Back to the "Multiple platform build/check report"
| IMPORTANT NOTE: R was configured with --enable-strict-barrier on lamb1 |
| Package 132/247 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
made41.11.1Aedin CulhaneLast Changed Date: 2007-08-17 15:33:39 -0700 Last Changed Rev: 26488 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | ERROR | |
| wellington | Linux (SUSE 9.2) | i686 | OK | ERROR | ||
| liverpool | Windows Server 2003 R2 (32-bit) | x64 | OK | [ ERROR ] | OK | |
| pitt | Mac OS X (10.4.10) | i386 | OK | ERROR | OK |
| Package: made4 |
| Version: 1.11.1 |
| Command: E:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check made4_1.11.1.tar.gz |
| RetCode: 1 |
| Time: 41.7 seconds |
| Status: ERROR |
| CheckDir: made4.Rcheck |
| Warnings: NA |
* checking for working latex ... OK
* using log directory 'E:/biocbld/bbs-2.1-bioc/meat/made4.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'made4/DESCRIPTION' ... OK
* this is package 'made4' version '1.11.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'made4' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... 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 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
getdata: no visible binding for global variable 'intensities'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'heatplot':
heatplot
Code: function(dataset, dend = TRUE, lowcol = "green", highcol =
"red", Colv = NULL, Rowv = NULL, cols.default = TRUE,
scale = "row", classvec = NULL, ...)
Docs: function(dataset, dend = TRUE, lowcol = "green", highcol =
"red", Colv = NULL, Rowv = NULL, cols.default = TRUE,
...)
Argument names in code not in docs:
scale classvec
Mismatches in argument names:
Position: 8 Code: scale Docs: ...
Codoc mismatches from documentation object 'ord':
plot.ord
Code: function(x, axis1 = 1, axis2 = 2, arraycol = NULL, genecol =
"gray25", nlab = 10, genelabels = NULL, arraylabels =
NULL, classvec = NULL, ...)
Docs: function(x, axis1 = 1, axis2 = 2, arraycol = NULL, genecol =
"gray25", nlab = 10, genelabels = NULL, classvec =
NULL, ...)
Argument names in code not in docs:
arraylabels
Mismatches in argument names:
Position: 8 Code: arraylabels Docs: classvec
Position: 9 Code: classvec Docs: ...
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'bga':
plot.bga
S3 methods shown with full name in documentation object 'cia':
plot.cia
S3 methods shown with full name in documentation object 'comparelists':
print.comparelists
S3 methods shown with full name in documentation object 'ord':
plot.ord
S3 methods shown with full name in documentation object 'suppl':
plot.suppl
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking data for non-ASCII characters ... OK
* creating made4-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'made4-Ex.R' failed.
The error most likely occurred in:
> ### * bga
>
> flush(stderr()); flush(stdout())
>
> ### Name: bga
> ### Title: Between group analysis
> ### Aliases: bga plot.bga
> ### Keywords: manip multivariate
>
> ### ** Examples
>
>
> data(khan)
>
> if (require(ade4, quiet = TRUE)) {
+ khan.bga<-bga(khan$train, classvec=khan$train.classes)
+ }
>
> khan.bga
$ord
$ord
Duality diagramm
class: coa dudi
$call: dudi.coa(df = data.tr, scannf = FALSE, nf = ord.nf)
$nf: 63 axis-components saved
$rank: 63
eigen values: 0.1713 0.1383 0.1032 0.05995 0.04965 ...
