- using R Under development (unstable) (2012-02-06 r58287)
- using platform: i686-pc-linux-gnu (32-bit)
- using session charset: UTF-8
- checking for file ‘digeR/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘digeR’ version ‘1.2’
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... NOTE
As from R 2.14.0 all packages need a namespace.
One will be generated on installation, but it is better to handcraft a
NAMESPACE file: R CMD build will produce a suitable starting point.
- checking for executable files ... OK
- checking whether package ‘digeR’ can be installed ... OK
- checking installed package size ... OK
- checking package directory ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level 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 for unstated dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... NOTE
digeR : whole.plot: warning in gpanedgroup(cont = gw.plot, horizontal =
TRUE): partial argument match of 'cont' to 'container'
digeR : whole.plot: warning in ggroup(horizontal = FALSE, cont = pg):
partial argument match of 'cont' to 'container'
digeR : whole.plot: warning in gnotebook(cont = lg): partial argument
match of 'cont' to 'container'
digeR : whole.plot: warning in glayout(label = " Score Plot ", cont =
nb): partial argument match of 'cont' to 'container'
digeR : whole.plot: warning in gseparator(cont = nb.tab1): partial
argument match of 'cont' to 'container'
digeR : whole.plot: warning in gradio(c("Top N Component",
"pair-wise"), horizontal = TRUE, cont = nb.tab1, handler =
function(h, ...) {: partial argument match of 'cont' to 'container'
digeR : whole.plot: warning in if (svalue(nComp) == "Top N Component")
{: partial argument match of 'cont' to 'container'
digeR : whole.plot: warning in enabled(secondCom) <- FALSE: partial
argument match of 'cont' to 'container'
digeR : whole.plot: warning in enabled(withLabel) <- FALSE: partial
argument match of 'cont' to 'container'
digeR : whole.plot: warning in }: partial argument match of 'cont' to
'container'
digeR : whole.plot: warning in if (svalue(nComp) == "pair-wise") {:
partial argument match of 'cont' to 'container'
digeR : whole.plot: warning in enabled(secondCom) <- TRUE: partial
argument match of 'cont' to 'container'
digeR : whole.plot: warning in enabled(withLabel) <- TRUE: partial
argument match of 'cont' to 'container'
digeR : whole.plot: warning in }): partial argument match of 'cont' to
'container'
digeR : whole.plot: warning in gdroplist(1:10, editable = TRUE, cont =
nb.tab1): partial argument match of 'cont' to 'container'
digeR : whole.plot: warning in gcheckbox("With label", cont = nb.tab1,
handler = ScorePlot): partial argument match of 'cont' to 'container'
digeR : whole.plot: warning in gbutton("Plot ", cont = nb.tab1, handler
= ScorePlot): partial argument match of 'cont' to 'container'
digeR : whole.class: warning in gpanedgroup(cont = gw.class, horizontal
= TRUE): partial argument match of 'cont' to 'container'
digeR : whole.class: warning in ggroup(horizontal = FALSE, cont = pg):
partial argument match of 'cont' to 'container'
digeR : whole.class: warning in gnotebook(cont = lg): partial argument
match of 'cont' to 'container'
digeR : whole.class: warning in glayout(label = "Classification", cont
= nb): partial argument match of 'cont' to 'container'
digeR : whole.class: warning in gnotebook(cont = arg.fr, closebuttons =
FALSE): partial argument match of 'cont' to 'container'
digeR : whole.class: warning in glayout(label = "LDA", cont = arg.nb):
partial argument match of 'cont' to 'container'
digeR : whole.class: warning in glayout(label = "PCR", cont = arg.nb):
partial argument match of 'cont' to 'container'
digeR : whole.class: warning in glayout(label = "PLSR", cont = arg.nb):
partial argument match of 'cont' to 'container'
digeR : whole.class: warning in glayout(label = "N-fold CV", cont =
arg.nb): partial argument match of 'cont' to 'container'
digeR : whole.class: warning in glayout(label = "bootstrap", cont =
arg.nb): partial argument match of 'cont' to 'container'
digeR : whole.class : <anonymous>: no visible binding for global
variable ‘feature’
digeR : whole.class: warning in gdroplist(c("leave-one-out cv", "N-fold
cv", "bootstrap"), cont = nb.tab2, handler = function(h, ..) {:
