Re: [Rd] object.size vs lobstr::obj_size

Thank you Tomas, Hervé and Hadley for the input. Much appreciated! Stefan Stefan Schreiber, PhD, P. Biol. Director EnviroStats Solutions Inc. Adjunct Professor, Faculty of Agricultural, Life & Environmental Sciences, University of Alberta Phone: 780-221-1838 https://envirostats.ca/ On Fri, 27

Re: [Rd] object.size vs lobstr::obj_size

On 3/27/20 15:19, Hadley Wickham wrote: On Fri, Mar 27, 2020 at 4:01 PM Hervé Pagès > wrote: On 3/27/20 12:00, Hadley Wickham wrote: > > > On Fri, Mar 27, 2020 at 10:39 AM Hervé Pagès mailto:hpa...@fredhutch.org> >

Re: [Rd] object.size vs lobstr::obj_size

On Fri, Mar 27, 2020 at 4:01 PM Hervé Pagès wrote: > > > On 3/27/20 12:00, Hadley Wickham wrote: > > > > > > On Fri, Mar 27, 2020 at 10:39 AM Hervé Pagès > > wrote: > > > > Hi Tomas, > > > > On 3/27/20 07:01, Tomas Kalibera wrote: > > > they provide an

Re: [Rd] object.size vs lobstr::obj_size

On 3/27/20 12:00, Hadley Wickham wrote: On Fri, Mar 27, 2020 at 10:39 AM Hervé Pagès > wrote: Hi Tomas, On 3/27/20 07:01, Tomas Kalibera wrote: > they provide an over-approximation They can also provide an "under-approximation" (to say the

Re: [Rd] object.size vs lobstr::obj_size

On Fri, Mar 27, 2020 at 11:08 AM Tomas Kalibera wrote: > On 3/27/20 4:39 PM, Hervé Pagès wrote: > > Hi Tomas, > > > > On 3/27/20 07:01, Tomas Kalibera wrote: > >> they provide an over-approximation > > > > They can also provide an "under-approximation" (to say the least) e.g. > > on reference

Re: [Rd] object.size vs lobstr::obj_size

On Fri, Mar 27, 2020 at 10:39 AM Hervé Pagès wrote: > Hi Tomas, > > On 3/27/20 07:01, Tomas Kalibera wrote: > > they provide an over-approximation > > They can also provide an "under-approximation" (to say the least) e.g. > on reference objects where the entire substance of the object is ignored

Re: [Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)

You should try and set up your system using SSH from your Github account as well. > On Mar 27, 2020, at 12:25 PM, Enio Gjerga wrote: > > Hi, > > Ahh apparently I cannot. I tried to clone a random repo (PHONEMeS) locally > through the command you provided, and then got the following: > >

[Bioc-devel] Fwd: Trying to access the source repository of a bioconductor package (Developer Access)

Seems the mailing list got dropped off. Forwarding to make sure the community is in the know. Begin forwarded message: From: Enio Gjerga mailto:enio.gje...@gmail.com>> Subject: Re: [Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access) Date: March 27,

Re: [Bioc-devel] Question regarding the error from build report

Try resending the email as plain text. The list strips HTML content, so if the message has no text part, there will be no message. On Thu, Mar 26, 2020 at 9:35 PM Hervé Pagès wrote: > > What is the question? > > On 3/26/20 17:36, 유도영 wrote: > > > > ___

Re: [Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)

Ok, can you also show my the result of ssh - T g...@git.bioconductor.org | grep CNORfeeder > On Mar 27, 2020, at 11:54 AM, Enio Gjerga wrote: > > Hi, > > Thank you for your reply. So according to #14: > > 1. I use "git remote -v" and then I get the following: > > origin

Re: [Rd] object.size vs lobstr::obj_size

On 3/27/20 4:39 PM, Hervé Pagès wrote: Hi Tomas, On 3/27/20 07:01, Tomas Kalibera wrote: they provide an over-approximation They can also provide an "under-approximation" (to say the least) e.g. on reference objects where the entire substance of the object is ignored which makes

Re: [Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)

Hi, Thank you for your reply. So according to #14: 1. I use "git remote -v" and then I get the following: origin https://github.com/saezlab/CNOv2.git (fetch) origin https://github.com/saezlab/CNOv2.git (push) upstream g...@git.bioconductor.org:packages/CNORfeeder.git (fetch) upstream

