a4Base 1.0.1
Tobias Verbeke
| Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/a4Base | | Last Changed Rev: 54837 / Revision: 59457 | | Last Changed Date: 2011-04-14 10:46:47 -0700 (Thu, 14 Apr 2011) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ ERROR ] | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/a4Base.Rcheck'
* using R version 2.13.2 (2011-09-30)
* 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 '1.0.1'
* 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 whether package 'a4Base' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'head' when loading 'utils'
Warning: replacing previous import 'tail' when loading 'utils'
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-2.8-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 ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
See section 'Generic functions and methods' of the 'Writing R
Extensions' manual.
* checking replacement functions ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... NOTE
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
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 ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
* checking Rd \usage sections ... NOTE
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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.
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
mpm version 1.0-18
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
mpm version 1.0-18
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
a4Base version 1.0.1
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)