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CHECK report for CellTrails on malbec1

This page was generated on 2020-08-12 11:22:11 -0400 (Wed, 12 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CellTrails PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 248/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellTrails 1.7.1
Daniel Ellwanger
Snapshot Date: 2020-08-11 14:50:16 -0400 (Tue, 11 Aug 2020)
URL: https://git.bioconductor.org/packages/CellTrails
Branch: master
Last Commit: d66623c
Last Changed Date: 2020-05-10 19:41:47 -0400 (Sun, 10 May 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CellTrails
Version: 1.7.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CellTrails.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CellTrails_1.7.1.tar.gz
StartedAt: 2020-08-12 05:19:20 -0400 (Wed, 12 Aug 2020)
EndedAt: 2020-08-12 05:24:20 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 300.0 seconds
RetCode: 0
Status:  OK 
CheckDir: CellTrails.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CellTrails.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CellTrails_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/CellTrails.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellTrails/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellTrails’ version ‘1.7.1’
* 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 ‘CellTrails’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
plotMap 7.764  0.052   7.835
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: OK


Installation output

CellTrails.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CellTrails
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘CellTrails’ ...
** 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 (CellTrails)

Tests output

CellTrails.Rcheck/tests/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("CellTrails")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Computing adjacency matrix ...
Computing spectral embedding ...
Calculating approximation of CellTrails manifold for 2D visualization...
Used tSNE perplexity: 30
Initialized 20 clusters with a minimum size of 1 sample(s) each.
Performing post-hoc test ...
Found 5 states.
Calculating layout of state trajectory graph component 1...
Computing adjacency matrix ...
Computing spectral embedding ...
Calculating approximation of CellTrails manifold for 2D visualization...
Used tSNE perplexity: 30
Initialized 20 clusters with a minimum size of 1 sample(s) each.
Performing post-hoc test ...
Found 5 states.
Calculating layout of state trajectory graph component 1...
Calculating layout of state trajectory graph component 2...
Calculating layout of state trajectory graph component 3...
Calculating layout of state trajectory graph component 4...
Calculating layout of state trajectory graph component 5...
Calculating layout of state trajectory graph component 1...
Computing adjacency matrix ...
Computing spectral embedding ...
Computing adjacency matrix ...
Computing spectral embedding ...
Calculating approximation of CellTrails manifold for 2D visualization...
Used tSNE perplexity: 30
Computing adjacency matrix ...
Computing spectral embedding ...
Calculating approximation of CellTrails manifold for 2D visualization...
Used tSNE perplexity: 30
Initialized 20 clusters with a minimum size of 1 sample(s) each.
Performing post-hoc test ...
Found 1 states.
Initialized 20 clusters with a minimum size of 1 sample(s) each.
Performing post-hoc test ...
Found 1 states.
Initialized 0 clusters with a minimum size of 1000 sample(s) each.
Initialized 20 clusters with a minimum size of 1 sample(s) each.
Performing post-hoc test ...
Found 20 states.
Initialized 20 clusters with a minimum size of 1 sample(s) each.
Performing post-hoc test ...
Found 1 states.
Initialized 20 clusters with a minimum size of 1 sample(s) each.
Performing post-hoc test ...
Found 19 states.
Initialized 20 clusters with a minimum size of 1 sample(s) each.
Performing post-hoc test ...
Found 5 states.
Initialized 20 clusters with a minimum size of 1 sample(s) each.
Performing post-hoc test ...
Found 5 states.
Computing adjacency matrix ...
Computing spectral embedding ...
Calculating approximation of CellTrails manifold for 2D visualization...
Used tSNE perplexity: 30
Initialized 20 clusters with a minimum size of 1 sample(s) each.
Performing post-hoc test ...
Found 5 states.
Calculating layout of state trajectory graph component 1...
Computing adjacency matrix ...
Computing spectral embedding ...
Calculating approximation of CellTrails manifold for 2D visualization...
Used tSNE perplexity: 30
Initialized 20 clusters with a minimum size of 1 sample(s) each.
Performing post-hoc test ...
Found 5 states.
Calculating layout of state trajectory graph component 1...
Computing adjacency matrix ...
Computing spectral embedding ...
Calculating approximation of CellTrails manifold for 2D visualization...
Used tSNE perplexity: 30
Initialized 20 clusters with a minimum size of 1 sample(s) each.
Performing post-hoc test ...
Found 5 states.
Calculating layout of state trajectory graph component 1...
Calculating 2D approximation of CellTrails manifold...
Calculating layout of state trajectory graph component 1...
Calculating layout of state trajectory graph component 2...
Calculating layout of state trajectory graph ...
Computing adjacency matrix ...
Computing spectral embedding ...
Calculating approximation of CellTrails manifold for 2D visualization...
Used tSNE perplexity: 30
Initialized 20 clusters with a minimum size of 1 sample(s) each.
Performing post-hoc test ...
Found 5 states.
Calculating layout of state trajectory graph component 1...


RUNIT TEST PROTOCOL -- Wed Aug 12 05:24:15 2020 
*********************************************** 
Number of test functions: 18 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CellTrails RUnit Tests - 18 test functions, 0 errors, 0 failures
Number of test functions: 18 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 48.876   0.592  49.794 

Example timings

CellTrails.Rcheck/CellTrails-Ex.timings

nameusersystemelapsed
addTrail0.8240.0120.842
connectStates0.2720.0000.270
contrastTrailExpr0.6000.0200.622
embedSamples1.0320.0441.079
enrichment.test0.0000.0000.003
featureNames-SingleCellExperiment-method0.0160.0000.016
filterTrajFeaturesByCOV3.3760.0323.413
filterTrajFeaturesByDL1.9920.0242.025
filterTrajFeaturesByFF2.9000.0282.931
findSpectrum0.6120.0040.616
findStates1.5920.0001.592
fitDynamic0.2760.0000.276
fitTrajectory0.7880.0080.796
landmarks0.0120.0000.015
latentSpace-set0.5080.0040.513
latentSpace0.2240.0000.223
manifold2D-set1.1240.0081.134
manifold2D0.1280.0000.130
pca0.3640.0040.371
phenoNames0.0240.0000.026
plotDynamic1.1320.0081.147
plotManifold1.1520.0001.150
plotMap7.7640.0527.835
plotStateExpression0.7320.0080.740
plotStateSize0.1840.0000.184
plotStateTrajectory1.3920.0081.402
plotTrail0.2800.0000.282
plotTrajectoryFit0.2880.0000.287
read.ygraphml0.0200.0000.018
removeTrail0.1280.0000.128
sampleNames-SingleCellExperiment-method0.0200.0040.026
selectTrajectory0.0240.0000.026
showTrajInfo0.7160.0000.716
simulate_exprs0.0040.0000.003
stateTrajLayout-set0.3640.0040.366
states-set0.0760.0000.075
states0.0120.0000.011
trailNames-set0.0960.0000.095
trailNames0.0200.0000.019
trails0.0640.0000.063
trajComponents0.0160.0040.019
trajFeatureNames-set0.0520.0000.051
trajFeatureNames0.0200.0080.028
trajLayout-set0.7880.0000.786
trajLayout0.0320.0000.032
trajResiduals0.020.000.02
trajSampleNames0.0280.0000.030
userLandmarks-set0.8800.0000.881
userLandmarks0.2720.0120.281
write.ygraphml0.0200.0000.019