Package: made4

Version: 1.33.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings made4_1.33.0.tar.gz

StartedAt: 2013-03-25 02:50:03 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:51:20 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 77.2 seconds

RetCode: 0

Status:  OK

CheckDir: made4.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/made4.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘made4/DESCRIPTION’ ... OK
* this is package ‘made4’ version ‘1.33.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘made4’ can be installed ... [4s/4s] OK
* checking installed package size ... OK
* checking package 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 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
bet.coinertia: warning in dudi.pca(df1, scan = FALSE): partial argument
  match of 'scan' to 'scannf'
cia: warning in dudi.nsc(df2, scan = FALSE, nf = cia.nf): partial
  argument match of 'scan' to 'scannf'
cia: warning in coinertia(t.dudi(coa1), t.dudi(coa2), nf = cia.nf, scan
  = cia.scan, ...): partial argument match of 'scan' to 'scannf'
cia: warning in coinertia(coa1, coa2, scan = cia.scan, nf = cia.nf,
  ...): partial argument match of 'scan' to 'scannf'
getdata: warning in require(affy, quiet = TRUE): partial argument match
  of 'quiet' to 'quietly'
plot.bga: warning in s.var(dudi.bga$bet$ls, xax = axis1, yax = axis2,
  col = as.vector(factor(dudi.bga$fac, labels = arraycol)), ...):
  partial argument match of 'col' to 'colpoints'
plot.ord: warning in s.var(dudi.ord$co, xax = axis1, yax = axis2, col =
  cols.array, label = arraylabels, ...): partial argument match of
  'col' to 'colpoints'
plot.ord: warning in s.var(dudi.ord$co, col = rep(arraycol,
  nrow(dudi.ord$li)), add.plot = TRUE, label = arraylabels, xax =
  axis1, yax = axis2, ...): partial argument match of 'col' to
  'colpoints'
plot.suppl: warning in s.var(sup, col = colsup, sub = "Supplementary
  data only (Colors:Predicted)", xax = axis1, yax = axis2, boxes =
  FALSE, ...): partial argument match of 'col' to 'colpoints'
plot.suppl: warning in s.var(sup, col = colsup, sub = "Supplementary
  data only (colors:true classes)", xax = axis1, yax = axis2, boxes =
  FALSE): partial argument match of 'col' to 'colpoints'
plotgenes: warning in s.var(coord, xax = axis1, yax = axis2, clab = 0,
  colpoints = rep(colpoints, nrow(coord)), ...): partial argument match
  of 'clab' to 'clabel'
s.match.col : arrow1: warning in arrows(x0, y0, x1, y1, ang = ang, len
  = len, lty = 1, col = col): partial argument match of 'len' to
  'length'
s.match.col : arrow1: warning in arrows(x0, y0, x1, y1, ang = ang, len
  = len, lty = 1, col = col): partial argument match of 'ang' to
  'angle'
* checking Rd files ... NOTE
prepare_Rd: array2ade4.Rd:38: Dropping empty section \references
prepare_Rd: between.graph.Rd:40-42: Dropping empty section \value
prepare_Rd: between.graph.Rd:47: Dropping empty section \note
prepare_Rd: checkfac.Rd:15-16: Dropping empty section \details
prepare_Rd: checkfac.Rd:22: Dropping empty section \note
prepare_Rd: checkfac.Rd:23: Dropping empty section \seealso
prepare_Rd: checkfac.Rd:24-25: Dropping empty section \examples
prepare_Rd: chime3D.Rd:56: Dropping empty section \seealso
prepare_Rd: chime3D.Rd:57-59: Dropping empty section \examples
prepare_Rd: cia.Rd:106: Dropping empty section \note
prepare_Rd: commonMap.Rd:29-30: Dropping empty section \value
prepare_Rd: commonMap.Rd:31: Dropping empty section \references
prepare_Rd: do3d.Rd:73: Dropping empty section \note
prepare_Rd: do3d.Rd:71: Dropping empty section \references
prepare_Rd: dudi.rwcoa.Rd:39-41: Dropping empty section \examples
prepare_Rd: forrwcoa.Rd:38-40: Dropping empty section \examples
prepare_Rd: genes.Rd:28: Dropping empty section \value
prepare_Rd: genes.Rd:32-33: Dropping empty section \examples
prepare_Rd: genes1d.Rd:34: Dropping empty section \references
prepare_Rd: getdata.Rd:36: Dropping empty section \examples
prepare_Rd: graph1D.Rd:33-34: Dropping empty section \details
prepare_Rd: graph1D.Rd:35-37: Dropping empty section \value
prepare_Rd: graph1D.Rd:40: Dropping empty section \note
prepare_Rd: graph1D.Rd:38: Dropping empty section \references
prepare_Rd: html3D.Rd:74: Dropping empty section \seealso
prepare_Rd: jmol3D.Rd:37: Dropping empty section \seealso
prepare_Rd: jmol3D.Rd:38-39: Dropping empty section \examples
prepare_Rd: ord.Rd:93: Dropping empty section \references
prepare_Rd: overview.Rd:26: Dropping empty section \value
prepare_Rd: overview.Rd:29: Dropping empty section \note
prepare_Rd: overview.Rd:27: Dropping empty section \references
prepare_Rd: prettyDend.Rd:27: Dropping empty section \value
prepare_Rd: prettyDend.Rd:30: Dropping empty section \note
prepare_Rd: prettyDend.Rd:28: Dropping empty section \references
prepare_Rd: sumstats.Rd:52: Dropping empty section \note
prepare_Rd: sumstats.Rd:50: Dropping empty section \references
prepare_Rd: sumstats.Rd:56: Dropping empty section \seealso
prepare_Rd: topgenes.Rd:40: Dropping empty section \note
prepare_Rd: topgenes.Rd:38: Dropping empty section \references
* 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 ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [27s/28s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/made4.Rcheck/00check.log’
for details.

* installing *source* package ‘made4’ ...
** R
** data
** inst
** preparing package for lazy loading
'.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘introduction.rnw’ 
** testing if installed package can be loaded
'.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")
* DONE (made4)

name	user	system	elapsed
NCI60	0.052	0.012	0.067
array2ade4	1.984	0.048	2.047
bet.coinertia	0.024	0.000	0.027
between.graph	1.244	0.024	1.273
bga	1.344	0.016	1.361
bga.jackknife	4.388	0.012	4.439
bga.suppl	1.420	0.008	1.432
cia	0.436	0.012	1.049
commonMap	0.144	0.012	0.173
comparelists	0.032	0.000	0.032
do3d	1.148	0.004	1.178
genes1d	0.492	0.004	0.494
getcol	0.056	0.004	0.059
graph1D	0.208	0.004	0.215
heatplot	3.385	0.052	3.749
html3D	0.828	0.008	0.951
khan	0.032	0.000	0.033
ord	0.592	0.008	0.616
overview	0.292	0.008	0.301
plotarrays	1.028	0.004	1.036
plotgenes	0.428	0.004	0.431
prettyDend	0.544	0.000	0.546
randomiser	0.060	0.000	0.062
s.var	1.012	0.000	1.012
sumstats	0.968	0.004	0.972
suppl	1.424	0.000	1.463
topgenes	0.292	0.012	0.322