partial argument match of 'cont' to 'container'
digeR : whole.class: warning in if (svalue(classMethod, index = TRUE)
== 2) {: partial argument match of 'cont' to 'container'
digeR : whole.class: warning in svalue(arg.nb) <- 4: partial argument
match of 'cont' to 'container'
digeR : whole.class: warning in }: partial argument match of 'cont' to
'container'
digeR : whole.class: warning in if (svalue(classMethod, index = TRUE)
== 3) {: partial argument match of 'cont' to 'container'
digeR : whole.class: warning in svalue(arg.nb) <- 5: partial argument
match of 'cont' to 'container'
digeR : whole.class: warning in }): partial argument match of 'cont' to
'container'
digeR : whole.class: warning in gbutton("Run Classfication", cont =
nb.tab2, handler = function(h, ...) {: partial argument match of
'cont' to 'container'
digeR : whole.class: warning in proceed <- TRUE: partial argument match
of 'cont' to 'container'
digeR : whole.class: warning in if (length(svalue(res.pred, index =
TRUE)) == 0) {: partial argument match of 'cont' to 'container'
digeR : whole.class: warning in gmessage("Please select a result item
to store the results", icon = "info"): partial argument match of
'cont' to 'container'
digeR : whole.class: warning in proceed <- FALSE: partial argument
match of 'cont' to 'container'
digeR : whole.class: warning in if (length(svalue(res.pred, index =
TRUE)) > 1) {: partial argument match of 'cont' to 'container'
digeR : whole.class: warning in gmessage("Please only select one result
item", icon = "info"): partial argument match of 'cont' to
'container'
digeR : whole.class: warning in svalue(res.pred, index = TRUE) <-
svalue(res.pred, index = TRUE)[1]: partial argument match of 'cont'
to 'container'
digeR : whole.class: warning in if (proceed) {: partial argument match
of 'cont' to 'container'
digeR : whole.class: warning in if (svalue(classMethod) ==
"leave-one-out cv") {: partial argument match of 'cont' to
'container'
digeR : whole.class: warning in cv.method <- svalue(classMethod):
partial argument match of 'cont' to 'container'
digeR : whole.class: warning in }: partial argument match of 'cont' to
'container'
digeR : whole.class: warning in if (svalue(classMethod) == "N-fold cv")
{: partial argument match of 'cont' to 'container'
digeR : whole.class: warning in cv.method <- paste(svalue(nFold), "fold
cv", sep = " "): partial argument match of 'cont' to 'container'
digeR : whole.class: warning in if (svalue(classMethod) == "bootstrap")
{: partial argument match of 'cont' to 'container'
digeR : whole.class: warning in cv.method <- paste(svalue(nboot),
"times bootstrap", sep = " "): partial argument match of 'cont' to
'container'
digeR : whole.class: warning in i <- svalue(res.pred, index = TRUE):
partial argument match of 'cont' to 'container'
digeR : whole.class: warning in res.pred[i] <-
paste(svalue(methodSelect), cv.method): partial argument match of
'cont' to 'container'
digeR : whole.class: warning in print("Classification..."): partial
argument match of 'cont' to 'container'
digeR : whole.class: warning in svalue(classbutton) <- "Processing..":
partial argument match of 'cont' to 'container'
digeR : whole.class: warning in enabled(nb) <- FALSE: partial argument
match of 'cont' to 'container'
digeR : whole.class: warning in if (svalue(useFeature) == TRUE) {:
partial argument match of 'cont' to 'container'
digeR : whole.class: warning in classResult[[i]] <<-
classification(expData[, feature.upload[[svalue(feature.gdrop, index
= TRUE)]]], label): partial argument match of 'cont' to 'container'
digeR : whole.class: warning in names(classResult)[i] <<-
svalue(methodSelect): partial argument match of 'cont' to 'container'
digeR : whole.class: warning in else if (svalue(useFeature) == FALSE)
{: partial argument match of 'cont' to 'container'
digeR : whole.class: warning in classResult[[i]] <<-
classification(expData, label): partial argument match of 'cont' to
'container'
digeR : whole.class: warning in names(classResult)[i] <<-
paste(svalue(methodSelect), cv.method): partial argument match of
'cont' to 'container'
digeR : whole.class: warning in print("Finished"): partial argument
match of 'cont' to 'container'
digeR : whole.class: warning in svalue(classbutton) <- "Run
Classfication": partial argument match of 'cont' to 'container'
