similar to: data.table not available as win binary for R 3.5

Dear all, to my astonishment data.table cannot be installed on R 3.5 Windows. When checking the package page, the Windows binary is available for download. When checking the server however, I can't seem to find data.table. Also install.packages() says the package is only available in source form and may need compilation. Compiling using Rtools 35 is no problem. Is this merely an issue of

Dear all, I tried to read in a 3.8Gb RDS file on a computer with 16Gb available memory. To my astonishment, the memory footprint of R rises quickly to over 13Gb and the attempt ends with an error that says "cannot allocate vector of size 5.8Gb". I would expect that 3 times the memory would be enough to read in that file, but apparently I was wrong. I checked the memory.limit() and that

I think you are confusing package and function here. Plus some of the R Core packages, that you mention, contain functions that should probably be replaced by functions with better implementation from packages on CRAN. Best regards Morgan On Fri, 11 Oct 2019 15:22 Joris Meys, <jorismeys at gmail.com> wrote: > > > On Fri, Oct 11, 2019 at 3:55 PM Morgan Morgan <morgan.emailbox

Dear all, as a follow-up to the question asked on R-package-devel (see link below): Someone sent a package to CRAN with a few problems. There's more things wrong with the submission, but one thing that really caught my eye was the following error: Warning message: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD BATCH --vanilla "testthat.R"

And now I've seen I copied the wrong part of ?is.na > The default method for is.na applied to an atomic vector returns a logical vector of the same length as its argument x, containing TRUE for those elements marked NA or, for numeric or complex vectors, NaN, and FALSE otherwise. Key point being "atomic vector" here. On Sat, Jun 9, 2018 at 1:41 PM, Joris Meys <jorismeys at

Thank you. I was just replying my own message with the same information. Sorry for not doing the research properly before filing. Cheers Joris On Sat, Mar 24, 2018 at 11:36 AM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote: > On 24/03/2018 6:16 AM, Joris Meys wrote: > >> Dear all, >> >> while preparing some exercises I came across some highly surprising

I fully agree with Joris and Hadley on roxygen2. Additionally: I wrote and published my first package before roxygen (or roxygen2) was available. I found editing .Rd extremely terse (especially when code is updated). For example, the fact that there are no spaces allowed between } and { in \param{}{} has hurt my brain quite a few times, especially since R CMD check did not give any useful error

Dear all, I asked this question on r-package-devel but Martin Maechler pointed out this was more suited on R-devel. So here it goes: per the manual, one should create and register both the S3 and a S4 method if one needs a method for an S4 class for a function using S3 dispatching. This is cumbersome, and not very optimal. I was wondering if there's a better way to do this. Currently I

Dear All: stepping in late, but @Joris, if you would like to take 'from a single file' literally, have a look at: https://github.com/bpfaff/lp4rp (lp4rp: literate programming for R packages); Cheers, Bernhard ps: incidentally, within the noweb-file roxygen is employed. -----Urspr?ngliche Nachricht----- Von: R-devel [mailto:r-devel-bounces at r-project.org] Im Auftrag von Joris

Dear all, while preparing some exercises I came across some highly surprising behaviour of file.exists(). The specific value "prn.us.txt" always returns TRUE, even though that file is nowhere to be found on my system. In a fresh R session 3.4.4 installed on Windows 10: > grep("prn.us.txt", dir(recursive = TRUE)) integer(0) > file.exists("prn.us.txt") [1] TRUE

On Thu, May 24, 2018 at 6:20 PM, Michael Lawrence <lawrence.michael at gene.com > wrote: > You only have to make an S4 method if there is already an S4 generic. > If there is just an S3 generic, then just define S3 methods on it. I was refering to the recommendations in ?Methods_for_S3 ( https://stat.ethz.ch/R-manual/R-devel/library/methods/html/Methods_for_S3.html). : "Two

I don't see the issue here. It would be helpful if people would report their sessionInfo() when reporting whether or not they see this issue. Mine is > sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Arch Linux Matrix products: default BLAS/LAPACK: /usr/lib/libopenblas_haswellp-r0.2.20.so locale: [1] LC_CTYPE=en_US.UTF-8

To my surprise, I can confirm on Windows 10 using R 3.4.3 . As tail is not recognized by Windows cmd, I replaced with: system('powershell -nologo "& "Get-Content -Path temp.csv -Tail 1') The last line shows only 7 digits after the decimal, whereas the first have 15 digits after the decimal. I agree with Dirk though, 1.6Gb csv files are not the best way to work with

Joris, the point is that 'z' is NOT used as a predictor in the model. Therefore it should not affect predictions. Also, I find it suspicious that the error only occurs when the response variable conitains missings and 'z' is unique (I have tested several other cases to confirm this). -Mark Op vr 16 mrt. 2018 om 13:03 schreef Joris Meys <jorismeys at gmail.com>: >

Dear all, quite a few package tools depend on R CMD INSTALL today for rapid testing of a package, eg: - devtools::install() - BiocCheck::BiocCheck() I've noticed that at least BiocCheck() doesn't ignore version control folders like .git. Trying to find out why this was, lead me to R CMD INSTALL. I know this R CMD build ignores these files and folders by default, but R CMD INSTALL

I'd add my support for mode = "wb" to (eventually) become the default, though I respect Tomas's comments about backwards-compatibility. Instead of making the argument mandatory (which would immediately break scripts -- even ones that won't be helped by changing to mode = 'wb') or otherwise changing behaviour, perhaps download.file could start to emit a message (not a

On Thu, Feb 1, 2018 at 1:29 PM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote: > On 31/01/2018 6:59 AM, Duncan Murdoch wrote: > >> On 30/01/2018 11:39 PM, Hadley Wickham wrote: >> > [ lots deleted ] > >> Personally, I don't find writing in comments any harder than writing >>> in .Rd files, especially now that you can write in markdown and

Emil et al., On Mon, Jun 11, 2018 at 1:08 AM, Emil Bode <emil.bode at dans.knaw.nl> wrote: > I don't think there's much wrong with is.na(as_date(Inf, > origin='1970-01-01'))==FALSE, as there still is some "non-NA-ness" about > the value (as difftime shows), but that the output when printing is > confusing. The way cat is treating it is clearer: it

The ratio of object size to rds file size depends on the object. Some variation is due to how header information is stored in memory and in the file but I suspect most is due to how compression works (e.g., a vector of repeated values can be compressed into a smaller file than a bunch of random bytes). f <- function (data, ...) { force(data) tf <- tempfile()

Dear all, I've noticed by trying to download gz files from here : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM907811 At the bottom one can download GSM907811.CEL.gz . If I download this manually and try oligo::read.celfiles("GSM907811.CEL.gz") everything works fine. (oligo is a bioConductor package) However, if I download using download.file("