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This page was generated on 2014-04-05 09:48:15 -0700 (Sat, 05 Apr 2014).
| Package 365/750 | Hostname | OS / Arch | BUILD | CHECK | BUILD BIN | ||||
| IdMappingAnalysis 1.6.0 Alex Lisovich
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ OK ] | |||||
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | |||||
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
| Package: IdMappingAnalysis |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.6.0.tar.gz |
| StartedAt: 2014-04-05 01:56:25 -0700 (Sat, 05 Apr 2014) |
| EndedAt: 2014-04-05 01:57:40 -0700 (Sat, 05 Apr 2014) |
| EllapsedTime: 74.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IdMappingAnalysis.Rcheck |
| Warnings: 0 |
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IdMappingAnalysis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IdMappingAnalysis’ version ‘1.6.0’
* 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 ‘IdMappingAnalysis’ can be installed ... [5s/6s] 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Biobase’
All declared Imports should be used.
Packages in Depends field not imported from:
‘R.oo’ ‘rChoiceDialogs’
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 ... OK
* checking Rd files ... NOTE
prepare_Rd: DataFilter.Rd:41-42: Dropping empty section \arguments
prepare_Rd: Display.Rd:41-42: Dropping empty section \arguments
prepare_Rd: Misc.Rd:41-42: Dropping empty section \arguments
* 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 ... [30s/30s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getBootstrap.JointUniquePairs 7.661 0.004 7.672
Bootstrap 6.816 0.044 6.905
* 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-2.13-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 ** testing if installed package can be loaded * DONE (IdMappingAnalysis)
IdMappingAnalysis.Rcheck/IdMappingAnalysis-Ex.timings:
| name | user | system | elapsed | |
| 000-LB-.IdMapBase | 0.304 | 0.008 | 0.313 | |
| Bootstrap | 6.816 | 0.044 | 6.905 | |
| Corr | 0.496 | 0.000 | 0.494 | |
| CorrData | 0.140 | 0.000 | 0.139 | |
| CsvList.merge.Misc | 0.004 | 0.000 | 0.005 | |
| IdMap | 0.008 | 0.000 | 0.009 | |
| IdMapBase | 0.000 | 0.000 | 0.003 | |
| IdMapCounts | 0.344 | 0.004 | 0.348 | |
| IdMapDiff | 0.512 | 0.004 | 0.540 | |
| IdMapDiffCounts | 0.328 | 0.000 | 0.329 | |
| JointIdMap | 0.072 | 0.000 | 0.072 | |
| JointUniquePairs | 0.676 | 0.008 | 0.682 | |
| Mixture | 0.376 | 0.000 | 0.377 | |
| UniquePairs | 0.008 | 0.000 | 0.010 | |
| aligned.IdMapBase | 0.016 | 0.000 | 0.016 | |
| as.IdMap.UniquePairs | 0.044 | 0.000 | 0.043 | |
| as.MultiSet.CorrData | 0.708 | 0.024 | 0.732 | |
| as.UniquePairs.IdMap | 0.024 | 0.000 | 0.025 | |
| as.data.frame.IdMapBase | 0.072 | 0.000 | 0.072 | |
| as.data.frame.JointIdMap | 0.064 | 0.000 | 0.067 | |
| as.list.IdMap | 0.016 | 0.000 | 0.018 | |
| boxplot.JointUniquePairs | 0.080 | 0.000 | 0.078 | |
| byColNames.Subset | 0.008 | 0.000 | 0.012 | |
| byColumn.Subset | 0.008 | 0.000 | 0.011 | |
| byRow.Subset | 0.012 | 0.000 | 0.010 | |
| byRowNames.Subset | 0.012 | 0.000 | 0.011 | |
| clust.Mixture | 0.004 | 0.000 | 0.006 | |
| copy.Display | 0.004 | 0.000 | 0.005 | |
| corr.boxplot.JointUniquePairs | 0.080 | 0.008 | 0.086 | |
| corr.plot.JointUniquePairs | 0.056 | 0.000 | 0.058 | |
| create.Display | 0.004 | 0.000 | 0.002 | |
| create.UniquePairs | 0.116 | 0.000 | 0.116 | |
| diffCounts.plot.JointIdMap | 0.488 | 0.000 | 0.490 | |
| dim.IdMapBase | 0.012 | 0.000 | 0.012 | |
| dimnames.IdMapBase | 0.084 | 0.000 | 0.083 | |
| do.glm.JointUniquePairs | 0.024 | 0.000 | 0.023 | |
| ecdf.plot.JointIdMap | 0.208 | 0.004 | 0.213 | |
| equals.UniquePairs | 0.044 | 0.000 | 0.043 | |
| fisherTransform.DataFilter | 0.068 | 0.000 | 0.068 | |
| fisherTransformInverse.DataFilter | 0.000 | 0.000 | 0.001 | |