digeR : whole.class: warning in enabled(nb) <- TRUE: partial argument
match of 'cont' to 'container'
digeR : whole.class: warning in gseparator(cont = nb.tab2): partial
argument match of 'cont' to 'container'
digeR : whole.class: warning in gtable(pred, cont = nb.tab2, multiple =
TRUE): partial argument match of 'cont' to 'container'
digeR : whole.class: warning in gbutton("ROC curve", cont = nb.tab2,
handler = function(h, ...) {: partial argument match of 'cont' to
'container'
digeR : whole.class: warning in gmessage("Please run classification
first", icon = "info"): partial argument match of 'cont' to
'container'
digeR : whole.class: warning in for (j in svalue(res.pred, index =
TRUE)) {: partial argument match of 'cont' to 'container'
digeR : whole.class: warning in if (is.null(classResult[[j]])) {:
partial argument match of 'cont' to 'container'
digeR : whole.class: warning in gmessage("Can not find the selected
result", icon = "info"): partial argument match of 'cont' to
'container'
digeR : whole.class: warning in proceed <- FALSE: partial argument
match of 'cont' to 'container'
digeR : whole.class: warning in break: partial argument match of 'cont'
to 'container'
digeR : whole.class: warning in }: partial argument match of 'cont' to
'container'
digeR : whole.class: warning in select.roc <- svalue(res.pred, index =
TRUE): partial argument match of 'cont' to 'container'
digeR : whole.class: warning in prd <- list(): partial argument match
of 'cont' to 'container'
digeR : whole.class: warning in lb <- list(): partial argument match of
'cont' to 'container'
digeR : whole.class: warning in a <- 1: partial argument match of
'cont' to 'container'
digeR : whole.class: warning in for (i in select.roc) {: partial
argument match of 'cont' to 'container'
digeR : whole.class: warning in prd[[a]] <- classResult[[i]]$pred:
partial argument match of 'cont' to 'container'
digeR : whole.class: warning in lb[[a]] <- classResult[[i]]$label:
partial argument match of 'cont' to 'container'
digeR : whole.class: warning in a <- a + 1: partial argument match of
'cont' to 'container'
digeR : whole.class: warning in roc(prd, lb, svalue(res.pred),
svalue(gleg)): partial argument match of 'cont' to 'container'
digeR : gwtCor: warning in ggroup(cont = gw.correlation): partial
argument match of 'cont' to 'container'
digeR : gwtCor: warning in ggroup(horizontal = FALSE, cont = BigGroup):
partial argument match of 'cont' to 'container'
digeR : gwtCor: warning in gradio(c("All", groupClass), horizontal =
FALSE, cont = tmp, handler = plotCor): partial argument match of
'cont' to 'container'
digeR : gwtCor: warning in gspinbutton(from = 1, to = ncol(expData), by
= 1, cont = tmp, editable = TRUE): partial argument match of 'cont'
to 'container'
digeR : gwtCor: warning in gcheckbox("Selected feature", cont = tmp,
handler = function(h, ...) {: partial argument match of 'cont' to
'container'
digeR : gwtCor: warning in if (svalue(useFeature)) {: partial argument
match of 'cont' to 'container'
digeR : gwtCor: warning in enabled(loadFeature.gb) <- TRUE: partial
argument match of 'cont' to 'container'
digeR : gwtCor: warning in enabled(feature.gdrop) <- TRUE: partial
argument match of 'cont' to 'container'
digeR : gwtCor: warning in enabled(spot.gdrop) <- TRUE: partial
argument match of 'cont' to 'container'
digeR : gwtCor: warning in enabled(glist) <- FALSE: partial argument
match of 'cont' to 'container'
digeR : gwtCor: warning in }: partial argument match of 'cont' to
'container'
digeR : gwtCor: warning in if (!svalue(useFeature)) {: partial argument
match of 'cont' to 'container'
digeR : gwtCor: warning in enabled(loadFeature.gb) <- FALSE: partial
argument match of 'cont' to 'container'
digeR : gwtCor: warning in enabled(feature.gdrop) <- FALSE: partial
argument match of 'cont' to 'container'
digeR : gwtCor: warning in enabled(spot.gdrop) <- FALSE: partial
argument match of 'cont' to 'container'
digeR : gwtCor: warning in enabled(glist) <- TRUE: partial argument
match of 'cont' to 'container'
digeR : gwtCor: warning in }): partial argument match of 'cont' to
'container'
digeR : gwtCor: warning in gbutton("load features", cont = tmp, handler
= function(h, ...) {: partial argument match of 'cont' to 'container'
