Alex Lisovich
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/IdMappingAnalysis |
| Branch: RELEASE_3_8 |
| Last Commit: 3e4929f |
| Last Changed Date: 2018-10-30 11:41:48 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:49:32 -0400 (Tue, 16 Apr 2019).
| Package 759/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| IdMappingAnalysis 1.26.0 Alex Lisovich
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: IdMappingAnalysis |
| Version: 1.26.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:IdMappingAnalysis.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings IdMappingAnalysis_1.26.0.tar.gz |
| StartedAt: 2019-04-16 00:44:38 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 00:45:48 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 70.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IdMappingAnalysis.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:IdMappingAnalysis.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings IdMappingAnalysis_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.26.0’
* 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 ... 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 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
.onAttach: no visible global function definition for
‘packageDescription’
Bootstrap: no visible global function definition for ‘extend’
Bootstrap : FUN: no visible global function definition for ‘cor’
Corr: no visible global function definition for ‘extend’
Corr: no visible global function definition for ‘throw’
Corr: no visible global function definition for ‘cor’
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’
Mixture: no visible global function definition for ‘density’
Mixture : <anonymous>: no visible global function definition for
‘dnorm’
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.MultiSet.CorrData: no visible global function definition for ‘new’
as.data.frame.IdMapBase: no visible global function definition for
‘getName’
as.data.frame.IdMapBase: no visible global function definition for
‘throw’
as.data.frame.IdMapBase: no visible global function definition for ‘as’
as.list.IdMap: no visible global function definition for ‘throw’
boxplot.JointUniquePairs: no visible global function definition for
‘par’
boxplot.JointUniquePairs: no visible global function definition for
‘axis’
boxplot.JointUniquePairs: no visible global function definition for
‘text’
boxplotdataJitter.JointUniquePairs: no visible global function
definition for ‘par’
copy.Display: no visible global function definition for ‘dev.cur’
copy.Display: no visible global function definition for ‘par’
copy.Display: no visible global function definition for ‘png’
copy.Display: no visible global function definition for ‘jpeg’
copy.Display: no visible global function definition for ‘tiff’
copy.Display: no visible global function definition for ‘bmp’
copy.Display: no visible global function definition for ‘pdf’
copy.Display: no visible global function definition for ‘dev.set’
copy.Display: no visible global function definition for ‘dev.copy’
copy.Display: no visible global function definition for ‘dev.next’
copy.Display: no visible global function definition for ‘dev.off’
corr.boxplot.JointUniquePairs: no visible global function definition
for ‘boxplot’
corr.boxplot.JointUniquePairs: no visible global function definition
for ‘abline’
create.Display: no visible global function definition for ‘dev.new’
create.Display: no visible global function definition for ‘par’
diffCounts.plot.JointIdMap: no visible global function definition for
‘rselect.list’
diffCounts.plot.JointIdMap: no visible global function definition for
‘par’
diffCounts.plot.JointIdMap: no visible global function definition for
‘plot’
ecdf.plot.JointIdMap: no visible global function definition for
‘rselect.list’
ecdf.plot.JointIdMap: no visible global function definition for ‘par’
ecdf.plot.JointIdMap: no visible global function definition for ‘plot’
fit2clusters: no visible global function definition for ‘rbinom’
fit2clusters: no visible global function definition for ‘rgamma’
fit2clusters: no visible global function definition for ‘rnorm’
fit2clusters: no visible global function definition for ‘dnorm’
fit2clusters: no visible global function definition for ‘plot’
fit2clusters: no visible global function definition for ‘lines’
fit2clusters: no visible global function definition for ‘density’
fit2clusters: no visible global function definition for ‘legend’
fit2clusters: no visible global function definition for ‘par’
getCorr.JointUniquePairs: no visible global function definition for
‘equals’
getExperimentSet.CorrData: no visible global function definition for
‘throw’
getExperimentSet.CorrData: no visible global function definition for
‘new’
getIdMapList.JointIdMap: no visible global function definition for
‘throw’
interactive.plot.CorrData: no visible global function definition for
‘rselect.list’
interactive.plot.CorrData: no visible global function definition for
‘plot’
interactive.plot.JointUniquePairs: no visible global function
definition for ‘rselect.list’
interactive.plot.JointUniquePairs: no visible global function
definition for ‘par’
line.loess.Display: no visible global function definition for ‘loess’
line.loess.Display: no visible global function definition for ‘lines’
line.unsorted.Display: no visible global function definition for
