- using R Under development (unstable) (2012-02-23 r58468)
- using platform: i686-pc-linux-gnu (32-bit)
- using session charset: UTF-8
- checking for file ‘OpenRepGrid/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘OpenRepGrid’ version ‘0.1.5’
- 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 executable files ... OK
- checking whether package ‘OpenRepGrid’ 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 whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace 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
alignByLoadings: warning in constructCor(x, trim = trim, out = 0):
partial argument match of 'out' to 'output'
alignByLoadings: warning in constructCor(x2, trim = trim, out = 0):
partial argument match of 'out' to 'output'
alignByLoadings: warning in constructCor(x2, out = 0): partial argument
match of 'out' to 'output'
alignByLoadings: warning in constructCor(x, trim = trim, col.index = F,
index = T, out = 2, digits = digits): partial argument match of 'out'
to 'output'
alignByLoadings: warning in constructCor(x2, trim = trim, col.index =
F, index = T, out = 2, digits = digits): partial argument match of
'out' to 'output'
biplot3dBase2: warning in matrix(0, nc = 3, nr = nrow(cl.l.xyz.outer)):
partial argument match of 'nr' to 'nrow'
biplot3dBase2: warning in matrix(0, nc = 3, nr = nrow(cl.l.xyz.outer)):
partial argument match of 'nc' to 'ncol'
biplot3dBase2: warning in matrix(c(mval, mval, mval, -mval, mval, mval,
-mval, mval, mval, -mval, -mval, mval, -mval, -mval, mval, mval,
-mval, mval, mval, -mval, mval, mval, mval, mval, mval, mval, -mval,
-mval, mval, -mval, -mval, mval, -mval, -mval, -mval, -mval, -mval,
-mval, -mval, mval, -mval, -mval, mval, -mval, -mval, mval, mval,
-mval, mval, mval, mval, mval, mval, -mval, -mval, mval, mval, -mval,
mval, -mval, -mval, -mval, mval, -mval, -mval, -mval, mval, -mval,
mval, mval, -mval, -mval), nc = 3, by = T): partial argument match of
'nc' to 'ncol'
biplot3dBase2: warning in matrix(c(mval, mval, mval, -mval, mval, mval,
-mval, mval, mval, -mval, -mval, mval, -mval, -mval, mval, mval,
-mval, mval, mval, -mval, mval, mval, mval, mval, mval, mval, -mval,
-mval, mval, -mval, -mval, mval, -mval, -mval, -mval, -mval, -mval,
-mval, -mval, mval, -mval, -mval, mval, -mval, -mval, mval, mval,
-mval, mval, mval, mval, mval, mval, -mval, -mval, mval, mval, -mval,
mval, -mval, -mval, -mval, mval, -mval, -mval, -mval, mval, -mval,
mval, mval, -mval, -mval), nc = 3, by = T): partial argument match of
'by' to 'byrow'
biplotDraw: warning in calcCoordsBorders(x["x"], x["y"], xm = max.ext *
(1 + strokes.x + offset.labels), ym = max.ext * (1 + strokes.y +
offset.labels)): partial argument match of 'xm' to 'xmax'
biplotDraw: warning in calcCoordsBorders(x["x"], x["y"], xm = max.ext *
(1 + strokes.x + offset.labels), ym = max.ext * (1 + strokes.y +
offset.labels)): partial argument match of 'ym' to 'ymax'
biplotDraw: warning in calcCoordsBorders(x["x"], x["y"], xm = max.ext,
ym = max.ext): partial argument match of 'xm' to 'xmax'
biplotDraw: warning in calcCoordsBorders(x["x"], x["y"], xm = max.ext,
ym = max.ext): partial argument match of 'ym' to 'ymax'
biplotDraw: warning in calcCoordsBorders(x["x"], x["y"], xm = max.ext *
(1 + strokes.x), ym = max.ext * (1 + strokes.y)): partial argument
match of 'xm' to 'xmax'
biplotDraw: warning in calcCoordsBorders(x["x"], x["y"], xm = max.ext *
(1 + strokes.x), ym = max.ext * (1 + strokes.y)): partial argument
match of 'ym' to 'ymax'
biplotDraw: warning in calcCoordsBorders(x[i, "x"], x[i, "y"], xm =
max.ext * (1 + strokes.x), ym = abs(x[i, "str.3.y"])): partial
argument match of 'xm' to 'xmax'
biplotDraw: warning in calcCoordsBorders(x[i, "x"], x[i, "y"], xm =
max.ext * (1 + strokes.x), ym = abs(x[i, "str.3.y"])): partial
argument match of 'ym' to 'ymax'
biplotSimple: warning in arrows(0, 0, -Cu[, d1], -Cu[, d2], len = 0.05,
col = c.point.col, lty = 1): partial argument match of 'len' to
'length'
biplotSimple: warning in arrows(0, 0, Cu[, d1], Cu[, d2], len = 0.05,
col = c.point.col, lty = 3): partial argument match of 'len' to
'length'
constructPca: warning in constructCor(x, method = method, trim = trim,
digits = 10, out = 0): partial argument match of 'out' to 'output'
constructRmsCor: warning in constructCor(x, method = method, trim =
trim, col.index = FALSE, digits = 10, out = 0): partial argument
match of 'out' to 'output'
distanceHartmann: warning in distanceSlater(x, digits = 10, out = 0):
partial argument match of 'out' to 'output'
distanceNormalized: warning in distanceHartmann(x, rep = rep, digits =
