Davis McCarthy
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/scater |
| Branch: RELEASE_3_9 |
| Last Commit: 1518dc2 |
| Last Changed Date: 2019-05-23 18:48:27 -0400 (Thu, 23 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:57:14 -0400 (Wed, 16 Oct 2019).
| Package 1461/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scater 1.12.2 Davis McCarthy
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: scater |
| Version: 1.12.2 |
| 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_1.12.2.tar.gz |
| StartedAt: 2019-10-16 06:34:29 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:48:50 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 861.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scater.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running 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_1.12.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/scater.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 ‘scater/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scater’ version ‘1.12.2’
* 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 ... 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 ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot_reddim 7.700 0.129 7.952
plotReducedDim 5.454 0.065 5.524
plotExpression 5.371 0.137 5.697
plotRLE 4.891 0.256 5.150
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.9-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/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:72:18: warning: unused variable 'ncells' [-Wunused-variable]
const size_t ncells=end_index - start_index;
^
sum_counts.cpp:96:18: warning: unused variable 'ncells' [-Wunused-variable]
const size_t ncells=mat->get_ncol();
^
2 warnings 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
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘filter’ in package ‘scater’
** 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 3.6.1 (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.
> 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
Attaching package: 'scater'
The following object is masked from 'package:S4Vectors':
rename
The following object is masked from 'package:stats':
filter
>
> test_check("scater")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 1224 | SKIPPED: 0 | WARNINGS: 15 | FAILED: 0 ]
>
> proc.time()
user system elapsed
238.794 18.427 525.291
scater.Rcheck/scater-Ex.timings
| name | user | system | elapsed | |
| accessors | 1.378 | 0.181 | 1.564 | |
| bootstraps | 0.123 | 0.010 | 0.133 | |
| calculateAverage | 0.112 | 0.007 | 0.120 | |
| calculateCPM | 0.129 | 0.007 | 0.136 | |
| calculateFPKM | 0.119 | 0.009 | 0.127 | |
| calculateQCMetrics | 0.611 | 0.015 | 0.628 | |
| calculateTPM | 0.232 | 0.050 | 0.282 | |
| centreSizeFactors | 0.169 | 0.044 | 0.214 | |
| getBMFeatureAnnos | 0.000 | 0.001 | 0.001 | |
| getExplanatoryPCs | 1.962 | 0.081 | 2.043 | |
| getVarianceExplained | 0.211 | 0.025 | 0.236 | |
| isOutlier | 0.364 | 0.013 | 0.378 | |
| librarySizeFactors | 0.014 | 0.006 | 0.019 | |
| multiplot | 3.175 | 0.145 | 3.320 | |
| nexprs | 0.093 | 0.006 | 0.099 | |
| normalize | 0.117 | 0.009 | 0.126 | |
| normalizeCounts | 0.009 | 0.004 | 0.012 | |
| plotColData | 2.875 | 0.042 | 2.921 | |
| plotExplanatoryPCs | 1.095 | 0.016 | 1.112 | |
| plotExplanatoryVariables | 0.887 | 0.051 | 0.938 | |
| plotExpression | 5.371 | 0.137 | 5.697 | |
| plotExprsFreqVsMean | 1.954 | 0.025 | 1.982 | |
| plotExprsVsTxLength | 4.004 | 0.097 | 4.107 | |
| plotHeatmap | 0.546 | 0.022 | 0.571 | |
| plotHighestExprs | 1.825 | 0.018 | 1.844 | |
| plotPlatePosition | 1.791 | 0.011 | 1.803 | |
| plotRLE | 4.891 | 0.256 | 5.150 | |
| plotReducedDim | 5.454 | 0.065 | 5.524 | |
| plotRowData | 2.099 | 0.037 | 2.140 | |
| plotScater | 3.823 | 0.213 | 4.040 | |
| plot_reddim | 7.700 | 0.129 | 7.952 | |
| readSparseCounts | 0.087 | 0.003 | 0.089 | |
| runDiffusionMap | 0.247 | 0.012 | 0.259 | |
| runMDS | 0.155 | 0.010 | 0.165 | |
| runPCA | 0.191 | 0.013 | 0.204 | |
| runTSNE | 0.261 | 0.013 | 0.275 | |
| runUMAP | 3.615 | 0.058 | 3.673 | |
| sumCountsAcrossCells | 0.108 | 0.029 | 0.138 | |
| sumCountsAcrossFeatures | 0.076 | 0.007 | 0.083 | |
| toSingleCellExperiment | 0.000 | 0.000 | 0.001 | |
| uniquifyFeatureNames | 0.001 | 0.000 | 0.002 | |