‘lines’
merge.IdMap: no visible global function definition for ‘getName’
mixture.boxplot.JointUniquePairs: no visible global function definition
for ‘boxplot’
mixture.boxplot.JointUniquePairs: no visible global function definition
for ‘abline’
mixture.plot.JointUniquePairs: no visible global function definition
for ‘plot’
plot.Bootstrap : BootstrapCorr.plot.internal: no visible global
function definition for ‘par’
plot.Bootstrap : BootstrapCorr.plot.internal: no visible global
function definition for ‘legend’
plot.Corr: no visible global function definition for ‘density’
plot.Corr: no visible global function definition for ‘plot.new’
plot.Corr: no visible global function definition for ‘plot.window’
plot.Corr: no visible global function definition for ‘axis’
plot.Corr: no visible global function definition for ‘par’
plot.Corr: no visible global function definition for ‘box’
plot.Corr: no visible global function definition for ‘lines’
plot.Corr: no visible global function definition for ‘legend’
plot.Corr: no visible global function definition for ‘abline’
plot.CorrData: no visible global function definition for ‘cor’
plot.CorrData: no visible global function definition for ‘par’
plot.CorrData: no visible global function definition for ‘plot’
plot.CorrData: no visible global function definition for ‘box’
plot.CorrData: no visible global function definition for ‘axis’
plot.CorrData: no visible global function definition for ‘points’
plot.CorrData: no visible global function definition for ‘title’
plot.IdMapCounts: no visible global function definition for ‘plot.new’
plot.IdMapCounts: no visible global function definition for
‘plot.window’
plot.IdMapCounts: no visible global function definition for ‘title’
plot.IdMapCounts: no visible global function definition for ‘axis’
plot.IdMapCounts: no visible global function definition for ‘par’
plot.IdMapCounts: no visible global function definition for ‘box’
plot.IdMapCounts: no visible global function definition for ‘ecdf’
plot.IdMapCounts: no visible global function definition for ‘lines’
plot.IdMapCounts: no visible global function definition for ‘legend’
plot.IdMapDiffCounts : plotValGroup: no visible global function
definition for ‘rect’
plot.IdMapDiffCounts: no visible global function definition for
‘plot.new’
plot.IdMapDiffCounts: no visible global function definition for ‘par’
plot.IdMapDiffCounts: no visible global function definition for
‘plot.window’
plot.IdMapDiffCounts: no visible global function definition for ‘title’
plot.IdMapDiffCounts: no visible global function definition for ‘axis’
plot.IdMapDiffCounts: no visible global function definition for ‘mtext’
plot.IdMapDiffCounts: no visible global function definition for ‘lines’
plot.IdMapDiffCounts: no visible global function definition for ‘text’
plot.IdMapDiffCounts: no visible global function definition for
‘abline’
plot.Mixture: no visible global function definition for ‘plot.new’
plot.Mixture: no visible global function definition for ‘plot.window’
plot.Mixture: no visible global function definition for ‘axis’
plot.Mixture: no visible global function definition for ‘par’
plot.Mixture: no visible global function definition for ‘box’
plot.Mixture: no visible global function definition for ‘lines’
plot.Mixture: no visible global function definition for ‘density’
plot.Mixture: no visible global function definition for ‘rug’
plot.Mixture: no visible global function definition for ‘dnorm’
plot.Mixture : <anonymous>: no visible global function definition for
‘dnorm’
plot.Mixture: no visible global function definition for ‘legend’
plot.Mixture: no visible global function definition for ‘abline’
progressMsg.Display: no visible global function definition for
‘flush.console’
textBoundingBox.Display: no visible global function definition for
‘strwidth’
textBoundingBox.Display: no visible global function definition for
‘strheight’
textBoundingBox.Display: no visible global function definition for
‘par’
to.index.expr.Misc: no visible global function definition for ‘tail’
unique.UniquePairs: no visible global function definition for ‘getName’
zoom.pars.Display: no visible global function definition for ‘par’
Undefined global functions or variables:
Object abline as axis bmp box boxplot cor density dev.copy dev.cur
dev.new dev.next dev.off dev.set dnorm ecdf equals extend
flush.console getName jpeg legend lines loess mtext new
packageDescription par pdf plot plot.new plot.window png points
rbinom rect rgamma rnorm rselect.list rug strheight strwidth tail
text throw tiff title
Consider adding
importFrom("grDevices", "bmp", "dev.copy", "dev.cur", "dev.new",
"dev.next", "dev.off", "dev.set", "jpeg", "pdf", "png",
"tiff")
importFrom("graphics", "abline", "axis", "box", "boxplot", "legend",
"lines", "mtext", "par", "plot", "plot.new", "plot.window",
"points", "rect", "rug", "strheight", "strwidth", "text",
"title")
importFrom("methods", "as", "new")
importFrom("stats", "cor", "density", "dnorm", "ecdf", "loess",
"rbinom", "rgamma", "rnorm")
importFrom("utils", "flush.console", "packageDescription", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getBootstrap.JointUniquePairs 7.888 0.004 8.106
Bootstrap 7.664 0.024 7.761
* 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-3.8-bioc/meat/IdMappingAnalysis.Rcheck/00check.log’
for details.
