search for: covr

Hi all, I would like to install a trace function that gets executed whenever *any* R function is called. In Python, for example, this functionality is provided by the `sys.settrace` function. I am not aware of any public interface, at the R or C level, that can accomplish this. The `trace` function is inadequate because it does not support nested functions. The `Rprof` function provides only

...nctions 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 r-devel (r70303). The parse data helps reliable coverage analysis [3]. Please advise. Best regards Kirill [1] https://github.com/krlmlr/covr.dummy [2] http://rpubs.com/krlmlr/getParseData [3] https://github.com/jimhester/covr/pull/154

...erddap, and I tested goodpractice on that. I get the error: > Error in set_makevars(new, path, makevars_file, assignment = assignment) : > Multiple results for CXXFLAGS found, something is wrong.FALSE > So after some playing around that is from the very first test, which uses the covr:package_coverage(), and sure enough running that produces the same error. Looking at the code, that error is being thrown by the function withr::set_makevars(). We are now too many layers deep into packages for me to follow what is going on, but the kicker is Scott Chamberlain can run it withou...

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 proble...

Hi all, I recently proposed a change in R that has led to the addition of new code to the R source code. The code added, as far as I know, has no tests and it might affect many packages in CRAN. I was wondering if adding a test would be helpful or it is already covered by some other test. Which brought me to the question: what is the coverage of R checks (check-devel)? My searches in the

...at. I get the error: > > > Error in set_makevars(new, path, makevars_file, assignment = assignment) > : > > Multiple results for CXXFLAGS found, something is wrong.FALSE > > > > > So after some playing around that is from the very first test, which uses > the covr:package_coverage(), and sure enough running that produces the same > error. Looking at the code, that error is being thrown by the function > withr::set_makevars(). We are now too many layers deep into packages for > me to follow what is going on, but the kicker is Scott Chamberlain ca...

...package tests; the R and C source code coverage has recently gone up from 59% to 96% (? and counting) [https://coveralls.io/r/HenrikBengtsson/matrixStats?branch=develop]. Some of the bugs were discovered as part of this effort. Here a special thank should go out to Jim Hester for his great work on covr [https://github.com/jimhester/covr], which provides me with on-the-fly coverage reports via Coveralls. (You can run covr locally or via GitHub + Travis CI, which is very easy if you're already up and running there. Try it!) I would also like to thank the R core team and the CRAN team for their...

...package tests; the R and C source code coverage has recently gone up from 59% to 96% (? and counting) [https://coveralls.io/r/HenrikBengtsson/matrixStats?branch=develop]. Some of the bugs were discovered as part of this effort. Here a special thank should go out to Jim Hester for his great work on covr [https://github.com/jimhester/covr], which provides me with on-the-fly coverage reports via Coveralls. (You can run covr locally or via GitHub + Travis CI, which is very easy if you're already up and running there. Try it!) I would also like to thank the R core team and the CRAN team for their...

...ave options(keep.source = TRUE, keep.source.pkgs = TRUE) in my .Rprofile . The srcrefs are all there, it's just that the parse data is not where I'd expect it to be. -Kirill >> >> Best regards >> >> Kirill >> >> >> [1] https://github.com/krlmlr/covr.dummy >> [2] http://rpubs.com/krlmlr/getParseData >> [3] https://github.com/jimhester/covr/pull/154 >> >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >

As Michael guessed my main use cases was code analysis. A concrete example where this would help is with my test code coverage tool covr. There is currently a bug when tracking coverage for if / else statements when the clauses do not contain brackets (https://github.com/jimhester/covr/issues/39). Because only one source reference is generated in this case (because it is parsed as a single expression), it is not possible to track e...

...: I have the impression that it is short of being installed, missing just a few simple packages (with no apparent non-R dependencies). Indeed, a first naive look shows following unavailable dependencies for tidyverse: ## missing for tidyverse: modelr (ok!?) reprex: -callr -debugme -covr -rex (ok!?) -rmarkdown (ok!?) rvest: selectr (ok!?) I hope that these package could be considered in a near future Michael? Thanks! :-) Best, Matthieu 2018-05-05 16:02 GMT-07:00 Dirk Eddelbuettel <edd at debian.org>: > > Salut Matthieu, > > On 5 May 2018 at 15:29...

