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CHECK report for TimeSeriesExperiment on merida1

This page was generated on 2019-04-16 12:14:03 -0400 (Tue, 16 Apr 2019).

Package 1563/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TimeSeriesExperiment 1.0.4
Lan Huong Nguyen
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/TimeSeriesExperiment
Branch: RELEASE_3_8
Last Commit: 63f9597
Last Changed Date: 2019-01-14 17:39:52 -0400 (Mon, 14 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: TimeSeriesExperiment
Version: 1.0.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TimeSeriesExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TimeSeriesExperiment_1.0.4.tar.gz
StartedAt: 2019-04-16 03:07:58 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:12:02 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 244.7 seconds
RetCode: 0
Status:  OK 
CheckDir: TimeSeriesExperiment.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TimeSeriesExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TimeSeriesExperiment_1.0.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/TimeSeriesExperiment.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TimeSeriesExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TimeSeriesExperiment’ version ‘1.0.4’
* package encoding: UTF-8
* 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 ‘TimeSeriesExperiment’ can be installed ... 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
Unexported object imported by a ':::' call: ‘S4Vectors:::selectSome’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
clusterTimeSeries: no visible binding for global variable ‘freq’
clusterTimeSeries: no visible binding for global variable ‘.’
Undefined global functions or variables:
  . freq
* checking Rd files ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
differentialExpression 15.273  0.349  15.756
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/TimeSeriesExperiment.Rcheck/00check.log’
for details.



Installation output

TimeSeriesExperiment.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TimeSeriesExperiment
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘TimeSeriesExperiment’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TimeSeriesExperiment)

Tests output


Example timings

TimeSeriesExperiment.Rcheck/TimeSeriesExperiment-Ex.timings

nameusersystemelapsed
TimeSeriesExperiment0.8770.0080.890
addLags0.4180.0140.435
clusterAssignment0.5060.0140.523
clusterData0.0990.0050.104
clusterTimeSeries0.5870.0110.603
colData0.0550.0020.059
collapseReplicates0.1390.0140.153
collapsed-data0.2870.0070.297
dataToTimeSeries0.0250.0010.026
differentialExpression15.273 0.34915.756
dimensionReduction0.0480.0020.050
filterFeatures0.0380.0010.040
groups0.0160.0010.017
makeTimeSeries0.1540.0100.165
makeTimeSeriesExperimentFromExpressionSet0.0020.0010.002
makeTimeSeriesExperimentFromSummarizedExperiment0.0830.0010.085
meltMatrix0.0070.0000.007
normalizeData0.0480.0030.050
pathwayEnrichment0.8840.0690.959
pipe0.0000.0000.001
plotEnrichment0.9830.0241.014
plotHeatmap0.0280.0020.031
plotSamplePCA0.4290.0090.449
plotTimeSeries1.9890.0172.031
plotTimeSeriesClusters2.4380.0132.469
plotTimeSeriesPCA3.1270.1893.346
replicates0.0210.0020.023
rowData0.0320.0020.034
row_and_colnames0.0140.0020.016
runPCA0.0810.0030.086
timeSeries0.7010.2080.913
timepointDE0.1310.0040.135
timepoints0.0210.0020.022
trajectoryDE0.1270.0030.131
varianceStabilization0.0050.0010.006