(igraph::igraph.from.graphNEL(g), from="GenomicScores", to="Matrix", mode="out")

Re: [Bioc-devel] how to trace 'Matrix' as package dependency for 'GenomicScores'

Excellent! I think there are other, independent, paths between your immediate dependents... RBGL::sp.between(g, start="DT", finish="Matrix", detail=TRUE)[[1]]$path_detail [1] "DT""crosstalk" "ggplot2" "mgcv" "Matrix" ?? Martin On 2/6/20, 10:47 AM, "Robert Castelo" wrote:

Re: [Bioc-devel] ptime ERROR

It might be a combination of both! Thanks for the information. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Andris Jankevics

Re: [Bioc-devel] ptime ERROR

My apologies for pointing in wrong direction, but I was getting the same error message in tests and it took me a while to figure out why. https://github.com/r-lib/devtools/issues/2167 [https://avatars0.githubusercontent.com/u/22618716?s=400=4]

Re: [Bioc-devel] ptime ERROR

Actually it looks like it has to do with having a conditional > 1 rather than a class() == There is this post: https://stat.ethz.ch/pipermail/bioc-devel/2020-January/016081.html And this: http://bioconductor.org/developers/how-to/troubleshoot-build-report/ Cheers, Lori Shepherd Bioconductor

Re: [Bioc-devel] ptime ERROR

This is the error, sorry my hand slipped when writing the last email. Thank you. http://bioconductor.org/checkResults/devel/bioc-LATEST/M3C/malbec2-checksrc.html checking examples ... ERROR Running examples in ‘M3C-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime",

[Bioc-devel] ptime ERROR

Hi I was wondering will this error disappear by itself? Because I did not change the package. Thanks, Chris [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] how to trace 'Matrix' as package dependency for 'GenomicScores'

hi Martin, thanks for hint!! i wasn't aware of 'tools::package_dependencies()', adding a bit of graph sorcery i get the result i was looking for: repos <- BiocManager::repositories()[c(1,5)] repos BioCsoft "https://bioconductor.org/packages/3.11/bioc;

Re: [Bioc-devel] Compatibility of S4 and tidyverse

OK sorry for this email chain, outlook in windows 10 is definitely doing weird stuff. I will reopen another thread. And after understanding the joke, I thought was a really good one XD Best wishes. *Stefano * Il giorno ven 7 feb 2020 alle ore 00:24 Martin Morgan < mtmorgan.b...@gmail.com>

Re: [Bioc-devel] Install and Build ERROR - CeTF package

Thanks for the reply, Lori and Andris! Best, Carlos > > On 6 Feb 2020, at 10:21, Shepherd, Lori wrote: > >  > I have already reached out to the maintainer of clusterProfile/enrichplot - > they are working on the updates and it should be fixed soon. > > Lori Shepherd > Bioconductor

Re: [Bioc-devel] how to trace 'Matrix' as package dependency for 'GenomicScores'

The first thing is to get the correct repositories repos = BiocManager::repositories() (maybe trim the experiment and annotation repos from this). I also tried pkgDepTools::makeDepGraph() but it took so long that I moved on... it has an option 'keep.builtin' which might include Matrix.

Re: [Bioc-devel] Compatibility of S4 and tidyverse

Sounds like an incompatibility with your mailer, maybe it tries to send the message as (signed / encrypted ?) attachement, which are always automatically stripped by the listserver. Try text only, or maybe use your webmailer ? Yours, Steffen On Thu, 2020-02-06 at 23:54 +1100, Stefano

Re: [Bioc-devel] Compatibility of S4 and tidyverse

It's still blank; the email list filters html content; make sure you send as 'text only' -- your client seemed to 'do the right thing' when responding to Martin Maechler, so responding again to that might do the trick... Martin Morgan On 2/6/20, 8:13 AM, "Bioc-devel on behalf of Stefano

Re: [Bioc-devel] Install and Build ERROR - CeTF package

I have already reached out to the maintainer of clusterProfile/enrichplot - they are working on the updates and it should be fixed soon. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets

Re: [Bioc-devel] Account Activation Issue

It is registered to, "c...@fgz.eth.ch". Would you like me to change the address? Best, Nitesh On 2/6/20, 5:18 AM, "Bioc-devel on behalf of Opitz Lennart" wrote: Dear BC-Devel-Team, I am the maintainer of the package ‘NextLink' and I tried to activate the relevant GIT accounts

Re: [Bioc-devel] Install and Build ERROR - CeTF package

Build of clusterProfiler is failing because it depends on enrichplot 1.7.1, while only 1.7.0 is available. I guess you will have to wait or contact maintainers of these two packages. BW, Andris From: Bioc-devel on behalf of cbiag...@gmail.com Sent: 06

Re: [Bioc-devel] Compatibility of S4 and tidyverse

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Re: [Bioc-devel] Compatibility of S4 and tidyverse

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[Bioc-devel] Install and Build ERROR - CeTF package

Dear all, I recently had an accepted package on the bioconductor and it's been a week since I got the error to install and build the package on Windows. The installation and build on Linux is OK. The error is: *ERROR: dependency 'clusterProfiler' is not available for package 'CeTF'* I already

Re: [Bioc-devel] Compatibility of S4 and tidyverse

Hi Stefano, Your message to the list was completely empty, thus the joke by Michael. I think you'll have to resend your message to the list and check it arrives as expected so you can get some feedback! :) Bernat El 2/6/20 a las 12:29 PM, stefano escribió: > Hello, > > Happy to trigger good

[Bioc-devel] how to trace 'Matrix' as package dependency for 'GenomicScores'

hi, when i load the package 'GenomicScores' in a clean session i see thorugh the 'sessionInfo()' that the package 'Matrix' is listed under "loaded via a namespace (and not attached)". i'd like to know what is the dependency that 'GenomicsScores' has that ends up requiring the package

Re: [Bioc-devel] Compatibility of S4 and tidyverse

Hello, Happy to trigger good laughs, although I did not understand the irony. If anyone has a clear idea of the issue or similar experience and can help out would be great! On Thu, 6 Feb 2020, 8:46 PM Martin Maechler wrote: > > Michael Lawrence via Bioc-devel > > on Wed, 5 Feb

[Bioc-devel] Account Activation Issue

Dear BC-Devel-Team, I am the maintainer of the package ‘NextLink' and I tried to activate the relevant GIT accounts via https://git.bioconductor.org/BiocCredentials/account_activation/ using the email 'lop...@fgcz.ethz.ch’ but I got the response that this address is not associated with a

Re: [Bioc-devel] Compatibility of S4 and tidyverse

> Michael Lawrence via Bioc-devel > on Wed, 5 Feb 2020 20:52:52 -0800 writes: > Yep that about sums it up. :-) ;-) Thank you, Michael !! I haven't laughed as much from reading e-mails in a long while !! Martin > On Wed, Feb 5, 2020 at 8:37 PM Stefano Mangiola >