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BioC 3.1: CHECK report for IdMappingAnalysis on moscato2

This page was generated on 2015-10-09 09:29:39 -0700 (Fri, 09 Oct 2015).

Package 487/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IdMappingAnalysis 1.12.0
Alex Lisovich , Roger Day
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/IdMappingAnalysis
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: IdMappingAnalysis
Version: 1.12.0
Command: rm -rf IdMappingAnalysis.buildbin-libdir IdMappingAnalysis.Rcheck && mkdir IdMappingAnalysis.buildbin-libdir IdMappingAnalysis.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IdMappingAnalysis.buildbin-libdir IdMappingAnalysis_1.12.0.tar.gz >IdMappingAnalysis.Rcheck\00install.out 2>&1 && cp IdMappingAnalysis.Rcheck\00install.out IdMappingAnalysis-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=IdMappingAnalysis.buildbin-libdir --install="check:IdMappingAnalysis-install.out" --force-multiarch --no-vignettes --timings IdMappingAnalysis_1.12.0.tar.gz
StartedAt: 2015-10-09 03:00:18 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 03:02:28 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 130.2 seconds
RetCode: 0
Status:  OK  
CheckDir: IdMappingAnalysis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf IdMappingAnalysis.buildbin-libdir IdMappingAnalysis.Rcheck && mkdir IdMappingAnalysis.buildbin-libdir IdMappingAnalysis.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IdMappingAnalysis.buildbin-libdir IdMappingAnalysis_1.12.0.tar.gz >IdMappingAnalysis.Rcheck\00install.out 2>&1 && cp IdMappingAnalysis.Rcheck\00install.out IdMappingAnalysis-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=IdMappingAnalysis.buildbin-libdir --install="check:IdMappingAnalysis-install.out" --force-multiarch --no-vignettes --timings IdMappingAnalysis_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/IdMappingAnalysis.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IdMappingAnalysis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IdMappingAnalysis' 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'IdMappingAnalysis' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [27s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
getBootstrap.JointUniquePairs 6.60   0.01    6.61
Bootstrap                     6.21   0.01    6.22
** running examples for arch 'x64' ... [28s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
getBootstrap.JointUniquePairs 7.25   0.01    7.27
Bootstrap                     6.60   0.00    6.59
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/IdMappingAnalysis.Rcheck/00check.log'
for details.


IdMappingAnalysis.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'IdMappingAnalysis' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IdMappingAnalysis' as IdMappingAnalysis_1.12.0.zip
* DONE (IdMappingAnalysis)

IdMappingAnalysis.Rcheck/examples_i386/IdMappingAnalysis-Ex.timings:

