SpeCond 1.20.0
Florence Cavalli
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/SpeCond | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings SpeCond_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/SpeCond.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpeCond/DESCRIPTION’ ... OK
* this is package ‘SpeCond’ version ‘1.20.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpeCond’ can be installed ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘Biobase’ ‘fields’ ‘hwriter’ ‘mclust’ ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* 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'
callMclustInStep2: no visible global function definition for ‘Mclust’
callMclustInStep2: no visible global function definition for
‘priorControl’
createSingleGeneHtmlPage: no visible global function definition for
‘openPage’
createSingleGeneHtmlPage: no visible global function definition for
‘hwrite’
createSingleGeneHtmlPage: no visible global function definition for
‘closePage’
fitNoPriorWithExclusion : <anonymous>: no visible global function
definition for ‘Mclust’
fitPrior : <anonymous>: no visible global function definition for
‘Mclust’
fitPrior : <anonymous>: no visible global function definition for
‘priorControl’
getExpressionpatternLegend: no visible global function definition for
‘hwrite’
getFullHtmlSpeCondResult: no visible global function definition for
‘openPage’
getFullHtmlSpeCondResult: no visible global function definition for
‘hwrite’
getFullHtmlSpeCondResult: no visible global function definition for
‘hwriteImage’
getFullHtmlSpeCondResult: no visible global function definition for
‘closePage’
getGeneHtmlPage: no visible global function definition for ‘openPage’
getGeneHtmlPage: no visible global function definition for ‘hwrite’
getGeneHtmlPage: no visible global function definition for ‘closePage’
getHeatmap: no visible global function definition for ‘colorbar.plot’
getMatrixFromExpressionSet: no visible global function definition for
‘exprs’
plotNormalMixture: no visible global function definition for
‘hwriteImage’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [55s/62s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getFullHtmlSpeCondResult 6.809 0.264 9.376
getGeneHtmlPage 6.108 0.284 7.598
writeSpeCondResult 5.101 0.016 5.264
SpeCond 5.016 0.012 5.856
getSpecificResult 4.916 0.016 5.066
writeGeneResult 4.896 0.008 5.020
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
NOTE: There were 2 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/SpeCond.Rcheck/00check.log’
for details.