digeR : gwtCor: warning in fpath <- gfile("Select the RData file
containing features", filter = list(.RData = list(patterns =
c("*.RData"))), type = "open"): partial argument match of 'cont' to
'container'
digeR : gwtCor: warning in if (fpath != "") {: partial argument match
of 'cont' to 'container'
digeR : gwtCor: warning in load(fpath): partial argument match of
'cont' to 'container'
digeR : gwtCor: warning in feature.upload <<- feature: partial argument
match of 'cont' to 'container'
digeR : gwtCor: warning in if (length(feature.upload) == 0) {: partial
argument match of 'cont' to 'container'
digeR : gwtCor: warning in gmessage("Can not find selected features",
icon = "info"): partial argument match of 'cont' to 'container'
digeR : gwtCor: warning in }: partial argument match of 'cont' to
'container'
digeR : gwtCor: warning in featureList <- rep("",
length(feature.upload)): partial argument match of 'cont' to
'container'
digeR : gwtCor: warning in for (j in 1:length(feature.upload)) {:
partial argument match of 'cont' to 'container'
digeR : gwtCor: warning in featureList[j] <- names(feature.upload)[j]:
partial argument match of 'cont' to 'container'
digeR : gwtCor: warning in feature.gdrop[] <- featureList: partial
argument match of 'cont' to 'container'
digeR : gwtCor : <anonymous>: no visible binding for global variable
‘feature’
digeR : gwtCor: warning in gdroplist(featureList, cont = tmp, handler =
function(h, ...) {: partial argument match of 'cont' to 'container'
digeR : gwtCor: warning in spot.gdrop[] <-
feature.upload[[svalue(feature.gdrop, index = TRUE)]]: partial
argument match of 'cont' to 'container'
digeR : gwtCor: warning in gdroplist(" ", cont = tmp): partial argument
match of 'cont' to 'container'
digeR : gwtCor: warning in gdroplist(c("pearson", "kendall",
"spearman"), cont = tmp, selected = 1): partial argument match of
'cont' to 'container'
digeR : gwtCor: warning in gbutton("Show the correlation", cont = tmp,
handler = plotCor): partial argument match of 'cont' to 'container'
digeR : gwtCor: warning in gtext("", cont = tmp, editable = TRUE,
horizontal = TRUE): partial argument match of 'cont' to 'container'
digeR : gwtCor: warning in gslider(from = 0.01, to = 0.99, by = 0.01,
value = 0, cont = leftpane, handler = plotCor): partial argument
match of 'cont' to 'container'
digeR : gwtCor: warning in gcheckbox("Show Number", cont = leftpane,
handler = plotCor): partial argument match of 'cont' to 'container'
digeR : gwtCor: warning in gimage(imagePath, cont = BigGroup): partial
argument match of 'cont' to 'container'
digeR : fs : ada: no visible global function definition for
‘adaboost.M1’
digeR : fs: warning in gpanedgroup(cont = gw.fs, horizontal = TRUE):
partial argument match of 'cont' to 'container'
digeR : fs: warning in ggroup(horizontal = FALSE, cont = pg): partial
argument match of 'cont' to 'container'
digeR : fs: warning in gnotebook(cont = lg): partial argument match of
'cont' to 'container'
digeR : fs: warning in glayout(label = "Feature Selection", cont = nb):
partial argument match of 'cont' to 'container'
digeR : fs: warning in gnotebook(cont = arg.fr, closebuttons = FALSE):
partial argument match of 'cont' to 'container'
digeR : fs: warning in glayout(label = "LDA", cont = arg.nb): partial
argument match of 'cont' to 'container'
digeR : fs: warning in glayout(label = "PLSR", cont = arg.nb): partial
argument match of 'cont' to 'container'
digeR : fs: warning in glayout(label = "RandomForest", cont = arg.nb):
partial argument match of 'cont' to 'container'
digeR : fs: warning in glayout(label = "Adaboost", cont = arg.nb):
partial argument match of 'cont' to 'container'
digeR : fs: warning in gseparator(cont = nb.tab2): partial argument
match of 'cont' to 'container'
digeR : fs: warning in gbutton("Run feature selection", cont = nb.tab2,
handler = function(h, ...) {: partial argument match of 'cont' to
'container'
digeR : fs: warning in proceed <- TRUE: partial argument match of
'cont' to 'container'
digeR : fs: warning in if (length(svalue(res.pred)) == 0) {: partial
argument match of 'cont' to 'container'
digeR : fs: warning in gmessage("Please select a result item to store
the features", icon = "info"): partial argument match of 'cont' to
'container'
