Re: [Rd] mclapply returns NULLs on MacOS when running GAM

On Tue, Apr 28, 2020 at 9:00 PM Shian Su wrote: > > Thanks Simon, > > I will take note of the sensible default for core usage. I’m trying to > achieve small scale parallelism, where tasks take 1-5 seconds and make fuller > use of consumer hardware. Its not a HPC-worthy computation but even

Re: [Bioc-devel] Bioconductor 3.11 is Released!

Congratulations to the entire Bioconductor team for another successful release! I have one question. I cannot find the package artMS in the News . Is there anything wrong with the

Re: [Rd] mclapply returns NULLs on MacOS when running GAM

Thanks Simon, I will take note of the sensible default for core usage. I’m trying to achieve small scale parallelism, where tasks take 1-5 seconds and make fuller use of consumer hardware. Its not a HPC-worthy computation but even laptops these days come with 4 cores and I don’t see a reason

Re: [Rd] mclapply returns NULLs on MacOS when running GAM

Do NOT use mcparallel() in packages except as a non-default option that user can set for the reasons Henrik explained. Multicore is intended for HPC applications that need to use many cores for computing-heavy jobs, but it does not play well with RStudio and more importantly you don't know the

Re: [Rd] mclapply returns NULLs on MacOS when running GAM

Thanks Henrik, That clears things up significantly. I did see the warning but failed to include it my initial email. It sounds like an RStudio issue, and it seems like that it’s quite intrinsic to how forks interact with RStudio. Given this code is eventually going to be a part of a package,

[Rd] R 4.0.0 build error with sysdata.rda on ppc64el architecture

The R 4.0.0 package migration on Debian is being held back by a failed build on ppc64el [1]. We can see from the history of builds logs [2] that it used to build, briefly failed, worked again and then failed leading to R 4.0.0's release. (And my bad for missing how the alpha1/alpha2/beta/rc

[Bioc-devel] Bioconductor 3.11 is Released!

Thanks to all developers and community members for contributing to the project! Please see the full release announcement: https://bioconductor.org/news/bioc_3_11_release/ The Bioconductor Core Team This email message may contain legally privileged and/or confidential information. If you

Re: [Rd] Rtools and R 4.0.0?

Absolutely; this is a complicated and frustrating procedure, and we owe Jeoren and all our gratitude! Avi On Tue, Apr 28, 2020 at 3:37 PM Gabriel Becker wrote: > > Huge thanks to you (Jeroen) and R-core for doing this. > > I wasn't involved with this directly but I know it was a pretty

Re: [Rd] Rtools and R 4.0.0?

Huge thanks to you (Jeroen) and R-core for doing this. I wasn't involved with this directly but I know it was a pretty seriously heavy list so well done all around! ~G On Tue, Apr 28, 2020, 11:04 AM Hervé Pagès wrote: > Thanks Jeroen! > > > On Tue, Apr 7, 2020 at 6:07 PM Kevin Ushey

Re: [Rd] Rtools and R 4.0.0?

Thanks Jeroen! On Tue, Apr 7, 2020 at 6:07 PM Kevin Ushey wrote: Regardless, I would like to thank R core, CRAN, and Jeroen for all of the time that has gone into creating and validating this new toolchain. This is arduous work at an especially arduous time, so I'd like to voice my

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

It is not clear what the purpose of these "if" statement is. Apparently to set the $os_name variable but then where is this variable used and for what? So you might want to revisit the need for these tests. Maybe you don't need them after all. Another problem is that the temporary files

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

Hi H, Thank you for pointing that out. I am currently not seeing errors on my Windows computer, but I see that I need to add "msys" for Windows on your system (and add quotes as well as make the error message more clear). I have a 64-bit Windows computer and I didn't get an error message,

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

Hi Charles, The error you get on Windows is because your Perl script integrate_island.pl fails on this platform. It contains the following code: if (($os eq "MacOS")||($os eq "darwin")||($os eq "linux")) { #Mac $os_name = "MAC"; }#end if ($os eq

Re: [Bioc-devel] Checking that last commit made the cut

That is the correct location to check. Notice the date at the top of the page is still yesterday. Today's report has not posted yet. When today's report is posted check to see if it is updated. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of

[Bioc-devel] Checking that last commit made the cut

Hi, I'm the developer for the package MOMA that was just accepted this past cycle. I was re-reading through the vignette on Sunday and realized I needed to add an additional link to a resource and committed the changes around 10 that evening (commit code: c305b841659c3de07ddaef83634cbd7338427462)

Re: [Bioc-devel] Fwd: About rcellminer package

Hi Fathi, You should update the version to 2.11.1, if you want a new build for your package. Developers should only change the version number in the "z" coordinate of the "x.y.z" versioning system. Best, Nitesh Hi Nitesh, My name is Fathi Elloumi one of the maintainer of package