IdMappingAnalysis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL IdMappingAnalysis ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘IdMappingAnalysis’ ... ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare 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 | 0.104 | 0.012 | 0.117 | |
| Bootstrap | 7.664 | 0.024 | 7.761 | |
| Corr | 0.480 | 0.008 | 0.496 | |
| CorrData | 0.04 | 0.00 | 0.04 | |
| CsvList.merge.Misc | 0.004 | 0.000 | 0.002 | |
| IdMap | 0.004 | 0.000 | 0.006 | |
| IdMapBase | 0.000 | 0.000 | 0.001 | |
| IdMapCounts | 0.352 | 0.008 | 0.360 | |
| IdMapDiff | 0.488 | 0.012 | 0.509 | |
| IdMapDiffCounts | 0.332 | 0.000 | 0.331 | |
| JointIdMap | 0.064 | 0.000 | 0.063 | |
| JointUniquePairs | 0.624 | 0.000 | 0.628 | |
| Mixture | 0.364 | 0.000 | 0.400 | |
| UniquePairs | 0.000 | 0.004 | 0.002 | |
| aligned.IdMapBase | 0.004 | 0.000 | 0.004 | |
| as.IdMap.UniquePairs | 0.044 | 0.000 | 0.043 | |
| as.MultiSet.CorrData | 0.608 | 0.000 | 0.616 | |
| as.UniquePairs.IdMap | 0.028 | 0.000 | 0.026 | |
| as.data.frame.IdMapBase | 0.116 | 0.000 | 0.117 | |
| as.data.frame.JointIdMap | 0.056 | 0.000 | 0.058 | |
| as.list.IdMap | 0.008 | 0.000 | 0.008 | |
| boxplot.JointUniquePairs | 0.060 | 0.000 | 0.062 | |
| byColNames.Subset | 0.016 | 0.000 | 0.015 | |
| byColumn.Subset | 0.004 | 0.000 | 0.003 | |
| byRow.Subset | 0.004 | 0.000 | 0.003 | |
| byRowNames.Subset | 0.004 | 0.000 | 0.006 | |
| clust.Mixture | 0.000 | 0.000 | 0.001 | |
| copy.Display | 0 | 0 | 0 | |
| corr.boxplot.JointUniquePairs | 0.092 | 0.000 | 0.089 | |
| corr.plot.JointUniquePairs | 0.048 | 0.000 | 0.048 | |
| create.Display | 0 | 0 | 0 | |
| create.UniquePairs | 0.152 | 0.000 | 0.153 | |
| diffCounts.plot.JointIdMap | 0.544 | 0.004 | 0.555 | |
| dim.IdMapBase | 0.000 | 0.000 | 0.001 | |
| dimnames.IdMapBase | 0.004 | 0.000 | 0.002 | |
| do.glm.JointUniquePairs | 0.016 | 0.000 | 0.016 | |
| ecdf.plot.JointIdMap | 0.212 | 0.000 | 0.233 | |
| equals.UniquePairs | 0.044 | 0.000 | 0.044 | |
| fisherTransform.DataFilter | 0 | 0 | 0 | |
| fisherTransformInverse.DataFilter | 0 | 0 | 0 | |
| fisherTransformJacobean.DataFilter | 0 | 0 | 0 | |
| getBootstrap.JointUniquePairs | 7.888 | 0.004 | 8.106 | |
| getCompoundEvents.IdMapDiffCounts | 0.360 | 0.012 | 0.373 | |
| getCompoundGroups.IdMapDiffCounts | 0.344 | 0.004 | 0.349 | |
| getCorr.JointUniquePairs | 0.044 | 0.000 | 0.048 | |
| getCorrData.JointUniquePairs | 0.04 | 0.00 | 0.04 | |
| getCorrDataFrame.JointUniquePairs | 0.016 | 0.000 | 0.018 | |
| getCounts.IdMap | 0.024 | 0.000 | 0.022 | |
| getCounts.JointIdMap | 0.144 | 0.016 | 0.158 | |
| getData.Corr | 0 | 0 | 0 | |
| getData.Mixture | 0.000 | 0.000 | 0.001 | |
| getDiff.JointIdMap | 0.220 | 0.000 | 0.222 | |
| getExperimentSet.CorrData | 0.1 | 0.0 | 0.1 | |
| getIdMapList.JointIdMap | 0.072 | 0.000 | 0.074 | |
| getMapNames.JointIdMap | 0.080 | 0.000 | 0.079 | |
