David Jenkins
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/singleCellTK |
| Branch: RELEASE_3_9 |
| Last Commit: 0285e0c |
| Last Changed Date: 2019-08-04 13:29:24 -0400 (Sun, 04 Aug 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:02:24 -0400 (Wed, 16 Oct 2019).
| Package 1532/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| singleCellTK 1.4.2 David Jenkins
| malbec2 | Linux (Ubuntu 18.04.2 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: 1.4.2 |
| 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_1.4.2.tar.gz |
| StartedAt: 2019-10-16 06:56:44 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:03:51 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 426.9 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_1.4.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/singleCellTK.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.2’
* 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
Namespace in Imports field not imported from: ‘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 or elapsed time > 5s
user system elapsed
visPlot 7.312 0.044 7.357
gsvaSCE 6.564 0.283 6.854
DownsampleCells 5.232 0.876 6.107
ComBatSCE 5.337 0.433 5.774
MAST 5.098 0.359 5.459
scDiffEx 4.875 0.401 5.274
* 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-3.9-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/3.6/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 3.6.1 (2019-07-05) -- "Action of the Toes"
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
0.415 0.157 0.521
singleCellTK.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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")
Estimating GSVA scores for 1 gene sets.
Computing observed enrichment scores
Estimating ECDFs with Gaussian kernels
Using parallel with 1 cores
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Estimating GSVA scores for 1 gene sets.
Computing observed enrichment scores
Estimating ECDFs with Gaussian kernels
Using parallel with 1 cores
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|======================================================================| 100%
Estimating GSVA scores for 402 gene sets.
Computing observed enrichment scores
Estimating ECDFs with Gaussian kernels
Using parallel with 1 cores
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Standardizing Data across genes
Standardizing Data across genes
Using batch = 3 as a reference batch (this batch won't change)
Standardizing Data across genes
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 78 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
110.680 4.258 114.959
singleCellTK.Rcheck/singleCellTK-Ex.timings
| name | user | system | elapsed | |
| ComBatSCE | 5.337 | 0.433 | 5.774 | |
| DownsampleCells | 5.232 | 0.876 | 6.107 | |
| DownsampleDepth | 1.018 | 0.108 | 1.125 | |
| MAST | 5.098 | 0.359 | 5.459 | |
| SCtkExperiment-class | 0.298 | 0.047 | 0.345 | |
| SCtkExperiment | 0.236 | 0.006 | 0.244 | |
| alignSingleCellData | 0 | 0 | 0 | |
| calcEffectSizes | 2.234 | 0.052 | 2.287 | |
| convertGeneIDs | 3.130 | 0.531 | 3.668 | |
| createSCE | 0.496 | 0.102 | 0.598 | |
| distinctColors | 0.005 | 0.000 | 0.005 | |
| enrichRSCE | 0.000 | 0.000 | 0.001 | |
| filterSCData | 1.151 | 0.045 | 1.196 | |
| generateSimulatedData | 0.238 | 0.049 | 0.287 | |
| getBiomarker | 0.012 | 0.001 | 0.013 | |
| getClusterInputData | 0.219 | 0.050 | 0.269 | |
| getPCA | 0.424 | 0.072 | 0.497 | |
| getTSNE | 0.523 | 0.108 | 0.631 | |
| getUMAP | 2.524 | 2.390 | 3.112 | |
| gsvaSCE | 6.564 | 0.283 | 6.854 | |
| iterateSimulations | 0.363 | 0.152 | 0.515 | |
| mouseBrainSubsetSCE | 0.001 | 0.003 | 0.004 | |
| pcaVariances-set | 0.394 | 0.089 | 0.482 | |
| pcaVariances | 0.186 | 0.024 | 0.209 | |
| plotBatchVariance | 2.990 | 0.305 | 3.296 | |
| plotBiomarker | 0.879 | 0.075 | 0.954 | |
| plotDiffEx | 2.545 | 0.288 | 2.834 | |
| plotPCA | 0.520 | 0.055 | 0.577 | |
| plotTSNE | 0.531 | 0.042 | 0.573 | |
| plotUMAP | 0.765 | 0.168 | 0.933 | |
| saveBiomarkerRes | 1.402 | 0.197 | 1.599 | |
| saveDiffExResults | 0.398 | 0.096 | 0.494 | |
| scDiffEx | 4.875 | 0.401 | 5.274 | |
| singleCellTK | 0.001 | 0.001 | 0.002 | |
| subDiffEx | 0.640 | 0.232 | 0.871 | |
| summarizeTable | 0.214 | 0.071 | 0.285 | |
| visPlot | 7.312 | 0.044 | 7.357 | |