SpeCond 1.11.0
Florence Cavalli
| Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SpeCond | | Last Changed Rev: 64680 / Revision: 66885 | | Last Changed Date: 2012-03-30 15:15:56 -0700 (Fri, 30 Mar 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | 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 |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/SpeCond.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'SpeCond/DESCRIPTION' ... OK
* this is package 'SpeCond' version '1.11.0'
* 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 'SpeCond' 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 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
SpeCond: warning in getSpecificOutliersStep1(expressionMatrix, fit =
fit1, param.detection = param.detection, multitest.correction.method
= "BY", prefix.file = prefix.file, print.hist.pv = FALSE): partial
argument match of 'fit' to 'fit1'
SpeCond: warning in getSpecificResult(expressionMatrix, fit = fit2,
specificOutlierStep1 = specificOutlierStep1, param.detection =
param.detection, multitest.correction.method =
multitest.correction.method, prefix.file = prefix.file, print.hist.pv
= print.hist.pv): partial argument match of 'fit' to 'fit2'
createSingleGeneHtmlPage: warning in matrix(c("color:#000DFE", NA), nr
= 1, nc = 2): partial argument match of 'nr' to 'nrow'
createSingleGeneHtmlPage: warning in matrix(c("color:#000DFE", NA), nr
= 1, nc = 2): partial argument match of 'nc' to 'ncol'
getExpressionpatternLegend: warning in matrix(" ", nr = 2, nc =
1): partial argument match of 'nr' to 'nrow'
getExpressionpatternLegend: warning in matrix(" ", nr = 2, nc =
1): partial argument match of 'nc' to 'ncol'
getHeatmap: warning in heatmap(M_values, scale = "none", margin = c(8,
8), col = colors): partial argument match of 'margin' to 'margins'
getHeatmap: warning in heatmap(M_values, scale = "none", margin = c(8,
8), col = colors, RowSideColors = colRowSide): partial argument match
of 'margin' to 'margins'
getHeatmap: warning in heatmap(M_values[rownames(M_values) %in%
probe_set, ], scale = "none", margin = c(8, 8), col = colors):
partial argument match of 'margin' to 'margins'
getProfileHeatmap: warning in heatmap(M_profile, scale = "none", margin
= c(8, 8), col = colors): partial argument match of 'margin' to
'margins'
* 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 ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There was 1 note.
See
'/Users/biocbuild/bbs-2.11-bioc/meat/SpeCond.Rcheck/00check.log'
for details.