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This page was generated on 2015-08-24 10:48:37 -0700 (Mon, 24 Aug 2015).
| Package 504/1071 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| IdMappingAnalysis 1.13.0 Alex Lisovich
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | 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 | |
| Package: IdMappingAnalysis |
| Version: 1.13.0 |
| Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.13.0.tar.gz |
| StartedAt: 2015-08-24 00:52:15 -0700 (Mon, 24 Aug 2015) |
| EndedAt: 2015-08-24 00:53:13 -0700 (Mon, 24 Aug 2015) |
| EllapsedTime: 57.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IdMappingAnalysis.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.13.0’
* 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 ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Bootstrap: no visible global function definition for ‘extend’
Corr: no visible global function definition for ‘extend’
Corr: no visible global function definition for ‘throw’
CorrData: no visible global function definition for ‘extend’
CorrData: no visible global function definition for ‘Object’
DataFilter: no visible global function definition for ‘extend’
DataFilter: no visible global function definition for ‘Object’
Display: no visible global function definition for ‘extend’
Display: no visible global function definition for ‘Object’
IdMap: no visible global function definition for ‘throw’
IdMap: no visible global function definition for ‘extend’
IdMapBase: no visible global function definition for ‘throw’
IdMapBase: no visible global function definition for ‘extend’
IdMapBase: no visible global function definition for ‘Object’
IdMapCounts: no visible global function definition for ‘throw’
IdMapCounts: no visible global function definition for ‘extend’
IdMapDiff: no visible global function definition for ‘throw’
IdMapDiff: no visible global function definition for ‘extend’
IdMapDiffCounts: no visible global function definition for ‘extend’
JointIdMap: no visible global function definition for ‘extend’
JointUniquePairs: no visible global function definition for ‘extend’
Misc: no visible global function definition for ‘extend’
Misc: no visible global function definition for ‘Object’
Mixture: no visible global function definition for ‘extend’
Mixture: no visible global function definition for ‘Object’
Subset: no visible global function definition for ‘extend’
Subset: no visible global function definition for ‘Object’
UniquePairs: no visible global function definition for ‘throw’
UniquePairs: no visible global function definition for ‘extend’
as.IdMap.UniquePairs: no visible global function definition for
‘getName’
as.data.frame.IdMapBase: no visible global function definition for
‘getName’
as.data.frame.IdMapBase: no visible global function definition for
‘throw’
as.list.IdMap: no visible global function definition for ‘throw’
diffCounts.plot.JointIdMap: no visible global function definition for
‘rselect.list’
ecdf.plot.JointIdMap: no visible global function definition for
‘rselect.list’
getCorr.JointUniquePairs: no visible global function definition for
‘equals’
getExperimentSet.CorrData: no visible global function definition for
