a4Base 1.1.3
Tobias Verbeke
| Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/a4Base | | Last Changed Rev: 55770 / Revision: 56603 | | Last Changed Date: 2011-05-21 07:15:35 -0700 (Sat, 21 May 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | ERROR | OK |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | [ ERROR ] | ERROR |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/a4Base.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'a4Base/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'a4Base' version '1.1.3'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* 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 ...
** running examples for arch 'i386' ... ERROR
Running examples in 'a4Base-Ex.R' failed
The error most likely occurred in:
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: logReg
> ### Title: Logistic regression for predicting the probability to belong to
> ### a certain class in binary classification problems.
> ### Aliases: logReg
>
> ### ** Examples
>
> if (require(ALL)){
+ data(ALL, package = "ALL")
+ ALL <- addGeneInfo(ALL)
+ ALL$BTtype <- as.factor(substr(ALL$BT,0,1))
+
+ logRegRes <- logReg(geneSymbol = "HLA-DPB1", object = ALL, groups = "BTtype")
+
+ # scoresplot
+ probabilitiesPlot(proportions = logRegRes$fit, classVar = logRegRes$y,
+ sampleNames = rownames(logRegRes), main = 'Probability of being a T-cell type ALL')
+ # barplot
+ probabilitiesPlot(proportions = logRegRes$fit, classVar = logRegRes$y, barPlot=TRUE,
+ sampleNames = rownames(logRegRes), main = 'Probability of being a T-cell type ALL')
+ }
Loading required package: ALL
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
Warning in logReg(geneSymbol = "HLA-DPB1", object = ALL, groups = "BTtype") :
Gene HLA-DPB1 corresponds to 2 probesets; only the first probeset ( 38095_i_at ) has been displayed on the plot.
Warning in mtext(sprintf("help(\"%s\")", nameEx()), side = 4, line = if (outer) max(1, :
Font family not found in Windows font database
Warning in mtext(sprintf("help(\"%s\")", nameEx()), side = 4, line = if (outer) max(1, :
Font family not found in Windows font database
Warning in title(...) : Font family not found in Windows font database
Warning in title(...) : Font family not found in Windows font database
Warning in title(...) : Font family not found in Windows font database
Warning in title(...) : Font family not found in Windows font database
Warning in title(...) : Font family not found in Windows font database
Warning in title(...) : Font family not found in Windows font database
Warning in title(...) : Font family not found in Windows font database
Warning in title(...) : Font family not found in Windows font database
Warning in title(...) : Font family not found in Windows font database
Warning in axis(1, las = 1) :
Font family not found in Windows font database
Error in plot.new() : figure margins too large
Calls: probabilitiesPlot -> plot -> plot -> plot.default -> plot.new
Execution halted
install for i386
* 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 1.7
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: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
Attaching package: 'gdata'
The following object(s) are masked from 'package:Biobase':
combine
The following object(s) are masked from 'package:stats':
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 1.7
a4Base version 1.1.3
add DLL for x64
* installing *source* package 'a4Base' ...
** testing if installed package can be loaded
mpm version 1.0-17
Loaded glmnet 1.7
a4Base version 1.1.3
* MD5 sums
packaged installation of 'a4Base' as a4Base_1.1.3.zip
* DONE (a4Base)