Multiple platform build/check report for BioC 3.8 - CHECK report for TimeSeriesExperiment on merida1

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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

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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/3.5/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

name	user	system	elapsed
TimeSeriesExperiment	0.877	0.008	0.890
addLags	0.418	0.014	0.435
clusterAssignment	0.506	0.014	0.523
clusterData	0.099	0.005	0.104
clusterTimeSeries	0.587	0.011	0.603
colData	0.055	0.002	0.059
collapseReplicates	0.139	0.014	0.153
collapsed-data	0.287	0.007	0.297
dataToTimeSeries	0.025	0.001	0.026
differentialExpression	15.273	0.349	15.756
dimensionReduction	0.048	0.002	0.050
filterFeatures	0.038	0.001	0.040
groups	0.016	0.001	0.017
makeTimeSeries	0.154	0.010	0.165
makeTimeSeriesExperimentFromExpressionSet	0.002	0.001	0.002
makeTimeSeriesExperimentFromSummarizedExperiment	0.083	0.001	0.085
meltMatrix	0.007	0.000	0.007
normalizeData	0.048	0.003	0.050
pathwayEnrichment	0.884	0.069	0.959
pipe	0.000	0.000	0.001
plotEnrichment	0.983	0.024	1.014
plotHeatmap	0.028	0.002	0.031
plotSamplePCA	0.429	0.009	0.449
plotTimeSeries	1.989	0.017	2.031
plotTimeSeriesClusters	2.438	0.013	2.469
plotTimeSeriesPCA	3.127	0.189	3.346
replicates	0.021	0.002	0.023
rowData	0.032	0.002	0.034
row_and_colnames	0.014	0.002	0.016
runPCA	0.081	0.003	0.086
timeSeries	0.701	0.208	0.913
timepointDE	0.131	0.004	0.135
timepoints	0.021	0.002	0.022
trajectoryDE	0.127	0.003	0.131
varianceStabilization	0.005	0.001	0.006

CHECK report for TimeSeriesExperiment on merida1

Summary

Command output

Installation output

Tests output

Example timings