Dear R-users, Half a year ago we put out the R package "glmmADMB" for fitting overdispersed count data. http://otter-rsch.com/admbre/examples/glmmadmb/glmmADMB.html Several people who used this package have requested additional features. We now have a new version ready. The major new feature is that glmmADMB allows Bernoulli responses with logistic and probit links. In addition there

...opm.R:167 /XML2R/R/utils.R:16 /assertive.base/tests/testthat/test-utils.R:14 /bigrquery/R/utils.r:13 /bold/R/zzz.R:29 /checkmate/R/checkList.r:56 /coin/R/ExactDistributions.R:80 /coin/R/ExactDistributions.R:97 /coin/R/ExactDistributions.R:234 /coin/R/SymmetryTests.R:217 /copula/R/aux-acopula.R:950 /covr/R/data_frame.R:13 /covr/R/display_name.R:40 /cplm/R/lme4_lmer.R:423 /crunch/R/batches.R:71 /crunch/R/batches.R:102 /crunch/R/categorical-array.R:87 /crunch/R/hide-variables.R:78 /crunch/R/misc.R:68 /crunch/R/share.R:11 /crunch/R/shoji-catalog.R:39 /crunch/R/show.R:88 /crunch/R/subvariables.R:76 /cr...

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

...ntinuous integration (CI) services provided for free by Travis (Linux and macOS) and AppVeyor (Windows) in combination with GitHub (or GitLab, ...). By adding simple .travis.yml and appveyor.yml to your Git repos (e.g. https://github.com/HenrikBengtsson/globals), they run R CMD check --as-cran and covr::package_coverage() etc for you more or less on the fly, e.g. * https://travis-ci.org/HenrikBengtsson/globals * https://ci.appveyor.com/project/HenrikBengtsson/globals /Henrik PS. Thanks to everyone who made all of the above possible. On Fri, Jan 27, 2017 at 2:17 PM, Dirk Eddelbuettel <edd a...

Hi, Both vapply() and sapply() support the 'USE.NAMES' argument. According to the man page: USE.NAMES: logical; if ?TRUE? and if ?X? is character, use ?X? as ?names? for the result unless it had names already. But if 'X' has names already and 'USE.NAMES' is FALSE, it's not clear what will happen to the names. Are they going to propagate to the result

...mvar is unequal to n.ahead.\n") } if (!is.null(Zdet)) { Zdet <- as.matrix(cbind(Zdet, dumvar)) } else { Zdet <- as.matrix(dumvar) } } Zy <- as.matrix(object$datamat[, 1:(K * (p + 1))]) cov<-summary(object)$covres forecast <- matrix(NA, ncol = K, nrow = n.ahead) lasty <- c(Zy[nrow(Zy), ]) for (i in 1:n.ahead) { lasty <- lasty[1:(K * p)] Z <- c(lasty, Zdet[i, ]) rv<-mult*matrix(rmvsnorm(1, dim = dim(cov)[1], Omega = cov), ncol = 1) forecast[i, ] &lt...

Hi I just upgraded to the Ubuntu 18.04 LTS, and tried to add both the "Ubuntu packages" source as well as ppa. I was not able to do this, trying to add for example: deb http://cran.cnr.berkeley.edu/bin/linux/ubuntu bionic/ or using: sudo add-apt-repository ppa:marutter/c2d4u am I doing something wrong, or just being impatient? Are there any plans to build these repos in the near

Hello everyone. I would like to find the sample covariance matrix using R. So far I read on the wikipedia what a sample_covariance is http://en.wikipedia.org/wiki/Sample_covariance according to wikipedia one vector is enough to calculate the sample covariance matrix. In R I tried cov(myvector) and I get the reply that I need to pass either two argument or one matrix with x,y values . How can I

Probably need a generic tree based on "ParseNode" objects that associate the line information with the symbol (for leaf nodes). As Duncan notes, it should be possible to gather that from the table. But it would be nice if there was an "expr" column in the parse data column in addition to "text". It would contain the parsed object. Otherwise, to use the table, one is