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This page was generated on 2022-04-13 12:08:55 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for TimeSeriesExperiment on machv2


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? 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 1.12.0  (landing page)
Lan Huong Nguyen
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/TimeSeriesExperiment
git_branch: RELEASE_3_14
git_last_commit: 858bcd5
git_last_commit_date: 2021-10-26 12:48:05 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TimeSeriesExperiment
Version: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2022-04-12 19:24:26 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 19:30:31 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 364.4 seconds
RetCode: 0
Status:   OK  
CheckDir: TimeSeriesExperiment.Rcheck
Warnings: 0

Command output

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### Running 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_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/TimeSeriesExperiment.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.12.0’
* 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 (user + system) or elapsed time > 5s
                         user system elapsed
differentialExpression 22.135  0.484  22.637
plotTimeSeriesPCA       9.097  0.613   9.788
* 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
TimeSeriesExperiment0.5950.0040.600
addLags0.8920.0380.931
clusterAssignment1.1980.0261.224
clusterData0.2440.0070.251
clusterTimeSeries0.8570.0280.885
colData0.0670.0030.069
collapseReplicates0.1720.0050.177
collapsed-data0.4690.0100.479
dataToTimeSeries0.0760.0020.077
differentialExpression22.135 0.48422.637
dimensionReduction0.1200.0030.123
filterFeatures0.1560.0040.159
groups0.0340.0030.037
makeTimeSeries0.3580.0180.376
makeTimeSeriesExperimentFromExpressionSet0.0020.0010.002
makeTimeSeriesExperimentFromSummarizedExperiment0.5460.0020.550
meltMatrix0.0280.0010.029
normalizeData0.0890.0040.093
pathwayEnrichment1.1250.0711.219
pipe0.0000.0010.001
plotEnrichment1.1610.0221.188
plotHeatmap0.0690.0030.072
plotSamplePCA0.4240.0050.429
plotTimeSeries2.9670.0463.087
plotTimeSeriesClusters2.8820.0312.915
plotTimeSeriesPCA9.0970.6139.788
replicates0.0370.0020.040
rowData0.0790.0030.082
row_and_colnames0.0330.0020.035
runPCA0.1210.0020.123
timeSeries0.6830.4821.166
timepointDE0.2310.0030.234
timepoints0.0590.0030.062
trajectoryDE0.2690.0150.284
varianceStabilization0.0040.0010.004