David Jenkins
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/singleCellTK |
| Branch: master |
| Last Commit: a761eb1 |
| Last Changed Date: 2019-10-29 13:43:06 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:51:06 -0500 (Thu, 16 Jan 2020).
| Package 1601/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| singleCellTK 1.7.0 David Jenkins
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: singleCellTK |
| Version: 1.7.0 |
| 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_1.7.0.tar.gz |
| StartedAt: 2020-01-16 08:59:27 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 09:05:29 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 361.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: singleCellTK.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/singleCellTK.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 ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘1.7.0’
* 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.
* 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 8.714 0.634 9.347
visPlot 6.837 0.146 6.985
DownsampleCells 5.609 0.920 6.528
ComBatSCE 6.041 0.412 6.458
gsvaSCE 6.022 0.238 6.265
getUMAP 3.000 2.810 3.410
* 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 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.
> if (requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
NULL
>
> proc.time()
user system elapsed
0.385 0.152 0.481
singleCellTK.Rcheck/tests/testthat.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.
> 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
Loading required package: BiocParallel
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
12.806 1.217 13.968
singleCellTK.Rcheck/singleCellTK-Ex.timings
| name | user | system | elapsed | |
| ComBatSCE | 6.041 | 0.412 | 6.458 | |
| DownsampleCells | 5.609 | 0.920 | 6.528 | |
| DownsampleDepth | 0.877 | 0.138 | 1.017 | |
| MAST | 3.028 | 0.257 | 3.286 | |
| SCtkExperiment-class | 0.324 | 0.052 | 0.375 | |
| SCtkExperiment | 0.256 | 0.004 | 0.260 | |
| alignSingleCellData | 0.000 | 0.001 | 0.000 | |
| calcEffectSizes | 2.549 | 0.051 | 2.600 | |
| convertGeneIDs | 3.330 | 0.536 | 3.869 | |
| createSCE | 0.389 | 0.070 | 0.459 | |
| distinctColors | 0.004 | 0.000 | 0.004 | |
| enrichRSCE | 0 | 0 | 0 | |
| filterSCData | 0.632 | 0.051 | 0.683 | |
| generateSimulatedData | 0.249 | 0.068 | 0.318 | |
| getBiomarker | 0.045 | 0.001 | 0.046 | |
| getClusterInputData | 1.033 | 0.101 | 1.134 | |
| getPCA | 0.554 | 0.077 | 0.631 | |
| getTSNE | 0.595 | 0.059 | 0.654 | |
| getUMAP | 3.00 | 2.81 | 3.41 | |
| gsvaSCE | 6.022 | 0.238 | 6.265 | |
| iterateSimulations | 0.493 | 0.175 | 0.668 | |
| mouseBrainSubsetSCE | 0.003 | 0.004 | 0.007 | |
| pcaVariances-set | 1.578 | 0.136 | 1.714 | |
| pcaVariances | 0.128 | 0.037 | 0.164 | |
| plotBatchVariance | 2.803 | 0.341 | 3.145 | |
| plotBiomarker | 0.842 | 0.078 | 0.921 | |
| plotDiffEx | 2.056 | 0.241 | 2.299 | |
| plotDimRed | 0.365 | 0.063 | 0.428 | |
| plotPCA | 0.710 | 0.066 | 0.776 | |
| plotTSNE | 0.822 | 0.045 | 0.867 | |
| plotUMAP | 0.899 | 0.136 | 1.035 | |
| saveBiomarkerRes | 1.498 | 0.175 | 1.673 | |
| saveDiffExResults | 0.509 | 0.140 | 0.649 | |
| scDiffEx | 8.714 | 0.634 | 9.347 | |
| singleCellTK | 0.000 | 0.000 | 0.001 | |
| subDiffEx | 1.034 | 0.228 | 1.263 | |
| summarizeTable | 0.225 | 0.067 | 0.291 | |
| visPlot | 6.837 | 0.146 | 6.985 | |