Re: [R-pkg-devel] Help Debugging Debian Error

Thanks for the tips. It appears the error is indeed related to the matchingMarkets package, but specifically an issue with rJava configuration. Now I get the following (see https://artifacts.r-hub.io/PAutilities_1.0.0.tar.gz-54a555386e924de6a53385479a1e199f/PAutilities.Rcheck/00check.log ):

Re: [Rd] [External] Re: Testing before release (was: edit() doubles backslashes when keep.source=TRUE)

On Fri, 15 May 2020, Abby Spurdle wrote: This perhaps diverges from the intent of the thread, but... I wanted to say I'm extremely grateful to the people who go the through the bug reports. It's an extremely important job (in the long run, particularly), but perhaps not quite as

Re: [Rd] Testing before release (was: edit() doubles backslashes when keep.source=TRUE)

This perhaps diverges from the intent of the thread, but... I wanted to say I'm extremely grateful to the people who go the through the bug reports. It's an extremely important job (in the long run, particularly), but perhaps not quite as "sexy"-sounding as other roles, and probably under-valued.

Re: [R-pkg-devel] Package submission failed with two warnings

The reason is that CRAN does not have an R-devel binary for data.table, and because of this install.packages() decides not to install it. Here is a workaround: https://github.com/r-hub/rhub/issues/367#issuecomment-621757715 Gabor On Fri, May 15, 2020 at 10:50 PM Max Turgeon wrote: > > Hi

Re: [R-pkg-devel] Package submission failed with two warnings

Hi Farshad, The error you get when compiling your vignette gives us a hint: Error: processing vignette 'Rpvt.Rmd' failed with diagnostics: package or namespace load failed for 'ggpubr' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called

Re: [R-pkg-devel] Package submission failed with two warnings

Hi Duncan, I changed the version, recreated the package, and then tested it with the rhub::check_for_cran(). The function failed to create a summary for all the platform results together, however individual results are available in the following links.

Re: [Rd] paste(character(0), collapse="", recycle0=FALSE) should be ""

There is still the situation where **both** 'sep' and 'collapse' are specified: > paste(integer(0), "nth", sep="", collapse=",") [1] "nth" In that case 'recycle0' should **not** be ignored i.e. paste(integer(0), "nth", sep="", collapse=",", recycle0=TRUE) should return the empty string

Re: [Bioc-devel] Vignette Building Latex Errors on Windows Release Branch

Dear bioc devel, We are having the same problem with our package FELLA. Any help is appreciated! Best, Sergi Missatge de petr smirnov del dia dv., 15 de maig 2020 a les 19:42: > I am having trouble reproducing some vignette build errors for our > PharmacoGx package on Windows (tokay2). > >

Re: [Rd] paste(character(0), collapse="", recycle0=FALSE) should be ""

Hi all, This makes sense to me, but I would think that recycle0 and collapse should actually be incompatible and paste should throw an error if recycle0 were TRUE and collapse were declared in the same call. I don't think the value of recycle0 should be silently ignored if it is actively

Re: [Rd] paste(character(0), collapse="", recycle0=FALSE) should be ""

Totally agree with that. H. On 5/15/20 10:34, William Dunlap via R-devel wrote: I agree: paste(collapse="something", ...) should always return a single character string, regardless of the value of recycle0. This would be similar to when there are no non-NULL arguments to paste; collapse="."

[Bioc-devel] Vignette Building Latex Errors on Windows Release Branch

I am having trouble reproducing some vignette build errors for our PharmacoGx package on Windows (tokay2). The error is a Latex error: LaTeX Error: Environment cslreferences undefined. It seems likely to be due to a missing dependency for the style file we are using, however, I do not understand

Re: [Rd] paste(character(0), collapse="", recycle0=FALSE) should be ""

I agree: paste(collapse="something", ...) should always return a single character string, regardless of the value of recycle0. This would be similar to when there are no non-NULL arguments to paste; collapse="." gives a single empty string and collapse=NULL gives a zero long character vector. >

Re: [Rd] edit() doubles backslashes when keep.source=TRUE

To discuss this further, we should probably move over to R-sig-mac and change the subject header. -pd > On 15 May 2020, at 19:26 , peter dalgaard wrote: > > Actually, it's not that hard to set up for a source compile for MacOS. -- Peter Dalgaard, Professor, Center for Statistics,

Re: [Rd] edit() doubles backslashes when keep.source=TRUE

Actually, it's not that hard to set up for a source compile for MacOS. The hard part is to do it precisely like the CRAN binaries so that you can run binary packages off CRAN, but in other setups you can just build packages from source. A stone in the shoe has been that the documentation on

Re: [Rd] edit() doubles backslashes when keep.source=TRUE

I build windows binaries from source. As of now, the only choice is R-revel unless I want to monkey around more with Jeroens’s PKGBUILD script (which is On my to-do list). It’s pretty straightforward, although I’m seeing a lot of issues with packages which had explicit calls to LOCALSOFT in

Re: [Rd] edit() doubles backslashes when keep.source=TRUE

Nightly binary builds of R-devel for macOS are available: http://mac.r-project.org ~~~ Kylie Ariel Bemis (she/her) Khoury College of Computer Sciences Northeastern University kuwisdelu.github.io On May 15, 2020, at 12:48 PM, brodie gaslam via R-devel

Re: [Rd] edit() doubles backslashes when keep.source=TRUE

> On Friday, May 15, 2020, 12:13:04 PM EDT, Dirk Eddelbuettel > wrote: > On 15 May 2020 at 15:41, Martin Maechler wrote: > | > | > |    Why does nobody anymore  help R development by working with > |    "R-devel", or at least then the alpha, beta and the "RC" > |    (Release Candidate)

