[Lme4-commits] r1742 - / pkgtests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed May 16 22:16:32 CEST 2012
Author: bbolker
Date: 2012-05-16 22:16:32 +0200 (Wed, 16 May 2012)
New Revision: 1742
Added:
pkgtests/
pkgtests/lme4_depends.csv
pkgtests/lme4depfuns.R
pkgtests/lme4deptests.R
pkgtests/lme4deptests.Rout
pkgtests/mkcheckdirs
pkgtests/runtests
Log:
downstream package testing code
Added: pkgtests/lme4_depends.csv
===================================================================
--- pkgtests/lme4_depends.csv (rev 0)
+++ pkgtests/lme4_depends.csv 2012-05-16 20:16:32 UTC (rev 1742)
@@ -0,0 +1,59 @@
+"","name","email"
+"agridat",Kevin Wright,<kw.stat at gmail.com>
+"AICcmodavg",Marc J. Mazerolle,<marc.mazerolle at uqat.ca>
+"amer",Fabian Scheipl,<fabian.scheipl at stat.uni-muenchen.de>
+"aod",Renaud Lancelot,<renaud.lancelot at cirad.fr>
+"arm",Yu-Sung Su,<yusung at gmail.com>
+"benchmark",Manuel J. A. Eugster,<manuel.eugster at stat.uni-muenchen.de>
+"blme",Vincent Dorie,<vincent at stat.columbia.edu>
+"boss",Arend Voorman,<voorma at u.washington.edu>
+"BradleyTerry2",Heather Turner,<ht at heatherturner.net>
+"car",John Fox,<jfox at mcmaster.ca>
+"catdata",Gunther Schauberger,
+"clusterPower",Nicholas G. Reich,<nick.reich at gmail.com>
+"cplm",Wayne Zhang,<actuary_zhang at hotmail.com>
+"DAAG",W. John Braun,<braun at stats.uwo.ca>
+"difR",David Magis,<david.magis at ulg.ac.be>
+"doBy",Søren Højsgaard,<sorenh at mail.dk>
+"effects",John Fox,<jfox at mcmaster.ca>
+"EquiNorm",Li-Xuan Qin,<qinl at mskcc.org>
+"ez",Michael A. Lawrence,<Mike.Lawrence at dal.ca>
+"flexmix",Bettina Gruen,<Bettina.Gruen at jku.at>
+"gamm4",Simon Wood,<simon.wood at r-project.org>
+"glmulti",Vincent Calcagno,<vincent.calcagno at sophia.inra.fr>
+"gmodels",Gregory R. Warnes,<greg at warnes.net>
+"GRRGI",Walter Resch,<walt55128 at msn.com>
+"HLMdiag",Adam Loy,<aloy at iastate.edu>
+"HSAUR",Torsten Hothorn,<Torsten.Hothorn at R-project.org>
+"HSAUR2",Torsten Hothorn,<Torsten.Hothorn at R-project.org>
+"influence.ME",Rense Nieuwenhuis,<r.nieuwenhuis at utwente.nl>
+"kulife",Claus Ekstrom,<ekstrom at life.ku.dk>
+"languageR",<harald.baayen at uni-tuebingen.de>,<harald.baayen at uni-tuebingen.de>
+"LMERConvenienceFunctions",Antoine Tremblay; IWK Health Center,<trea26 at gmail.com>
+"longpower",Michael C. Donohue,<mdonohue at ucsd.edu>
+"MEMSS",<lme4-authors at R-forge.wu-wien.ac.at>,<lme4-authors at R-forge.wu-wien.ac.at>
+"MethComp",Bendix Carstensen,<bxc at steno.dk>
+"mi",Yu-Sung Su,<suyusung at tsinghua.edu.cn>
+"mice",Stef van Buuren,<stef.vanbuuren at tno.nl>
+"mixAK",Arnošt Komárek,<arnost.komarek at mff.cuni.cz>
+"MixMod",Alexandra Kuznetsova,<alku at imm.dtu.dk>
+"mlmRev",<lme4-authors at R-forge.wu-wien.ac.at>,<lme4-authors at R-forge.wu-wien.ac.at>
