Package: TimeSeriesExperiment

Version: 1.5.0

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_1.5.0.tar.gz

StartedAt: 2020-01-16 09:28:35 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 09:34:55 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 379.5 seconds

RetCode: 0

Status:  OK

CheckDir: TimeSeriesExperiment.Rcheck

Warnings: 0

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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_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/TimeSeriesExperiment.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.5.0’
* 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 (user + system) or elapsed time > 5s
                         user system elapsed
differentialExpression 19.039  2.076  21.117
plotTimeSeriesPCA       5.554  0.535   6.098
* 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-3.11-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/4.0/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	0.348	0.062	0.411
addLags	0.671	0.119	0.791
clusterAssignment	0.581	0.018	0.599
clusterData	0.117	0.008	0.126
clusterTimeSeries	0.479	0.028	0.507
colData	0.073	0.007	0.079
collapseReplicates	0.221	0.009	0.230
collapsed-data	0.263	0.008	0.272
dataToTimeSeries	0.024	0.000	0.024
differentialExpression	19.039	2.076	21.117
dimensionReduction	0.083	0.006	0.089
filterFeatures	0.060	0.004	0.065
groups	0.033	0.004	0.037
makeTimeSeries	0.171	0.016	0.187
makeTimeSeriesExperimentFromExpressionSet	0.002	0.000	0.002
makeTimeSeriesExperimentFromSummarizedExperiment	0.247	0.001	0.249
meltMatrix	0.012	0.000	0.012
normalizeData	0.066	0.005	0.071
pathwayEnrichment	1.255	0.141	1.396
pipe	0.001	0.000	0.001
plotEnrichment	1.278	0.058	1.336
plotHeatmap	0.032	0.003	0.035
plotSamplePCA	0.510	0.018	0.527
plotTimeSeries	2.319	0.158	2.477
plotTimeSeriesClusters	2.757	0.045	2.803
plotTimeSeriesPCA	5.554	0.535	6.098
replicates	0.019	0.002	0.021
rowData	0.052	0.004	0.056
row_and_colnames	0.018	0.005	0.022
runPCA	0.086	0.006	0.093
timeSeries	1.015	0.528	1.542
timepointDE	0.173	0.006	0.179
timepoints	0.082	0.005	0.086
trajectoryDE	0.151	0.020	0.169
varianceStabilization	0.007	0.002	0.008