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Package 329/658 | Hostname | OS / Arch | BUILD | CHECK | BUILD BIN | ||||
IdMappingAnalysis 1.3.1 Alex Lisovich
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | WARNINGS | |||||
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK | |||||
petty | Mac OS X Leopard (10.5.8) / i386 | OK | [ WARNINGS ] | OK |
Package: IdMappingAnalysis |
Version: 1.3.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IdMappingAnalysis_1.3.1.tar.gz |
StartedAt: 2013-03-25 03:09:48 -0700 (Mon, 25 Mar 2013) |
EndedAt: 2013-03-25 03:12:01 -0700 (Mon, 25 Mar 2013) |
EllapsedTime: 132.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: IdMappingAnalysis.Rcheck |
Warnings: 1 |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/IdMappingAnalysis.Rcheck' * using R Under development (unstable) (2013-02-26 r62077) * using platform: i386-apple-darwin9.8.0 (32-bit) * using session charset: ASCII * using option '--no-vignettes' * checking for file 'IdMappingAnalysis/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'IdMappingAnalysis' version '1.3.1' * 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 'IdMappingAnalysis' can be installed ... [11s/12s] OK * checking installed package size ... OK * checking package 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 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 NB: .First.lib is obsolete and will not be used in R >= 3.0.0 * checking Rd files ... WARNING checkRd: (3) CsvList.merge.Misc.Rd:22: \synopsis will be removed in R 3.1.0 checkRd: (3) as.list.IdMap.Rd:26: \synopsis will be removed in R 3.1.0 checkRd: (3) boxplotdataJitter.JointUniquePairs.Rd:23: \synopsis will be removed in R 3.1.0 checkRd: (3) byColNames.Subset.Rd:26: \synopsis will be removed in R 3.1.0 checkRd: (3) byColumn.Subset.Rd:26: \synopsis will be removed in R 3.1.0 checkRd: (3) byRow.Subset.Rd:26: \synopsis will be removed in R 3.1.0 checkRd: (3) byRowNames.Subset.Rd:26: \synopsis will be removed in R 3.1.0 checkRd: (3) copy.Display.Rd:22: \synopsis will be removed in R 3.1.0 checkRd: (3) create.Display.Rd:20: \synopsis will be removed in R 3.1.0 checkRd: (3) create.UniquePairs.Rd:26: \synopsis will be removed in R 3.1.0 checkRd: (3) do.apply.DataFilter.Rd:27: \synopsis will be removed in R 3.1.0 checkRd: (3) fisherTransform.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0 checkRd: (3) fisherTransformInverse.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0 checkRd: (3) fisherTransformJacobean.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0 checkRd: (3) interleave.Misc.Rd:20: \synopsis will be removed in R 3.1.0 checkRd: (3) line.loess.Display.Rd:20: \synopsis will be removed in R 3.1.0 checkRd: (3) line.unsorted.Display.Rd:20: \synopsis will be removed in R 3.1.0 checkRd: (3) log10.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0 checkRd: (3) minAvgCountConstraint.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0 checkRd: (3) minCountConstraint.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0 checkRd: (3) minCountGroupConstraint.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0 checkRd: (3) pack.experiments.CorrData.Rd:21: \synopsis will be removed in R 3.1.0 checkRd: (3) progressMsg.Display.Rd:22: \synopsis will be removed in R 3.1.0 checkRd: (3) removeNASeries.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0 checkRd: (3) swapKeys.IdMap.Rd:19: \synopsis will be removed in R 3.1.0 checkRd: (3) swapKeys.UniquePairs.Rd:19: \synopsis will be removed in R 3.1.0 checkRd: (3) textBoundingBox.Display.Rd:28: \synopsis will be removed in R 3.1.0 checkRd: (3) to.base.Misc.Rd:20: \synopsis will be removed in R 3.1.0 checkRd: (3) to.binary.logical.Misc.Rd:22: \synopsis will be removed in R 3.1.0 checkRd: (3) to.index.expr.Misc.Rd:25: \synopsis will be removed in R 3.1.0 checkRd: (3) words.Misc.Rd:22: \synopsis will be removed in R 3.1.0 checkRd: (3) zoom.pars.Display.Rd:20: \synopsis will be removed in R 3.1.0 * 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 ... [52s/52s] OK Examples with CPU or elapsed time > 5s user system elapsed getBootstrap.JointUniquePairs 11.278 0.600 11.888 Bootstrap 8.699 0.539 9.254 * 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 WARNING: There was 1 warning. NOTE: There was 1 note. See '/Users/biocbuild/bbs-2.12-bioc/meat/IdMappingAnalysis.Rcheck/00check.log' for details.
