BioC 3.3: CHECK report for scater on morelia

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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scater_0.99.10.tar.gz
###
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* 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.

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

* 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)

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