SpeCond 1.12.0
Florence Cavalli
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/SpeCond | | Last Changed Rev: 70050 / Revision: 74773 | | Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | 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 2.15.3 (2013-03-01)
* 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 '1.12.0'
* 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 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 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
Examples with CPU or elapsed time > 5s
user system elapsed
getFullHtmlSpeCondResult 8.617 0.479 9.377
getGeneHtmlPage 8.030 0.374 8.590
SpeCond 5.900 0.082 6.018
getProfile 5.596 0.051 5.694
writeSpeCondResult 5.532 0.049 5.595
writeUniqueProfileSpecificResult 5.481 0.050 5.546
writeGeneResult 5.409 0.049 5.504
getSpecificResult 5.381 0.046 5.448
fitNoPriorWithExclusion 5.036 0.056 5.135
* 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.