made4 1.34.0
Aedin Culhane
| Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/made4 | | Last Changed Rev: 75263 / Revision: 81334 | | Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/made4.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'made4/DESCRIPTION' ... OK
* this is package 'made4' version '1.34.0'
* 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 ... [5s/5s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [24s/25s] 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
'/Users/biocbuild/bbs-2.12-bioc/meat/made4.Rcheck/00check.log'
for details.