digeR : fs: warning in proceed <- FALSE: partial argument match of
'cont' to 'container'
digeR : fs: warning in }: partial argument match of 'cont' to
'container'
digeR : fs: warning in if (proceed) {: partial argument match of 'cont'
to 'container'
digeR : fs: warning in i <- svalue(res.pred, index = TRUE): partial
argument match of 'cont' to 'container'
digeR : fs: warning in res.pred[i] <- paste(svalue(methodSelect)):
partial argument match of 'cont' to 'container'
digeR : fs: warning in svalue(fs.button) <- "Processing..": partial
argument match of 'cont' to 'container'
digeR : fs: warning in enabled(nb) <- FALSE: partial argument match of
'cont' to 'container'
digeR : fs: warning in print("Feature Selection..."): partial argument
match of 'cont' to 'container'
digeR : fs: warning in if (svalue(methodSelect) == "LDA") {: partial
argument match of 'cont' to 'container'
digeR : fs: warning in feature[[i]] <<- coef.ft(expData, l,
svalue(lda.n), "lda"): partial argument match of 'cont' to
'container'
digeR : fs: warning in names(feature)[i] <<- "LDA": partial argument
match of 'cont' to 'container'
digeR : fs: warning in }: partial argument match of 'cont' to
'container'
digeR : fs: warning in if (svalue(methodSelect) == "PLSR") {: partial
argument match of 'cont' to 'container'
digeR : fs: warning in feature[[i]] <<- coef.ft(expData, l,
svalue(pls.n), "pls"): partial argument match of 'cont' to
'container'
digeR : fs: warning in names(feature)[i] <<- "PLSR": partial argument
match of 'cont' to 'container'
digeR : fs: warning in if (svalue(methodSelect) == "RandomForest") {:
partial argument match of 'cont' to 'container'
digeR : fs: warning in feature[[i]] <<- randf(h, ...): partial argument
match of 'cont' to 'container'
digeR : fs: warning in names(feature)[i] <<- "RandomForest": partial
argument match of 'cont' to 'container'
digeR : fs: warning in if (svalue(methodSelect) == "Adaboost") {:
partial argument match of 'cont' to 'container'
digeR : fs: warning in feature[[i]] <<- ada(h, ...): partial argument
match of 'cont' to 'container'
digeR : fs: warning in names(feature)[i] <<- "Adaboost": partial
argument match of 'cont' to 'container'
digeR : fs: warning in print("Finished"): partial argument match of
'cont' to 'container'
digeR : fs: warning in svalue(fs.button) <- "Run feature selection":
partial argument match of 'cont' to 'container'
digeR : fs: warning in enabled(nb) <- TRUE: partial argument match of
'cont' to 'container'
digeR : fs: warning in }): partial argument match of 'cont' to
'container'
digeR : fs: warning in gtable(pred, cont = nb.tab2, multiple = TRUE):
partial argument match of 'cont' to 'container'
digeR : power.call: warning in gpanedgroup(cont = gw.power, horizontal
= TRUE): partial argument match of 'cont' to 'container'
digeR : power.call: warning in ggroup(horizontal = FALSE, cont = pg):
partial argument match of 'cont' to 'container'
digeR : power.call: warning in gnotebook(cont = lg): partial argument
match of 'cont' to 'container'
digeR : power.call: warning in glayout(label = "Power Analysis", cont =
nb): partial argument match of 'cont' to 'container'
digeR : power.call: warning in glayout(label = "parameters", cont =
arg.fr): partial argument match of 'cont' to 'container'
digeR: warning in gimage(paste(file.path(.path.package(package =
"digeR")[1]), "/data/cover.jpg", sep = ""), cont = digeR.menu):
partial argument match of 'cont' to 'container'
digeR: warning in gmenu(mblst, cont = digeR.menu): partial argument
match of 'cont' to 'container'
- checking Rd files ... OK
- checking Rd metadata ... 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 ... WARNING
Files not of a type allowed in a ‘data’ directory:
‘Thumbs.db’ ‘cover.jpg’ ‘gel.jpg’
Please use e.g. ‘inst/extdata’ for non-R data files
- checking data for non-ASCII characters ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking sizes of PDF files under ‘inst/doc’ ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking examples ... NONE
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in ‘inst/doc’ ... OK
- checking running R code from vignettes ... [1s/1s] OK
- checking re-building of vignette PDFs ... [1s/1s] OK
- checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/digeR.Rcheck/00check.log’
for details.