+"multcomp",Torsten Hothorn,<Torsten.Hothorn at R-project.org>
+"MuMIn",Kamil Bartoń,<kamil.barton at go2.pl>
+"NanoStringNorm",Daryl Waggott,<Daryl.Waggott at oicr.on.ca>
+"NetworkAnalysis",Cedric E Ginestet,<cedric.ginestet at kcl.ac.uk>
+"odprism",Martijn van de Pol,<m.van.de.pol at myscience.eu>
+"ordinal",Rune Haubo B Christensen,<rhbc at imm.dtu.dk>
+"pamm",Julien Martin,<julien.martin2 at usherbrooke.ca>
+"pbkrtest",Søren Højsgaard,<sorenh at mail.dk>
+"pedigreemm",Ana Ines Vazquez,<anainesvs at gmail.com>
+"phmm",Michael Donohue,<mdonohue at ucsd.edu>
+"polytomous",Antti Arppe,<antti.arppe at helsinki.fi>
+"prLogistic",Raydonal Ospina,<raydonal at de.ufpe.br>
+"R2admb",Ben Bolker,<bolker at mcmaster.ca>
+"R2STATS",Yvonnick Noel,<yvonnick.noel at uhb.fr>
+"RLRsim",Fabian Scheipl,<fabian.scheipl at stat.uni-muenchen.de>
+"SASmixed",<lme4-authors at R-forge.wu-wien.ac.at>,<lme4-authors at R-forge.wu-wien.ac.at>
+"sdtalt",Dan Wright,<dwright at fiu.edu>
+"TripleR",Felix Schönbrodt,<felix.schoenbrodt at psy.lmu.de>
+"Zelig",Kosuke Imai,<kimai at Princeton.Edu>
Added: pkgtests/lme4depfuns.R
===================================================================
--- pkgtests/lme4depfuns.R (rev 0)
+++ pkgtests/lme4depfuns.R 2012-05-16 20:16:32 UTC (rev 1742)
@@ -0,0 +1,187 @@
+pkgmax <- function(x,y) {
+ if (missing(y)) {
+ if (length(x)==1) return(x)
+ return(Reduce(pkgmax,x))
+ }
+ if (package_version(x)>package_version(y)) x else y
+}
+
+
+checkPkg <- function(pn,verbose=FALSE,tarballdir="./tarballs",libdir="./library",
+ checkdir=".",skip=FALSE) {
+ ## FIXME: check for/document local version of tarball more recent than R-forge/CRAN versions
+ ## FIXME: consistent implementation of checkdir
+ rforge <- "http://r-forge.r-project.org"
+ if (!exists("availCRAN")) {
+ if (verbose) cat("getting list of available packages from CRAN\n")
+ availCRAN <<- available.packages()
+ }
+ if (!exists("availRforge")) {
+ if (verbose) cat("getting list of available packages from R-forge\n")
+ availRforge <<- available.packages(contriburl=contrib.url(rforge))
+ }
+ .libPaths(libdir)
+ instPkgs <- installed.packages()
+ if (verbose) cat("checking package",pn,"\n")
+ loc <- "none"
+ if (pn %in% rownames(availRforge)) {
+ loc <- "Rforge"
+ pkginfo <- availRforge[pn,]
+ } else if (pn %in% rownames(availCRAN)) {
+ loc <- "CRAN"
+ pkginfo <- availCRAN[pn,]
+ }
+ locpkg <- list.files(tarballdir,paste0("^",pn))
+ if (length(locpkg)>0) {
+ locver <- gsub(paste0(pn,"_([-0-9.]+).tar.gz"),"\\1",locpkg)
+ } else locver <- NULL
+ if (loc=="none" && is.null(locver)) stop("package seems to be unavailable")
+ ver <- pkginfo["Version"]
+ if (!is.null(locver)) {
+ if (length(locver)>1) {
+ locver <- pkgmax(locver)
+ }
+ ## FIXME: could figure out most recent version?