| fisherTransformJacobean.DataFilter | 0.000 | 0.000 | 0.002 | |
| getBootstrap.JointUniquePairs | 7.661 | 0.004 | 7.672 | |
| getCompoundEvents.IdMapDiffCounts | 0.372 | 0.000 | 0.372 | |
| getCompoundGroups.IdMapDiffCounts | 0.388 | 0.000 | 0.390 | |
| getCorr.JointUniquePairs | 0.068 | 0.000 | 0.070 | |
| getCorrData.JointUniquePairs | 0.156 | 0.000 | 0.153 | |
| getCorrDataFrame.JointUniquePairs | 0.032 | 0.000 | 0.032 | |
| getCounts.IdMap | 0.028 | 0.000 | 0.029 | |
| getCounts.JointIdMap | 0.184 | 0.000 | 0.186 | |
| getData.Corr | 0.004 | 0.000 | 0.003 | |
| getData.Mixture | 0.004 | 0.000 | 0.004 | |
| getDiff.JointIdMap | 0.208 | 0.000 | 0.211 | |
| getExperimentSet.CorrData | 0.108 | 0.004 | 0.113 | |
| getIdMapList.JointIdMap | 0.076 | 0.000 | 0.074 | |
| getMapNames.JointIdMap | 0.136 | 0.000 | 0.137 | |
| getMapNames.JointUniquePairs | 0.008 | 0.000 | 0.006 | |
| getMatch.UniquePairs | 0.048 | 0.000 | 0.048 | |
| getMatchInfo.JointIdMap | 0.072 | 0.000 | 0.074 | |
| getMatchInfo.JointUniquePairs | 0.408 | 0.000 | 0.410 | |
| getMixture.JointUniquePairs | 0.220 | 0.000 | 0.222 | |
| getSampleNames.CorrData | 0.008 | 0.000 | 0.005 | |
| getStats.IdMapCounts | 0.192 | 0.004 | 0.199 | |
| getStats.Mixture | 0.008 | 0.000 | 0.007 | |
| getUnionIdMap.JointIdMap | 0.464 | 0.000 | 0.510 | |
| getUniquePairs.Corr | 0.008 | 0.000 | 0.010 | |
| getUniquePairs.CorrData | 0.008 | 0.000 | 0.008 | |
| getUniquePairs.JointUniquePairs | 0.012 | 0.000 | 0.010 | |
| interactive.corr.boxplot.JointUniquePairs | 0.108 | 0.000 | 0.224 | |
| interactive.corr.plot.JointUniquePairs | 0.060 | 0.004 | 0.065 | |
| interactive.mixture.boxplot.JointUniquePairs | 0.300 | 0.004 | 0.303 | |
| interactive.mixture.plot.JointUniquePairs | 0.248 | 0.000 | 0.251 | |
| interactive.plot.CorrData | 0.056 | 0.000 | 0.054 | |
| interactive.plot.JointUniquePairs | 0.004 | 0.000 | 0.006 | |
| interleave.Misc | 0.004 | 0.000 | 0.003 | |
| line.loess.Display | 0.004 | 0.000 | 0.004 | |
| line.unsorted.Display | 0.004 | 0.000 | 0.004 | |
| logTen.DataFilter | 0.204 | 0.000 | 0.204 | |
| merge.IdMap | 0.628 | 0.000 | 0.630 | |
| minAvgCountConstraint.DataFilter | 0.140 | 0.000 | 0.138 | |
| minCountConstraint.DataFilter | 0.152 | 0.004 | 0.154 | |
| minCountGroupConstraint.DataFilter | 0.256 | 0.000 | 0.259 | |
| mixture.boxplot.JointUniquePairs | 0.292 | 0.000 | 0.292 | |
| mixture.plot.JointUniquePairs | 0.236 | 0.000 | 0.237 | |
| plot.Bootstrap | 0.080 | 0.000 | 0.079 | |
| plot.Corr | 0.064 | 0.000 | 0.064 | |
| plot.CorrData | 0.036 | 0.000 | 0.035 | |
| plot.IdMapCounts | 0.176 | 0.000 | 0.177 | |
| plot.IdMapDiffCounts | 0.576 | 0.000 | 0.577 | |
| plot.Mixture | 0.028 | 0.000 | 0.028 | |
| primaryIDs.IdMapBase | 0.020 | 0.000 | 0.021 | |
| primaryKey.CorrData | 0.004 | 0.000 | 0.005 | |
| primaryKey.IdMapBase | 0.004 | 0.000 | 0.003 | |
| primaryKey.Mixture | 0.004 | 0.000 | 0.003 | |
| progressMsg.Display | 0.004 | 0.000 | 0.004 | |
| removeNASeries.DataFilter | 0.156 | 0.000 | 0.156 | |
| secondaryKey.CorrData | 0.004 | 0.000 | 0.005 | |
| secondaryKey.IdMapBase | 0.004 | 0.000 | 0.006 | |
| secondaryKey.Mixture | 0.004 | 0.000 | 0.003 | |
| subsetCorr.JointUniquePairs | 0.020 | 0.000 | 0.021 | |
| subsetData.JointUniquePairs | 0.016 | 0.000 | 0.018 | |
| subsetGroups.JointUniquePairs | 0.620 | 0.000 | 0.622 | |
| summary.IdMapDiffCounts | 0.424 | 0.000 | 0.425 | |
| swapKeys.IdMap | 0.06 | 0.00 | 0.06 | |
| swapKeys.UniquePairs | 0.024 | 0.000 | 0.022 | |
| textBoundingBox.Display | 0.000 | 0.000 | 0.001 | |
| to.base.Misc | 0.000 | 0.000 | 0.002 | |
| to.binary.logical.Misc | 0.004 | 0.000 | 0.005 | |
| to.index.expr.Misc | 0.000 | 0.000 | 0.004 | |
| unique.UniquePairs | 0.064 | 0.000 | 0.061 | |
| words.Misc | 0.004 | 0.000 | 0.004 | |
| zoom.pars.Display | 0.004 | 0.000 | 0.003 | |