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

Paul et al, I will try to do this tonight or tomorrow, though it will not be built with th system tools because I have yet to get that tto work locally (spent a good chunk of this morning trying). I will send a separate messaage regarding those difficulties as well so that we can at least

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

The R-symfam branch (r78176) is now working, for my basic tests, on ... Ubuntu (pango < 1.44) Ubuntu (no pango) Fedora (pango > 1.44) Windows I need help to confirm that this builds on macOS and that the basic tests work ... https://github.com/pmur002/R-symfam-testing Brian has been

Re: [R-pkg-devel] Windows specific install error

This is the same as https://stat.ethz.ch/pipermail/r-package-devel/2020q1/005256.html and due I believe to stale packages on the CRAN windows builder; the solution is I believe on the CRAN side. Martin Morgan On 4/7/20, 6:14 PM, "R-package-devel on behalf of Ryan Sartor" wrote:

[R-pkg-devel] Windows specific install error

Hello everyone, My package seems to pass all the CRAN checks for Linux but fails to install on Windows. This is the contents of 00install.out: * installing *source* package 'DiPALM' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Error:

[Rd] ASAN

I'm trying to chase down a possible issue with the survival package, and so was trying to resurrect my ASAN version of r-devel.   I added the lines to config.site for CC, CFLAGS and MAIN_LDFLAGS per section 4.3.3 of the  'packages' documentation, and lines to ~/.R/Makevars. I followed that

Re: [R-pkg-devel] [FWD] [CRAN-pretest-archived] CRAN submission JuliaConnectoR 0.5.0

I did not say "interfere"... I said "problems with consistency". I don't think your wholesale import of functions without corresponding help pages is consistent with the normal use of R, which will make reading R code written with this mechanism in place a painful source of trouble for help

Re: [Rd] Hard memory limit of 16GB under Windows?

Agreed. I don't see any evidence of a "hard limit" here. It just looks like the code you're running has exhausted the memory of your machine. It doesn't require creating a lot of 12.6 Gb vectors to do that, even on a machine with a lot of memory ;-) H. On 4/7/20 08:05, Thierry Onkelinx via

Re: [R-pkg-devel] [FWD] [CRAN-pretest-archived] CRAN submission JuliaConnectoR 0.5.0

Thank you very much for your comment. Could you elaborate how you think that it could interfere with the help system? I haven't yet connected the Julia help with the R help, as the R help system is quite complex and RStudio handles it again differently. So it's simply like the functions were

Re: [Rd] [SPAM] Hard memory limit of 16GB under Windows?

Dear Samuel Does the FAQ for Windows section 2.9 help you here? Michael On 07/04/2020 12:35, Samuel Granjeaud IR/Inserm wrote: Hi, I am not not sure whether this topic belongs to this mail list, but I feel the subscribers here should be the right audience. I noticed that the memory limit

Re: [Rd] Rtools and R 4.0.0?

That's great to see, although I suspect it's still a speculative change and could be backed out if any non-trivial issues were encountered. 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

Re: [Bioc-devel] Unit tests pass locally but fail on Bioconductor machines

Dear Vincent, you've hit the nail on the head! Indeed the error was raised by the fact that ExpressionSet objects store the R version. I followed your suggestion and create this object now every time I run the tests. And also thanks @Lori, part of the solution was indeed to update to R4.0

Re: [Rd] Hard memory limit of 16GB under Windows?

Dear Samuel, The most important information from your mail was the actual error message: "cannot allocate vector of size 12.6 Gb". You'll need to know what code generated this error message. And then figure out if the code does something sensible. Often that is not the case when you get a

Re: [Rd] Rtools and R 4.0.0?

There appears to have been some progress on this matter: -Note that @command{g++} 4.9.x (as used for @R{} on Windows up to 3.6.x) +Note that @command{g++} 4.9.x (as used on Windows prior to @R{} 4.0.0) See SVN commit r78169 titled 'anticipate change in Windows toolchain', or the mirrored git

Re: [Rd] Hard memory limit of 16GB under Windows?

Hi Samuel, You may already be aware, but if not, RStudio has their own support mechanisms here: https://support.rstudio.com/hc/en-us If this does turn out to be RStudio specific, you may wish to check there for additional insights. Regards, Marc Schwartz > On Apr 7, 2020, at 10:24 AM,

Re: [Rd] Hard memory limit of 16GB under Windows?

Hi Samuel, please also have a look at ?memory.limit. You can set this limit at R startup. It is in megabytes. Maybe R Studio sets it at runtime. Best Tomas On 4/7/20 3:57 PM, Samuel Granjeaud IR/Inserm wrote: Hi Tomas, Many thanks for your answer. Here is a copy of a fresh session under

Re: [Rd] Hard memory limit of 16GB under Windows?