+ if (package_version(locver)>package_version(ver)) {
+ ver <- locver
+ loc <- "local"
+ if (verbose) cat("local package is more recent than CRAN or R-forge\n")
+ }
+ }
+ ## FIXME: can we safely assume if the file is in 'available.packages(Rforge)' that
+ ## the tarball is really there??
+ tn <- paste0(pn,"_",ver,".tar.gz")
+ if (loc!="local" && !file.exists(tdn <- file.path(tarballdir,tn)))
+ {
+ if (verbose) cat("downloading tarball\n")
+ basepath <- switch(loc,CRAN=contrib.url(getOption("repos")),
+ Rforge=contrib.url(rforge),
+ loc=stop("tarball not available"))
+ download.file(file.path(basepath,tn),
+ destfile=tdn)
+ ## install suggested packages that aren't already installed
+ depList <-lapply(c("Suggests","Depends"),
+ tools:::package.dependencies,
+ x=pkginfo,
+ check=FALSE)
+ depList <- unlist(lapply(depList,function(x) {
+ if (!is.matrix(x[[1]])) character(0) else x[[1]][,1] }))
+ depMiss <- setdiff(depList,c("R",rownames(instPkgs)))
+ if (length(depMiss)>0) {
+ if (verbose) cat("installing dependencies",depMiss,"\n")
+ install.packages(depMiss,lib=libdir)
+ rPath <- if (loc=="CRAN") getOption("repos") else c(rforge,getOption("repos"))
+ instPkgs <- installed.packages(noCache=TRUE) ## update installed package info
+ }
+ }
+ ## how to force altered .libPaths in R CMD check? this doesn't seem to work ...
+ if (verbose) cat("running R CMD check ...\n")
+ unlink(file.path(checkdir,paste0(pn,".Rcheck"))) ## erase existing check directory
+ ## FIXME: run R CMD check in checkdir ...
+ if (!skip) {
+ tt <- system.time(ss <- suppressWarnings(system(paste("R CMD check",
+ file.path(tarballdir,tn)),
+ intern=TRUE)))
+ if (verbose) print(ss)
+ stat <- attr(ss,"status")
+ ss <- paste0(seq(ss),": ",ss)
+ t0 <- tt["elapsed"]
+ } else {
+ stat <- "skipped"
+ t0 <- NA
+ msg <- ""
+ ss <- ""
+ }
+ list(status=stat,msg=ss,time=t0,location=loc,version=ver)
+}
+
+
+dumbBrackets <- function(x) {
+ gsub("<","<",
+ gsub(">",">",x))
+}
+dumbQuotes <- function(x) {
+ gsub("[“”]","\"",
+ gsub("[‘’]","'",x))
+}
+colorCode <- function(x) {
+ fcol <- ifelse(grepl("skipped",x),"gray",
+ ifelse(grepl("error_depfail",x),"purple",
+ ifelse(grepl("error_[[:alpha:]]+",x),"red",
+ "blue")))
+ paste0("<font style=\"color:",fcol,"\">",x,"</font>")
+}
+
+errstrings <- c(error_ex="checking examples \\.\\.\\. ERROR",
+ error_depfail="Package (suggested|required) but not available",
+ error_install="checking whether package.+can be installed.+ERROR",
+ error_vignette="Errors in running code in vignettes")
+
+procError <- function(z,pkgname=NULL,debug=FALSE) {
+ if (is.null(loc <- z$location)) loc <- ""
+ if (is.null(ver <- z$version)) ver <- ""
+ L <- list(pkgname=pkgname,location=loc,version=ver)
+ if (!is.null(z$status) && z$status=="skipped") {
+ m <- list(result="skipped",diag="")
+ } else {
+ if (any(grepl(errstrings["error_ex"],z$msg))) {
+ m <- list(result="error_examples",diag=tail(z$msg,3))
+ } else if (any(grepl(errstrings["error_depfail"],z$msg))) {
+ m <- list(result="error_depfail",diag=grep(errstrings["error_depfail"],z$msg,value=TRUE))
+ } else if (any(grepl(errstrings["error_install"],z$msg))) {
+ m <- list(result="error_install",
+ diag=tail(readLines(file.path(paste0(pkgname,".Rcheck"),"00install.out"))))
+ } else if (any(grepl(errstrings["error_vignette"],z$msg))) {
+ m <- list(result="error_vignette",diag=tail(z$msg,3))
+ } else m <- list(result="OK",diag="")
+ }
+ c(L,m)
+}
+
+genReport <- function(X,testresults,
+ contact="lme4-authors <at> r-forge.wu-wien.ac.at",
+ verbose=FALSE) {
+ require(lme4) ## for lme4 package version (FIXME: should be stored with test results!)
