Davis McCarthy
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/scater |
| Branch: RELEASE_3_10 |
| Last Commit: ba37f4d |
| Last Changed Date: 2019-12-13 22:59:26 -0400 (Fri, 13 Dec 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:43:07 -0400 (Wed, 15 Apr 2020).
| Package 1524/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scater 1.14.6 Davis McCarthy
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | TIMEOUT | skipped | skipped | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: scater |
| Version: 1.14.6 |
| 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_1.14.6.tar.gz |
| StartedAt: 2020-04-15 05:27:48 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:39:16 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 687.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scater.Rcheck |
| Warnings: 2 |
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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_1.14.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/scater.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.14.6’
* 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 ... 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 ... WARNING
Output for data("sc_example_cell_info", package = "scater"):
Warning message:
'data(sc_example_cell_info)' is deprecated.
Use mockSCE() instead.
Output for data("sc_example_counts", package = "scater"):
Warning message:
'data(sc_example_counts)' is deprecated.
Use mockSCE() instead.
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... WARNING
Found the following significant warnings:
Warning: 'calculateQCMetrics' is deprecated.
Warning: 'calculateQCMetrics' is deprecated.
Warning: 'calculateQCMetrics' is deprecated.
Warning: 'type=' is deprecated.
Warning: 'type=' is deprecated.
Warning: 'centreSizeFactors' is deprecated.
Warning: 'type=' is deprecated.
Warning: 'normalizeSCE' is deprecated.
Warning: 'centreSizeFactors' is deprecated.
Warning: 'ncomponents' is deprecated.
Warning: 'calculateQCMetrics' is deprecated.
Warning: 'plotExprsFreqVsMean' is deprecated.
Warning: 'plotExprsFreqVsMean' is deprecated.
Warning: 'plotExprsVsTxLength' is deprecated.
Warning: 'plotExprsVsTxLength' is deprecated.
Warning: 'plotExprsVsTxLength' is deprecated.
Warning: 'plotExprsVsTxLength' is deprecated.
Warning: 'plotExprsVsTxLength' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
plotRLE 10.736 0.337 11.177
plot_reddim 9.292 0.155 9.564
plotScater 8.397 0.538 9.035
plotExpression 5.413 0.111 5.597
plotReducedDim 4.933 0.030 5.023
* 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 WARNINGs, 1 NOTE
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/scater.Rcheck/00check.log’
for details.
scater.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scater
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘scater’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c calc_exprs.cpp -o calc_exprs.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c combined_qc.cpp -o combined_qc.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c init.cpp -o init.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c num_exprs.cpp -o num_exprs.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c sum_counts.cpp -o sum_counts.o
sum_counts.cpp:94:18: warning: unused variable 'ncells' [-Wunused-variable]
const size_t ncells=mat->get_ncol();
^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o
clang++ -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 calc_exprs.o combined_qc.o init.o num_exprs.o sum_counts.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-scater/00new/scater/libs
** 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
** 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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.
> 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
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: ggplot2
>
> test_check("scater")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 1649 | SKIPPED: 0 | WARNINGS: 26 | FAILED: 0 ]
>
> proc.time()
user system elapsed
267.613 37.053 370.246
scater.Rcheck/scater-Ex.timings
| name | user | system | elapsed | |
| accessors | 1.523 | 0.043 | 1.578 | |
| addPerCellQC | 0.906 | 0.024 | 0.940 | |
| annotateBMFeatures | 0 | 0 | 0 | |
| bootstraps | 0.306 | 0.027 | 0.341 | |
| calculateAverage | 0.357 | 0.031 | 0.397 | |
| calculateCPM | 0.371 | 0.001 | 0.386 | |
| calculateFPKM | 0.811 | 0.003 | 0.828 | |
| calculateQCMetrics | 0.756 | 0.003 | 0.768 | |
| calculateTPM | 0.322 | 0.008 | 0.335 | |
| centreSizeFactors | 0.306 | 0.005 | 0.315 | |
| getExplanatoryPCs | 0.878 | 0.022 | 0.919 | |
| getVarianceExplained | 0.983 | 0.059 | 1.050 | |
| isOutlier | 0.569 | 0.008 | 0.580 | |
| librarySizeFactors | 0.265 | 0.007 | 0.275 | |
| logNormCounts | 0.352 | 0.029 | 0.383 | |
| medianSizeFactors | 0.328 | 0.014 | 0.347 | |
| mockSCE | 0.320 | 0.016 | 0.343 | |
| multiplot | 2.175 | 0.029 | 2.216 | |
| nexprs | 0.280 | 0.002 | 0.282 | |
| normalize | 0.336 | 0.001 | 0.342 | |
| normalizeCounts | 0.280 | 0.011 | 0.292 | |
| numDetectedAcrossCells | 0.270 | 0.007 | 0.277 | |
| numDetectedAcrossFeatures | 0.304 | 0.006 | 0.311 | |
| perCellQCMetrics | 1.295 | 0.012 | 1.318 | |
| perFeatureQCMetrics | 0.418 | 0.002 | 0.422 | |
| plotColData | 2.779 | 0.042 | 2.841 | |
| plotDots | 0.967 | 0.004 | 0.985 | |
| plotExplanatoryPCs | 1.249 | 0.006 | 1.272 | |
| plotExplanatoryVariables | 0.919 | 0.042 | 0.973 | |
| plotExpression | 5.413 | 0.111 | 5.597 | |
| plotExprsFreqVsMean | 1.693 | 0.036 | 1.746 | |
| plotExprsVsTxLength | 4.083 | 0.116 | 4.236 | |
| plotHeatmap | 0.922 | 0.026 | 0.968 | |
| plotHighestExprs | 1.628 | 0.024 | 1.665 | |
| plotPlatePosition | 1.424 | 0.019 | 1.453 | |
| plotRLE | 10.736 | 0.337 | 11.177 | |
| plotReducedDim | 4.933 | 0.030 | 5.023 | |
| plotRowData | 0.719 | 0.008 | 0.738 | |
| plotScater | 8.397 | 0.538 | 9.035 | |
| plot_reddim | 9.292 | 0.155 | 9.564 | |
| quickPerCellQC | 0.667 | 0.008 | 0.685 | |
| readSparseCounts | 0.025 | 0.000 | 0.027 | |
| retrieveCellInfo | 0.430 | 0.014 | 0.446 | |
| retrieveFeatureInfo | 0.461 | 0.018 | 0.493 | |
| runColDataPCA | 0.762 | 0.010 | 0.783 | |
| runDiffusionMap | 0.684 | 0.023 | 0.712 | |
| runMDS | 0.541 | 0.026 | 0.568 | |
| runMultiUMAP | 4.385 | 0.046 | 4.502 | |
| runPCA | 0.692 | 0.012 | 0.708 | |
| runTSNE | 1.321 | 0.026 | 1.353 | |
| runUMAP | 3.655 | 0.048 | 3.765 | |
| sumCountsAcrossCells | 0.618 | 0.008 | 0.628 | |
| sumCountsAcrossFeatures | 0.267 | 0.002 | 0.270 | |
| toSingleCellExperiment | 0 | 0 | 0 | |
| uniquifyFeatureNames | 0.000 | 0.000 | 0.001 | |