Re: [Bioc-devel] regutools: request to add more git push access

I've resolved this with Carmina, but I haven't received Emiliano's email. Best, Nitesh On 4/27/2020 11:17 AM, Carmina Barjon wrote: Hi Nitesh! Yes, this it's the email address I will be using (car.bar...@gmail.com ). Thank you Carmina El lun., 27 abr. 2020 a

Re: [Rd] mclapply returns NULLs on MacOS when running GAM

Hi, a few comments below. First, from my experience and troubleshooting similar reports from others, a returned NULL from parallel::mclapply() is often because the corresponding child process crashed/died. However, when this happens you should see a warning, e.g. > y <- parallel::mclapply(1:2,

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

Hi Lori, Thank you very much. I was thinking about reverting the change to test not specifying the full file path at one point (in v1.33.6), but I was planning on keeping the change to using a temporary directory in v1.33.4. Essentially, I tested making that change in v1.33.6 because there

Re: [Bioc-devel] Images from vignettes

I am not a lawyer, but if you wrote the vignette, then you likely could claim any "rights" to it. In other words, I don't see a problem. Perhaps others have something deeper to add. Sean On Tue, Apr 28, 2020 at 10:14 AM Diego Morais wrote: > Hi everyone, > > a collaborator intends to use an

Re: [R-pkg-devel] Problems importing packages with SystemRequirements

Yeah, this is a bug in whoami I think. It has a tryCatch() but it does not suppress the error message from system(). Gabor On Tue, Apr 28, 2020 at 2:35 PM wrote: > > Dear Uwe, > thanks for your reply. > But wouldn't checking for the SystemRequirements be the dependencies' jobs? > Looking at

[Bioc-devel] Images from vignettes

Hi everyone, a collaborator intends to use an image from the vignette of my package in a book chapter. Do I have to ask permission to publish such image? I don't know if there are copyright issues related to the vignette I wrote. -- Best regards, Diego Morais [[alternative HTML

Re: [R-pkg-devel] Problems importing packages with SystemRequirements

Dear Uwe, thanks for your reply. But wouldn't checking for the SystemRequirements be the dependencies' jobs? Looking at `whoami`'s code (which is basically a single very well structured and clearly written file of 350 lines including roxygen comments by Gabor Csardi), I see exactly a single call

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

I can investigate more on the windows machine after we are done with the release (later this week -- possibly early next) I would highly recommend not reverting the change to using a temporary directory. We don't normally allow anyone to write to anywhere but a temporary directory except in

Re: [R-pkg-devel] Problems importing packages with SystemRequirements

On 28.04.2020 09:28, fvaf...@mailbox.org wrote: Dear Jeff, thanks for your reply, I exactly know, where gitr and whoami are called, since I constitently use the `::` operator to import from any dependency. I am pretty sure that I use those packages for intended purposes only. Furthermore,

Re: [Rd] mclapply returns NULLs on MacOS when running GAM

Yes I am running on Rstudio 1.2.5033. I was also running this code without error on Ubuntu in Rstudio. Checking again on the terminal and it does indeed work fine even with large data.frames. Any idea as to what interaction between Rstudio and mclapply causes this? Thanks, Shian On 28 Apr

Re: [Rd] mclapply returns NULLs on MacOS when running GAM

Sorry, the code works perfectly fine for me in R even for 1e6 observations (but I was testing with R 4.0.0). Are you using some kind of GUI? Cheers, Simon > On 28/04/2020, at 8:11 PM, Shian Su wrote: > > Dear R-devel, > > I am experiencing issues with running GAM models using mclapply, it

[Rd] mclapply returns NULLs on MacOS when running GAM

Dear R-devel, I am experiencing issues with running GAM models using mclapply, it fails to return any values if the data input becomes large. For example here the code runs fine with a df of 100 rows, but fails at 1000. library(mgcv) library(parallel) > df <- data.frame( + x = 1:100, +

Re: [R-pkg-devel] Problems importing packages with SystemRequirements

Dear Jeff, thanks for your reply, I exactly know, where gitr and whoami are called, since I constitently use the `::` operator to import from any dependency. I am pretty sure that I use those packages for intended purposes only. Furthermore, CRAN reports issues for system calls (made by `git2r`

Re: [R-pkg-devel] Problems importing packages with SystemRequirements

Maybe your use of those packages represent use cases that are not tested by those packages. If you pare down your code that triggers these problems to small reproducible examples then you can contribute them to those packages? On April 27, 2020 11:05:49 PM PDT, fvaf...@mailbox.org wrote: >Dear

[R-pkg-devel] Problems importing packages with SystemRequirements

Dear All, I maintain a package that has issues `sh: whoami: not found` and `sh: git: not found` (see https://cran.r-project.org/web/checks/check_results_packager.html), albeit not having any (declared or undeclared) external dependencies -- no calls to system() or system2(). It does import