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This page was generated on 2021-10-15 15:05:55 -0400 (Fri, 15 Oct 2021).

CHECK results for TimeSeriesExperiment on nebbiolo1

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 1921/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TimeSeriesExperiment 1.10.1  (landing page)
Lan Huong Nguyen
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/TimeSeriesExperiment
git_branch: RELEASE_3_13
git_last_commit: 543ffaf
git_last_commit_date: 2021-08-31 05:15:55 -0400 (Tue, 31 Aug 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.10.1
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:TimeSeriesExperiment.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings TimeSeriesExperiment_1.10.1.tar.gz
StartedAt: 2021-10-14 11:52:00 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:55:30 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 210.8 seconds
RetCode: 0
Status:   OK  
CheckDir: TimeSeriesExperiment.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:TimeSeriesExperiment.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings TimeSeriesExperiment_1.10.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/TimeSeriesExperiment.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.10.1’
* 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 9.963  0.028   9.992
* 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-3.13-bioc/meat/TimeSeriesExperiment.Rcheck/00check.log’
for details.



Installation output

TimeSeriesExperiment.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL TimeSeriesExperiment
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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)

Tests output


Example timings

TimeSeriesExperiment.Rcheck/TimeSeriesExperiment-Ex.timings

nameusersystemelapsed
TimeSeriesExperiment0.2360.0000.237
addLags0.3330.0400.373
clusterAssignment0.4060.0060.412
clusterData0.0900.0020.091
clusterTimeSeries0.4090.0000.409
colData0.0630.0000.063
collapseReplicates0.1190.0000.120
collapsed-data0.2540.0040.258
dataToTimeSeries0.0250.0000.026
differentialExpression9.9630.0289.992
dimensionReduction0.0640.0120.076
filterFeatures0.0780.0000.078
groups0.020.000.02
makeTimeSeries0.1460.0000.146
makeTimeSeriesExperimentFromExpressionSet0.0010.0000.001
makeTimeSeriesExperimentFromSummarizedExperiment0.2160.0000.216
meltMatrix0.0090.0000.009
normalizeData0.0410.0000.041
pathwayEnrichment0.5710.1870.776
pipe0.0010.0000.000
plotEnrichment0.6260.0120.638
plotHeatmap0.0330.0000.033
plotSamplePCA0.230.000.23
plotTimeSeries0.9620.0160.979
plotTimeSeriesClusters1.2920.0521.345
plotTimeSeriesPCA2.7200.1602.882
replicates0.0190.0040.023
rowData0.0400.0000.039
row_and_colnames0.0180.0000.017
runPCA0.0620.0000.063
timeSeries0.3260.3800.705
timepointDE0.0830.0000.084
timepoints0.0390.0000.040
trajectoryDE0.1590.0000.159
varianceStabilization0.0030.0000.004