| getMapNames.JointUniquePairs | 0.004 | 0.000 | 0.001 | |
| getMatch.UniquePairs | 0.056 | 0.000 | 0.058 | |
| getMatchInfo.JointIdMap | 0.072 | 0.000 | 0.070 | |
| getMatchInfo.JointUniquePairs | 0.372 | 0.000 | 0.371 | |
| getMixture.JointUniquePairs | 0.248 | 0.000 | 0.247 | |
| getSampleNames.CorrData | 0.000 | 0.000 | 0.002 | |
| getStats.IdMapCounts | 0.176 | 0.000 | 0.180 | |
| getStats.Mixture | 0.000 | 0.000 | 0.003 | |
| getUnionIdMap.JointIdMap | 0.504 | 0.000 | 0.507 | |
| getUniquePairs.Corr | 0.004 | 0.000 | 0.004 | |
| getUniquePairs.CorrData | 0.004 | 0.000 | 0.003 | |
| getUniquePairs.JointUniquePairs | 0.000 | 0.000 | 0.004 | |
| interactive.corr.boxplot.JointUniquePairs | 0.072 | 0.000 | 0.074 | |
| interactive.corr.plot.JointUniquePairs | 0.044 | 0.004 | 0.048 | |
| interactive.mixture.boxplot.JointUniquePairs | 0.284 | 0.000 | 0.286 | |
| interactive.mixture.plot.JointUniquePairs | 0.252 | 0.004 | 0.258 | |
| interactive.plot.CorrData | 0.036 | 0.004 | 0.040 | |
| interactive.plot.JointUniquePairs | 0 | 0 | 0 | |
| interleave.Misc | 0 | 0 | 0 | |
| line.loess.Display | 0.000 | 0.000 | 0.001 | |
| line.unsorted.Display | 0 | 0 | 0 | |
| logTen.DataFilter | 0.104 | 0.004 | 0.105 | |
| merge.IdMap | 0.752 | 0.000 | 0.752 | |
| minAvgCountConstraint.DataFilter | 0.108 | 0.000 | 0.107 | |
| minCountConstraint.DataFilter | 0.108 | 0.004 | 0.114 | |
| minCountGroupConstraint.DataFilter | 0.140 | 0.000 | 0.141 | |
| mixture.boxplot.JointUniquePairs | 0.284 | 0.000 | 0.284 | |
| mixture.plot.JointUniquePairs | 0.236 | 0.000 | 0.236 | |
| plot.Bootstrap | 0.096 | 0.000 | 0.095 | |
| plot.Corr | 0.072 | 0.000 | 0.071 | |
| plot.CorrData | 0.028 | 0.000 | 0.028 | |
| plot.IdMapCounts | 0.180 | 0.000 | 0.182 | |
| plot.IdMapDiffCounts | 0.580 | 0.004 | 0.582 | |
| plot.Mixture | 0.028 | 0.000 | 0.029 | |
| primaryIDs.IdMapBase | 0.004 | 0.000 | 0.002 | |
| primaryKey.CorrData | 0 | 0 | 0 | |
| primaryKey.IdMapBase | 0.004 | 0.000 | 0.002 | |
| primaryKey.Mixture | 0.000 | 0.000 | 0.001 | |
| progressMsg.Display | 0.000 | 0.000 | 0.001 | |
| removeNASeries.DataFilter | 0.136 | 0.000 | 0.136 | |
| secondaryKey.CorrData | 0.000 | 0.000 | 0.001 | |
| secondaryKey.IdMapBase | 0.004 | 0.000 | 0.001 | |
| secondaryKey.Mixture | 0 | 0 | 0 | |
| subsetCorr.JointUniquePairs | 0.012 | 0.000 | 0.014 | |
| subsetData.JointUniquePairs | 0.008 | 0.000 | 0.009 | |
| subsetGroups.JointUniquePairs | 0.716 | 0.000 | 0.715 | |
| summary.IdMapDiffCounts | 0.360 | 0.000 | 0.362 | |
| swapKeys.IdMap | 0.060 | 0.004 | 0.065 | |
| swapKeys.UniquePairs | 0.024 | 0.000 | 0.026 | |
| textBoundingBox.Display | 0 | 0 | 0 | |
| to.base.Misc | 0.000 | 0.000 | 0.001 | |
| to.binary.logical.Misc | 0.000 | 0.004 | 0.002 | |
| to.index.expr.Misc | 0 | 0 | 0 | |
| unique.UniquePairs | 0.072 | 0.000 | 0.073 | |
| words.Misc | 0.000 | 0.000 | 0.001 | |
| zoom.pars.Display | 0 | 0 | 0 | |