‘throw’
getIdMapList.JointIdMap: no visible global function definition for
‘throw’
interactive.plot.CorrData: no visible global function definition for
‘rselect.list’
interactive.plot.JointUniquePairs: no visible global function
definition for ‘rselect.list’
merge.IdMap: no visible global function definition for ‘getName’
unique.UniquePairs: no visible global function definition for ‘getName’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/24s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getBootstrap.JointUniquePairs 5.972 0.016 5.999
Bootstrap 5.722 0.003 5.846
* 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
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.2-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 | 0.178 | 0.012 | 0.191 | |
| Bootstrap | 5.722 | 0.003 | 5.846 | |
| Corr | 0.396 | 0.001 | 0.396 | |
| CorrData | 0.028 | 0.007 | 0.035 | |
| CsvList.merge.Misc | 0.001 | 0.000 | 0.002 | |
| IdMap | 0.006 | 0.000 | 0.005 | |
| IdMapBase | 0.001 | 0.000 | 0.002 | |
| IdMapCounts | 0.301 | 0.003 | 0.304 | |
| IdMapDiff | 0.324 | 0.008 | 0.332 | |
| IdMapDiffCounts | 0.251 | 0.000 | 0.252 | |
| JointIdMap | 0.049 | 0.000 | 0.049 | |
| JointUniquePairs | 0.476 | 0.000 | 0.475 | |
| Mixture | 0.326 | 0.000 | 0.325 | |
| UniquePairs | 0.003 | 0.000 | 0.003 | |
| aligned.IdMapBase | 0.005 | 0.000 | 0.005 | |
| as.IdMap.UniquePairs | 0.037 | 0.000 | 0.037 | |
| as.MultiSet.CorrData | 0.499 | 0.004 | 0.509 | |
| as.UniquePairs.IdMap | 0.023 | 0.001 | 0.023 | |
| as.data.frame.IdMapBase | 0.051 | 0.000 | 0.051 | |
| as.data.frame.JointIdMap | 0.062 | 0.000 | 0.062 | |
| as.list.IdMap | 0.011 | 0.000 | 0.011 | |
| boxplot.JointUniquePairs | 0.066 | 0.000 | 0.066 | |
| byColNames.Subset | 0.001 | 0.000 | 0.004 | |
| byColumn.Subset | 0.004 | 0.001 | 0.004 | |
| byRow.Subset | 0.004 | 0.000 | 0.004 | |
| byRowNames.Subset | 0.005 | 0.000 | 0.005 | |
| clust.Mixture | 0.001 | 0.000 | 0.002 | |
| copy.Display | 0.001 | 0.000 | 0.000 | |
| corr.boxplot.JointUniquePairs | 0.076 | 0.000 | 0.076 | |
| corr.plot.JointUniquePairs | 0.047 | 0.000 | 0.048 | |
| create.Display | 0.001 | 0.000 | 0.000 | |
| create.UniquePairs | 0.104 | 0.000 | 0.104 | |
| diffCounts.plot.JointIdMap | 0.354 | 0.000 | 0.354 | |
| dim.IdMapBase | 0.000 | 0.000 | 0.001 | |
| dimnames.IdMapBase | 0.001 | 0.000 | 0.002 | |
| do.glm.JointUniquePairs | 0.012 | 0.000 | 0.012 | |
| ecdf.plot.JointIdMap | 0.175 | 0.000 | 0.175 | |
| equals.UniquePairs | 0.035 | 0.000 | 0.035 | |
| fisherTransform.DataFilter | 0.001 | 0.000 | 0.000 | |
| fisherTransformInverse.DataFilter | 0.000 | 0.000 | 0.001 | |
| fisherTransformJacobean.DataFilter | 0.001 | 0.000 | 0.000 | |
| getBootstrap.JointUniquePairs | 5.972 | 0.016 | 5.999 | |
| getCompoundEvents.IdMapDiffCounts | 0.272 | 0.000 | 0.273 | |
| getCompoundGroups.IdMapDiffCounts | 0.277 | 0.000 | 0.277 | |
| getCorr.JointUniquePairs | 0.049 | 0.000 | 0.049 | |
| getCorrData.JointUniquePairs | 0.047 | 0.000 | 0.047 | |
| getCorrDataFrame.JointUniquePairs | 0.019 | 0.000 | 0.019 | |
| getCounts.IdMap | 0.02 | 0.00 | 0.02 | |
| getCounts.JointIdMap | 0.157 | 0.000 | 0.157 | |
| getData.Corr | 0.001 | 0.000 | 0.001 | |
