Package: TimeSeriesExperiment

Version: 1.4.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:TimeSeriesExperiment.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings TimeSeriesExperiment_1.4.0.tar.gz

StartedAt: 2020-04-15 06:08:33 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:13:02 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 269.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: TimeSeriesExperiment.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:TimeSeriesExperiment.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings TimeSeriesExperiment_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/TimeSeriesExperiment.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.4.0’
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'plotHeatmap':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 14.312      0  14.341
* 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/TimeSeriesExperiment.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL TimeSeriesExperiment
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* installing to library ‘/home/biocbuild/bbs-3.10-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	0.176	0.000	0.174
addLags	1.280	0.000	1.284
clusterAssignment	0.712	0.040	0.752
clusterData	0.060	0.008	0.068
clusterTimeSeries	1.168	0.004	1.174
colData	0.096	0.000	0.098
collapseReplicates	0.164	0.000	0.167
collapsed-data	0.260	0.004	0.269
dataToTimeSeries	0.036	0.000	0.035
differentialExpression	14.312	0.000	14.341
dimensionReduction	0.068	0.000	0.069
filterFeatures	0.060	0.000	0.058
groups	0.024	0.000	0.024
makeTimeSeries	0.488	0.000	0.492
makeTimeSeriesExperimentFromExpressionSet	0.000	0.000	0.001
makeTimeSeriesExperimentFromSummarizedExperiment	0.124	0.000	0.125
meltMatrix	0.008	0.000	0.011
normalizeData	0.040	0.000	0.039
pathwayEnrichment	1.600	0.036	1.639
pipe	0.004	0.000	0.000
plotEnrichment	0.944	0.004	0.950
plotHeatmap	0.036	0.000	0.036
plotSamplePCA	0.492	0.000	0.499
plotTimeSeries	1.648	0.000	1.664
plotTimeSeriesClusters	2.412	0.000	2.417
plotTimeSeriesPCA	4.604	0.136	4.758
replicates	0.012	0.004	0.016
rowData	0.032	0.000	0.031
row_and_colnames	0.020	0.000	0.017
runPCA	0.064	0.000	0.067
timeSeries	0.960	0.152	1.115
timepointDE	0.168	0.000	0.169
timepoints	0.108	0.000	0.109
trajectoryDE	0.540	0.000	0.544
varianceStabilization	0.004	0.000	0.003