David Jenkins
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/singleCellTK |
| Branch: RELEASE_3_11 |
| Last Commit: ed17c59 |
| Last Changed Date: 2020-04-27 15:16:09 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:59:38 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE singleCellTK PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1673/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| singleCellTK 1.8.0 David Jenkins
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: singleCellTK |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings singleCellTK_1.8.0.tar.gz |
| StartedAt: 2020-10-17 05:25:17 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:30:18 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 301.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: singleCellTK.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings singleCellTK_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/singleCellTK.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘1.8.0’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘singleCellTK’ 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 ... NOTE
Namespaces in Imports field not imported from:
‘celda’ ‘shinyBS’ ‘shinythemes’
All declared Imports should be used.
Missing or unexported object: ‘SingleCellExperiment::isSpike’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
scDiffEx 6.655 0.151 6.812
visPlot 6.377 0.104 6.534
gsvaSCE 5.615 0.083 5.703
ComBatSCE 5.298 0.179 5.485
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’
Running ‘testthat.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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.
singleCellTK.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL singleCellTK ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘singleCellTK’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (singleCellTK)
singleCellTK.Rcheck/tests/spelling.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.
> if (requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
NULL
>
> proc.time()
user system elapsed
0.290 0.069 0.338
singleCellTK.Rcheck/tests/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.
> library(testthat)
> library(singleCellTK)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
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
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
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
Loading required package: SingleCellExperiment
Attaching package: 'singleCellTK'
The following object is masked from 'package:BiocGenerics':
plotPCA
>
> test_check("singleCellTK")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 3 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
12.198 0.622 12.837
singleCellTK.Rcheck/singleCellTK-Ex.timings
| name | user | system | elapsed | |
| ComBatSCE | 5.298 | 0.179 | 5.485 | |
| DownsampleCells | 3.928 | 0.526 | 4.456 | |
| DownsampleDepth | 1.282 | 0.043 | 1.326 | |
| MAST | 3.523 | 0.116 | 3.644 | |
| SCtkExperiment-class | 1.069 | 0.019 | 1.090 | |
| SCtkExperiment | 0.401 | 0.007 | 0.410 | |
| alignSingleCellData | 0.000 | 0.001 | 0.001 | |
| calcEffectSizes | 1.841 | 0.026 | 1.870 | |
| convertGeneIDs | 3.263 | 0.522 | 3.787 | |
| createSCE | 0.434 | 0.004 | 0.438 | |
| distinctColors | 0.004 | 0.001 | 0.005 | |
| enrichRSCE | 0.000 | 0.001 | 0.000 | |
| filterSCData | 1.257 | 0.034 | 1.293 | |
| generateSimulatedData | 0.310 | 0.034 | 0.343 | |
| getBiomarker | 0.029 | 0.002 | 0.031 | |
| getClusterInputData | 1.107 | 0.034 | 1.142 | |
| getPCA | 0.628 | 0.016 | 0.651 | |
| getTSNE | 0.725 | 0.027 | 0.761 | |
| getUMAP | 0.697 | 0.032 | 0.732 | |
| gsvaSCE | 5.615 | 0.083 | 5.703 | |
| iterateSimulations | 1.063 | 0.038 | 1.101 | |
| mouseBrainSubsetSCE | 0.002 | 0.002 | 0.004 | |
| pcaVariances-set | 0.515 | 0.010 | 0.525 | |
| pcaVariances | 0.156 | 0.002 | 0.158 | |
| plotBatchVariance | 1.369 | 0.062 | 1.431 | |
| plotBiomarker | 0.793 | 0.017 | 0.811 | |
| plotDiffEx | 2.830 | 0.082 | 2.932 | |
| plotDimRed | 0.204 | 0.018 | 0.223 | |
| plotPCA | 0.669 | 0.050 | 0.720 | |
| plotTSNE | 0.627 | 0.011 | 0.638 | |
| plotUMAP | 0.617 | 0.035 | 0.653 | |
| saveBiomarkerRes | 1.338 | 0.065 | 1.402 | |
| saveDiffExResults | 0.483 | 0.024 | 0.508 | |
| scDiffEx | 6.655 | 0.151 | 6.812 | |
| singleCellTK | 0.000 | 0.000 | 0.001 | |
| subDiffEx | 0.989 | 0.063 | 1.053 | |
| summarizeTable | 0.241 | 0.003 | 0.244 | |
| visPlot | 6.377 | 0.104 | 6.534 | |