[Rd] ftable <-> data.frame etc {was "justify hard coded in format.ftable"}

> Gabor Grothendieck > on Thu, 14 May 2020 06:56:06 -0400 writes: > If you are looking at ftable could you also consider adding > a way to convert an ftable into a usable data.frame such as > the ftable2df function defined here: >

Re: [Rd] edit() doubles backslashes when keep.source=TRUE

On 15 May 2020 at 15:41, Martin Maechler wrote: | | | Why does nobody anymore help R development by working with | "R-devel", or at least then the alpha, beta and the "RC" | (Release Candidate) versions that we release daily for about one | month before the final release? | |

Re: [Rd] Daily News about R-devel/NEWS is not updating

Thank you! Jen On Fri, May 15, 2020 at 9:02 AM Duncan Murdoch wrote: > On 15/05/2020 10:39 a.m., Jennifer Lyon wrote: > > Hi: > > > > The "Daily News about R-devel/NEWS" webpage at > > http://developer.r-project.org/blosxom.cgi/R-devel/NEWS seems to not be > > updating. As of today, the latest

Re: [R-pkg-devel] Package submission failed with two warnings

For your first warning, see the CRAN policy: "Updates to previously-published packages must have an increased version. Increasing the version number at each submission reduces confusion so is preferred even when a previous submission was not accepted." For the second, it's hard to say what's

Re: [R-pkg-devel] Package submission failed with two warnings

On Fri, 15 May 2020 at 10:34, FARSHAD TABASINEJAD wrote: > > Dear R-package-devel experts, > > This is the first time I’m writing to this platform about a package I > recently submitted to CRAN (my first package). > While the package is already available on CRAN, I still must fix a few >

Re: [Rd] Daily News about R-devel/NEWS is not updating

On 15/05/2020 10:39 a.m., Jennifer Lyon wrote: Hi: The "Daily News about R-devel/NEWS" webpage at http://developer.r-project.org/blosxom.cgi/R-devel/NEWS seems to not be updating. As of today, the latest entry is Tue, 14 Apr 2020. Thanks. Thanks for noticing that. It's now fixed. (The

[Rd] Testing before release (was: edit() doubles backslashes when keep.source=TRUE)

On 15/05/2020 9:41 a.m., Martin Maechler wrote: [ deletions ] Why does nobody anymore help R development by working with "R-devel", or at least then the alpha, beta and the "RC" (Release Candidate) versions that we release daily for about one month before the final

[Rd] Daily News about R-devel/NEWS is not updating

Hi: The "Daily News about R-devel/NEWS" webpage at http://developer.r-project.org/blosxom.cgi/R-devel/NEWS seems to not be updating. As of today, the latest entry is Tue, 14 Apr 2020. Thanks. Jen [[alternative HTML version deleted]] __

[R-pkg-devel] Package submission failed with two warnings

Dear R-package-devel experts, This is the first time I’m writing to this platform about a package I recently submitted to CRAN (my first package). While the package is already available on CRAN, I still must fix a few warnings and one error as reported on the CRAN package check results page:

Re: [Rd] edit() doubles backslashes when keep.source=TRUE

> Sebastian Meyer > on Fri, 15 May 2020 10:47:55 +0200 writes: > I can confirm this changed behaviour. I just compared R-3.6.3 with > yesterday's R-devel. Using R-devel, the tempfile opened by the editor > (Emacs for me, but shouldn't matter) contains doubled backslashes.

Re: [Rd] justify hard coded in format.ftable

Thanks for the links. I agree that such a feature would be a nice addition, and could make ftable even more useful. In the same spirit, I think it could be useful to mention the undocumented base::as.data.frame.matrix function in documentation of table and xtabs (in addition to the already

Re: [Rd] justify hard coded in format.ftable

If you are looking at ftable could you also consider adding a way to convert an ftable into a usable data.frame such as the ftable2df function defined here: https://stackoverflow.com/questions/11141406/reshaping-an-array-to-data-frame/11143126#11143126 and there is an example of using it here:

Re: [Rd] justify hard coded in format.ftable

One can use as.data.frame(as.matrix(tab)) to avoid calling as.data.frame.matrix directly (although I find I do use as.data.frame.matrix anyways sometimes even though it is generally better to call the generic.). Also note that the various as.data.frame methods do not address the examples in the

Re: [R-pkg-devel] Help Debugging Debian Error

You don't need to move the files around, though, just use a more verbose testthat reporter, e.g. in testthat.R use test_check("PAutilities", reporter = "summary") and then at least you'll know where it crashes. But to fix this, you'll probably need to debug it locally. You can do that in Docker

Re: [R-pkg-devel] Help Debugging Debian Error

On Fri, 15 May 2020 03:50:12 -0400 Paul Hibbing wrote: > Complete output: > > library(testthat) > > library(PAutilities) > > > > test_check("PAutilities") It seems to me that the R process crashes while running your tests, but since testthat::test_check captures everything to

Re: [Rd] edit() doubles backslashes when keep.source=TRUE

I can confirm this changed behaviour. I just compared R-3.6.3 with yesterday's R-devel. Using R-devel, the tempfile opened by the editor (Emacs for me, but shouldn't matter) contains doubled backslashes. This could be related to https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17800 Best

Re: [R-pkg-devel] Help Debugging Debian Error

Removing the startup message did not resolve the issue. Now I have just: * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(PAutilities) > > test_check("PAutilities") See