Package: TimeSeriesExperiment

Version: 1.2.0

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_1.2.0.tar.gz

StartedAt: 2019-10-16 07:22:55 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:28:52 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 356.5 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TimeSeriesExperiment.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.2.0’
* 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 20.335  1.863  22.198
* 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.

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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	0.334	0.027	0.361
addLags	0.631	0.053	0.683
clusterAssignment	0.625	0.026	0.651
clusterData	0.654	0.011	0.665
clusterTimeSeries	0.927	0.052	0.979
colData	0.069	0.014	0.083
collapseReplicates	0.168	0.039	0.206
collapsed-data	0.259	0.021	0.281
dataToTimeSeries	0.034	0.002	0.036
differentialExpression	20.335	1.863	22.198
dimensionReduction	0.080	0.005	0.085
filterFeatures	0.057	0.005	0.062
groups	0.025	0.004	0.030
makeTimeSeries	0.189	0.033	0.222
makeTimeSeriesExperimentFromExpressionSet	0.003	0.000	0.004
makeTimeSeriesExperimentFromSummarizedExperiment	0.207	0.001	0.208
meltMatrix	0.011	0.001	0.011
normalizeData	0.053	0.004	0.057
pathwayEnrichment	1.159	0.143	1.308
pipe	0.001	0.001	0.002
plotEnrichment	1.411	0.079	1.489
plotHeatmap	0.049	0.004	0.052
plotSamplePCA	0.669	0.065	0.734
plotTimeSeries	2.006	0.026	2.033
plotTimeSeriesClusters	2.921	0.037	2.958
plotTimeSeriesPCA	4.364	0.409	4.777
replicates	0.015	0.004	0.019
rowData	0.030	0.005	0.035
row_and_colnames	0.019	0.005	0.023
runPCA	0.076	0.004	0.081
timeSeries	1.196	0.509	1.705
timepointDE	0.156	0.005	0.161
timepoints	0.043	0.003	0.046
trajectoryDE	0.208	0.021	0.229
varianceStabilization	0.007	0.002	0.009