Davis McCarthy
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/scater |
| Branch: RELEASE_3_11 |
| Last Commit: e01dfed |
| Last Changed Date: 2020-06-26 14:17:15 -0400 (Fri, 26 Jun 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:59:31 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE scater PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1584/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scater 1.16.2 Davis McCarthy
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: scater |
| Version: 1.16.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scater.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scater_1.16.2.tar.gz |
| StartedAt: 2020-10-17 05:00:42 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:13:46 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 784.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scater.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scater.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scater_1.16.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/scater.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 ‘scater/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scater’ version ‘1.16.2’
* 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 ‘scater’ 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
'library' or 'require' call to ‘NMF’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runNMF 17.824 1.409 19.289
plotRLE 8.057 0.346 8.414
plot_reddim 8.160 0.133 8.319
plotScater 5.582 0.216 5.807
plotExpression 5.396 0.094 5.504
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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/scater.Rcheck/00check.log’
for details.
scater.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scater ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘scater’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/beachmat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/beachmat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c combined_qc.cpp -o combined_qc.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/beachmat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c sum_counts.cpp -o sum_counts.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/beachmat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o scater.so RcppExports.o combined_qc.o sum_counts.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-scater/00new/scater/libs ** R ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scater)
scater.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.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(scater)
Loading required package: SingleCellExperiment
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: ggplot2
>
> test_check("scater")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 1815 | SKIPPED: 0 | WARNINGS: 11 | FAILED: 0 ]
>
> proc.time()
user system elapsed
398.236 15.493 418.945
scater.Rcheck/scater-Ex.timings
| name | user | system | elapsed | |
| accessors | 1.745 | 0.044 | 1.795 | |
| addPerCellQC | 1.429 | 0.046 | 1.480 | |
| annotateBMFeatures | 0.000 | 0.001 | 0.000 | |
| bootstraps | 0.398 | 0.031 | 0.429 | |
| calculateAverage | 0.400 | 0.036 | 0.437 | |
| calculateCPM | 0.469 | 0.032 | 0.501 | |
| calculateFPKM | 0.393 | 0.010 | 0.404 | |
| calculateTPM | 0.413 | 0.007 | 0.420 | |
| defunct | 0.001 | 0.000 | 0.002 | |
| getExplanatoryPCs | 1.034 | 0.021 | 1.056 | |
| getVarianceExplained | 0.579 | 0.040 | 0.621 | |
| ggsce | 3.217 | 0.092 | 3.316 | |
| isOutlier | 0.778 | 0.003 | 0.782 | |
| librarySizeFactors | 0.375 | 0.004 | 0.380 | |
| logNormCounts | 0.495 | 0.007 | 0.505 | |
| makePerCellDF | 0.882 | 0.023 | 0.906 | |
| makePerFeatureDF | 0.545 | 0.009 | 0.555 | |
| medianSizeFactors | 0.387 | 0.014 | 0.402 | |
| mockSCE | 0.379 | 0.002 | 0.383 | |
| multiplot | 1.836 | 0.016 | 1.856 | |
| nexprs | 0.308 | 0.001 | 0.310 | |
| normalizeCounts | 0.374 | 0.010 | 0.384 | |
| numDetectedAcrossCells | 1.048 | 0.032 | 1.080 | |
| numDetectedAcrossFeatures | 0.346 | 0.003 | 0.352 | |
| perCellQCMetrics | 1.737 | 0.028 | 1.769 | |
| perFeatureQCMetrics | 0.599 | 0.004 | 0.607 | |
| plotColData | 2.495 | 0.034 | 2.575 | |
| plotDots | 0.963 | 0.012 | 0.975 | |
| plotExplanatoryPCs | 1.853 | 0.020 | 1.875 | |
| plotExplanatoryVariables | 0.962 | 0.038 | 1.001 | |
| plotExpression | 5.396 | 0.094 | 5.504 | |
| plotHeatmap | 0.957 | 0.015 | 0.973 | |
| plotHighestExprs | 1.536 | 0.023 | 1.566 | |
| plotPlatePosition | 1.601 | 0.014 | 1.623 | |
| plotRLE | 8.057 | 0.346 | 8.414 | |
| plotReducedDim | 4.111 | 0.039 | 4.157 | |
| plotRowData | 0.910 | 0.009 | 0.923 | |
| plotScater | 5.582 | 0.216 | 5.807 | |
| plot_reddim | 8.160 | 0.133 | 8.319 | |
| quickPerCellQC | 0.863 | 0.005 | 0.868 | |
| readSparseCounts | 0.025 | 0.001 | 0.027 | |
| retrieveCellInfo | 0.495 | 0.012 | 0.509 | |
| retrieveFeatureInfo | 0.581 | 0.004 | 0.586 | |
| runColDataPCA | 1.018 | 0.011 | 1.030 | |
| runDiffusionMap | 0.852 | 0.011 | 0.863 | |
| runMDS | 0.641 | 0.002 | 0.645 | |
| runMultiUMAP | 4.638 | 0.068 | 4.711 | |
| runNMF | 17.824 | 1.409 | 19.289 | |
| runPCA | 0.932 | 0.012 | 0.946 | |
| runTSNE | 1.748 | 0.007 | 1.759 | |
| runUMAP | 4.092 | 0.066 | 4.159 | |
| sumCountsAcrossCells | 1.282 | 0.006 | 1.288 | |
| sumCountsAcrossFeatures | 0.370 | 0.003 | 0.374 | |
| toSingleCellExperiment | 0.001 | 0.001 | 0.001 | |
| uniquifyFeatureNames | 0.000 | 0.001 | 0.001 | |