a4Base 1.1.1
Tobias Verbeke
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/a4Base | | Last Changed Rev: 54828 / Revision: 55359 | | Last Changed Date: 2011-04-14 10:39:51 -0700 (Thu, 14 Apr 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | ERROR | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | ERROR | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | ERROR | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | [ ERROR ] | OK |
* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/a4Base.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘a4Base/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Base’ version ‘1.1.1’
* checking package name space information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
‘gridSVG’ ‘JavaGD’
* checking if this is a source package ... OK
* checking whether package ‘a4Base’ 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... WARNING
‘library’ or ‘require’ call not declared from: ‘gridSVG’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotLogRatio: no visible global function definition for ‘JavaGD’
plotLogRatio: no visible global function definition for ‘grid.garnish’
plotLogRatio: no visible global function definition for
‘grid.hyperlink’
plotLogRatio: no visible global function definition for ‘grid.script’
plotLogRatio: no visible global function definition for ‘gridToSVG’
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
‘library’ or ‘require’ call not declared from: ‘nlcv’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in ‘a4Base-Ex.R’ failed
The error most likely occurred in:
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lassoReg
> ### Title: Multiple regression using the Lasso algorithm as implemented in
> ### the glmnet package
> ### Aliases: lassoReg
>
> ### ** Examples
>
> if (require(ALL)){
+ data(ALL, package = "ALL")
+ ALL <- addGeneInfo(ALL)
+ ALL$BTtype <- as.factor(substr(ALL$BT,0,1))
+
+ resultLasso <- lassoReg(object = ALL[1:100,], covariate = "age")
+ plot(resultLasso, label = TRUE,
+ main = "Lasso coefficients in relation to degree of penalization.")
+ featResultLasso <- topTable(resultLasso, n = 15)
+ }
Loading required package: ALL
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "topTable", for signature "elnet"
Calls: topTable -> <Anonymous>
Execution halted
* installing *source* package ‘a4Base’ ...
** R
** data
** inst
** preparing package for lazy loading
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.
Loading required package: GO.db
Loading required package: DBI
Loading required package: KEGG.db
Loading required package: MASS
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
mpm version 1.0-17
Attaching package: ‘genefilter’
The following object(s) are masked from ‘package:MASS’:
area
Loading required package: Matrix
Loading required package: lattice
Attaching package: ‘Matrix’
The following object(s) are masked from ‘package:base’:
det
Loaded glmnet 1.6
Attaching package: ‘a4Core’
The following object(s) are masked from ‘package:limma’:
topTable
Loading required package: gtools
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.
gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.
Attaching package: ‘gdata’
The following object(s) are masked from ‘package:Biobase’:
combine
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nobs
The following object(s) are masked from ‘package:utils’:
object.size
Loading required package: caTools
Loading required package: bitops
Attaching package: ‘gplots’
The following object(s) are masked from ‘package:multtest’:
wapply
The following object(s) are masked from ‘package:stats’:
lowess
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
mpm version 1.0-17
Loaded glmnet 1.6
a4Base version 1.1.1
* DONE (a4Base)