Multiple platform build/check report for BioC 3.17 - CHECK results for CellTrails on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.2 LTS)	x86_64	4.3.1 (2023-06-16) -- "Beagle Scouts"	4626
palomino3	Windows Server 2022 Datacenter	x64	4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"	4379
merida1	macOS 12.6.4 Monterey	x86_64	4.3.1 (2023-06-16) -- "Beagle Scouts"	4395
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*

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CellTrails.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CellTrails_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/CellTrails.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellTrails/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellTrails’ version ‘1.18.0’
* 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 ‘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 (user + system) or elapsed time > 5s
                          user system elapsed
plotMap                 10.571  0.498  15.623
filterTrajFeaturesByFF   5.717  0.402   8.583
filterTrajFeaturesByCOV  4.828  0.224   7.133
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CellTrails
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars


Attaching package: 'BiocGenerics'

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, aperm, 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:utils':

    findMatches

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

    I, expand.grid, unname

Welcome to Bioconductor

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

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...
This graph was created by an old(er) igraph version.
  Call upgrade_graph() on it to use with the current igraph version
  For now we convert it on the fly...
Calculating layout of state trajectory graph component 1...
Calculating layout of state trajectory graph component 2...
Calculating layout of state trajectory graph ...
This graph was created by an old(er) igraph version.
  Call upgrade_graph() on it to use with the current igraph version
  For now we convert it on the fly...
This graph was created by an old(er) igraph version.
  Call upgrade_graph() on it to use with the current igraph version
  For now we convert it on the fly...
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 -- Sun Oct 15 23:46:43 2023 
*********************************************** 
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 
Warning message:
The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as
of ggplot2 3.3.4.
ℹ The deprecated feature was likely used in the CellTrails package.
  Please report the issue to the authors. 
> 
> proc.time()
   user  system elapsed 
 77.007   2.093 104.372

Example timings

name	user	system	elapsed
addTrail	0.927	0.015	1.246
connectStates	0.180	0.007	0.244
contrastTrailExpr	1.146	0.020	1.569
embedSamples	0.587	0.055	0.900
enrichment.test	0.005	0.001	0.006
featureNames-SingleCellExperiment-method	0.018	0.005	0.023
filterTrajFeaturesByCOV	4.828	0.224	7.133
filterTrajFeaturesByDL	1.768	0.069	2.575
filterTrajFeaturesByFF	5.717	0.402	8.583
findSpectrum	1.184	0.074	1.782
findStates	2.088	0.064	2.902
fitDynamic	0.220	0.009	0.313
fitTrajectory	0.575	0.012	0.787
landmarks	0.011	0.004	0.018
latentSpace-set	0.642	0.018	0.875
latentSpace	0.131	0.008	0.198
manifold2D-set	0.946	0.032	1.328
manifold2D	0.070	0.005	0.100
pca	0.551	0.015	0.875
phenoNames	0.012	0.004	0.017
plotDynamic	1.696	0.024	2.314
plotManifold	1.785	0.027	2.361
plotMap	10.571	0.498	15.623
plotStateExpression	1.083	0.039	1.585
plotStateSize	0.525	0.041	0.799
plotStateTrajectory	2.404	0.048	3.373
plotTrail	0.552	0.012	0.771
plotTrajectoryFit	0.613	0.013	0.886
read.ygraphml	0.007	0.004	0.016
removeTrail	0.063	0.005	0.096
sampleNames-SingleCellExperiment-method	0.019	0.004	0.027
selectTrajectory	0.018	0.004	0.034
showTrajInfo	0.502	0.012	0.698
simulate_exprs	0.002	0.001	0.003
stateTrajLayout-set	0.391	0.011	0.571
states-set	0.072	0.006	0.119
states	0.010	0.004	0.017
trailNames-set	0.038	0.005	0.060
trailNames	0.006	0.004	0.010
trails	0.030	0.005	0.050
trajComponents	0.008	0.005	0.016
trajFeatureNames-set	0.047	0.004	0.070
trajFeatureNames	0.022	0.004	0.035
trajLayout-set	1.053	0.020	1.485
trajLayout	0.021	0.005	0.047
trajResiduals	0.009	0.006	0.015
trajSampleNames	0.021	0.004	0.031
userLandmarks-set	0.986	0.016	1.335
userLandmarks	0.173	0.005	0.235
write.ygraphml	0.007	0.005	0.018

CHECK results for CellTrails on merida1

Summary

Command output

Installation output

Tests output

Example timings