vector length mode content
1 $cw 306 numeric column weights
2 $lw 64 numeric row weights
3 $eig 63 numeric eigen values
data.frame nrow ncol content
1 $tab 64 306 modified array
2 $li 64 63 row coordinates
3 $l1 64 63 row normed scores
4 $co 306 63 column coordinates
5 $c1 306 63 column normed scores
other elements: N
$fac
[1] EWS EWS EWS EWS EWS EWS EWS EWS EWS EWS
[11] EWS EWS EWS EWS EWS EWS EWS EWS EWS EWS
[21] EWS EWS EWS BL-NHL BL-NHL BL-NHL BL-NHL BL-NHL BL-NHL BL-NHL
[31] BL-NHL NB NB NB NB NB NB NB NB NB
[41] NB NB NB RMS RMS RMS RMS RMS RMS RMS
[51] RMS RMS RMS RMS RMS RMS RMS RMS RMS RMS
[61] RMS RMS RMS RMS
Levels: EWS BL-NHL NB RMS
attr(,"class")
[1] "coa" "ord"
$bet
Between analysis
call: between(dudi = data.ord$ord, fac = classvec, scannf = FALSE,
nf = nclasses - 1)
class: between dudi
$nf (axis saved) : 3
$rank: 3
$ratio: 0.3599779
eigen values: 0.1522 0.1218 0.08981
vector length mode content
1 $eig 3 numeric eigen values
2 $lw 4 numeric group weigths
3 $cw 306 numeric col weigths
data.frame nrow ncol content
1 $tab 4 306 array class-variables
2 $li 4 3 class coordinates
3 $l1 4 3 class normed scores
4 $co 306 3 column coordinates
5 $c1 306 3 column normed scores
6 $ls 64 3 row coordinates
7 $as 63 3 inertia axis onto between axis
$fac
[1] EWS EWS EWS EWS EWS EWS EWS EWS EWS EWS
[11] EWS EWS EWS EWS EWS EWS EWS EWS EWS EWS
[21] EWS EWS EWS BL-NHL BL-NHL BL-NHL BL-NHL BL-NHL BL-NHL BL-NHL
[31] BL-NHL NB NB NB NB NB NB NB NB NB
[41] NB NB NB RMS RMS RMS RMS RMS RMS RMS
[51] RMS RMS RMS RMS RMS RMS RMS RMS RMS RMS
[61] RMS RMS RMS RMS
Levels: EWS BL-NHL NB RMS
attr(,"class")
[1] "coa" "bga"
> plot(khan.bga, genelabels=khan$annotation$Symbol)
>
> # Provide a view of the principal components (axes) of the bga
> heatplot(khan.bga$bet$ls, dend=FALSE,lowcol="blue")
Loading required package: gtools
Loading required package: gdata
Attaching package: 'gplots'
The following object(s) are masked from package:stats :
lowess
Error in if ((Colv == "Rowv") && (!isTRUE(Rowv) || is.null(Rowv))) Colv <- FALSE :
missing value where TRUE/FALSE needed
Calls: heatplot -> heatmap.2
Execution halted
made4.Rcheck/00install.out:
installing R.css in E:/biocbld/bbs-2.1-bioc/meat/made4.Rcheck
---------- Making package made4 ------------
adding build stamp to DESCRIPTION
installing R files
installing inst files
installing data files
installing man source files
installing indices
not zipping data
installing help
Note: unmatched right brace in 'cia' on or after line 102
Note: unmatched right brace in 'cia.Rd' on or after line 102
Note: unmatched right brace in 'genes' on or after line 40
Note: unmatched right brace in 'genes.Rd' on or after line 40
Note: unmatched right brace in 'jmol3D' on or after line 42
Note: unmatched right brace in 'jmol3D.Rd' on or after line 42
Note: unmatched right brace in 'plotgenes' on or after line 48
Note: unmatched right brace in 'plotgenes.Rd' on or after line 48
>>> Building/Updating help pages for package 'made4'
Formats: text html latex example chm
NCI60 text html latex example chm
array2ade4 text html latex example chm
bet.coinertia text html latex example chm
between.graph text html latex example chm
bga text html latex example chm
bga.jackknife text html latex example chm
bga.suppl text html latex example chm
checkfac text html latex example chm
chime3D text html latex example chm
cia text html latex example chm
commonMap text html latex example chm
comparelists text html latex example chm
do3d text html latex example chm
dudi.rwcoa text html latex example chm
forrwcoa text html latex example chm
genes text html latex example chm
genes1d text html latex example chm
getcol text html latex example chm
getdata text html latex example chm
graph1D text html latex example chm
heatplot text html latex example chm
html3D text html latex example chm
jmol3D text html latex example chm
khan text html latex example chm
ord text html latex example chm
overview text html latex example chm
plotarrays text html latex example chm
plotgenes text html latex example chm
randomiser text html latex example chm
s.var text html latex example chm
sumstats text html latex example chm
suppl text html latex example chm
topgenes text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.1-bioc\meat\made4.Rcheck\00_pkg_src\made4\chm\made4.chm
Compile time: 0 minutes, 0 seconds
34 Topics
167 Local links
20 Internet links
1 Graphic
Created e:\biocbld\bbs-2.1-bioc\meat\made4.Rcheck\00_pkg_src\made4\chm\made4.chm, 81,096 bytes
Compression decreased file by 107,654 bytes.
preparing package made4 for lazy loading
Loading required package: ade4
Loading required package: scatterplot3d
adding MD5 sums
* DONE (made4)