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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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

Package 308/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellTrails 1.22.0  (landing page)
Daniel Ellwanger
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/CellTrails
git_branch: RELEASE_3_19
git_last_commit: 0904a4a
git_last_commit_date: 2024-04-30 11:07:25 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for CellTrails on nebbiolo1

To the developers/maintainers of the CellTrails package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CellTrails.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: CellTrails
Version: 1.22.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CellTrails.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CellTrails_1.22.0.tar.gz
StartedAt: 2024-06-12 21:26:46 -0400 (Wed, 12 Jun 2024)
EndedAt: 2024-06-12 21:30:50 -0400 (Wed, 12 Jun 2024)
EllapsedTime: 243.5 seconds
RetCode: 0
Status:   OK  
CheckDir: CellTrails.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CellTrails.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CellTrails_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CellTrails.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘CellTrails/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellTrails’ version ‘1.22.0’
* 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 code 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 loading without being on the library search path ... 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 ... NOTE
checkRd: (-1) connectStates.Rd:55: Lost braces; missing escapes or markup?
    55 | where D is a matrix containing all collected {l}-nearest neighbor sample
       |                                              ^
checkRd: (-1) dot-bhtsne.Rd:10-14: Lost braces
    10 | .reduceDimensions_def <- function(x, s) {
       |                                         ^
checkRd: (-1) dot-trajLandmark-set.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{type}{A character in {"type", "id", "shape"}}
       |                            ^
checkRd: (-1) dot-trajLandmark.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{type}{A character in {"type", "id", "shape"}}
       |                            ^
checkRd: (-1) dot-validatePlotParams.Rd:24: Lost braces; missing escapes or markup?
    24 | {'featureName', 'phenoName'}. Parameter \code{name} needs
       | ^
checkRd: (-1) dot-validatePlotParams.Rd:26: Lost braces; missing escapes or markup?
    26 | {colnames(colData(object)), state, landmark}.
       | ^
checkRd: (-1) plotMap.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{type}{Type of map; one of {"raw","surface.fit","surface.se"}}
       |                                 ^
checkRd: (-1) write.ygraphml.Rd:52: Lost braces; missing escapes or markup?
    52 | \code{color_by='phenoName'} and {name='landmark'}. States can be indicated
       |                                 ^
checkRd: (-1) write.ygraphml.Rd:53: Lost braces; missing escapes or markup?
    53 | by \code{color_by='phenoName'} and {name='state'}.
       |                                    ^
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'dot-adjustLayoutByPtime.Rd':
  ‘layout’

Documented arguments not in \usage in Rd file 'dot-findStates_def.Rd':
  ‘ming.g’

Documented arguments not in \usage in Rd file 'dot-plotStateTrajectory_def.Rd':
  ‘label’

Documented arguments not in \usage in Rd file 'dot-rbf.Rd':
  ‘x’ ‘sigma’

Documented arguments not in \usage in Rd file 'dot-spatmed.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'dot-write_ygraphml_def.Rd':
  ‘tlayout’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 5.055  0.236   5.291
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/CellTrails.Rcheck/00check.log’
for details.


Installation output

CellTrails.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CellTrails
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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, 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 -- Wed Jun 12 21:30:34 2024 
*********************************************** 
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 
 31.312   0.963  32.280 

Example timings

CellTrails.Rcheck/CellTrails-Ex.timings

nameusersystemelapsed
addTrail0.9030.0520.955
connectStates0.0710.0040.075
contrastTrailExpr0.2240.0160.239
embedSamples0.2260.0240.250
enrichment.test0.0040.0000.003
featureNames-SingleCellExperiment-method0.0090.0000.009
filterTrajFeaturesByCOV2.9070.1763.083
filterTrajFeaturesByDL0.8540.0160.870
filterTrajFeaturesByFF2.6740.0602.734
findSpectrum0.5380.0320.571
findStates0.7570.0160.773
fitDynamic0.0980.0140.112
fitTrajectory0.2490.0210.270
landmarks0.0020.0040.006
latentSpace-set0.2910.0040.294
latentSpace0.0520.0000.051
manifold2D-set0.4080.0120.420
manifold2D0.0290.0040.033
pca0.2420.0280.270
phenoNames0.0070.0000.007
plotDynamic0.5750.0160.591
plotManifold0.6810.0120.692
plotMap5.0550.2365.291
plotStateExpression0.4000.0080.407
plotStateSize0.1710.0080.179
plotStateTrajectory0.8960.0240.920
plotTrail0.2180.0030.222
plotTrajectoryFit0.2760.0000.276
read.ygraphml0.0040.0000.004
removeTrail0.0330.0000.032
sampleNames-SingleCellExperiment-method0.0090.0000.009
selectTrajectory0.0090.0000.009
showTrajInfo0.1850.0000.185
simulate_exprs0.0010.0000.001
stateTrajLayout-set0.1330.0000.134
states-set0.0310.0000.031
states0.0050.0000.006
trailNames-set0.0160.0010.016
trailNames0.0010.0030.004
trails0.0150.0000.015
trajComponents0.0050.0000.005
trajFeatureNames-set0.020.000.02
trajFeatureNames0.0090.0000.009
trajLayout-set0.4110.0160.427
trajLayout0.0060.0040.010
trajResiduals0.0050.0000.004
trajSampleNames0.010.000.01
userLandmarks-set0.3630.0040.367
userLandmarks0.0720.0000.072
write.ygraphml0.0050.0000.004