GeneAnswers 1.10.0
Gang Feng , Pan Du and Tian Xia
| 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/GeneAnswers | | Last Changed Rev: 59920 / Revision: 61898 | | Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 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 | OK | OK |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/GeneAnswers.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneAnswers/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneAnswers' version '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'GeneAnswers' can be installed ... OK
* checking installed package size ... NOTE
installed size is 37.8Mb
sub-directories of 1Mb or more:
data 1.5Mb
doc 3.4Mb
External 32.4Mb
* 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
File 'GeneAnswers/R/zzz.R':
.onLoad calls:
require(Biobase)
Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.
* checking Rd files ... NOTE
prepare_Rd: DO.Rd:32-34: Dropping empty section \references
prepare_Rd: geneFunSummarize.Rd:21-23: Dropping empty section \details
prepare_Rd: plotGeneFunSummary.Rd:30-32: Dropping empty section \details
prepare_Rd: plotOntologyGraph.Rd:28-30: Dropping empty section \details
prepare_Rd: saveGeneFunSummary.Rd:18-20: Dropping empty section \details
prepare_Rd: saveGeneFunSummary.Rd:24-26: Dropping empty section \references
prepare_Rd: simplifyGeneFunSummary.Rd:18-20: Dropping empty section \details
* 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 ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... NOTE
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
DO.rda 702Kb 417Kb xz
DOLite.rda 86Kb 46Kb xz
DmIALite.rda 114Kb 84Kb xz
HsIALite.rda 536Kb 414Kb xz
MmIALite.rda 43Kb 34Kb xz
RnIALite.rda 19Kb 16Kb xz
sampleGroupsData.rda 25Kb 17Kb bzip2
* checking examples ... ERROR
Running examples in 'GeneAnswers-Ex.R' failed
The error most likely occurred in:
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chartPlots
> ### Title: Pie Chart and Bar Plots
> ### Aliases: chartPlots
> ### Keywords: methods
>
> ### ** Examples
>
> x <- matrix(c(6,9,3,30,13,2,15,20), nrow = 4, ncol=2, byrow=FALSE,
+ dimnames = list(c("group1", "group2", "group3", "group4"),
+ c("value1", "value2")))
> chartPlots(x, chartType='all', specifiedCol = "value2", top = 3)
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 text.default(1.1 * P$x, 1.1 * P$y, labels[i], xpd = TRUE, adj = ifelse(P$x < :
Font family not found in Windows font database
Warning in title(main = main, ...) :
Font family not found in Windows font database
Warning in x11() : Unable to open window
Warning in x11() : opening device failed
Error in x11() : unable to start windows() device
Calls: chartPlots -> x11
Execution halted
* installing *source* package 'GeneAnswers' ...
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class "connection" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class "file" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'GeneAnswersCWAnnotation.Rnw'
'geneAnswers.Rnw'
'geneFunctionSummarize.Rnw'
** testing if installed package can be loaded
Warning message:
In rgl.init(initValue) : RGL: error: window class registration failed
* DONE (GeneAnswers)