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This page was generated on 2016-04-21 13:27:49 -0700 (Thu, 21 Apr 2016).
Package 1041/1210 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
scater 0.99.10 Davis McCarthy
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | ERROR | ||||||
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | ERROR | OK | ||||||
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ ERROR ] | OK |
Package: scater |
Version: 0.99.10 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scater_0.99.10.tar.gz |
StartedAt: 2016-04-21 07:20:18 -0700 (Thu, 21 Apr 2016) |
EndedAt: 2016-04-21 07:24:15 -0700 (Thu, 21 Apr 2016) |
EllapsedTime: 237.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: scater.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scater_0.99.10.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/scater.Rcheck’ * using R version 3.3.0 beta (2016-04-06 r70435) * using platform: x86_64-apple-darwin13.4.0 (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 ‘0.99.10’ * 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 ... [11s/11s] OK * checking installed package size ... NOTE installed size is 6.1Mb sub-directories of 1Mb or more: doc 3.9Mb * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [81s/87s] OK Examples with CPU or elapsed time > 5s user system elapsed plotPCA 7.776 0.081 7.879 plotTSNE 7.494 0.053 10.774 plotReducedDim 6.035 0.046 7.971 plotExpression 5.348 0.046 5.413 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [33s/35s] ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Collapsing expression to 500 features.Kallisto log not provided - assuming all runs successfultestthat results ================================================================ OK: 29 SKIPPED: 0 FAILED: 7 1. Failure: we can produce PCA plots with different expression values (@test-plotting.R#12) 2. Failure: we can produce t-SNE plots with different expression values (@test-plotting.R#22) 3. Failure: we can produce Diffusion Map plots with different expression values (@test-plotting.R#34) 4. Failure: we can produce MDS plots with different expression values (@test-plotting.R#48) 5. Failure: we can produce MDS plots with different expression values (@test-plotting.R#49) 6. Failure: we can produce expression plots with different expression values (@test-plotting.R#65) 7. Failure: we can produce expression plots with different expression values (@test-plotting.R#66) Error: testthat unit tests failed Execution halted * 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 ERROR, 1 NOTE See ‘/Users/biocbuild/bbs-3.3-bioc/meat/scater.Rcheck/00check.log’ for details.
testthat.Rout.fail:
R version 3.3.0 beta (2016-04-06 r70435) -- "Supposedly Educational" Copyright (C) 2016 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin13.4.0 (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. > 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, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit 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 Attaching package: 'scater' The following objects are masked from 'package:Biobase': fData<-, pData<- > > test_check("scater") Kallisto log not provided - assuming all runs successful1. Failure: we can produce PCA plots with different expression values (@test-plotting.R#12) class(plotPCA(example_sceset)) produced no output 2. Failure: we can produce t-SNE plots with different expression values (@test-plotting.R#22) class(plotTSNE(example_sceset)) produced no output 3. Failure: we can produce Diffusion Map plots with different expression values (@test-plotting.R#34) class(plotDiffusionMap(example_sceset)) produced no output 4. Failure: we can produce MDS plots with different expression values (@test-plotting.R#48) class(plotMDS(example_sceset)) produced no output 5. Failure: we can produce MDS plots with different expression values (@test-plotting.R#49) class(...) produced no output 