search for: cleanex

Dear listers, I was used to package pgirmess under Windows with everything OK, but, for the first time, I had a trial this afternoon on Ubuntu 7.10 gutsy (I have a double boot computer and work more and more under unix) and R 2.7.0. Everything went OK except this: sudo R CMD check pgirmess ..... * checking examples ... ERROR Running examples in 'pgirmess-Ex.R' failed. The error most

Good morning, we recently observed a problem with importing S3 generics from a foreign package (without namespace), defining a S3 method in a package _with_ namespace and the `cleanEx()' function which is automatically generated and executed before examples are run by R CMD check. To be more precise. Package `strucchange' defines a S3 generic sctest <- function(x, ...) UseMethod("sctest") and the development version of `party' defines scte...

....nameEx, ")"), + x=unit(1, "npc") + unit(0.5, "lines"), + y=unit(0.8, "npc"), rot=90, + gp=gpar(col="orchid")) + } > setHook("grid.newpage", .gridplot.hook) > rm(.gridplot.hook) > assign("cleanEx", + function(env = .GlobalEnv) { + rm(list = ls(envir = env, all.names = TRUE), envir = env) + RNGkind("default", "default") + set.seed(1) + options(warn = 1) + assign("T", delay(stop("T used instead of TR...

...at uses a mock of a rook request for their examples. The mock is an R6 object containing a rawConnection, along with a finalizer that closes this connection when the object is removed. So far so good. I?ve recently been getting CRAN errors due to the rawConnection not being closed in examples > cleanEx() Error: connections left open: content (rawConnection) and the only way to remove this is by removing the objects and calling gc() as part of the example code. While it is possible to hide all that inside a \dontshow{} block, it appears to me that it would be better if cleanEx() did a cleaning o...

...o through CRAN MacOSX checks, just because I have this command in one of the examples. text(mydata[,3],mydata[,4],paste(round(dirs,0),"?"),cex=0.7) It makes: <ERROR: re-encoding failure from encoding 'latin1'> text(mydata[,3],mydata[,4],paste(round(dirs,0),"+ + + + cleanEx() + nameEx("distNode") Error: unexpected symbol in: "cleanEx() nameEx("distNode" Execution halted The description file (following some earlier recommandation) includes: Encoding: latin1 Is there any way to make "?" accepted by MacOSX checks ? Cheers, Patrick

...heck but runs fine on console. > foos <- c("aaa", "bbb", "ccc") > cat(sapply(foos, + function(foo) { + sprintf("name: + foo, + toupper(foo)) + }), sep="") + + + + cleanEx(); nameEx("sc80-registerNormalizationMethod") Error: unexpected string constant in: " cleanEx(); nameEx("" Execution halted Yet on console, it provides the expected: name: aaa upper: AAA name: bbb upper: BBB name: ccc upper: C...

...mock of a rook request for their examples. The mock is an R6 object containing a rawConnection, along with a finalizer that closes this connection when the object is removed. So far so good. I?ve recently been getting CRAN errors due to the rawConnection not being closed in examples > >> cleanEx() > Error: connections left open: > content (rawConnection) > > and the only way to remove this is by removing the objects and calling gc() as part of the example code. While it is possible to hide all that inside a \dontshow{} block, it appears to me that it would be better if cleanE...

...I used "\dontrun{} % enddontrun" in all the examples of my functions that should be no problem, i think. I checked my package before and did not find errors. I also browsed the checking results in 'stam-Ex.R'. It listed all the example codes in that file, something like this, cleanEx(); nameEx("stcdt") ### * stcdt flush(stderr()); flush(stdout()) ###example codes I did not met this problem before. Any ideas on solving this? Thanks a lot. -- ----------------- Jane Chang Queen's [[alternative HTML version deleted]]

...text(paste("help(", ..nameEx, ")"), side = 4, + line = if(outer)max(1, oma4 - 1) else min(1, mar4 - 1), + outer = outer, adj = 1, cex = .8, col = "orchid") + } + }, + env = environment(plot)) > assign("cleanEx", + function(env = .GlobalEnv) { + rm(list = ls(envir = env, all.names = TRUE), envir = env) + RNGkind("Wichmann-Hill", "default") + assign(".Random.seed", c(0, rep(7654, 3)), pos = 1) + assign("T", delay(stop("T used i...

On a SUN 280R running Solaris 9... The configure and make steps completed without errors. But when I try to perform the make check step, I get the following: $ make check FORCE=FORCE `Makedeps' is up to date. running code in 'base-Ex.R' ...*** Error code 1 make: Fatal error: Command failed for target `base-Ex.Rout' Current working directory /usr/local/R-2.0.0/tests/Examples ***

...et", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > ### * <FOOTER> > ### > cleanEx() > options(digits = 7L) > base::cat("Time elapsed: ", proc.time() - base::g + Error: unexpected end of input Execution halted The code without the offending comment is available here: https://github.com/rob-ward-psych/iac at revision c2f3529. To add the offending...

