BioC 3.4: CHECK report for scater on morelia

Package: scater

Version: 1.1.14

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scater_1.1.14.tar.gz

StartedAt: 2016-09-20 12:48:11 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 12:51:24 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 193.2 seconds

RetCode: 0

Status:  OK

CheckDir: scater.Rcheck

Warnings: 0

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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_1.1.14.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/scater.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.1.14’
* 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  5.6Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
* 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 ... 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
plotPCA        6.015  0.041   6.102
plotExpression 5.752  0.068   5.850
plotTSNE       5.073  0.030   5.129
* 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-3.4-bioc/meat/scater.Rcheck/00check.log’
for details.

* installing *source* package ‘scater’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c calc_cpm.cpp -o calc_cpm.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c init.cpp -o init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c matrix_info.cpp -o matrix_info.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c utils.cpp -o utils.o
clang++ -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_cpm.o init.o matrix_info.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-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’
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
arrange	0.510	0.007	0.517
bootstraps	0.254	0.008	0.263
calcIsExprs	0.433	0.003	0.435
calculateFPKM	0.319	0.008	0.328
calculateQCMetrics	0.329	0.004	0.332
calculateTPM	0.482	0.002	0.484
cellNames	0.276	0.001	0.277
cellPairwiseDistances	0.342	0.009	0.351
counts	0.367	0.135	0.502
cpm	0.233	0.001	0.234
fData	0.000	0.000	0.001
featurePairwiseDistances	0.241	0.002	0.242
filter	0.353	0.003	0.356
findImportantPCs	1.247	0.011	1.259
fpkm	0.414	0.003	0.416
fromCellDataSet	1.308	0.024	1.334
getBMFeatureAnnos	0.001	0.000	0.000
getExprs	0.587	0.005	0.592
get_exprs	0.606	0.146	0.753
isOutlier	0.310	0.001	0.311
is_exprs	0.263	0.002	0.265
multiplot	1.441	0.005	1.447
mutate	0.259	0.011	0.270
newSCESet	0.265	0.002	0.267
nexprs	0.328	0.002	0.329
norm_counts	0.278	0.003	0.280
norm_cpm	0.320	0.003	0.324
norm_exprs	0.274	0.002	0.275
norm_fpkm	0.257	0.001	0.259
norm_tpm	0.418	0.002	0.420
normaliseExprs	1.236	0.016	1.278
normalize	1.517	0.009	1.526
pData	0.001	0.000	0.001
plot	3.249	0.069	3.350
plotDiffusionMap	4.058	0.057	4.153
plotExplanatoryVariables	0.871	0.013	0.884
plotExpression	5.752	0.068	5.850
plotExprsFreqVsMean	1.767	0.017	1.786
plotFeatureData	1.098	0.006	1.106
plotHighestExprs	1.142	0.008	1.153
plotMDS	1.378	0.005	1.568
plotMetadata	0.442	0.002	0.607
plotPCA	6.015	0.041	6.102
plotPhenoData	0.773	0.004	0.778
plotQC	2.442	0.027	2.470
plotReducedDim	4.681	0.024	4.714
plotTSNE	5.073	0.030	5.129
readKallistoResults	0	0	0
readKallistoResultsOneSample	0	0	0
readSalmonResults	0	0	0
readSalmonResultsOneSample	0.001	0.000	0.000
readTxResults	0.001	0.000	0.001
reducedDimension	0.514	0.004	0.518
rename	0.571	0.004	0.575
runKallisto	0.000	0.001	0.000
scater_gui	0.677	0.004	0.682
set_exprs	0.576	0.006	0.581
sizeFactors	0.950	0.005	0.957
stand_exprs	0.537	0.003	0.540
summariseExprsAcrossFeatures	1.987	0.028	2.016
toCellDataSet	0.881	0.005	0.888
tpm	0.484	0.002	0.488
updateSCESet	0.745	0.004	0.750