nameusersystemelapsed
000-LB-.IdMapBase0.180.000.19
Bootstrap6.210.016.22
Corr0.480.000.48
CorrData0.040.000.03
CsvList.merge.Misc000
IdMap000
IdMapBase000
IdMapCounts0.340.020.36
IdMapDiff0.390.000.39
IdMapDiffCounts0.270.000.26
JointIdMap0.080.000.08
JointUniquePairs0.470.000.47
Mixture0.450.000.59
UniquePairs000
aligned.IdMapBase0.010.000.02
as.IdMap.UniquePairs0.040.000.03
as.MultiSet.CorrData0.710.010.73
as.UniquePairs.IdMap000
as.data.frame.IdMapBase0.050.000.05
as.data.frame.JointIdMap0.060.000.06
as.list.IdMap0.010.000.01
boxplot.JointUniquePairs0.070.020.08
byColNames.Subset000
byColumn.Subset000
byRow.Subset000
byRowNames.Subset000
clust.Mixture000
copy.Display000
corr.boxplot.JointUniquePairs0.100.000.09
corr.plot.JointUniquePairs0.040.000.24
create.Display000
create.UniquePairs0.060.000.06
diffCounts.plot.JointIdMap0.360.020.38
dim.IdMapBase000
dimnames.IdMapBase000
do.glm.JointUniquePairs0.020.000.01
ecdf.plot.JointIdMap0.170.000.18
equals.UniquePairs0.010.000.01
fisherTransform.DataFilter000
fisherTransformInverse.DataFilter000
fisherTransformJacobean.DataFilter000
getBootstrap.JointUniquePairs6.600.016.61
getCompoundEvents.IdMapDiffCounts0.310.000.31
getCompoundGroups.IdMapDiffCounts0.300.000.29
getCorr.JointUniquePairs0.050.000.05
getCorrData.JointUniquePairs0.060.000.06
getCorrDataFrame.JointUniquePairs0.030.000.04
getCounts.IdMap0.020.000.01
getCounts.JointIdMap0.180.000.19
getData.Corr000
getData.Mixture000
getDiff.JointIdMap0.180.000.17
getExperimentSet.CorrData0.060.000.06
getIdMapList.JointIdMap0.060.020.08
getMapNames.JointIdMap0.060.000.06
getMapNames.JointUniquePairs000
getMatch.UniquePairs0.030.000.03
getMatchInfo.JointIdMap0.070.000.07
getMatchInfo.JointUniquePairs0.310.000.31
getMixture.JointUniquePairs0.280.000.28
getSampleNames.CorrData000
getStats.IdMapCounts0.160.000.15
getStats.Mixture000
getUnionIdMap.JointIdMap0.320.000.33
getUniquePairs.Corr0.020.000.02
getUniquePairs.CorrData000
getUniquePairs.JointUniquePairs000
interactive.corr.boxplot.JointUniquePairs0.220.000.48
interactive.corr.plot.JointUniquePairs0.060.060.13
interactive.mixture.boxplot.JointUniquePairs0.450.010.46
interactive.mixture.plot.JointUniquePairs0.390.040.43
interactive.plot.CorrData0.050.000.04
interactive.plot.JointUniquePairs000
interleave.Misc000
line.loess.Display000
line.unsorted.Display000
logTen.DataFilter0.280.000.28
merge.IdMap0.560.000.57
minAvgCountConstraint.DataFilter0.140.000.14
minCountConstraint.DataFilter0.140.000.14
minCountGroupConstraint.DataFilter0.170.000.17
mixture.boxplot.JointUniquePairs0.320.000.31
mixture.plot.JointUniquePairs0.280.000.28
plot.Bootstrap0.090.000.09
plot.Corr0.080.000.08
plot.CorrData0.010.000.02
plot.IdMapCounts0.230.000.24
plot.IdMapDiffCounts0.600.000.62
plot.Mixture0.040.000.05
primaryIDs.IdMapBase000
primaryKey.CorrData000
primaryKey.IdMapBase000
primaryKey.Mixture000
progressMsg.Display000
removeNASeries.DataFilter0.270.000.26
secondaryKey.CorrData000
secondaryKey.IdMapBase000
secondaryKey.Mixture000
subsetCorr.JointUniquePairs0.010.000.02
subsetData.JointUniquePairs0.020.000.02
subsetGroups.JointUniquePairs0.470.000.46
summary.IdMapDiffCounts0.250.000.25
swapKeys.IdMap0.040.000.05
swapKeys.UniquePairs0.020.000.02
textBoundingBox.Display000
to.base.Misc000
to.binary.logical.Misc0.020.000.01
to.index.expr.Misc000
unique.UniquePairs0.030.000.03
words.Misc0.010.000.02
zoom.pars.Display000

IdMappingAnalysis.Rcheck/examples_x64/IdMappingAnalysis-Ex.timings:

