similar to: codetools really optional for R CMD check?

I just uploaded R 2.5.0 to Debian's unstable distribution. As Peter's announcement says, it now contains two new packages'rcompgen' and 'codetools'. About two or three weeks ago, I also packaged these, just like other 'recommended' packages as r-cran-rcompgen and r-cran-codetools. However, as "new" packages, they are still in the NEW queue awaiting

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

Dear list, R 2.5.0 packages for Debian stable (i386 and amd64) are now available from CRAN. The new recommended codetools and rcompgen packages haven't completely made it to Debian yet, but can of course be installed in the standard non-Debian ways. Please consult the README file in the Debian directory, and report problems to me directly or to this list. Best regards, Johannes Ranke --

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: "=" "{" "+"

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 all I'm updating a package for submission to CRAN, and I am getting an error message I never have seen before, and can't find out what it implies or means (and hence, what I need to do to fix it). After running R CMD check, I get this: <snip> * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd

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

Hello All, I'm actually the system administrator of a UNIX system where several users use R version 2.6.0. I have a user who is trying to use the SURVEY package, and when he does, he gets the message: survey' is not a valid package -- installed < 2.0.0? When I run the library() command, I get (see below): Anything that is listed as ** No title available (pre-2.0.0 install?) **

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)

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

In a package, I define a method for not-yet-generic function 'qr.X' like so: > setOldClass("qr") > setMethod("qr.X", signature(qr = "qr"), function(qr, complete, ncol) NULL) The formals of the newly generic 'qr.X' are inherited from the non-generic function in the base namespace. Notably, the inherited default value of formal

On 4/9/16 10:54 AM, Dirk Eddelbuettel wrote: > On 9 April 2016 at 10:28, Mick Jordan wrote: > | Can someone explain a message of this form from an rscript execution: > | > | Note: no visible global function definition for 'foo' > | > | > | This happens right at the start of execution. 'foo' is only executed in > | a branch of an 'if' that is not

I'm observing that the new staged installation in R 3.6.0 can produce: mv: cannot move ?/home/alice/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-codetools/00new/codetools? to ?/home/alice/R/x86_64-pc-linux-gnu-library/3.6/codetools?: File exists ERROR: moving to final location failed on some file systems. # EXAMPLE $ R --vanilla R version 3.6.0 (2019-04-26) -- "Planting of a Tree"

On Tue, May 7, 2019 at 9:05 AM Tomas Kalibera <tomas.kalibera at gmail.com> wrote: > > Thanks for the report. According to my reading, this use of "mv" is ok > and the renameat2() call which the invocation of "mv" leads to is also > ok and allowed by POSIX in this context. It could only fail with EEXIST > if the target directory (path/pkg) was not empty.

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is

Not certain this is actually a bug, so posting here. I'm on Ubuntu 18.04.4 LTS, building R version 4.0.0. The "configure" and "make" steps are successful, but the "make check" step fails when it gets to this part of ./tests/reg-tests-1b.R: ?? > ## methods() gave two wrong warnings in some cases: ?? > op <- options(warn = 2)# no warning, please! ??

I just built R-devel from source on OS X (Tiger), using the subversion sources. Running ./tools/rsync-recommended didn't download rcompgen. I checked http://cran.r-project/src/contrib/2.7.0/Recommended and indeed, this package is not there. If I try to install using install.packages I get > install.packages("rcompgen", type="source") --- Please select a CRAN

Dear all, can somebody point me from where to download "rcompgen" package? CRAN does not seem to hold that. Installing this package through install.packages() tells this package is not available. Thanks [[alternative HTML version deleted]]

Readers, Using version 251 I tried the following command: lm(y~a+b,data=datafile) Resulting in, inter alia: ... coefficients (intercept) a 1.2 3.4 Packages installed: acepack ace() and avas() for selecting regression transformations adlift An adaptive lifting scheme algorithm akima Interpolation of irregularly spaced