+ ## FIXME: should store/pull date from test results too
+ require(R2HTML)
+
+ isOK <- !sapply(testresults,inherits,what="try-error")
+ tOK <- testresults[isOK]
+
+ if (FALSE) {
+ ## testing
+ for (i in seq_along(tOK)) {
+ print(procError(tOK[[i]],names(tOK)[[i]]))
+ scan()
+ }
+ }
+ rpt <- mapply(procError,tOK,names(tOK),SIMPLIFY=FALSE)
+ rpt <- lapply(rpt,
+ function(x) {
+ x$diag <- paste(dumbQuotes(x$diag),collapse="<br>")
+ data.frame(x,stringsAsFactors=FALSE)
+ })
+ rpt <- do.call(rbind,rpt)
+ rpt$result <- colorCode(rpt$result)
+ rpt <- merge(rpt,X,by.x="pkgname",by.y="X")
+ rpt <- rpt[,c("pkgname","location","version","name","result","diag")] ## drop e-mail, reorder
+ names(rpt)[4] <- "maintainer"
+ rpt$maintainer <- dumbBrackets(rpt$maintainer)
+
+ ## write file
+ HTMLInitFile(filename="lme4_compat_report",outdir=".",
+ Title="lme4 downstream package report")
+ HTML("<meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\">") ## for special chars in names etc.
+ HTML.title("downstream lme4 package test report",HR=1)
+ HTML(paste("lme4 version: ",dumbQuotes(packageVersion(sessionInfo()$otherPkgs$lme4))))
+ HTML(paste("Test date: ",date()))
+ HTML.title("Notes",HR=2)
+ HTML("<ul>")
+ HTMLli(paste("contact:",dumbBrackets(contact)))
+ HTMLli("'error_depfail' results are due to packages I haven't managed to get installed yet")
+ ## HTMLli("'error_install' results due to missing dependencies are probably spurious (packages that are installed elsewhere on my machine but not seen during testing")
+ HTMLli("'PIRLS step failed' errors are due to known, current GLMM issues (not your fault)")
+ HTML("</ul>")
+ HTML(rpt,innerBorder=1,sortableDF=TRUE)
+ HTMLEndFile()
+}
Added: pkgtests/lme4deptests.R
===================================================================
--- pkgtests/lme4deptests.R (rev 0)
+++ pkgtests/lme4deptests.R 2012-05-16 20:16:32 UTC (rev 1742)
@@ -0,0 +1,67 @@
+## code for testing lme4 downstream packages
+##
+## include all downstream packages from CRAN, r-forge:
+## packages to check, loaded from package-dependency scan
+X <- read.csv("lme4_depends.csv",as.is=TRUE,fileEncoding="UTF8")
+source("lme4depfuns.R")
+skippkgs <- "polytomous"
+
+## * must export R_LIBS_SITE=./library before running R CMD BATCH? (why?)
+## * make sure that .R/check.Renviron is set, e.g.
+## mv /home/bolker/.R/check.Renviron.old ~/.R/check.Renviron
+## ~/.R/check.Renviron:
+## R_LIBS_SITE=/home/bolker/R/pkgs/lme4/testpkgs/library
+
+## (repeated from lme4depfuns.R):
+## FIXME: check for/document local version of tarball more recent than R-forge/CRAN versions
+## FIXME: consistent implementation of checkdir
+
+## FIXME: set up an appropriate makefile structure for this ? (a little tricky if it also depends on
+## checking CRAN/R-forge versions?