10, prob = prob, quant = quant, out = 0): partial argument match of
'out' to 'output'
distanceSlater: warning in distance(x, along = 2, digits = 10, out =
0): partial argument match of 'out' to 'output'
importGridcor: warning in tk_choose.files(filter = Filters, multi =
TRUE): partial argument match of 'filter' to 'filters'
importGridstat: warning in tk_choose.files(filter = Filters, multi =
TRUE): partial argument match of 'filter' to 'filters'
importGridsuite: warning in tk_choose.files(filter = Filters, multi =
TRUE): partial argument match of 'filter' to 'filters'
importScivesco: warning in tk_choose.files(filter = Filters, multi =
TRUE): partial argument match of 'filter' to 'filters'
importTxt: warning in tk_choose.files(filter = Filters, multi = TRUE):
partial argument match of 'filter' to 'filters'
indexConflict1: warning in constructCor(x, out = 0): partial argument
match of 'out' to 'output'
indexConflict2: warning in constructCor(x, out = 0): partial argument
match of 'out' to 'output'
indexConflict3 : out3: warning in formatMatrix(x$disc, rnames =
paste("c", seq_len(nrow(x$disc)), sep = ""), cnames = paste("e",
seq_len(ncol(x$disc)), sep = ""), pre.ind = c(F, F), mode = 2, diag =
F): partial argument match of 'pre.ind' to 'pre.index'
indexDilemmaInternal: warning in constructCor(x, digits = digits, out =
0): partial argument match of 'out' to 'output'
indexDilemmaInternal: warning in constructCor(x[, -c(self, ideal)],
digits = digits, out = 0): partial argument match of 'out' to
'output'
indexDilemmaShowCorrelationDistribution: warning in constructCor(x, out
= 0): partial argument match of 'out' to 'output'
indexDilemmaShowCorrelationDistribution: warning in constructCor(x[,
-c(e1, e2)], out = 0): partial argument match of 'out' to 'output'
indexIntensity: warning in constructCor(x, trim = trim, digits = 8, out
= 0): partial argument match of 'out' to 'output'
indexIntensity: warning in elementCor(x, rc = rc, trim = trim, digits =
8, out = 0): partial argument match of 'out' to 'output'
indexPvaff: warning in constructCor(x, out = 0): partial argument match
of 'out' to 'output'
indexPvaff2: warning in constructCor(x, out = 0): partial argument
match of 'out' to 'output'
loadgrid: warning in tk_choose.files(filter = Filters): partial
argument match of 'filter' to 'filters'
makeRepgrid: warning in matrix(args$scores, ncol = getNoOfElements(x),
by = T): partial argument match of 'by' to 'byrow'
pointLabel : GA : crossbreed: warning in sample(c(0, 1), length(g1),
repl = TRUE): partial argument match of 'repl' to 'replace'
pointLabel : GA: warning in sample(1:8, n_labels * n_startgenes, repl =
TRUE): partial argument match of 'repl' to 'replace'
prepareBiplotData: warning in mapCoordinatesToColor(z, color =
e.label.col, val.range = e.color.map): partial argument match of
'color' to 'colors'
prepareBiplotData: warning in mapCoordinatesToColor(z, color =
e.point.col, val.range = e.color.map): partial argument match of
'color' to 'colors'
prepareBiplotData: warning in mapCoordinatesToColor(z, color =
c.label.col, val.range = c.color.map): partial argument match of
'color' to 'colors'
prepareBiplotData: warning in mapCoordinatesToColor(z, color =
c.point.col, val.range = c.color.map): partial argument match of
'color' to 'colors'
randomGrid: warning in sample(range[1]:range[2], nc * ne, rep = TRUE,
prob = prob): partial argument match of 'rep' to 'replace'
randomSentences: warning in sample(nwords, n, rep = TRUE): partial
argument match of 'rep' to 'replace'
randomWords: warning in sample(words, n, rep = TRUE): partial argument
match of 'rep' to 'replace'
random_df: warning in sample(1:5, nrow, rep = TRUE): partial argument
match of 'rep' to 'replace'
rglDrawConstructLabels: warning in texts3d(coords, text = labels, adj =
c(0.5, 0.5), cex = c.cex, col = c.text.col, aspect = F): partial
argument match of 'text' to 'texts'
rglDrawElementLabels: warning in texts3d(x = coords.text[, 1], y =
coords.text[, 2], z = coords.text[, 3], text = labels, adj = c(1, 1),
cex = e.cex, col = e.text.col, aspect = F): partial argument match of
'text' to 'texts'
- 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 ... NOTE
S3 methods shown with full name in documentation object 'dim.repgrid':
‘dim.repgrid’
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
- 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 examples ... [1s/1s] OK
- checking PDF version of manual ... OK
NOTE: There were 2 notes.
See
‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/OpenRepGrid.Rcheck/00check.log’
for details.