Package: TimeSeriesExperiment

Version: 1.4.0

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_1.4.0.tar.gz

StartedAt: 2020-04-15 06:09:19 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:14:02 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 283.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: TimeSeriesExperiment.Rcheck

Warnings: 1

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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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/TimeSeriesExperiment.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.4.0’
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'plotHeatmap':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 16.055   0.45  16.655
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/TimeSeriesExperiment.Rcheck/00check.log’
for details.

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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’ ...
** 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)

name	user	system	elapsed
TimeSeriesExperiment	0.208	0.002	0.211
addLags	1.603	0.041	1.652
clusterAssignment	1.107	0.036	1.151
clusterData	0.091	0.004	0.096
clusterTimeSeries	1.228	0.015	1.256
colData	0.086	0.004	0.091
collapseReplicates	0.130	0.006	0.136
collapsed-data	0.226	0.012	0.239
dataToTimeSeries	0.043	0.002	0.044
differentialExpression	16.055	0.450	16.655
dimensionReduction	0.055	0.002	0.059
filterFeatures	0.048	0.002	0.050
groups	0.023	0.002	0.025
makeTimeSeries	0.558	0.010	0.571
makeTimeSeriesExperimentFromExpressionSet	0.001	0.000	0.002
makeTimeSeriesExperimentFromSummarizedExperiment	0.184	0.001	0.186
meltMatrix	0.017	0.001	0.017
normalizeData	0.048	0.002	0.050
pathwayEnrichment	0.923	0.067	0.998
pipe	0.001	0.000	0.001
plotEnrichment	1.122	0.039	1.170
plotHeatmap	0.038	0.003	0.041
plotSamplePCA	0.445	0.008	0.457
plotTimeSeries	2.385	0.012	2.407
plotTimeSeriesClusters	3.204	0.020	3.244
plotTimeSeriesPCA	4.364	0.235	4.650
replicates	0.019	0.002	0.023
rowData	0.034	0.002	0.036
row_and_colnames	0.035	0.001	0.036
runPCA	0.054	0.002	0.056
timeSeries	1.121	0.222	1.352
timepointDE	0.100	0.002	0.102
timepoints	0.045	0.002	0.047
trajectoryDE	0.530	0.006	0.541
varianceStabilization	0.003	0.001	0.004