+
+## FIXME (?)/warning: need to make sure that latest version of lme4 is installed in libdir ...
+
+## FIXME: why are R2admb, RLRsim, sdtalt, Zelig not getting checked?
+
+testdir <- "~/R/pkgs/lme4/pkgtests"
+tarballdir <- file.path(testdir,"tarballs")
+libdir <- file.path(testdir,"library")
+
+suppressWarnings(rm(list=c("availCRAN","availRforge"))) ## clean up
+options(repos="http://probability.ca/cran")
+
+require(tools)
+## assume wd is test dir, already
+if (FALSE) {
+ setwd(testdir)
+}
+
+## auto-generated list -- cleaned up by hand (removed 'lme4', fixed R2STATS maintainer syntax,
+## fixed comma in LMERconveniencefunctions author)
+
+dir.create(tarballdir,showWarnings=FALSE)
+dir.create(libdir,showWarnings=FALSE)
+## want to install additional dependencies etc. out of the way
+## to keep original installed base clean, but this may not be feasible
+## it would be nice to use tools:::testInstalledPackages(), but I may simply
+## have to do R CMD check
+
+pkgnames <- X$X
+names(pkgnames) <- pkgnames ## so results are named
+pkgnames <- pkgnames[!pkgnames %in% skippkgs]
+require(parallel)
+## FIXME (maybe): mclapply doesn't work on Windows ?
+testresults <- mclapply(pkgnames,function(x) try(checkPkg(x,verbose=TRUE)))
+skipresults <- mclapply(skippkgs,function(x) try(checkPkg(x,skip=TRUE,verbose=TRUE)))
+testresults <- c(testresults,skipresults)
+
+save("testresults",file="lme4tests_out.RData")
+
+if (FALSE) {
+ ## playing with results
+ load("lme4tests_out.RData")
+ checkPkg("HSAUR2")
+}
+## names(testresults) <- X$X ## should be obsolete after next run
+genReport(X,testresults)
+
Added: pkgtests/lme4deptests.Rout
===================================================================
--- pkgtests/lme4deptests.Rout (rev 0)
+++ pkgtests/lme4deptests.Rout 2012-05-16 20:16:32 UTC (rev 1742)
@@ -0,0 +1,4899 @@
+
+R Under development (unstable) (2012-05-12 r59340) -- "Unsuffered Consequences"
+Copyright (C) 2012 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: i686-pc-linux-gnu (32-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+ Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> ## code for testing lme4 downstream packages
+> ##
+> ## include all downstream packages from CRAN, r-forge:
+> ## packages to check, loaded from package-dependency scan
+> X <- read.csv("lme4_depends.csv",as.is=TRUE,fileEncoding="UTF8")
+> source("lme4depfuns.R")
+> skippkgs <- "polytomous"
+>
+> ## pkgs missing: arm, BradleyTerry2, HSAUR, HSAUR2? (something wrong with genReport)
+> ## FIXME: Bioconductor dependencies?
+> ## clean-up directory structure etc.
+> ##
+>
+> ## * must export R_LIBS_SITE=./library before running R CMD BATCH? (why?)
+> ## * make sure that .R/check.Renviron is set, e.g.
+> ## mv /home/bolker/.R/check.Renviron.old ~/.R/check.Renviron
+> ## ~/.R/check.Renviron:
+> ## R_LIBS_SITE=/home/bolker/R/pkgs/lme4/testpkgs/library
+>
+> ## (repeated from lme4depfuns.R):
+> ## FIXME: check for/document local version of tarball more recent than R-forge/CRAN versions
+> ## FIXME: consistent implementation of checkdir
+>
+> ## FIXME: set up an appropriate makefile structure for this ? (a little tricky if it also depends on
+> ## checking CRAN/R-forge versions?
