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CHECK report for CellTrails on merida1

This page was generated on 2019-04-16 12:10:46 -0400 (Tue, 16 Apr 2019).

Package 222/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellTrails 1.0.1
Daniel Ellwanger
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/CellTrails
Branch: RELEASE_3_8
Last Commit: 548bced
Last Changed Date: 2019-01-04 13:09:06 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CellTrails
Version: 1.0.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CellTrails.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CellTrails_1.0.1.tar.gz
StartedAt: 2019-04-15 22:51:31 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:56:07 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 275.3 seconds
RetCode: 0
Status:  OK 
CheckDir: CellTrails.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CellTrails.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CellTrails_1.0.1.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/CellTrails.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.0.1’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
plotMap                9.000  0.634   9.740
filterTrajFeaturesByFF 5.376  0.169   5.632
* 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

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CellTrails
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘CellTrails’ ...
** 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
* DONE (CellTrails)

Tests output

CellTrails.Rcheck/tests/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, 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: '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

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 samples 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 samples 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 samples each.
Performing post-hoc test ...
Found 1 states.
Initialized 20 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Found 1 states.
Initialized 0 clusters with a minimum size of 1000 samples each.
Initialized 20 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Found 20 states.
Initialized 20 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Found 1 states.
Initialized 20 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Found 19 states.
Initialized 20 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Found 5 states.
Initialized 20 clusters with a minimum size of 1 samples 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 samples 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 samples 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 samples 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 samples each.
Performing post-hoc test ...
Found 5 states.
Calculating layout of state trajectory graph component 1...


RUNIT TEST PROTOCOL -- Mon Apr 15 22:56:01 2019 
*********************************************** 
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 
 43.633   0.959  45.434 

Example timings

CellTrails.Rcheck/CellTrails-Ex.timings

nameusersystemelapsed
addTrail0.9840.0161.009
connectStates0.0520.0120.064
contrastTrailExpr0.3560.0190.384
embedSamples0.4400.0400.486
enrichment.test0.0060.0000.005
featureNames-SingleCellExperiment-method0.0150.0090.024
filterTrajFeaturesByCOV4.1480.1544.354
filterTrajFeaturesByDL1.6310.0551.707
filterTrajFeaturesByFF5.3760.1695.632
findSpectrum0.5270.0150.549
findStates0.9900.0121.006
fitDynamic0.1520.0050.156
fitTrajectory0.4670.0060.477
landmarks0.0180.0050.023
latentSpace-set0.3550.0050.360
latentSpace0.0120.0030.015
manifold2D-set0.3550.0030.361
manifold2D0.0150.0030.017
pca0.3100.0070.319
phenoNames0.0150.0020.017
plotDynamic0.9630.0061.075
plotManifold0.7350.0060.749
plotMap9.0000.6349.740
plotStateExpression0.7040.0190.734
plotStateSize0.2470.0040.251
plotStateTrajectory1.2600.0141.298
plotTrail0.3990.0060.406
plotTrajectoryFit0.4700.0040.476
read.ygraphml0.0120.0040.016
removeTrail0.0280.0040.031
sampleNames-SingleCellExperiment-method0.0130.0040.017
selectTrajectory0.0180.0030.025
showTrajInfo0.0600.0040.065
simulate_exprs0.0020.0000.001
stateTrajLayout-set0.0680.0040.072
states-set0.0240.0040.029
states0.0200.0040.025
trailNames-set0.0190.0030.023
trailNames0.0150.0040.019
trails0.0300.0040.035
trajComponents0.0110.0020.014
trajFeatureNames-set0.0160.0020.018
trajFeatureNames0.0150.0030.019
trajLayout-set0.3840.0040.396
trajLayout0.0220.0040.026
trajResiduals0.0150.0050.020
trajSampleNames0.0210.0050.027
userLandmarks-set0.3170.0050.339
userLandmarks0.1350.0060.148
write.ygraphml0.0120.0040.016