similar to: suggested patch for messages

Dear R-devs, Scenario: When checking a package via `R CMD check package_tar.ball`, required / suggested packages may be missing. R subsequently returns a list of packages that are missing (delimited by spaces). Example: ``` R CMD check glmSparseNet_0.99.13.tar.gz * using log directory '/home/ubuntu/Bioconductor/glmSparseNet.Rcheck' * using R Under development (unstable) (2018-06-06

On 18/09/2018 2:16 PM, Marcel Ramos wrote: > Dear R-devs, > > > Scenario: > > When checking a package via `R CMD check package_tar.ball`, required / suggested packages may be missing. R subsequently returns a list of packages that are missing (delimited by spaces). > > Example: > > ``` > R CMD check glmSparseNet_0.99.13.tar.gz > * using log directory

Hi the reference to R Internals https://cran.r-project.org/doc/manuals/r-release/R-ints.html#Tools in ?check (PkgUtils.Rd in utils package) is stale. Here is my proposed patch (use named reference rather than numeric reference to avoid any similar broken links in the future). Index: src/library/utils/man/PkgUtils.Rd =================================================================== ---

Dear R-core devs, I hope this email finds you well. Please see the proposed patch to R-devel below: Scenario: When loading a package using `library`, a package may not be found if the cases are not matching: ``` > library(ORG.Hs.eg.db) Error in library(ORG.Hs.eg.db) : there is no package called 'ORG.Hs.eg.db' ``` Suggested Patch: Returns a message matching what

Full_Name: Martin C. Martin Version: 2.7.1 OS: Ubuntu Submission from: (NULL) (75.150.115.86) The function write.arff, in the foreign library: - Can produce relation names with invalid characters - Doesn't use colnames() for attribute names when writing a matrix. Here's a better version: write.arff <- function (x, file, eol = "\n") { if (file == "")

Hi guRus, i'm running R-2.15.1 and the R CMD CHECK output appears to have changed substantially, in that instead of pointing me to the offending functions or files, I get lots of 'call sequence' traces as below. I've been using R CMD CHECK for years & never seen anything like this before. This is on a pretty fresh OSX 10.8 Mountain Lion installation, where I installed R from

Dear all When comparing sQuote("text") and dQuote("text") on MacOS X and Linux FC4 I get an inconsistent behavior (using the new release version R-2.6.0): sQuote: On Mac I get the correct result "'text'", but on FC4 the incorrect result "`text?". dQuote: On Mac I get the correct result "\"text\"", but on FC4 the incorrect

Hi Luke, Thank you for your response. On 6/21/19 10:56 AM, Tierney, Luke wrote: Thanks for the suggestion. However I don't think it is the right way to go. I also don't care for what install.packages() does. Signaling a warning and then an error means someone has to catch both the error and the warning, or suppress the warning, in order to handle the error programmatically. I do care

Dear all, Maybe, I am doing something wrong, but using R-2.5.0 on my Intel-Mac, I have problems using function callNextMethod() in method initialize. I am loading the following code as file "testS4.R": setClass("baseClass", representation(myname = "character", mydir = "character", "VIRTUAL"),

With a pretty recent version of R 2.11.0 (devel,unstable, svn 50178) on Linux I could not install version 1.5-8 of zoo (the current on on CRAN): % R-devel CMD INSTALL -l Rlib3 zoo * installing *source* package 'zoo' ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package 'zoo' finding

Logic.Rd has been changed again in r74377. After change: ? \item{x, y}{raw or logical or \sQuote{number-like} vectors (i.e., of ? ? types \code{\link{double}} (class \code{\link{numeric}}, ? ? \code{\link{integer}}) and \code{\link{complex}}), or objects for It is still inappropriate. As I said before, integer is not double. Right: numeric includes double and integer Wrong: double includes

Calling library(..., quietly=TRUE) may still output: Loading required package: <other pkg> in some cases, e.g. > library("R.utils", quietly=TRUE) Loading required package: R.methodsS3 [...] I traced this to base:::.getRequiredPackages2(), which forgets to pass 'quietly' to an internal library() call: if (!attached) { if (!quietly)

There was a discussion on r-help of getting the output from print.packageInfo into a file. Spencer and I have added a file= argument to print.packageInfo for consideration in R. Had this been available it would have simplified the answer to that thread. If the file= argument is used then the packageInfo information is sent to the file specified rather than displayed using file.show .

In the context of installing a Bioconductor package using our biocLite() function, install.packages() warns > install.packages("RUVSeq", repos="http://bioconductor.org/packages/2.14/bioc") Installing package into '/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.1-2.14' (as 'lib' is unspecified) Warning message: package 'RUVSeq' is not available

Please, do not ask why you would do this. I have simplified my complicated code to just the basic problem occuring to be able to make it easier to understand the actual problem. I have two function getArgs() and extractArgs() - code and test results provided below. I test them using getArgs(id = 's1002') from the command line. getArgs() prints the name of the argument as id and the

Hi, I notice in R-3.1.1, if a package specifies a VignetteBuilder (such as knitr) in its DESCRIPTION file, but does not also depend on the specified package (in either Depends, Imports, or Suggests), that R CMD check will say: * checking package dependencies ... ERROR VignetteBuilder package not declared: ?knitr? I'm glad this situation is now caught by R CMD check, but I think the message

Hello, when trying to write an R-file, which automatically installs and updates a given list of packages, I had two problems with install.packages() 1) install.packages("<package>") will install <package>, no matter if <package> has already been installed. 2) the readline() at the end of install.packages, which asks the user, if the downloaded files should be

I am writing a rd doc, and need to use "#" in a url adress. This would make: \url{http://www.xxxx.org/myfolder/#myanchor} Of course, I suppose this will not work because # is a special character starting a comment line in the rd dialect. I did not found a similar example in "Writing R exentions". I am not sure bout using \dQuote{a quotation}), and use \sQuote and \dQuote

Dear All, I have a question, suppose X is a dataframe, with column names as "x1", "x2", "x3", ..... And I would like to use the i-th column by X[,'xi']. But it seems the single quote and double quote are different. So if I run X[, names(X)[i]], it has some error. Please use the below example code X = matrix(rnorm(50),ncol = 5) X = data.frame(X)

Doing it like this: genericForPrimitive <- function(f, where = topenv(parent.frame()), mustFind = TRUE) { ans = .BasicFunsList[[f]] ## this element may not exist (yet, during loading), dom't test null if(mustFind && identical(ans, FALSE)) stop(gettextf("methods may not be defined for primitive function %s in this version of R",