+> ## FIXME (?)/warning: need to make sure that latest version of lme4 is installed in libdir ...
+> ## (done in runtests)
+>
+>
+> testdir <- "~/R/pkgs/lme4/pkgtests"
+> tarballdir <- file.path(testdir,"tarballs")
+> libdir <- file.path(testdir,"library")
+>
+> suppressWarnings(rm(list=c("availCRAN","availRforge"))) ## clean up
+> options(repos="http://probability.ca/cran")
+>
+> require(tools)
+Loading required package: tools
+> ## assume wd is test dir, already
+> if (FALSE) {
++ setwd(testdir)
++ }
+>
+> ## auto-generated -- cleaned up by hand (removed 'lme4', fixed R2STATS maintainer syntax,
+> ## fixed comma in LMERconveniencefunctions author)
+>
+> dir.create(tarballdir,showWarnings=FALSE)
+> dir.create(libdir,showWarnings=FALSE)
+> ## want to install additional dependencies etc. out of the way
+> ## to keep original installed base clean, but this may not be feasible
+> ## it would be nice to use tools:::testInstalledPackages(), but I may simply
+> ## have to do R CMD check
+>
+> pkgnames <- X$X
+> names(pkgnames) <- pkgnames ## so results are named
+> names(skippkgs) <- skippkgs
+> pkgnames <- pkgnames[!pkgnames %in% skippkgs]
+>
+> require(parallel)
+Loading required package: parallel
+> ## FIXME (maybe): mclapply doesn't work on Windows ?
+> testresults <- mclapply(pkgnames,function(x) try(checkPkg(x,verbose=TRUE)))
+getting list of available packages from CRAN
+getting list of available packages from CRAN
+getting list of available packages from R-forge
+getting list of available packages from R-forge
+checking package agridat
+running R CMD check ...
+checking package AICcmodavg
+running R CMD check ...
+ [1] "* using log directory ‘/mnt/hgfs/bolker/Documents/R/pkgs/lme4/pkgtests/AICcmodavg.Rcheck’"
+ [2] "* using R Under development (unstable) (2012-05-12 r59340)"
+ [3] "* using platform: i686-pc-linux-gnu (32-bit)"
+ [4] "* using session charset: UTF-8"
+ [5] "* checking for file ‘AICcmodavg/DESCRIPTION’ ... OK"
+ [6] "* checking extension type ... Package"
+ [7] "* this is package ‘AICcmodavg’ version ‘1.24’"
+ [8] "* checking package namespace information ... OK"
+ [9] "* checking package dependencies ... OK"
+ [10] "* checking if this is a source package ... OK"
+ [11] "* checking if there is a namespace ... OK"
+ [12] "* checking for executable files ... OK"
+ [13] "* checking whether package ‘AICcmodavg’ can be installed ... OK"
+ [14] "* checking installed package size ... OK"
+ [15] "* checking package directory ... OK"
+ [16] "* checking for portable file names ... OK"
+ [17] "* checking for sufficient/correct file permissions ... OK"
+ [18] "* checking DESCRIPTION meta-information ... OK"
+ [19] "* checking top-level files ... OK"
+ [20] "* checking index information ... OK"
+ [21] "* checking package subdirectories ... OK"
+ [22] "* checking R files for non-ASCII characters ... OK"
+ [23] "* checking R files for syntax errors ... OK"
+ [24] "* checking whether the package can be loaded ... OK"
+ [25] "* checking whether the package can be loaded with stated dependencies ... OK"
+ [26] "* checking whether the package can be unloaded cleanly ... OK"
+ [27] "* checking whether the namespace can be loaded with stated dependencies ... OK"
+ [28] "* checking whether the namespace can be unloaded cleanly ... OK"
+ [29] "* checking loading without being on the library search path ... OK"
+ [30] "* checking for unstated dependencies in R code ... OK"
+ [31] "* checking S3 generic/method consistency ... OK"
+ [32] "* checking replacement functions ... OK"
+ [33] "* checking foreign function calls ... OK"
+ [34] "* checking R code for possible problems ... OK"
+ [35] "* checking Rd files ... OK"
+ [36] "* checking Rd metadata ... OK"
+ [37] "* checking Rd cross-references ... WARNING"
+ [38] "Missing link(s) in documentation object ‘/mnt/hgfs/bolker/Documents/R/pkgs/lme4/pkgtests/AICcmodavg.Rcheck/00_pkg_src/AICcmodavg/man/predictSE.mer.Rd’:"
+ [39] " ‘[lme4]{mer-class}’"
+ [40] ""
+ [41] "See the information in section ‘Cross-references’ of the ‘Writing R"
+ [42] "Extensions’ manual."
