Davis McCarthy
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/scater |
| Branch: RELEASE_3_6 |
| Last Commit: 964effb |
| Last Changed Date: 2018-02-13 08:43:57 -0400 (Tue, 13 Feb 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:14:34 -0400 (Thu, 12 Apr 2018).
| Package 1253/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scater 1.6.3 Davis McCarthy
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: scater |
| Version: 1.6.3 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings scater_1.6.3.tar.gz |
| StartedAt: 2018-04-12 02:45:18 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:49:42 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 263.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scater.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings scater_1.6.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/scater.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.6.3’
* 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 12.1Mb
sub-directories of 1Mb or more:
doc 5.0Mb
extdata 2.9Mb
libs 2.6Mb
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotExpression 8.404 0.024 8.442
plotPCA 5.644 0.004 5.656
* 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
‘/home/biocbuild/bbs-3.6-bioc/meat/scater.Rcheck/00check.log’
for details.
scater.Rcheck/00install.out
* installing *source* package ‘scater’ ... ** libs g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I/usr/local/include -fpic -g -O2 -c calc_variance.cpp -o calc_variance.o g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I/usr/local/include -fpic -g -O2 -c downsample_matrix.cpp -o downsample_matrix.o g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I/usr/local/include -fpic -g -O2 -c margin_summary.cpp -o margin_summary.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o scater.so calc_exprs.o calc_top_features.o calc_variance.o downsample_matrix.o init.o margin_summary.o -L/home/biocbuild/bbs-3.6-bioc/R/library/beachmat/lib -Wl,-rpath,/home/biocbuild/bbs-3.6-bioc/R/library/beachmat/lib -lbeachmat -pthread -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.6-bioc/meat/scater.Rcheck/scater/libs ** R ** data *** moving datasets to lazyload DB ** inst ** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, 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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
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: 278 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
25.960 0.220 26.189
scater.Rcheck/scater-Ex.timings
| name | user | system | elapsed | |
| accessors | 0.680 | 0.016 | 0.696 | |
| areSizeFactorsCentred | 0.2 | 0.0 | 0.2 | |
| arrange | 0.100 | 0.000 | 0.103 | |
| bootstraps | 0.432 | 0.000 | 0.430 | |
| calcAverage | 0.036 | 0.000 | 0.035 | |
| calcIsExprs | 0.040 | 0.000 | 0.039 | |
| calculateCPM | 0.040 | 0.000 | 0.043 | |
| calculateFPKM | 0.040 | 0.004 | 0.044 | |
| calculateQCMetrics | 0.364 | 0.012 | 0.375 | |
| calculateTPM | 0.064 | 0.012 | 0.077 | |
| deprecated | 0 | 0 | 0 | |
| downsampleCounts | 0.200 | 0.004 | 0.207 | |
| filter | 0.104 | 0.000 | 0.105 | |
| findImportantPCs | 2.560 | 0.000 | 2.561 | |
| getBMFeatureAnnos | 0 | 0 | 0 | |
| isOutlier | 0.148 | 0.000 | 0.146 | |
| kallisto-wrapper | 0.000 | 0.000 | 0.001 | |
| multiplot | 2.672 | 0.004 | 2.680 | |
| mutate | 0.040 | 0.000 | 0.037 | |
| newSCESet | 0.012 | 0.000 | 0.011 | |
| nexprs | 0.036 | 0.000 | 0.035 | |
| normaliseExprs | 0.240 | 0.004 | 0.244 | |
| normalize | 0.160 | 0.004 | 0.165 | |
| plotDiffusionMap | 0.140 | 0.000 | 0.137 | |
| plotExplanatoryVariables | 1.132 | 0.004 | 1.137 | |
| plotExpression | 8.404 | 0.024 | 8.442 | |
| plotExprsFreqVsMean | 1.436 | 0.000 | 1.438 | |
| plotExprsVsTxLength | 1.716 | 0.008 | 1.729 | |
| plotFeatureData | 0.488 | 0.004 | 0.493 | |
| plotHighestExprs | 1.736 | 0.004 | 1.741 | |
| plotMDS | 1.700 | 0.000 | 1.703 | |
| plotMetadata | 0.200 | 0.000 | 0.199 | |
| plotPCA | 5.644 | 0.004 | 5.656 | |
| plotPhenoData | 0.668 | 0.000 | 0.669 | |
| plotPlatePosition | 0.552 | 0.000 | 0.555 | |
| plotQC | 1.904 | 0.000 | 1.905 | |
| plotRLE | 4.276 | 0.016 | 4.295 | |
| plotReducedDim | 3.108 | 0.000 | 3.108 | |
| plotScater | 2.588 | 0.008 | 2.602 | |
| plotTSNE | 3.076 | 0.004 | 3.079 | |
| read10XResults | 0.268 | 0.000 | 0.270 | |
| readTxResults | 0.000 | 0.000 | 0.001 | |
| rename | 0.032 | 0.000 | 0.032 | |
| salmon-wrapper | 0.004 | 0.000 | 0.001 | |
| scater_gui | 0.172 | 0.000 | 0.172 | |
| summariseExprsAcrossFeatures | 0.6 | 0.0 | 0.6 | |
| toSingleCellExperiment | 0 | 0 | 0 | |