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CHECK report for TimeSeriesExperiment on malbec2

This page was generated on 2019-10-16 12:16:49 -0400 (Wed, 16 Oct 2019).

Package 1648/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TimeSeriesExperiment 1.2.0
Lan Huong Nguyen
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/TimeSeriesExperiment
Branch: RELEASE_3_9
Last Commit: df56189
Last Changed Date: 2019-05-02 11:54:13 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TimeSeriesExperiment
Version: 1.2.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:TimeSeriesExperiment.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings TimeSeriesExperiment_1.2.0.tar.gz
StartedAt: 2019-10-16 05:26:46 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:30:46 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 239.9 seconds
RetCode: 0
Status:  OK 
CheckDir: TimeSeriesExperiment.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:TimeSeriesExperiment.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings TimeSeriesExperiment_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/TimeSeriesExperiment.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.0’
* 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 10.772  0.004  10.784
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/TimeSeriesExperiment.Rcheck/00check.log’
for details.



Installation output

TimeSeriesExperiment.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL TimeSeriesExperiment
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘TimeSeriesExperiment’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TimeSeriesExperiment)

Tests output


Example timings

TimeSeriesExperiment.Rcheck/TimeSeriesExperiment-Ex.timings

nameusersystemelapsed
TimeSeriesExperiment0.2080.0080.216
addLags0.2770.0080.285
clusterAssignment0.3180.0000.318
clusterData0.5480.0040.552
clusterTimeSeries0.4010.0000.401
colData0.0420.0000.043
collapseReplicates0.0850.0120.097
collapsed-data0.1650.0080.173
dataToTimeSeries0.0160.0000.016
differentialExpression10.772 0.00410.784
dimensionReduction0.0640.0000.064
filterFeatures0.0470.0000.046
groups0.0190.0000.019
makeTimeSeries0.1680.0000.169
makeTimeSeriesExperimentFromExpressionSet0.0020.0000.001
makeTimeSeriesExperimentFromSummarizedExperiment0.1830.0000.184
meltMatrix0.0090.0000.008
normalizeData0.0460.0000.047
pathwayEnrichment0.9720.0201.455
pipe0.0000.0000.001
plotEnrichment0.8580.0080.866
plotHeatmap0.0320.0040.036
plotSamplePCA0.4390.0160.455
plotTimeSeries2.5360.0242.561
plotTimeSeriesClusters2.2650.0202.286
plotTimeSeriesPCA2.9250.1283.055
replicates0.0180.0000.018
rowData0.0290.0000.029
row_and_colnames0.0050.0040.009
runPCA0.0350.0000.035
timeSeries0.3360.0640.399
timepointDE0.0700.0060.076
timepoints0.0200.0010.021
trajectoryDE0.120.000.12
varianceStabilization0.0030.0000.003