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This page was generated on 2021-10-23 14:07:21 -0400 (Sat, 23 Oct 2021).

CHECK results for TimeSeriesExperiment on merida1

To the developers/maintainers of the TimeSeriesExperiment package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TimeSeriesExperiment.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1959/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TimeSeriesExperiment 1.11.1  (landing page)
Lan Huong Nguyen
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/TimeSeriesExperiment
git_branch: master
git_last_commit: fcb85c7
git_last_commit_date: 2021-08-31 04:49:06 -0400 (Tue, 31 Aug 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TimeSeriesExperiment
Version: 1.11.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TimeSeriesExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TimeSeriesExperiment_1.11.1.tar.gz
StartedAt: 2021-10-23 10:09:32 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 10:14:54 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 322.6 seconds
RetCode: 0
Status:   OK  
CheckDir: TimeSeriesExperiment.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TimeSeriesExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TimeSeriesExperiment_1.11.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/TimeSeriesExperiment.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.11.1’
* 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 (user + system) or elapsed time > 5s
                         user system elapsed
differentialExpression 17.232  0.309  17.558
plotTimeSeriesPCA       4.842  0.536   5.387
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/TimeSeriesExperiment.Rcheck/00check.log’
for details.



Installation output

TimeSeriesExperiment.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TimeSeriesExperiment
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)

Tests output


Example timings

TimeSeriesExperiment.Rcheck/TimeSeriesExperiment-Ex.timings

nameusersystemelapsed
TimeSeriesExperiment0.4190.0050.425
addLags0.6080.0210.630
clusterAssignment0.7440.0200.766
clusterData0.2500.0080.258
clusterTimeSeries0.7150.0210.737
colData0.0710.0020.074
collapseReplicates0.2110.0020.214
collapsed-data0.4420.0090.452
dataToTimeSeries0.0370.0020.039
differentialExpression17.232 0.30917.558
dimensionReduction0.1100.0040.115
filterFeatures0.1300.0030.133
groups0.0330.0030.036
makeTimeSeries0.2650.0130.280
makeTimeSeriesExperimentFromExpressionSet0.0010.0010.001
makeTimeSeriesExperimentFromSummarizedExperiment0.4380.0030.441
meltMatrix0.0150.0000.014
normalizeData0.0730.0030.076
pathwayEnrichment0.9050.0700.997
pipe000
plotEnrichment0.9240.0170.943
plotHeatmap0.0600.0020.063
plotSamplePCA0.4410.0040.446
plotTimeSeries1.7570.0251.785
plotTimeSeriesClusters2.4740.0292.507
plotTimeSeriesPCA4.8420.5365.387
replicates0.0260.0020.027
rowData0.0500.0020.052
row_and_colnames0.0230.0010.025
runPCA0.0770.0010.079
timeSeries0.4370.1650.602
timepointDE0.1720.0060.178
timepoints0.0660.0030.068
trajectoryDE0.2290.0110.240
varianceStabilization0.0040.0000.004