IdMappingAnalysis.Rcheck/00install.out:
* installing *source* package 'IdMappingAnalysis' ... ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes 'IdMappingAnalysis.Rnw' using 'latin-9' ** testing if installed package can be loaded * DONE (IdMappingAnalysis)
IdMappingAnalysis.Rcheck/IdMappingAnalysis-Ex.timings:
name | user | system | elapsed | |
000-LB-.IdMapBase | 0.402 | 0.067 | 0.497 | |
Bootstrap | 8.699 | 0.539 | 9.254 | |
Corr | 0.634 | 0.019 | 0.652 | |
CorrData | 0.218 | 0.030 | 0.250 | |
CsvList.merge.Misc | 0.010 | 0.007 | 0.016 | |
IdMap | 0.016 | 0.008 | 0.024 | |
IdMapBase | 0.009 | 0.006 | 0.014 | |
IdMapCounts | 0.747 | 0.042 | 0.792 | |
IdMapDiff | 0.810 | 0.032 | 0.846 | |
IdMapDiffCounts | 0.580 | 0.022 | 0.601 | |
JointIdMap | 0.182 | 0.014 | 0.196 | |
JointUniquePairs | 0.820 | 0.039 | 0.861 | |
Mixture | 0.284 | 0.012 | 0.296 | |
UniquePairs | 0.012 | 0.008 | 0.021 | |
aligned.IdMapBase | 0.020 | 0.012 | 0.032 | |
as.IdMap.UniquePairs | 0.061 | 0.009 | 0.070 | |
as.MultiSet.CorrData | 0.952 | 0.055 | 1.009 | |
as.UniquePairs.IdMap | 0.031 | 0.011 | 0.042 | |
as.data.frame.IdMapBase | 0.092 | 0.034 | 0.127 | |
as.data.frame.JointIdMap | 0.195 | 0.015 | 0.210 | |
as.list.IdMap | 0.022 | 0.009 | 0.030 | |
boxplot.JointUniquePairs | 0.150 | 0.021 | 0.172 | |
byColNames.Subset | 0.011 | 0.010 | 0.021 | |
byColumn.Subset | 0.013 | 0.011 | 0.029 | |
byRow.Subset | 0.014 | 0.015 | 0.028 | |
byRowNames.Subset | 0.017 | 0.010 | 0.028 | |
clust.Mixture | 0.006 | 0.007 | 0.013 | |
copy.Display | 0.009 | 0.007 | 0.016 | |
corr.boxplot.JointUniquePairs | 0.103 | 0.021 | 0.124 | |
corr.plot.JointUniquePairs | 0.075 | 0.017 | 0.093 | |
create.Display | 0.005 | 0.006 | 0.011 | |
create.UniquePairs | 0.136 | 0.016 | 0.152 | |
diffCounts.plot.JointIdMap | 0.662 | 0.025 | 0.688 | |
dim.IdMapBase | 0.011 | 0.009 | 0.020 | |
dimnames.IdMapBase | 0.025 | 0.014 | 0.039 | |
do.glm.JointUniquePairs | 0.032 | 0.010 | 0.043 | |
ecdf.plot.JointIdMap | 0.365 | 0.021 | 0.386 | |
equals.UniquePairs | 0.053 | 0.015 | 0.068 | |
fisherTransform.DataFilter | 0.007 | 0.006 | 0.013 | |
fisherTransformInverse.DataFilter | 0.005 | 0.007 | 0.013 | |
fisherTransformJacobean.DataFilter | 0.005 | 0.007 | 0.012 | |
getBootstrap.JointUniquePairs | 11.278 | 0.600 | 11.888 | |
getCompoundEvents.IdMapDiffCounts | 0.621 | 0.023 | 0.645 | |
getCompoundGroups.IdMapDiffCounts | 1.004 | 0.032 | 1.036 | |
getCorr.JointUniquePairs | 0.114 | 0.017 | 0.133 | |
getCorrData.JointUniquePairs | 0.402 | 0.035 | 0.437 | |
getCorrDataFrame.JointUniquePairs | 0.043 | 0.011 | 0.054 | |
getCounts.IdMap | 0.053 | 0.009 | 0.062 | |
getCounts.JointIdMap | 0.561 | 0.020 | 0.580 | |
getData.Corr | 0.008 | 0.008 | 0.017 | |
getData.Mixture | 0.010 | 0.008 | 0.017 | |
getDiff.JointIdMap | 0.676 | 0.020 | 0.697 | |
getExperimentSet.CorrData | 0.307 | 0.031 | 0.339 | |
getIdMapList.JointIdMap | 0.343 | 0.019 | 0.363 | |
