Davis McCarthy
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/scater |
| Branch: RELEASE_3_7 |
| Last Commit: d560a9a |
| Last Changed Date: 2018-08-13 06:13:02 -0400 (Mon, 13 Aug 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:28:32 -0400 (Wed, 17 Oct 2018).
| Package 1320/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scater 1.8.4 Davis McCarthy
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: scater |
| Version: 1.8.4 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:scater.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings scater_1.8.4.tar.gz |
| StartedAt: 2018-10-16 03:34:15 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 03:38:04 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 229.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scater.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:scater.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings scater_1.8.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/scater.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.4’
* 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 ... NOTE
installed size is 6.8Mb
sub-directories of 1Mb or more:
extdata 2.9Mb
libs 2.2Mb
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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: 'read10xResults' is deprecated.
Warning: 'downsampleCounts' is deprecated.
Warning: 'normalizeExprs' is deprecated.
Warning: 'normalizeExprs' is deprecated.
Warning: 'normalizeExprs' is deprecated.
Warning: 'normalizeExprs' is deprecated.
Warning: 'normalizeExprs' is deprecated.
Warning: 'normalizeExprs' is deprecated.
Warning: 'read10xResults' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/scater.Rcheck/00check.log’
for details.
scater.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL scater ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘scater’ ... ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I/usr/local/include -fpic -g -O2 -c calc_exprs.cpp -o calc_exprs.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I/usr/local/include -fpic -g -O2 -c calc_top_features.cpp -o calc_top_features.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I/usr/local/include -fpic -g -O2 -c init.cpp -o init.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/beachmat/include" -I/usr/local/include -fpic -g -O2 -c matrix_stats.cpp -o matrix_stats.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o scater.so calc_exprs.o calc_top_features.o init.o matrix_stats.o -L/home/biocbuild/bbs-3.7-bioc/R/library/beachmat/lib -Wl,-rpath,/home/biocbuild/bbs-3.7-bioc/R/library/beachmat/lib -lbeachmat -pthread -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.7-bioc/R/library/scater/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘mutate’ in package ‘scater’ 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 * DONE (scater)
scater.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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: Biobase
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: ggplot2
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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: 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
Attaching package: 'scater'
The following object is masked from 'package:S4Vectors':
rename
The following object is masked from 'package:stats':
filter
>
> test_check("scater")
Collapsing expression to 500 features.Collapsing expression to 500 features.Collapsing expression to 500 features.Collapsing expression to 500 features.Collapsing expression to 500 features.Kallisto log not provided - assuming all runs successfulCollapsing expression to 500 features.Kallisto log not provided - assuming all runs successful══ testthat results ═══════════════════════════════════════════════════════════
OK: 1014 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
55.732 0.476 56.318
scater.Rcheck/scater-Ex.timings
| name | user | system | elapsed | |
| accessors | 0.552 | 0.016 | 0.571 | |
| areSizeFactorsCentred | 0.084 | 0.004 | 0.088 | |
| arrange | 0.076 | 0.000 | 0.078 | |
| bootstraps | 0.060 | 0.000 | 0.058 | |
| calcAverage | 0.064 | 0.004 | 0.069 | |
| calcIsExprs | 0.052 | 0.004 | 0.057 | |
| calculateCPM | 0.072 | 0.000 | 0.074 | |
| calculateFPKM | 0.064 | 0.000 | 0.067 | |
| calculateQCMetrics | 0.824 | 0.000 | 0.825 | |
| calculateTPM | 0.132 | 0.000 | 0.133 | |
| centreSizeFactors | 0.064 | 0.000 | 0.063 | |
| downsampleCounts | 0.172 | 0.000 | 0.207 | |
| filter | 0.052 | 0.000 | 0.051 | |
| findImportantPCs | 1.344 | 0.000 | 1.347 | |
| getBMFeatureAnnos | 0.004 | 0.000 | 0.000 | |
| isOutlier | 0.412 | 0.000 | 0.413 | |
| kallisto-wrapper | 0.000 | 0.000 | 0.001 | |
| librarySizeFactors | 0.004 | 0.000 | 0.006 | |
| multiplot | 1.492 | 0.000 | 1.490 | |
| mutate | 0.04 | 0.00 | 0.04 | |
| nexprs | 0.048 | 0.000 | 0.046 | |
| normalize | 0.284 | 0.008 | 0.293 | |
| normalizeExprs | 0.232 | 0.000 | 0.232 | |
| plotColData | 1.956 | 0.060 | 2.033 | |
| plotExplanatoryVariables | 1.040 | 0.004 | 1.048 | |
| plotExpression | 3.468 | 0.008 | 3.482 | |
| plotExprsFreqVsMean | 1.064 | 0.000 | 1.066 | |
| plotExprsVsTxLength | 1.896 | 0.012 | 1.910 | |
| plotHeatmap | 0.524 | 0.012 | 0.542 | |
| plotHighestExprs | 1.112 | 0.000 | 1.114 | |
| plotPlatePosition | 1.128 | 0.000 | 1.126 | |
| plotQC | 1.968 | 0.008 | 1.978 | |
| plotRLE | 3.556 | 0.020 | 3.579 | |
| plotReducedDim | 2.720 | 0.000 | 2.727 | |
| plotRowData | 1.068 | 0.004 | 1.073 | |
| plotScater | 2.156 | 0.000 | 2.157 | |
| plot_reddim | 3.940 | 0.008 | 3.948 | |
| read10xResults | 0.200 | 0.000 | 0.199 | |
| readTxResults | 0.000 | 0.000 | 0.001 | |
| rename | 0.052 | 0.000 | 0.050 | |
| runDiffusionMap | 0.136 | 0.004 | 0.139 | |
| runMDS | 0.084 | 0.004 | 0.088 | |
| runPCA | 0.092 | 0.000 | 0.093 | |
| runTSNE | 0.196 | 0.000 | 0.196 | |
| salmon-wrapper | 0.000 | 0.000 | 0.001 | |
| scater_gui | 0.520 | 0.000 | 0.523 | |
| summariseExprsAcrossFeatures | 0.672 | 0.000 | 0.670 | |
| toSingleCellExperiment | 0.004 | 0.000 | 0.002 | |
| uniquifyFeatureNames | 0.000 | 0.000 | 0.001 | |