| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:37:34 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 304/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CellTrails 1.20.0 (landing page) Daniel Ellwanger
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: CellTrails |
| Version: 1.20.0 |
| Command: /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_1.20.0.tar.gz |
| StartedAt: 2024-04-16 00:29:37 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 00:38:18 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 521.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CellTrails.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /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_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/CellTrails.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellTrails/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellTrails’ version ‘1.20.0’
* 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 9.346 0.374 10.309
filterTrajFeaturesByFF 5.295 0.175 5.720
filterTrajFeaturesByCOV 4.937 0.157 5.340
* 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
CellTrails.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CellTrails ### ############################################################################## ############################################################################## * 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)
CellTrails.Rcheck/tests/runTests.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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 -- Tue Apr 16 00:37:58 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
78.085 1.838 83.904
CellTrails.Rcheck/CellTrails-Ex.timings
| name | user | system | elapsed | |
| addTrail | 0.748 | 0.014 | 0.794 | |
| connectStates | 0.181 | 0.008 | 0.197 | |
| contrastTrailExpr | 0.509 | 0.016 | 0.556 | |
| embedSamples | 0.722 | 0.036 | 0.794 | |
| enrichment.test | 0.005 | 0.001 | 0.007 | |
| featureNames-SingleCellExperiment-method | 0.018 | 0.005 | 0.024 | |
| filterTrajFeaturesByCOV | 4.937 | 0.157 | 5.340 | |
| filterTrajFeaturesByDL | 2.336 | 0.041 | 2.485 | |
| filterTrajFeaturesByFF | 5.295 | 0.175 | 5.720 | |
| findSpectrum | 1.262 | 0.030 | 1.339 | |
| findStates | 2.044 | 0.102 | 2.249 | |
| fitDynamic | 0.217 | 0.006 | 0.228 | |
| fitTrajectory | 0.573 | 0.010 | 0.616 | |
| landmarks | 0.036 | 0.004 | 0.040 | |
| latentSpace-set | 0.619 | 0.019 | 0.655 | |
| latentSpace | 0.125 | 0.006 | 0.135 | |
| manifold2D-set | 0.883 | 0.019 | 0.952 | |
| manifold2D | 0.070 | 0.005 | 0.076 | |
| pca | 0.621 | 0.012 | 0.668 | |
| phenoNames | 0.012 | 0.004 | 0.016 | |
| plotDynamic | 1.434 | 0.022 | 1.524 | |
| plotManifold | 1.525 | 0.022 | 1.609 | |
| plotMap | 9.346 | 0.374 | 10.309 | |
| plotStateExpression | 0.909 | 0.017 | 0.977 | |
| plotStateSize | 0.414 | 0.013 | 0.482 | |
| plotStateTrajectory | 2.322 | 0.050 | 2.478 | |
| plotTrail | 0.536 | 0.008 | 0.564 | |
| plotTrajectoryFit | 0.661 | 0.012 | 0.715 | |
| read.ygraphml | 0.006 | 0.004 | 0.010 | |
| removeTrail | 0.064 | 0.005 | 0.071 | |
| sampleNames-SingleCellExperiment-method | 0.018 | 0.004 | 0.022 | |
| selectTrajectory | 0.018 | 0.004 | 0.024 | |
| showTrajInfo | 0.494 | 0.007 | 0.527 | |
| simulate_exprs | 0.002 | 0.000 | 0.002 | |
| stateTrajLayout-set | 0.369 | 0.007 | 0.393 | |
| states-set | 0.070 | 0.005 | 0.082 | |
| states | 0.010 | 0.004 | 0.014 | |
| trailNames-set | 0.037 | 0.004 | 0.042 | |
| trailNames | 0.006 | 0.004 | 0.012 | |
| trails | 0.029 | 0.005 | 0.035 | |
| trajComponents | 0.007 | 0.005 | 0.013 | |
| trajFeatureNames-set | 0.044 | 0.004 | 0.050 | |
| trajFeatureNames | 0.021 | 0.004 | 0.027 | |
| trajLayout-set | 1.036 | 0.010 | 1.098 | |
| trajLayout | 0.020 | 0.005 | 0.026 | |
| trajResiduals | 0.009 | 0.004 | 0.014 | |
| trajSampleNames | 0.022 | 0.005 | 0.028 | |
| userLandmarks-set | 0.993 | 0.009 | 1.045 | |
| userLandmarks | 0.176 | 0.005 | 0.185 | |
| write.ygraphml | 0.007 | 0.005 | 0.016 | |