a4Base 1.2.1
Tobias Verbeke
| Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/a4Base | | Last Changed Rev: 60978 / Revision: 61898 | | Last Changed Date: 2011-11-30 02:11:49 -0800 (Wed, 30 Nov 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | ERROR | OK |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ ERROR ] | OK |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | ERROR | OK |
| 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 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-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 '1.2.1'
* checking package namespace 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 if there is a namespace ... OK
* checking whether package 'a4Base' can be installed ... WARNING
Found the following significant warnings:
Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
See 'D:/biocbld/bbs-2.9-bioc/meat/a4Base.Rcheck/00install.out' for details.
* 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
* 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
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: 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
* installing *source* package 'a4Base' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'head' when loading 'utils'
Warning: replacing previous import 'tail' when loading 'utils'
File type 'perl' not found or no open command associated with it.
Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
File type 'perl' not found or no open command associated with it.
Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
Warning messages:
1: replacing previous import 'head' when loading 'utils'
2: replacing previous import 'tail' when loading 'utils'
3: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
4: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
* DONE (a4Base)