Multiple platform build/check report for BioC 3.9 - CHECK report for TimeSeriesExperiment on merida2

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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_1.1.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TimeSeriesExperiment.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.1.4’
* 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 14.816  0.419  15.376
* 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-3.9-bioc/meat/TimeSeriesExperiment.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TimeSeriesExperiment
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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

name	user	system	elapsed
TimeSeriesExperiment	0.275	0.002	0.281
addLags	0.444	0.039	0.485
clusterAssignment	0.419	0.011	0.433
clusterData	0.089	0.004	0.093
clusterTimeSeries	0.598	0.011	0.616
colData	0.057	0.004	0.061
collapseReplicates	0.124	0.005	0.130
collapsed-data	0.328	0.018	0.354
dataToTimeSeries	0.022	0.000	0.022
differentialExpression	14.816	0.419	15.376
dimensionReduction	0.058	0.002	0.063
filterFeatures	0.030	0.001	0.032
groups	0.013	0.002	0.014
makeTimeSeries	0.114	0.005	0.120
makeTimeSeriesExperimentFromExpressionSet	0.002	0.000	0.002
makeTimeSeriesExperimentFromSummarizedExperiment	0.162	0.003	0.167
meltMatrix	0.006	0.000	0.006
normalizeData	0.032	0.001	0.034
pathwayEnrichment	0.804	0.058	0.870
pipe	0.001	0.001	0.001
plotEnrichment	0.931	0.019	0.955
plotHeatmap	0.029	0.001	0.031
plotSamplePCA	0.359	0.006	0.367
plotTimeSeries	1.683	0.008	1.707
plotTimeSeriesClusters	2.056	0.014	2.079
plotTimeSeriesPCA	2.984	0.186	3.198
replicates	0.016	0.003	0.019
rowData	0.029	0.002	0.030
row_and_colnames	0.014	0.001	0.016
runPCA	0.046	0.002	0.048
timeSeries	0.668	0.197	0.869
timepointDE	0.123	0.004	0.126
timepoints	0.024	0.001	0.026
trajectoryDE	0.111	0.005	0.116
varianceStabilization	0.004	0.000	0.005

CHECK report for TimeSeriesExperiment on merida2

Summary

Command output

Installation output

Tests output

Example timings