Re: [Rd] object.size vs lobstr::obj_size

Hi Tomas, On 3/27/20 07:01, Tomas Kalibera wrote: they provide an over-approximation They can also provide an "under-approximation" (to say the least) e.g. on reference objects where the entire substance of the object is ignored which makes object.size() completely meaningless in that case:

Re: [Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)

As given in #14 of the FAQ, please send me git remote -v > On Mar 27, 2020, at 10:54 AM, Enio Gjerga wrote: > > Hello, > > Thank you very much for your reply. I have added a new key on my > BiocCredentials and on Github, however, I am afraid that the same issue still > persists.

Re: [Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)

Hello, Thank you very much for your reply. I have added a new key on my BiocCredentials and on Github, however, I am afraid that the same issue still persists. If I try to check whether I have access to the package (using the "ssh -T g...@git.bioconductor.org" command) or clone it locally

Re: [Rd] object.size vs lobstr::obj_size

On 2/19/20 3:55 AM, Stefan Schreiber wrote: I have posted this question on R-help where it was suggested to me that I might get a better response on R-devel. So far I have gotten no response. The post I am talking about is here: https://stat.ethz.ch/pipermail/r-help/2020-February/465700.html My

[Bioc-devel] Bioconductor 3.11 db0s are available

Hello Bioconductor Community! The newest db0s for the upcoming Bioconductor 3.11 release are up and available for download in the devel version of Bioconductor. They are: anopheles.db0_3.11.0.tar.gz arabidopsis.db0_3.11.0.tar.gz bovine.db0_3.11.0.tar.gz canine.db0_3.11.0.tar.gz

Re: [Rd] [External] Re: Expressions from boxplot() passed to bxp()

On Fri, 27 Mar 2020, peter dalgaard wrote: It's not new anyway. You see the same behaviour with boxplot(dat, ylab=quote(X[2])) and it boils down to the use of do.call("bxp", ...) in the internals. As a general matter, expression() exists to prevent this sort of confusion, e.g., in this

Re: [Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)

Try adding another key. If that doesn't work, show us your git set up. http://bioconductor.org/developers/how-to/git/faq/ #13 and #14 Best, Nitesh On 3/27/20, 6:15 AM, "Bioc-devel on behalf of Enio Gjerga" wrote: Hello, I am Enio Gjerga and I am the maintainer of the

Re: [Rd] Plotmath on Fedora 31 broken with with pango >= 1.44 - workarounds?

On Wed, 25 Mar 2020 at 12:25, Nicolas Mailhot wrote: > > > > R brought this all on itself by hardcoding a Windows-only “Symbol” font > family name in its default conf. Linux systems are UTF-8 by default for > ~20 years now, they don’t need the forcing of magic font families to > handle symbols

[Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)

Hello, I am Enio Gjerga and I am the maintainer of the CNORfeeder and the CNORode package, a role which I got recently. I am facing trouble trying to access the source packages for then later syncing it with a Github repository and do a few necessary updates. I try first to obtain developer

[Rd] Possibility of Less Verbose Stack Trace

Good day, Is there a setting the user can change to make R CMD check stack traces output less and make it easier to spot the line of code that's the problem? I use R Under development. Part of the trace I see looks like: --- R stacktrace --- where 1: .local(model, test, ...) where 2:

Re: [Rd] Expressions from boxplot() passed to bxp()

It's not new anyway. You see the same behaviour with boxplot(dat, ylab=quote(X[2])) and it boils down to the use of do.call("bxp", ...) in the internals. As a general matter, expression() exists to prevent this sort of confusion, e.g., in this construction, > X <- quote(Y+1); bquote(f(.(X)))

Re: [Bioc-devel] Drosophila virilis BioPackage forthcoming?

Hi Ilkka, On 3/26/20 02:11, Ilkka Havukkala wrote: Hello there Is it possible to get Drosophila virilis genome as a BSGenome data package? e.g. this one https://metazoa.ensembl.org/Drosophila_virilis/Info/Annotation/ I wrapped up this genome in the BSgenome.Dvirilis.Ensembl.dvircaf1 package.