R Development Page
extendedForest log file (check_x86_64_windows)
* using log directory 'R:/run/building/build_2023-12-12-05-24/RF_PKG_CHECK/PKGS/extendedForest.Rcheck'
* using R version 4.3.2 Patched (2023-12-01 r85665 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* running under: Windows 10 x64 (build 19045)
* using session charset: UTF-8
* using option '--as-cran'
* checking for file 'extendedForest/DESCRIPTION' ... OK
* this is package 'extendedForest' version '1.6.2'
* checking CRAN incoming feasibility ... [13s] NOTE
Maintainer: 'Nick Ellis '
New submission
Problems when reading CITATION file:
It is recommended to use 'given' instead of 'first'.
It is recommended to use 'family' instead of 'last'.
Package CITATION file contains call(s) to old-style personList() or
as.personList(). Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry(). Please
use bibentry() instead.
Found the following (possibly) invalid URLs:
URL: http://CRAN.R-project.org/doc/Rnews/
From: inst/CITATION
Status: 200
Message: OK
CRAN URL not in canonical form
URL: http://oz.berkeley.edu/users/breiman/Using_random_forests_V3.1.pdf
From: man/randomForest.Rd
Status: 404
Message: Not Found
URL: http://oz.berkeley.edu/users/breiman/Using_random_forests_v4.0.pdf
From: man/rfImpute.Rd
Status: 404
Message: Not Found
URL: http://stat-www.berkeley.edu/users/breiman/RandomForests
From: DESCRIPTION
Status: 404
Message: Not Found
URL: http://www.ics.uci.edu/~mlearn/MLSummary.html
From: man/imports85.Rd
Status: 404
Message: Not Found
Canonical CRAN.R-project.org URLs use https.
The Title field should be in title case. Current version is:
'Breiman and Cutler's random forests for classification and regression'
In title case that is:
'Breiman and Cutler's Random Forests for Classification and Regression'
The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking serialization versions ... OK
* checking whether package 'extendedForest' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used Fortran compiler: 'GNU Fortran (GCC) 12.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'RColorBrewer' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Calls with DUP:
.C("regForest", as.double(x), ypred = double(ntest), as.integer(mdim),
as.integer(ntest), as.integer(ntree), as.integer(object$forest$leftDaughter),
as.integer(object$forest$rightDaughter), as.integer(object$forest$nodestatus),
as.integer(object$forest$nrnodes), as.double(object$forest$xbestsplit),
as.double(object$forest$nodepred), as.integer(object$forest$bestvar),
as.integer(object$forest$ndbigtree), as.integer(object$forest$ncat),
as.integer(maxcat), as.integer(predict.all), treepred = as.double(treepred),
as.integer(proximity), proximity = as.double(proxmatrix),
nodes = as.integer(nodes), nodexts = as.integer(nodexts),
DUP = FALSE, PACKAGE = "extendedForest")
.C("classRF", x = x, xdim = as.integer(c(p, n)), y = as.integer(y),
nclass = as.integer(nclass), ncat = as.integer(ncat), maxcat = as.integer(maxcat),
sampsize = as.integer(sampsize), strata = if (Stratify) as.integer(strata) else integer(1),
Options = as.integer(c(addclass, importance, localImp, proximity,
oob.prox, do.trace, keep.forest, replace, Stratify, keep.inbag,
keep.group)), ntree = as.integer(ntree), mtry = as.integer(mtry),
ipi = as.integer(ipi), classwt = as.double(classwt), cutoff = as.double(cutoff),
nodesize = as.integer(nodesize), outcl = integer(nsample),
counttr = integer(nclass * nsample), prox = prox, impout = impout,
impSD = impSD, impmat = impmat, nrnodes = as.integer(nrnodes),
ndbigtree = integer(ntree), nodestatus = integer(nt * nrnodes),
bestvar = integer(nt * nrnodes), treemap = integer(nt * 2 *
nrnodes), nodepred = integer(nt * nrnodes), xbestsplit = double(nt *
nrnodes), errtr = double((nclass + 1) * ntree), testdat = as.integer(testdat),
xts = as.double(xtest), clts = as.integer(ytest), nts = as.integer(ntest),
countts = double(nclass * ntest), outclts = as.integer(numeric(ntest)),
labelts = as.integer(labelts), proxts = proxts, errts = error.test,
inbag = if (keep.inbag) matrix(integer(n * ntree), n) else integer(n),
nodeImprove = double(nt * nrnodes), as.integer(maxLevel),
group = if (keep.group) matrix(integer(n * p), n) else integer(1),
permX = if (keep.group) matrix(double(n * p), n) else double(1),
as.integer(abs(corr) > corr.threshold), DUP = FALSE, PACKAGE = "extendedForest")
.C("regRF", x, as.double(y), as.integer(c(n, p)), as.integer(sampsize),
as.integer(nodesize), as.integer(nrnodes), as.integer(ntree),
as.integer(mtry), as.integer(c(importance, localImp, nPerm)),
as.integer(ncat), as.integer(maxcat), as.integer(do.trace),
as.integer(proximity), as.integer(oob.prox), as.integer(corr.bias),
ypred = double(n), impout = impout, impmat = impmat, impSD = impSD,
prox = prox, ndbigtree = integer(ntree), nodestatus = matrix(integer(nrnodes *
nt), ncol = nt), leftDaughter = matrix(integer(nrnodes *
nt), ncol = nt), rightDaughter = matrix(integer(nrnodes *
nt), ncol = nt), nodepred = matrix(double(nrnodes * nt),
ncol = nt), bestvar = matrix(integer(nrnodes * nt), ncol = nt),
xbestsplit = matrix(double(nrnodes * nt), ncol = nt), mse = double(ntree),
keep = as.integer(c(keep.forest, keep.inbag, keep.group)),
replace = as.integer(replace), testdat = as.integer(testdat),
xts = xtest, ntest = as.integer(ntest), yts = as.double(ytest),
labelts = as.integer(labelts), ytestpred = double(ntest),
proxts = proxts, msets = double(if (labelts) ntree else 1),
coef = double(2), oob.times = integer(n), inbag = if (keep.inbag) matrix(integer(n *
ntree), n) else integer(1), nodeSS = matrix(double(nrnodes *
nt), ncol = nt), nodeImprove = matrix(double(nrnodes *
nt), ncol = nt), as.integer(maxLevel), group = if (keep.group) matrix(integer(n *
p), n) else integer(1), permX = if (keep.group) matrix(double(n *
p), n) else double(1), as.integer(abs(corr) > corr.threshold),
DUP = FALSE, PACKAGE = "extendedForest")
DUP is no longer supported and will be ignored.
