Daniel Ellwanger
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/CellTrails |
| Branch: master |
| Last Commit: 92ef7e2 |
| Last Changed Date: 2019-10-29 13:43:15 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:51:37 -0500 (Thu, 16 Jan 2020).
| Package 248/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CellTrails 1.5.0 Daniel Ellwanger
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: CellTrails |
| Version: 1.5.0 |
| 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_1.5.0.tar.gz |
| StartedAt: 2020-01-16 02:38:30 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 02:45:40 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 429.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CellTrails.Rcheck |
| Warnings: 1 |
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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_1.5.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CellTrails.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.5.0’
* 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 ... WARNING
Found the following significant warnings:
Warning: 'isSpike' is deprecated.
Warning: 'isSpike' is deprecated.
Warning: 'isSpike' is deprecated.
Warning: 'isSpike' is deprecated.
Warning: 'isSpike' is deprecated.
Warning: 'isSpike' is deprecated.
Warning: 'isSpike' is deprecated.
Warning: 'isSpike' is deprecated.
Warning: 'isSpike' is deprecated.
Warning: 'isSpike' is deprecated.
Warning: 'isSpike' is deprecated.
Warning: 'isSpike' is deprecated.
Warning: 'isSpike' is deprecated.
Warning: 'isSpike' is deprecated.
Warning: 'isSpike' is deprecated.
Warning: 'isSpike' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotMap 12.080 1.182 13.290
filterTrajFeaturesByFF 5.353 0.359 5.748
filterTrajFeaturesByCOV 4.700 0.387 5.090
* 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: 1 WARNING
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/CellTrails.Rcheck/00check.log’
for details.
CellTrails.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CellTrails ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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, 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, 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, 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 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 -- Thu Jan 16 02:45:30 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
There were 23 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
60.927 2.599 64.048
CellTrails.Rcheck/CellTrails-Ex.timings
| name | user | system | elapsed | |
| addTrail | 0.924 | 0.030 | 0.955 | |
| connectStates | 0.143 | 0.008 | 0.151 | |
| contrastTrailExpr | 0.987 | 0.017 | 1.004 | |
| embedSamples | 0.634 | 0.100 | 0.732 | |
| enrichment.test | 0.006 | 0.001 | 0.008 | |
| featureNames-SingleCellExperiment-method | 0.025 | 0.005 | 0.030 | |
| filterTrajFeaturesByCOV | 4.700 | 0.387 | 5.090 | |
| filterTrajFeaturesByDL | 2.040 | 0.144 | 2.185 | |
| filterTrajFeaturesByFF | 5.353 | 0.359 | 5.748 | |
| findSpectrum | 0.845 | 0.060 | 1.088 | |
| findStates | 2.115 | 0.090 | 2.298 | |
| fitDynamic | 0.269 | 0.010 | 0.280 | |
| fitTrajectory | 0.932 | 0.017 | 0.951 | |
| landmarks | 0.029 | 0.009 | 0.038 | |
| latentSpace-set | 0.731 | 0.012 | 0.744 | |
| latentSpace | 0.100 | 0.009 | 0.109 | |
| manifold2D-set | 0.964 | 0.026 | 0.991 | |
| manifold2D | 0.095 | 0.009 | 0.103 | |
| pca | 0.480 | 0.012 | 0.492 | |
| phenoNames | 0.025 | 0.008 | 0.034 | |
| plotDynamic | 1.369 | 0.022 | 1.393 | |
| plotManifold | 1.451 | 0.012 | 1.464 | |
| plotMap | 12.080 | 1.182 | 13.290 | |
| plotStateExpression | 0.980 | 0.045 | 1.031 | |
| plotStateSize | 0.267 | 0.009 | 0.276 | |
| plotStateTrajectory | 1.754 | 0.013 | 1.767 | |
| plotTrail | 0.546 | 0.009 | 0.556 | |
| plotTrajectoryFit | 0.539 | 0.011 | 0.551 | |
| read.ygraphml | 0.018 | 0.008 | 0.026 | |
| removeTrail | 0.058 | 0.010 | 0.068 | |
| sampleNames-SingleCellExperiment-method | 0.031 | 0.008 | 0.040 | |
| selectTrajectory | 0.024 | 0.009 | 0.032 | |
| showTrajInfo | 0.412 | 0.011 | 0.424 | |
| simulate_exprs | 0.001 | 0.000 | 0.002 | |
| stateTrajLayout-set | 0.204 | 0.008 | 0.212 | |
| states-set | 0.036 | 0.004 | 0.041 | |
| states | 0.013 | 0.005 | 0.018 | |
| trailNames-set | 0.022 | 0.009 | 0.031 | |
| trailNames | 0.014 | 0.006 | 0.020 | |
| trails | 0.045 | 0.007 | 0.053 | |
| trajComponents | 0.019 | 0.008 | 0.028 | |
| trajFeatureNames-set | 0.052 | 0.009 | 0.061 | |
| trajFeatureNames | 0.020 | 0.006 | 0.026 | |
| trajLayout-set | 0.758 | 0.012 | 0.769 | |
| trajLayout | 0.032 | 0.007 | 0.040 | |
| trajResiduals | 0.019 | 0.008 | 0.027 | |
| trajSampleNames | 0.021 | 0.007 | 0.029 | |
| userLandmarks-set | 0.736 | 0.010 | 0.746 | |
| userLandmarks | 0.181 | 0.009 | 0.190 | |
| write.ygraphml | 0.011 | 0.005 | 0.016 | |