Package: TimeSeriesExperiment

Version: 1.0.4

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:TimeSeriesExperiment.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TimeSeriesExperiment_1.0.4.tar.gz

StartedAt: 2019-04-16 03:25:37 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:29:04 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 207.1 seconds

RetCode: 0

Status:  OK

CheckDir: TimeSeriesExperiment.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:TimeSeriesExperiment.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TimeSeriesExperiment_1.0.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/TimeSeriesExperiment.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.4’
* 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 10.38      0  10.387
* 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-3.8-bioc/meat/TimeSeriesExperiment.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL TimeSeriesExperiment
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘TimeSeriesExperiment’ ...
** 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
* DONE (TimeSeriesExperiment)

name	user	system	elapsed
TimeSeriesExperiment	0.756	0.000	0.757
addLags	0.248	0.004	0.252
clusterAssignment	0.296	0.000	0.297
clusterData	0.060	0.000	0.059
clusterTimeSeries	0.392	0.000	0.393
colData	0.036	0.000	0.036
collapseReplicates	0.084	0.000	0.083
collapsed-data	0.176	0.004	0.180
dataToTimeSeries	0.020	0.000	0.017
differentialExpression	10.380	0.000	10.387
dimensionReduction	0.040	0.000	0.037
filterFeatures	0.024	0.004	0.028
groups	0.008	0.004	0.011
makeTimeSeries	0.108	0.004	0.113
makeTimeSeriesExperimentFromExpressionSet	0.004	0.000	0.002
makeTimeSeriesExperimentFromSummarizedExperiment	0.108	0.000	0.108
meltMatrix	0.012	0.000	0.010
normalizeData	0.052	0.000	0.051
pathwayEnrichment	0.980	0.036	1.198
pipe	0.000	0.000	0.001
plotEnrichment	0.692	0.008	0.700
plotHeatmap	0.024	0.000	0.023
plotSamplePCA	0.384	0.008	0.393
plotTimeSeries	1.824	0.008	1.831
plotTimeSeriesClusters	2.324	0.004	2.331
plotTimeSeriesPCA	2.088	0.072	2.166
replicates	0.012	0.000	0.012
rowData	0.024	0.000	0.026
row_and_colnames	0.008	0.000	0.010
runPCA	0.060	0.000	0.058
timeSeries	0.324	0.060	0.384
timepointDE	0.096	0.004	0.100
timepoints	0.012	0.004	0.016
trajectoryDE	0.096	0.000	0.097
varianceStabilization	0.004	0.000	0.003