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Package 318/553HostnameOS / ArchBUILDCHECKBUILD BIN
made4 1.30.0
Aedin Culhane
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/made4
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: made4
Version: 1.30.0
Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings made4_1.30.0.tar.gz
StartedAt: 2012-09-24 02:00:16 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 02:01:06 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 49.8 seconds
RetCode: 0
Status:  OK 
CheckDir: made4.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/made4.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘1.30.0’
* 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 whether package ‘made4’ 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
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 ... 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
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/made4.Rcheck/00check.log’
for details.

made4.Rcheck/00install.out:

* installing *source* package ‘made4’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘introduction.rnw’ 
** testing if installed package can be loaded

* DONE (made4)

made4.Rcheck/made4-Ex.timings:

nameusersystemelapsed
NCI600.0280.0000.027
array2ade41.3280.0481.379
bet.coinertia000
between.graph0.7760.0080.782
bga0.7760.0000.776
bga.jackknife2.7640.0162.841
bga.suppl0.8960.0080.946
cia0.3000.0000.311
commonMap0.0440.0000.043
comparelists000
do3d0.8680.0000.866
genes1d0.1760.0040.181
getcol0.0160.0000.012
graph1D0.2200.0000.224
heatplot2.0960.0322.137
html3D0.4720.0000.472
khan0.0120.0000.012
ord0.3760.0000.374
overview0.2000.0000.201
plotarrays0.6520.0040.658
plotgenes0.2120.0040.214
prettyDend0.2840.0000.283
randomiser0.0000.0000.002
s.var0.4480.0000.448
sumstats0.5560.0080.563
suppl0.9240.0000.928
topgenes0.1320.0000.132