SpeCond 1.18.0
Florence Cavalli
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/SpeCond | | Last Changed Rev: 88838 / Revision: 95116 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
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### Running command:
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### /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings SpeCond_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/SpeCond.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.18.0’
* 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 ... [4s/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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [57s/61s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getFullHtmlSpeCondResult 7.161 0.040 7.925
getGeneHtmlPage 6.648 0.060 6.855
getSpecificResult 5.116 0.064 5.388
getProfile 5.097 0.020 5.363
writeSpeCondResult 5.061 0.008 5.137
writeUniqueProfileSpecificResult 5.028 0.016 5.154
writeGeneResult 5.024 0.012 5.071
SpeCond 4.812 0.016 5.489
fitNoPriorWithExclusion 4.540 0.016 5.143
* 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
NOTE: There were 2 notes.
See
‘/home/biocbuild/bbs-2.14-bioc/meat/SpeCond.Rcheck/00check.log’
for details.