similar to: matrixStats 0.13.1 - Methods that Apply to Rows and Columns of a Matrix (and Vectors)

Second this. As the CRAN Policies suggests, there's also the very handy winbuilder service (https://win-builder.r-project.org/) you can use to check your package on Windows. This service has been a valuable workhorse for years. We should also mention the continuous integration (CI) services provided for free by Travis (Linux and macOS) and AppVeyor (Windows) in combination with GitHub (or

Hi. On Sun, Feb 13, 2011 at 10:18 AM, TakeoKatsuki <takeo.katsuki at gmail.com> wrote: > > Hi Henrik, > > It would be nice if functions of the matrixStats package can handle array > data. > For example, rowSums() of the base package sums along the third axis of an > array by rowSums(x, dim=2). That is a good idea. This was indeed the initial objective before starting

Hi, I'm using this mailing list for the first time and I hope this is the right one. I don't think that the following is a bug but it can be a performance issue. By my opinion, there is no need to filter by [w != 0] in last sum of weighted.mean.default method defined in src/library/stats/R/weighted.mean.R. There is no need to do it because you can always sum zero numbers and

I can't seem to reliably obtain parse data via getParseData() for functions from installed packages. The parse data seems to be available only for the *last* file in the package. See [1] for a small example package with just two functions f and g in two files a.R and b.R. See [2] for a documented test run on installed package (Ubuntu 15.10, UTF-8 locale, R 3.2.3). Same behavior with

Hi, I have recently tried to check the test coverage using library("covr") and, interestingly, the command > covr::package_coverage() fails, while > covr::package_coverage(quiet = FALSE) runs through without problem. I traced the problem to a call to utils::install.packages(), where the option quiet is passed on. In utils::install.packages(), the problem seems to lie in the

>>>>> Henrik Bengtsson <henrik.bengtsson at gmail.com> >>>>> on Thu, 25 Jan 2018 09:30:42 -0800 writes: > Just following up on this old thread since matrixStats 0.53.0 is now > out, which supports this use case: >> x <- rep(TRUE, times = 2^31) >> y <- sum(x) >> y > [1] NA > Warning message:

It looks like OP uses a data.frame, so in order to use matrixStats (I'm the author) one would have to pay the price to coerce to a matrix before using matrixStats::rowMaxs(). However, if it is that the original data could equally well live in a matrix, then matrixStats should be computational efficient for this task. (I've seen cases where an original matrix was turned into a data.frame

Does anyone know if it is possible to add a dictionary file of known words that becomes part of the *built* package to tell 'R CMD check --as-cran' not to report these words as misspelled. I want this dictionary to come with the *.tar.gz such that it will be available regardless where the package is checked. For instance, currently I get: * using log directory

>>>>> Herv? Pag?s <hpages at fredhutch.org> >>>>> on Tue, 30 Jan 2018 13:30:18 -0800 writes: > Hi Martin, Henrik, > Thanks for the follow up. > @Martin: I vote for 2) without *any* hesitation :-) > (and uniformity could be restored at some point in the > future by having prod(), rowSums(), colSums(), and others >

Just following up on this old thread since matrixStats 0.53.0 is now out, which supports this use case: > x <- rep(TRUE, times = 2^31) > y <- sum(x) > y [1] NA Warning message: In sum(x) : integer overflow - use sum(as.numeric(.)) > y <- matrixStats::sum2(x, mode = "double") > y [1] 2147483648 > str(y) num 2.15e+09 No coercion is taking place, so the

Hi, I am trying to using SAMseq() to analyze my RNA-seq experiment (20000 genes x 550 samples) with survival endpoint. It quickly give the following error: > library(samr)Loading required package: imputeLoading required package: matrixStats Attaching package: ?matrixStats? The following objects are masked from ?package:Biobase?: ? ? anyMissing, rowMedians Warning messages:1: package ?samr? was

Sorry forgot to use plain text format, hope this time it works: Hi, I am trying to using SAMseq() to analyze my RNA-seq experiment (20000 genes x 550 samples) with survival endpoint. It quickly give the following error: > library(samr) Loading required package: impute Loading required package: matrixStats Attaching package: ?matrixStats? The following objects are masked from

Hi Martin, Henrik, Thanks for the follow up. @Martin: I vote for 2) without *any* hesitation :-) (and uniformity could be restored at some point in the future by having prod(), rowSums(), colSums(), and others align with the behavior of length() and sum()) Cheers, H. On 01/27/2018 03:06 AM, Martin Maechler wrote: >>>>>> Henrik Bengtsson <henrik.bengtsson at gmail.com>

SUMMARY: I'm proposing that R assert that 'connection' options have not changed since first created such that R will produce the following error: > fh <- file("a.txt", open = "w+") > cat("hello\n", file = fh) > close(fh) > fh2 <- file("b.txt", open = "w+") > cat("world\n", file = fh2) >

On 10.03.2016 15:49, Duncan Murdoch wrote: > On 10/03/2016 8:27 AM, Kirill M?ller wrote: >> I can't seem to reliably obtain parse data via getParseData() for >> functions from installed packages. The parse data seems to be available >> only for the *last* file in the package. >> >> See [1] for a small example package with just two functions f and g in >>

On 27 January 2017 at 21:54, G?bor Cs?rdi wrote: | On Fri, Jan 27, 2017 at 9:28 PM, Da Zheng <zhengda1936 at gmail.com> wrote: | > What major R platforms does this policy refer to? | > | | Linux, macOS, Windows. | | | > Currently, my package runs in Ubuntu. If it works on both Ubuntu and | > Redhat, does it count as two platforms? | > | | I think that Linux is just one. Is

Sorry, posting back to the list. Thank you all. Morgan On Thu, 21 May 2020, 16:33 Henrik Bengtsson, <henrik.bengtsson at gmail.com> wrote: > Hi. > > Good point and a good example. Feel free to post to the list. The purpose > of my reply wasn't to take away Peter's point but to emphasize that > base::mean() does a two-pass scan over the elements too lower the impact

Aaaah ... and argh - I should have better not to post R question at midnight, especially when I know it forks the process and it's not using threads. Brain meltdown. (So, we'll proceed trying to use pthreads in matrixStats also for Windows). Sorry for the noise and thanks Kasper. Henrik On Aug 15, 2015 02:52, "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com> wrote:

withr:::set_makevars() can give that error if the makefile named by the 'old_path' argument (default "~/.R/Makevars) contains more than one definition of a variable of the form 'name=value'. You can see what file it is reading and its contents by using the trace() function: trace(withr:::set_makevars, quote({ cat(old_path, "\n"); writeLines(paste0(" ",

On Tue, Feb 20, 2018 at 11:58 AM, Bert Gunter <bgunter.4567 at gmail.com> wrote: > Ista, et. al: efficiency? > (Note: I needed to correct my previous post: do.call() is required for > pmax() over the data frame) > > > x <- data.frame(matrix(runif(12e6), ncol=12)) > > > system.time(r1 <- do.call(pmax,x)) > user system elapsed > 0.049 0.000