Package: TimeSeriesExperiment

Version: 1.1.4

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_1.1.4.tar.gz

StartedAt: 2019-04-09 05:58:08 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 06:03:53 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 345.0 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_1.1.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TimeSeriesExperiment.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.1.4’
* 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 17.216  1.648  18.866
* 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	0.245	0.004	0.250
addLags	0.386	0.052	0.438
clusterAssignment	0.389	0.021	0.409
clusterData	0.117	0.010	0.127
clusterTimeSeries	0.693	0.028	0.722
colData	0.066	0.005	0.071
collapseReplicates	0.177	0.005	0.182
collapsed-data	0.461	0.040	0.502
dataToTimeSeries	0.027	0.001	0.028
differentialExpression	17.216	1.648	18.866
dimensionReduction	0.046	0.003	0.049
filterFeatures	0.035	0.003	0.038
groups	0.014	0.002	0.016
makeTimeSeries	0.112	0.006	0.119
makeTimeSeriesExperimentFromExpressionSet	0.002	0.000	0.002
makeTimeSeriesExperimentFromSummarizedExperiment	0.130	0.001	0.130
meltMatrix	0.006	0.001	0.007
normalizeData	0.033	0.003	0.035
pathwayEnrichment	1.699	0.141	1.845
pipe	0.000	0.000	0.001
plotEnrichment	1.264	0.092	1.356
plotHeatmap	0.040	0.004	0.044
plotSamplePCA	0.615	0.011	0.625
plotTimeSeries	2.519	0.026	2.545
plotTimeSeriesClusters	2.568	0.043	2.610
plotTimeSeriesPCA	3.785	0.406	4.194
replicates	0.022	0.004	0.027
rowData	0.041	0.004	0.046
row_and_colnames	0.017	0.003	0.020
runPCA	0.079	0.005	0.084
timeSeries	0.924	0.403	1.327
timepointDE	0.104	0.003	0.108
timepoints	0.032	0.004	0.035
trajectoryDE	0.113	0.008	0.121
varianceStabilization	0.004	0.000	0.005