6. Failure: we can produce expression plots with different expression values (@test-plotting.R#65) class(plotExpression(example_sceset, 1:4, "Cell_Cycle")) produced no output 7. Failure: we can produce expression plots with different expression values (@test-plotting.R#66) class(plotExpression(example_sceset, 1:4, "Gene_0004")) produced no output Collapsing expression to 500 features.Kallisto log not provided - assuming all runs successfultestthat results ================================================================ OK: 29 SKIPPED: 0 FAILED: 7 1. Failure: we can produce PCA plots with different expression values (@test-plotting.R#12) 2. Failure: we can produce t-SNE plots with different expression values (@test-plotting.R#22) 3. Failure: we can produce Diffusion Map plots with different expression values (@test-plotting.R#34) 4. Failure: we can produce MDS plots with different expression values (@test-plotting.R#48) 5. Failure: we can produce MDS plots with different expression values (@test-plotting.R#49) 6. Failure: we can produce expression plots with different expression values (@test-plotting.R#65) 7. Failure: we can produce expression plots with different expression values (@test-plotting.R#66) Error: testthat unit tests failed Execution halted
scater.Rcheck/00install.out:
* installing *source* package ‘scater’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading Creating a new generic function for ‘pData<-’ in package ‘scater’ Creating a new generic function for ‘fData<-’ in package ‘scater’ Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘scater’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (scater)
scater.Rcheck/scater-Ex.timings:
name | user | system | elapsed | |
bootstraps | 0.734 | 0.016 | 0.752 | |
calcIsExprs | 0.784 | 0.013 | 0.798 | |
calculateFPKM | 0.562 | 0.004 | 0.566 | |
calculateQCMetrics | 0.590 | 0.005 | 0.596 | |
calculateTPM | 1.018 | 0.010 | 1.030 | |
cellNames | 0.524 | 0.003 | 0.527 | |
cellPairwiseDistances | 0.614 | 0.010 | 0.624 | |
counts | 0.829 | 0.224 | 1.053 | |
cpm | 0.438 | 0.005 | 0.443 | |
fData | 0.000 | 0.000 | 0.001 | |
featurePairwiseDistances | 0.540 | 0.004 | 0.546 | |
findImportantPCs | 1.433 | 0.011 | 1.443 | |
fpkm | 0.662 | 0.008 | 0.672 | |
fromCellDataSet | 1.713 | 0.032 | 1.744 | |
getBMFeatureAnnos | 0.000 | 0.000 | 0.001 | |
getExprs | 1.319 | 0.028 | 1.350 | |
get_exprs | 0.917 | 0.227 | 1.147 | |
is_exprs | 0.696 | 0.189 | 0.885 | |
multiplot | 1.310 | 0.012 | 1.324 | |
newSCESet | 0.538 | 0.002 | 0.542 | |
norm_counts | 0.581 | 0.004 | 0.587 | |
norm_cpm | 0.567 | 0.004 | 0.572 | |
norm_exprs | 0.465 | 0.003 | 0.468 | |
norm_fpkm | 0.441 | 0.003 | 0.444 | |
norm_tpm | 0.501 | 0.004 | 0.504 | |
normaliseExprs | 1.688 | 0.019 | 1.725 | |
pData | 0.001 | 0.000 | 0.000 | |
plot | 4.072 | 0.154 | 4.268 | |
plotDiffusionMap | 4.258 | 0.057 | 4.358 | |
plotExplanatoryVariables | 1.611 | 0.026 | 1.639 | |
plotExpression | 5.348 | 0.046 | 5.413 | |
plotExprsFreqVsMean | 1.044 | 0.009 | 1.053 | |
plotFeatureData | 1.080 | 0.027 | 1.108 | |
plotHighestExprs | 1.457 | 0.022 | 1.482 | |
plotMDS | 1.960 | 0.015 | 1.979 | |
plotMetadata | 0.807 | 0.005 | 0.814 | |
plotPCA | 7.776 | 0.081 | 7.879 | |
plotPhenoData | 1.150 | 0.009 | 1.161 | |
plotQC | 2.606 | 0.049 | 2.675 | |
plotReducedDim | 6.035 | 0.046 | 7.971 | |
plotTSNE | 7.494 | 0.053 | 10.774 | |
readKallistoResults | 0.000 | 0.001 | 0.001 | |
readKallistoResultsOneSample | 0.001 | 0.000 | 0.000 | |
readSalmonResults | 0.001 | 0.000 | 0.001 | |
readSalmonResultsOneSample | 0.000 | 0.001 | 0.001 | |
readTxResults | 0.001 | 0.000 | 0.001 | |
reducedDimension | 0.819 | 0.009 | 0.842 | |
runKallisto | 0.000 | 0.000 | 0.001 | |
scater_gui | 1.329 | 0.011 | 1.347 | |
set_exprs | 1.418 | 0.024 | 1.445 | |
stand_exprs | 0.822 | 0.018 | 0.851 | |
summariseExprsAcrossFeatures | 2.745 | 0.049 | 2.799 | |
toCellDataSet | 1.087 | 0.011 | 1.098 | |
tpm | 0.592 | 0.003 | 0.595 | |