...about a use of T that occurs not in the example, but rather in the implementation of the function called by the example. I have searched the R-devel archives for a reference to that error message and in https://stat.ethz.ch/pipermail/r-devel/2006-February/036520.html found a mention of function cleanEx() that is apparently generated by R CMD check(?) and that contains delayedAssign("T", stop("T used instead of TRUE"), assign.env = .CheckExEnv) delayedAssign("F", stop("F used instead of FALSE"), assign.env = .CheckExEnv) (BTW: A rather fascinatin...

...: Leaving directory `/home/gavin/R/devel/build/tests' make[1]: *** [test-all-basics] Error 1 make[1]: Leaving directory `/home/gavin/R/devel/build/tests' make: *** [check-all] Error 2 And the Rout file contains this at the failure: $ tail -n 20 tests/Examples/stats-Ex.Rout.fail > > cleanEx(); nameEx("scatter.smooth") > ### * scatter.smooth > > flush(stderr()); flush(stdout()) > > ### Name: scatter.smooth > ### Title: Scatter Plot with Smooth Curve Fitted by Loess > ### Aliases: scatter.smooth loess.smooth > ### Keywords: smooth > > ### ** Ex...

....format_ptime", pos = > 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", > file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > > ### * <FOOTER> > > ### > > cleanEx() > > options(digits = 7L) > > base::cat("Time elapsed: ", proc.time() - base::g > + Error: unexpected end of input > Execution halted > > The code without the offending comment is available here: > > https://github.com/rob-ward-psych/ia...

...,...) The package works fine when I'm writing scripts, but all heck breaks loose when I try to write a package that depends on futile.paradigm. When I run R CMD check, it doesn't seem that the guard commands are being executed. A less likely hypothesis is that they are being deleted by the cleanEx() function. * checking examples ... ERROR Running examples in 'pars.core-Ex.R' failed. The error most likely occurred in: > set_date(20100921) Error: could not find function "set_date" Execution halted If I add the explicit function definition for 'month' as shown a...

Hi all, Today, i just installed the newest R version 2.10.1 and other necessary tools for building R package under windows,e.g. Rtools, perl. All are the newest version. After the correct configuration under windows, i use it to re-check my old package. I found the following prolem when checking EXAMPLE, which did not exist before this re-installation. ######## * checking examples ... ERROR

...]: *** [test-Examples] Error 2 make[2]: Leaving directory `/usr/local/src/R/R-alpha/tests' make[1]: *** [test-all-basics] Error 1 make[1]: Leaving directory `/usr/local/src/R/R-alpha/tests' make: *** [check] Error 2 59 (0) $ The final part of tests/Examples/utils-Ex.Rout.fail reads > cleanEx(); ..nameEx <- "help.search" > > ### * help.search > > flush(stderr()); flush(stdout()) > > ### Name: help.search > ### Title: Search the Help System > ### Aliases: help.search print.hsearch > ### Keywords: documentation > > ### ** Examples > &g...

...ake pkg-track', and encounter no errors. Loading the package, my 'examples' work fine. Returning to the ERROR, it is clear how this has come about. ls(.GlobalEnv) [1] "plotT" So the genericFunction object plotT resides in frame 1 i.e. .GlobalEnv. It gets deleted when cleanEx(env=.GlobalEnv) does its job in Rcmd CHECK. The other object defined in this package, plotTrack, is in frame 2: ls(2) [1] "plotTrack" I have tried unsuccessfully to put the genericFunction object plotT into frame 2, using the 'where' argument in setGeneric. To cut a long stor...

...Fax: 01524 594459 Lancaster University, Lancaster LA1 4YW ----- Tail end of tools-Ex.Rout.fail: > library('tools') > > assign(".oldSearch", search(), pos = 'CheckExEnv') > assign(".oldNS", loadedNamespaces(), pos = 'CheckExEnv') > cleanEx(); nameEx("Rdutils"); > ### * Rdutils > > flush(stderr()); flush(stdout()) > > ### Name: Rdutils > ### Title: Rd Utilities > ### Aliases: Rd_db Rd_parse > ### Keywords: utilities documentation > > ### ** Examples > > ## Build the Rd db for the (inst...

Hi all, I'm preparing a package which uses .Fortran to interface a Fortran 95 function. This F95 function simply receives the name of a file from R, opens this file and forwards its content to a F95 module, which, in turn, makes the real computation. The F95 module is a pre-existing one and I'm trying to use it in its actual state. Thus, data transfer between R and this F95 module is