Hi Tomas, Many thanks for your answer. Here is a copy of a fresh session under RStudio, and after a copy under Rgui. Strangely enough the result of memory.limit() is not the same. Without your question I would not have looked to RGui, being used to work with RStudio. The value under RGui

Re: [Bioc-devel] HDF5Array failure on windows

Thanks for the two pointers. Herve: we are using a number of unexpected functions from HDF5Array: ‘HDF5Array:::.create_dir’, ‘HDF5Array:::.replace_dir’, ‘HDF5Array:::.shorten_assay2h5_links’ That might be relevant in light of that specific test error. On Mon, Apr 6, 2020 at 1:13 PM Hervé

Re: [Rd] Hard memory limit of 16GB under Windows?

Hi Samuel, could you please provide more information? Where do you see the limit reported or how did you trigger it, what version of Windows do you have, are you using 64-bit build of R (sessionInfo()) Please check help("Memory-limits") and section 8 of R Admin manual Best, Tomas On 4/7/20

Re: [Bioc-devel] Unit tests pass locally but fail on Bioconductor machines

I will chime in because the error is a bit obscure. You serialized ExpressionSet instances for testing. In the expected_res in your tests we have ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slot .. .. ..@ .Data:List of 4 .. .. .. ..$ : int [1:3] 3 6 1 ..

Re: [Bioc-devel] Unit tests pass locally but fail on Bioconductor machines

There are many changes to base R hence the switch from 3.6 to 4.0. I would highly suggest using R 4.0. There is a R-alpha version now available for all platforms with the R - 4.0 release schedule for later this month. Please use the R-alpha version . on CRAN.r-project.org you should see a

[Rd] Hard memory limit of 16GB under Windows?

Hi, I am not not sure whether this topic belongs to this mail list, but I feel the subscribers here should be the right audience. I noticed that the memory limit reported under Windows is 16 GB. I am wondering how to increase it. I didn't found anything in Rprofile.site nor .Rprofile. Is this

[Bioc-devel] Unit tests pass locally but fail on Bioconductor machines

Hi there, the unit tests (implemented with testthat) of my package (https://github.com/saezlab/dorothea ) run smoothly on local machines (tested for Linux, Windows and macOS). However, on the Bioconductor machines (both Linux and Window) a particular test

Re: [Bioc-devel] git.bioconductor identifies me as a different person

Sorry the term concatenate was poorly chosen. I meant to say that my BiocCredential ssh key list consist of all the keys both from my public github and from koen's. Adding a new key did not fix the issue though and lead to the same error. Hector Roux de Bezieux UC Berkeley - PhD Student in

Re: [Bioc-devel] git.bioconductor identifies me as a different person

Hi, Please add another SSH key in BiocCredentials and it'll give you access. Feel free to remove any key in that list which you think is not needed. There cannot be keys which are concatenated, it will not work that way. Let me know if there is problem. Best, Nitesh > On Apr 7, 2020, at

Re: [Bioc-devel] git.bioconductor identifies me as a different person

Hi, There is no overlap between https://github.com/HectorRDB.keys and https://github.com/koenvandenberge.keys. However, the keys listed in my BiocCredential page (https://git.bioconductor.org/BiocCredentials/profile/) are a concatenation of koen's public github keys and mine. However, none of the

Re: [Bioc-devel] git.bioconductor identifies me as a different person

Do you have koenvandenberge's public key in your github repository? On 4/7/20, 3:51 AM, "Bioc-devel on behalf of Hector Roux de Bezieux" wrote: Hi, My github usernameis HectorRDB but this is what happens if I try to connect to git.bioconductor ssh

[Bioc-devel] git.bioconductor identifies me as a different person

Hi, My github usernameis HectorRDB but this is what happens if I try to connect to git.bioconductor ssh g...@git.bioconductor.org PTY allocation request failed on channel 0 hello koenvandenberge, this is ... However, I am not koenvandenberge. I am working with him on the tradeSeq package but the

[R-pkg-devel] RIOT 2020: canceled

After carefully considering the current situation regarding COVID-19, we decided to cancel this year's RIOT workshop. Best regards, Stepan On 25. 02. 20 17:47, Stepan wrote: I hope you don’t mind us using this mailing list for a small advertisement, but we think it is relevant for this group:

Re: [Rd] RIOT 2020

After carefully considering the current situation regarding COVID-19, we decided to cancel this year's RIOT workshop. Best regards, Stepan On 25. 02. 20 17:38, Stepan wrote: I hope you don’t mind us using this mailing list for a small advertisement, but we think it is most relevant for this

Re: [R-pkg-devel] About dataset in my own package

Either use the data() function to retrieve it or use the LazyData: true line in your DESCRIPTION file. On April 6, 2020 11:25:21 PM PDT, jared_wood wrote: >Dear all， > >I have three datasets (drugbank.rda edgar.rda mala.rda) in my package >and I put them in the document folder which called

[R-pkg-devel] About dataset in my own package

Dear all， I have three datasets (drugbank.rda edgar.rda mala.rda) in my package and I put them in the document folder which called “data”. And I just use the dataset in the function. However, here comes a note: drugbank_disease_gene: no visible binding for global variable 'drugbank'