similar to: codetools wrongly complains about lazy evaluation in S4 methods

We're seeing many warnings like this: Warning: S3 method 'print.check_code_usage_in_package' was declared in NAMESPACE but not found But the package's NAMESPACE does not contain such a declaration. Seeing this in many Bioconductor packages when running R CMD check on Windows with R-devel built 1 Sept. Below is a snip of the output from R CMD check. Any ideas of what this

Hi I''m trying to compile R packages on my vista (I''m very new on vista...). I installed Rtools, RExcel on a specific folder: c:\Rtools and gave full access. Unfortunately, I am still unable to compile any packages (may be still because of the security properties of vista). I checked several mailing list/forums/website but I did not found any solution. Does anybody have the

I am having some difficulty understanding the implication of lazy evaluation mixed with DUP=F in a .Fortran call. In qr.qty from base DUP is not used as an argument so defaults to T. I am calling qr.qty with a very large array and would like to set DUP=F in the .Fortran call so that qr.qty would be defined as copied below. Is there some risk that a variable used as the argument in the original

Hello, I am new to R and I am trying to figure out how to build and install a package with nothing but R code inside. I have run 'package.skeleton' to get the basic structure. When I run 'Rcmd INSTALL testPackage' I get this error message: make: *** No rule to make target `Files/R/rw1080'. Stop. *** Installation of testPackage failed *** When I run 'Rcmd build

Jiefei, you did not commit all files into the example package - your example has things like RcppExports.cpp as well as additional flags which are not in your GH project. I suspect the issue is with the extra flags you're adding - those don't come from R. Please make sure you can replicate the issue with the GH package you created. Cheers, Simon * installing *source* package

Thanks a lot for your suggestions. I see what you mean. I have removed all unnecessary files and dependences on https://github.com/Jiefei-Wang/example, but still no luck. I've tried to install the package as a user, not admin, but I got the same error. Also, I apologize for spamming the mail list. I will keep my reply as neat as possible. Martin has suggested checking the encoding of the file

Thanks, Jiefei, unfortunately your example does not work on my system, and also it is far from minimal. The error message you are getting is from Windows and could be caused for example by accidental quoting of the path using single quotes. Issues with RStudio or devtools would have to be discussed in their mailing lists/with their authors, but my guess is that the problem is in your local

See R_RegisterCFinalizerEx() and set onexit to nonzero. Here: https://github.com/wch/r-source/blob/9353ddfa8d30069ad8975e0364307d710f2488d5/src/include/Rinternals.h#L1279-L1280 Gabor On Fri, Apr 3, 2020 at 1:56 PM Wang Jiefei <szwjf08 at gmail.com> wrote: > > Hi all, > > I found that the finalizer of the externalPtr is not called when R is > quitting. However, manually

Use R_RegisterFinalizerEx in your C code. See https://cran.r-project.org/doc/manuals/r-release/R-exts.html#External-pointers-and-weak-references This still gives you only "best effort"; for anything stronger you would need a different approach. In general, finalizers should only be used as a backstop, not as a primary resource management tool (in R or any other garbage-collected

Hi all, I found that the finalizer of the externalPtr is not called when R is quitting. However, manually calling GC() works fine. This behavior is observed on devel R 2020-04-02 r78142 on Win and R 3.6.3 on Ubuntu. I make a reproducible package here: https://github.com/Jiefei-Wang/example Here is the detail of how to reproduce the problem, I create a temporary file in the package root path and

After upgrading to R 2.5.1 on Debian, R CMD check gives * checking Rd cross-references ... WARNING Error in .find.package(package, lib.loc) : there is no package called 'codetools' Execution halted * checking for missing documentation entries ... WARNING etc The NEWS file says (for 2.5.0; I was on 2.4 before the recent upgrade) o New recommended package 'codetools' by Luke

Sorry for reposting, i keep forgetting this should be plain text. Will not make this mistake again Hello, The following code moo <- function(a=1){ x=1; x=x+y} funs <- new.env() enter <- function(type, v, e, w){ assign(v, TRUE, funs) } library(codetools) collectUsage(moo, enterGlobal = enter) adds + to the environment funs i.e. funs: "=" "{" "+"

I've put together a package codetools with some tools for examining R source code. It is available at http://www.stat.uiowa.edu/~luke/R/codetools/codetools.tar.gz It requires a reasonably current version of R-devel. The main user functions are: checkUsage, checkUsageEnv, checkUsagePackage: Examine closure, closures in an environment, closures in a package, and report

Hello, Is this a bug in codetools: > codetools::showTree( body( glm) ) ("{" (<- call (match.call)) (if (is.character family) (<- family (get family "function" (parent.frame)))) (if (is.function family) (<- family(family))) (if (is.null ($ family family)) ("{" (print family) (stop "'family' not recognized"))) (if (missing data)

Dear R Users, Using codetools I obtained the text representation of the parse tree for this snippet z=quote({x[1]<-2}) showTree(z) > ("{" (<- ([ x 1) 2)) (A) If I understand correctly, x[1]<-2 ought to be "[<-"(x,1,2), so shouldn't i see ("{" ( [<- x 1 2 ) ) If indeed the parse tree in (A) is correct, the operation ([ x 1) returns the

Dear list members, I frequently program small scripts and wrap them into functions to be able to check them with checkUsage. In case these functions (loaded via source or copy pasted to the R console) use functions from other packages, I get this error: no visible global function definition for ?xxxxxxx? For example: test = function() { require(plotrix) color.legend() }

Hi Mr Tierney, I have noticed an error message from R 1.12.x's CMD check for a while (apparently prof Ripley completely rewrote CMD check in R 1.12+) e.g.: http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html ---------------- * checking R code for possible problems ... NOTE Warning: non-unique value when setting 'row.names': ?new? Error in

Hi the list Is there any tutorial to learn codetools ? It seems to be a very interesting pacakge, but the help gives not that much detail, and there is not that much examples provided... Christophe

This is just a note/wishlist/for the record: With foo1 <- function() { res; } foo2 <- function() { for (i in c()) res <- 1; res; } foo3 <- function() { while (FALSE) res <- 1; res; } foo4 <- function() { if (FALSE) res <- 1; res; } we get: > foo1() Error in foo1() : object 'res' not found > foo2() Error in foo2() : object 'res' not

Oops, I think both of us forget to cite the r-devel channel. Best, Jiefei On Tue, Mar 10, 2020 at 5:13 AM Wang Jiefei <szwjf08 at gmail.com> wrote: > Thanks for your quick response, Tomas. > > Yes, this is a path issue, I think the problem is related to R, not the > Rtools make. I built an example package for reproducing the problem: > https://github.com/Jiefei-Wang/example