nameusersystemelapsed
000-LB-.IdMapBase0.190.030.22
Bootstrap6.600.006.59
Corr0.50.00.5
CorrData0.050.000.05
CsvList.merge.Misc0.010.000.02
IdMap000
IdMapBase000
IdMapCounts0.330.000.32
IdMapDiff0.420.000.42
IdMapDiffCounts0.310.000.32
JointIdMap0.060.000.06
JointUniquePairs0.520.000.51
Mixture0.420.000.63
UniquePairs000
aligned.IdMapBase0.010.000.02
as.IdMap.UniquePairs0.030.000.03
as.MultiSet.CorrData0.610.000.61
as.UniquePairs.IdMap0.010.000.02
as.data.frame.IdMapBase0.060.000.06
as.data.frame.JointIdMap0.070.000.06
as.list.IdMap0.010.000.02
boxplot.JointUniquePairs0.070.000.06
byColNames.Subset0.010.000.02
byColumn.Subset000
byRow.Subset000
byRowNames.Subset0.020.000.01
clust.Mixture000
copy.Display000
corr.boxplot.JointUniquePairs0.090.000.10
corr.plot.JointUniquePairs0.060.000.06
create.Display000
create.UniquePairs0.160.000.16
diffCounts.plot.JointIdMap0.40.00.4
dim.IdMapBase000
dimnames.IdMapBase000
do.glm.JointUniquePairs0.020.000.02
ecdf.plot.JointIdMap0.190.020.20
equals.UniquePairs0.030.000.03
fisherTransform.DataFilter000
fisherTransformInverse.DataFilter000
fisherTransformJacobean.DataFilter000
getBootstrap.JointUniquePairs7.250.017.27
getCompoundEvents.IdMapDiffCounts0.420.000.42
getCompoundGroups.IdMapDiffCounts0.320.000.31
getCorr.JointUniquePairs0.040.020.07
getCorrData.JointUniquePairs0.060.000.06
getCorrDataFrame.JointUniquePairs0.020.000.01
getCounts.IdMap0.020.000.02
getCounts.JointIdMap0.150.000.16
getData.Corr000
getData.Mixture000
getDiff.JointIdMap0.220.000.21
getExperimentSet.CorrData0.160.000.16
getIdMapList.JointIdMap0.060.000.06
getMapNames.JointIdMap0.060.000.06
getMapNames.JointUniquePairs000
getMatch.UniquePairs0.030.000.03
getMatchInfo.JointIdMap0.080.000.08
getMatchInfo.JointUniquePairs0.370.000.37
getMixture.JointUniquePairs0.270.000.27
getSampleNames.CorrData000
getStats.IdMapCounts0.150.000.16
getStats.Mixture0.020.000.01
getUnionIdMap.JointIdMap0.370.000.38
getUniquePairs.Corr0.020.000.01
getUniquePairs.CorrData000
getUniquePairs.JointUniquePairs000
interactive.corr.boxplot.JointUniquePairs0.150.000.22
interactive.corr.plot.JointUniquePairs0.070.030.09
interactive.mixture.boxplot.JointUniquePairs0.320.010.35
interactive.mixture.plot.JointUniquePairs0.280.020.29
interactive.plot.CorrData0.050.000.05
interactive.plot.JointUniquePairs000
interleave.Misc000
line.loess.Display000
line.unsorted.Display000
logTen.DataFilter0.130.000.12
merge.IdMap0.570.010.60
minAvgCountConstraint.DataFilter0.110.000.11
minCountConstraint.DataFilter0.140.000.14
minCountGroupConstraint.DataFilter0.170.000.17
mixture.boxplot.JointUniquePairs0.320.000.31
mixture.plot.JointUniquePairs0.350.000.36
plot.Bootstrap0.100.000.09
plot.Corr0.060.000.06
plot.CorrData0.030.000.04
plot.IdMapCounts0.160.000.15
plot.IdMapDiffCounts0.530.000.53
plot.Mixture0.030.000.03
primaryIDs.IdMapBase000
primaryKey.CorrData000
primaryKey.IdMapBase000
primaryKey.Mixture000
progressMsg.Display0.010.000.02
removeNASeries.DataFilter0.190.000.19
secondaryKey.CorrData000
secondaryKey.IdMapBase000
secondaryKey.Mixture000
subsetCorr.JointUniquePairs0.010.000.02
subsetData.JointUniquePairs0.020.000.01
subsetGroups.JointUniquePairs0.530.000.53
summary.IdMapDiffCounts0.310.000.31
swapKeys.IdMap0.050.000.05
swapKeys.UniquePairs0.010.000.01
textBoundingBox.Display000
to.base.Misc000
to.binary.logical.Misc000
to.index.expr.Misc000
unique.UniquePairs0.050.000.05
words.Misc000
zoom.pars.Display000