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

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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.

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### Running command:
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###   /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)

name	user	system	elapsed
TimeSeriesExperiment	0.208	0.008	0.216
addLags	0.277	0.008	0.285
clusterAssignment	0.318	0.000	0.318
clusterData	0.548	0.004	0.552
clusterTimeSeries	0.401	0.000	0.401
colData	0.042	0.000	0.043
collapseReplicates	0.085	0.012	0.097
collapsed-data	0.165	0.008	0.173
dataToTimeSeries	0.016	0.000	0.016
differentialExpression	10.772	0.004	10.784
dimensionReduction	0.064	0.000	0.064
filterFeatures	0.047	0.000	0.046
groups	0.019	0.000	0.019
makeTimeSeries	0.168	0.000	0.169
makeTimeSeriesExperimentFromExpressionSet	0.002	0.000	0.001
makeTimeSeriesExperimentFromSummarizedExperiment	0.183	0.000	0.184
meltMatrix	0.009	0.000	0.008
normalizeData	0.046	0.000	0.047
pathwayEnrichment	0.972	0.020	1.455
pipe	0.000	0.000	0.001
plotEnrichment	0.858	0.008	0.866
plotHeatmap	0.032	0.004	0.036
plotSamplePCA	0.439	0.016	0.455
plotTimeSeries	2.536	0.024	2.561
plotTimeSeriesClusters	2.265	0.020	2.286
plotTimeSeriesPCA	2.925	0.128	3.055
replicates	0.018	0.000	0.018
rowData	0.029	0.000	0.029
row_and_colnames	0.005	0.004	0.009
runPCA	0.035	0.000	0.035
timeSeries	0.336	0.064	0.399
timepointDE	0.070	0.006	0.076
timepoints	0.020	0.001	0.021
trajectoryDE	0.12	0.00	0.12
varianceStabilization	0.003	0.000	0.003