* checking R code for possible problems ... NOTE
MDSplot: no visible global function definition for 'par'
MDSplot: no visible global function definition for 'brewer.pal'
MDSplot: no visible global function definition for 'rainbow'
MDSplot: no visible global function definition for 'pairs'
classCenter : : no visible binding for global variable
'median'
grow.randomForest: no visible global function definition for 'update'
na.roughfix.data.frame: no visible global function definition for
'median'
na.roughfix.default: no visible global function definition for 'median'
outlier.default: no visible global function definition for 'median'
outlier.default: no visible global function definition for 'mad'
partialPlot.randomForest: no visible global function definition for
'predict'
partialPlot.randomForest: no visible global function definition for
'weighted.mean'
partialPlot.randomForest: no visible global function definition for
'points'
partialPlot.randomForest: no visible global function definition for
'barplot'
partialPlot.randomForest: no visible global function definition for
'lines'
partialPlot.randomForest: no visible global function definition for
'quantile'
plot.margin: no visible global function definition for 'brewer.pal'
plot.margin: no visible global function definition for 'rainbow'
plot.margin: no visible global function definition for 'plot.default'
plot.randomForest: no visible global function definition for 'matplot'
predict.randomForest: no visible global function definition for
'delete.response'
predict.randomForest: no visible global function definition for
'model.frame'
predict.randomForest: no visible binding for global variable 'na.omit'
randomForest.default: no visible global function definition for 'cor'
randomForest.default: no visible global function definition for 'var'
randomForest.formula: no visible binding for global variable 'na.fail'
randomForest.formula: no visible global function definition for
'model.response'
randomForest.formula: no visible global function definition for
'model.frame'
randomForest.formula: no visible global function definition for 'terms'
randomForest.formula: no visible global function definition for
'reformulate'
rfImpute.formula: no visible global function definition for
'model.response'
tuneRF: no visible global function definition for 'axis'
varImpPlot: no visible global function definition for 'par'
varImpPlot: no visible global function definition for 'dotchart'
varImpPlot: no visible global function definition for 'mtext'
Undefined global functions or variables:
axis barplot brewer.pal cor delete.response dotchart lines mad
matplot median model.frame model.response mtext na.fail na.omit pairs
par plot.default points predict quantile rainbow reformulate terms
update var weighted.mean
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "axis", "barplot", "dotchart", "lines",
"matplot", "mtext", "pairs", "par", "plot.default",
"points")
importFrom("stats", "cor", "delete.response", "mad", "median",
"model.frame", "model.response", "na.fail", "na.omit",
"predict", "quantile", "reformulate", "terms", "update",
"var", "weighted.mean")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (7) combine.Rd:31: Invalid email address: andy\_liaw@merck.com
checkRd: (7) getTree.Rd:62: Invalid email address: andy\_liaw@merck.com
checkRd: (7) grow.Rd:37: Invalid email address: andy\_liaw@merck.com
checkRd: (7) partialPlot.Rd:79: Invalid email address: andy\_liaw@merck.com
checkRd: (7) predict.randomForest.Rd:73: Invalid email address: andy\_liaw@merck.com
checkRd: (7) predict.randomForest.Rd:74: Invalid email address: matthew\_wiener@merck.com
checkRd: (7) randomForest.Rd:212: Invalid email address: andy\_liaw@merck.com
checkRd: (7) randomForest.Rd:213: Invalid email address: matthew\_wiener@merck.com
checkRd: (7) treesize.Rd:34: Invalid email address: andy\_liaw@merck.com
checkRd: (7) varImpPlot.Rd:37: Invalid email address: andy\_liaw@merck.com
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File 'extendedForest/libs/x64/extendedForest.dll':
Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'
It is good practice to register native routines and to disable symbol
search.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... NOTE
Unable to find GhostScript executable to run checks on size reduction
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [82s] OK
* checking PDF version of manual ... [10s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING, 6 NOTEs
See
'R:/run/building/build_2023-12-12-05-24/RF_PKG_CHECK/PKGS/extendedForest.Rcheck/00check.log'
for details.
Run time: 146.45 seconds.