getMapNames.JointIdMap | 0.323 | 0.016 | 0.339 | |
getMapNames.JointUniquePairs | 0.010 | 0.007 | 0.016 | |
getMatch.UniquePairs | 0.092 | 0.017 | 0.107 | |
getMatchInfo.JointIdMap | 0.337 | 0.018 | 0.356 | |
getMatchInfo.JointUniquePairs | 0.775 | 0.009 | 0.783 | |
getMixture.JointUniquePairs | 0.319 | 0.022 | 0.342 | |
getSampleNames.CorrData | 0.009 | 0.008 | 0.016 | |
getStats.IdMapCounts | 0.605 | 0.025 | 0.633 | |
getStats.Mixture | 0.011 | 0.006 | 0.018 | |
getUnionIdMap.JointIdMap | 1.183 | 0.025 | 1.209 | |
getUniquePairs.Corr | 0.021 | 0.009 | 0.032 | |
getUniquePairs.CorrData | 0.011 | 0.006 | 0.017 | |
getUniquePairs.JointUniquePairs | 0.015 | 0.008 | 0.022 | |
interactive.corr.boxplot.JointUniquePairs | 0.113 | 0.025 | 0.140 | |
interactive.corr.plot.JointUniquePairs | 0.115 | 0.113 | 0.230 | |
interactive.mixture.boxplot.JointUniquePairs | 0.442 | 0.100 | 0.542 | |
interactive.mixture.plot.JointUniquePairs | 0.430 | 0.087 | 0.521 | |
interactive.plot.CorrData | 0.090 | 0.016 | 0.107 | |
interactive.plot.JointUniquePairs | 0.008 | 0.010 | 0.018 | |
interleave.Misc | 0.007 | 0.007 | 0.014 | |
line.loess.Display | 0.008 | 0.009 | 0.017 | |
line.unsorted.Display | 0.008 | 0.009 | 0.017 | |
log10.DataFilter | 0.037 | 0.016 | 0.054 | |
merge.IdMap | 1.436 | 0.031 | 1.470 | |
minAvgCountConstraint.DataFilter | 0.270 | 0.082 | 0.352 | |
minCountConstraint.DataFilter | 0.286 | 0.086 | 0.372 | |
minCountGroupConstraint.DataFilter | 0.379 | 0.083 | 0.463 | |
mixture.boxplot.JointUniquePairs | 0.375 | 0.028 | 0.403 | |
mixture.plot.JointUniquePairs | 0.210 | 0.017 | 0.230 | |
plot.Bootstrap | 0.114 | 0.012 | 0.130 | |
plot.Corr | 0.122 | 0.024 | 0.147 | |
plot.CorrData | 0.041 | 0.010 | 0.050 | |
plot.IdMapCounts | 0.352 | 0.021 | 0.373 | |
plot.IdMapDiffCounts | 0.887 | 0.032 | 0.922 | |
plot.Mixture | 0.039 | 0.011 | 0.051 | |
primaryIDs.IdMapBase | 0.018 | 0.008 | 0.025 | |
primaryKey.CorrData | 0.007 | 0.007 | 0.014 | |
primaryKey.IdMapBase | 0.008 | 0.008 | 0.016 | |
primaryKey.Mixture | 0.007 | 0.007 | 0.014 | |
progressMsg.Display | 0.006 | 0.007 | 0.013 | |
removeNASeries.DataFilter | 0.205 | 0.059 | 0.263 | |
secondaryKey.CorrData | 0.004 | 0.005 | 0.008 | |
secondaryKey.IdMapBase | 0.006 | 0.005 | 0.011 | |
secondaryKey.Mixture | 0.003 | 0.005 | 0.006 | |
subsetCorr.JointUniquePairs | 0.024 | 0.009 | 0.033 | |
subsetData.JointUniquePairs | 0.020 | 0.014 | 0.039 | |
subsetGroups.JointUniquePairs | 1.409 | 0.062 | 1.473 | |
summary.IdMapDiffCounts | 0.995 | 0.030 | 1.027 | |
swapKeys.IdMap | 0.247 | 0.023 | 0.270 | |
swapKeys.UniquePairs | 0.058 | 0.016 | 0.074 | |
textBoundingBox.Display | 0.009 | 0.007 | 0.016 | |
to.base.Misc | 0.010 | 0.008 | 0.018 | |
to.binary.logical.Misc | 0.011 | 0.008 | 0.019 | |
to.index.expr.Misc | 0.009 | 0.008 | 0.017 | |
unique.UniquePairs | 0.154 | 0.030 | 0.185 | |
words.Misc | 0.004 | 0.005 | 0.010 | |
zoom.pars.Display | 0.008 | 0.008 | 0.016 | |