| getData.Mixture | 0.002 | 0.000 | 0.002 | |
| getDiff.JointIdMap | 0.234 | 0.000 | 0.248 | |
| getExperimentSet.CorrData | 0.072 | 0.000 | 0.072 | |
| getIdMapList.JointIdMap | 0.052 | 0.000 | 0.053 | |
| getMapNames.JointIdMap | 0.048 | 0.000 | 0.047 | |
| getMapNames.JointUniquePairs | 0.002 | 0.000 | 0.002 | |
| getMatch.UniquePairs | 0.036 | 0.000 | 0.036 | |
| getMatchInfo.JointIdMap | 0.055 | 0.000 | 0.055 | |
| getMatchInfo.JointUniquePairs | 0.312 | 0.000 | 0.311 | |
| getMixture.JointUniquePairs | 0.235 | 0.000 | 0.244 | |
| getSampleNames.CorrData | 0.002 | 0.000 | 0.002 | |
| getStats.IdMapCounts | 0.166 | 0.000 | 0.166 | |
| getStats.Mixture | 0.003 | 0.000 | 0.002 | |
| getUnionIdMap.JointIdMap | 0.371 | 0.000 | 0.372 | |
| getUniquePairs.Corr | 0.003 | 0.000 | 0.003 | |
| getUniquePairs.CorrData | 0.004 | 0.000 | 0.004 | |
| getUniquePairs.JointUniquePairs | 0.004 | 0.000 | 0.004 | |
| interactive.corr.boxplot.JointUniquePairs | 0.054 | 0.007 | 0.063 | |
| interactive.corr.plot.JointUniquePairs | 0.031 | 0.008 | 0.042 | |
| interactive.mixture.boxplot.JointUniquePairs | 0.252 | 0.000 | 0.263 | |
| interactive.mixture.plot.JointUniquePairs | 0.238 | 0.000 | 0.238 | |
| interactive.plot.CorrData | 0.033 | 0.000 | 0.032 | |
| interactive.plot.JointUniquePairs | 0.000 | 0.000 | 0.001 | |
| interleave.Misc | 0.001 | 0.000 | 0.000 | |
| line.loess.Display | 0.000 | 0.000 | 0.001 | |
| line.unsorted.Display | 0.001 | 0.000 | 0.001 | |
| logTen.DataFilter | 0.11 | 0.00 | 0.11 | |
| merge.IdMap | 0.604 | 0.000 | 0.603 | |
| minAvgCountConstraint.DataFilter | 0.104 | 0.000 | 0.104 | |
| minCountConstraint.DataFilter | 0.114 | 0.000 | 0.114 | |
| minCountGroupConstraint.DataFilter | 0.151 | 0.000 | 0.155 | |
| mixture.boxplot.JointUniquePairs | 0.259 | 0.000 | 0.259 | |
| mixture.plot.JointUniquePairs | 0.205 | 0.000 | 0.208 | |
| plot.Bootstrap | 0.074 | 0.000 | 0.074 | |
| plot.Corr | 0.051 | 0.000 | 0.051 | |
| plot.CorrData | 0.022 | 0.000 | 0.022 | |
| plot.IdMapCounts | 0.159 | 0.000 | 0.159 | |
| plot.IdMapDiffCounts | 0.478 | 0.000 | 0.482 | |
| plot.Mixture | 0.027 | 0.000 | 0.027 | |
| primaryIDs.IdMapBase | 0.003 | 0.000 | 0.003 | |
| primaryKey.CorrData | 0.001 | 0.000 | 0.001 | |
| primaryKey.IdMapBase | 0.003 | 0.000 | 0.003 | |
| primaryKey.Mixture | 0.001 | 0.000 | 0.002 | |
| progressMsg.Display | 0 | 0 | 0 | |
| removeNASeries.DataFilter | 0.136 | 0.000 | 0.136 | |
| secondaryKey.CorrData | 0.001 | 0.000 | 0.002 | |
| secondaryKey.IdMapBase | 0.003 | 0.000 | 0.002 | |
| secondaryKey.Mixture | 0.000 | 0.000 | 0.001 | |
| subsetCorr.JointUniquePairs | 0.019 | 0.000 | 0.018 | |
| subsetData.JointUniquePairs | 0.009 | 0.000 | 0.009 | |
| subsetGroups.JointUniquePairs | 0.536 | 0.000 | 0.537 | |
| summary.IdMapDiffCounts | 0.300 | 0.000 | 0.301 | |
| swapKeys.IdMap | 0.055 | 0.000 | 0.055 | |
| swapKeys.UniquePairs | 0.02 | 0.00 | 0.02 | |
| textBoundingBox.Display | 0.000 | 0.000 | 0.001 | |
| to.base.Misc | 0.001 | 0.000 | 0.001 | |
| to.binary.logical.Misc | 0.002 | 0.000 | 0.002 | |
| to.index.expr.Misc | 0 | 0 | 0 | |
| unique.UniquePairs | 0.055 | 0.000 | 0.055 | |
| words.Misc | 0.002 | 0.000 | 0.002 | |
| zoom.pars.Display | 0 | 0 | 0 | |