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This page was generated on 2022-01-06 11:05:28 -0500 (Thu, 06 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2021-11-10 r81171) -- "Unsuffered Consequences" 4310
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4045
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2021-11-01 r81125) -- "Unsuffered Consequences" 4123
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 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 1948/2072HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TimeSeriesExperiment 1.13.0  (landing page)
Lan Huong Nguyen
Snapshot Date: 2022-01-05 13:55:14 -0500 (Wed, 05 Jan 2022)
git_url: https://git.bioconductor.org/packages/TimeSeriesExperiment
git_branch: master
git_last_commit: 33e5983
git_last_commit_date: 2021-10-26 12:48:05 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TimeSeriesExperiment
Version: 1.13.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TimeSeriesExperiment.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TimeSeriesExperiment_1.13.0.tar.gz
StartedAt: 2022-01-05 21:25:22 -0500 (Wed, 05 Jan 2022)
EndedAt: 2022-01-05 21:29:00 -0500 (Wed, 05 Jan 2022)
EllapsedTime: 217.7 seconds
RetCode: 0
Status:   OK  
CheckDir: TimeSeriesExperiment.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TimeSeriesExperiment.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TimeSeriesExperiment_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/TimeSeriesExperiment.Rcheck’
* using R Under development (unstable) (2021-11-10 r81171)
* 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 ‘1.13.0’
* 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 10.472  0.076  10.549
* 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-3.15-bioc/meat/TimeSeriesExperiment.Rcheck/00check.log’
for details.



Installation output

TimeSeriesExperiment.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL TimeSeriesExperiment
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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
TimeSeriesExperiment0.1870.0000.188
addLags0.3490.0120.361
clusterAssignment0.3810.0000.380
clusterData0.1570.0040.161
clusterTimeSeries0.3340.0000.333
colData0.0430.0040.047
collapseReplicates0.0880.0000.089
collapsed-data0.1720.0000.173
dataToTimeSeries0.0230.0040.027
differentialExpression10.472 0.07610.549
dimensionReduction0.0470.0000.047
filterFeatures0.0510.0120.063
groups0.0090.0080.017
makeTimeSeries0.1440.0000.143
makeTimeSeriesExperimentFromExpressionSet0.0020.0000.001
makeTimeSeriesExperimentFromSummarizedExperiment0.1600.0040.163
meltMatrix0.0110.0000.011
normalizeData0.0320.0080.039
pathwayEnrichment0.5660.2440.825
pipe000
plotEnrichment0.5760.0120.588
plotHeatmap0.0260.0000.026
plotSamplePCA0.2350.0000.236
plotTimeSeries0.9420.0080.950
plotTimeSeriesClusters1.3460.0201.365
plotTimeSeriesPCA2.8670.1363.004
replicates0.0170.0000.017
rowData0.0240.0000.024
row_and_colnames0.0100.0000.011
runPCA0.0440.0000.044
timeSeries0.2780.4400.717
timepointDE0.0920.0000.092
timepoints0.0250.0040.029
trajectoryDE0.1220.0000.122
varianceStabilization0.0000.0030.004