+ [43] ""
+ [44] "* checking for missing documentation entries ... OK"
+ [45] "* checking for code/documentation mismatches ... OK"
+ [46] "* checking Rd \\usage sections ... OK"
+ [47] "* checking Rd contents ... OK"
+ [48] "* checking for unstated dependencies in examples ... OK"
+ [49] "* checking contents of ‘data’ directory ... OK"
+ [50] "* checking data for non-ASCII characters ... OK"
+ [51] "* checking data for ASCII and uncompressed saves ... OK"
+ [52] "* checking examples ... ERROR"
+ [53] "Running examples in ‘AICcmodavg-Ex.R’ failed"
+ [54] "The error most likely occurred in:"
+ [55] ""
+ [56] "> ### Name: aictab"
+ [57] "> ### Title: Create Model Selection Tables"
+ [58] "> ### Aliases: aictab aictab.glm aictab.gls aictab.lme aictab.mer aictab.mult"
+ [59] "> ### aictab.nls aictab.polr aictab.unmarked print.aictab"
+ [60] "> ### Keywords: models"
+ [61] "> "
+ [62] "> ### ** Examples"
+ [63] "> "
+ [64] "> ##Mazerolle (2006) frog water loss example"
+ [65] "> data(dry.frog)"
+ [66] "> "
+ [67] "> ##setup a subset of models of Table 1"
+ [68] "> Cand.models <- list( )"
+ [69] "> Cand.models[[1]] <- lm(log_Mass_lost ~ Shade + Substrate +"
+ [70] "+ cent_Initial_mass + Initial_mass2,"
+ [71] "+ data = dry.frog)"
+ [72] "> Cand.models[[2]] <- lm(log_Mass_lost ~ Shade + Substrate +"
+ [73] "+ cent_Initial_mass + Initial_mass2 +"
+ [74] "+ Shade:Substrate, data = dry.frog)"
+ [75] "> Cand.models[[3]] <- lm(log_Mass_lost ~ cent_Initial_mass +"
+ [76] "+ Initial_mass2, data = dry.frog)"
+ [77] "> Cand.models[[4]] <- lm(log_Mass_lost ~ Shade + cent_Initial_mass +"
+ [78] "+ Initial_mass2, data = dry.frog)"
+ [79] "> Cand.models[[5]] <- lm(log_Mass_lost ~ Substrate + cent_Initial_mass +"
+ [80] "+ Initial_mass2, data = dry.frog)"
+ [81] "> "
+ [82] "> ##create a vector of names to trace back models in set"
+ [83] "> Modnames <- paste(\"mod\", 1:length(Cand.models), sep = \" \")"
+ [84] "> "
+ [85] "> ##generate AICc table"
+ [86] "> aictab(cand.set = Cand.models, modnames = Modnames, sort = TRUE)"
+ [87] ""
+ [88] "Model selection based on AICc :"
+ [89] ""
+ [90] " K AICc Delta_AICc AICcWt Cum.Wt LL"
+ [91] "mod 2 9 89.98 0.00 0.8 0.8 -35.18"
+ [92] "mod 1 7 92.77 2.79 0.2 1.0 -38.89"
+ [93] "mod 5 6 115.52 25.54 0.0 1.0 -51.39"
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/lme4 -r 1742
More information about the Lme4-commits
mailing list