BioC 3.5: CHECK report for scater on oaxaca

Package: scater

Version: 1.3.35

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scater_1.3.35.tar.gz

StartedAt: 2017-03-04 08:46:40 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 08:51:59 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 319.0 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_1.3.35.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/scater.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.3.35’
* 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  9.9Mb
  sub-directories of 1Mb or more:
    doc   7.5Mb
* 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
plotExpression   14.767  0.099  16.194
plotPCA           8.968  0.039  10.051
plotDiffusionMap  5.833  0.059   5.953
plotTSNE          5.391  0.039   5.532
plotReducedDim    5.111  0.064   5.414
* 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-3.5-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_exprs.cpp -o calc_exprs.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
utils.cpp:86:13: warning: unused variable 's' [-Wunused-variable]
        int s;
            ^
1 warning generated.
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_exprs.o init.o matrix_info.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-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)

name	user	system	elapsed
areSizeFactorsCentred	1.229	0.009	1.238
arrange	0.549	0.002	0.552
bootstraps	0.421	0.005	0.426
calcAverage	0.359	0.003	0.361
calcIsExprs	0.489	0.002	0.492
calculateCPM	0.426	0.002	0.428
calculateFPKM	0.512	0.004	0.516
calculateQCMetrics	0.698	0.003	0.701
calculateTPM	0.881	0.005	0.886
cellNames	0.793	0.026	0.819
cellPairwiseDistances	0.312	0.002	0.315
counts	0.542	0.230	0.771
cpm	0.326	0.003	0.330
fData	0.001	0.000	0.000
featureControlInfo	0.420	0.004	0.425
featurePairwiseDistances	0.344	0.001	0.346
filter	0.496	0.004	0.500
findImportantPCs	3.205	0.026	3.231
fpkm	0.381	0.003	0.385
fromCellDataSet	0.797	0.016	0.814
getBMFeatureAnnos	0.000	0.000	0.001
get_exprs	0.701	0.229	0.939
isOutlier	0.388	0.002	0.391
isSpike	0.419	0.003	0.422
is_exprs	0.397	0.003	0.400
mergeSCESet	2.942	0.017	2.961
multiplot	3.085	0.010	3.097
mutate	0.333	0.001	0.334
newSCESet	0.310	0.001	0.312
nexprs	0.302	0.003	0.306
norm_counts	0.355	0.003	0.358
norm_cpm	0.374	0.002	0.377
norm_exprs	0.385	0.003	0.388
norm_fpkm	0.661	0.006	0.666
norm_tpm	0.358	0.010	0.368
normaliseExprs	1.672	0.031	1.703
normalize	1.532	0.007	1.539
pData	0.000	0.000	0.001
plot	4.601	0.169	4.803
plotDiffusionMap	5.833	0.059	5.953
plotExplanatoryVariables	2.407	0.031	2.440
plotExpression	14.767	0.099	16.194
plotExprsFreqVsMean	2.992	0.027	3.416
plotExprsVsTxLength	3.189	0.043	3.661
plotFeatureData	1.774	0.011	2.012
plotHighestExprs	2.091	0.013	2.389
plotMDS	2.915	0.015	3.325
plotMetadata	0.903	0.004	1.028
plotPCA	8.968	0.039	10.051
plotPhenoData	1.250	0.007	1.417
plotPlatePosition	1.311	0.008	1.409
plotQC	3.399	0.033	3.757
plotReducedDim	5.111	0.064	5.414
plotTSNE	5.391	0.039	5.532
read10XResults	0	0	0
readKallistoResults	0.000	0.000	0.001
readKallistoResultsOneSample	0.001	0.001	0.000
readSalmonResults	0.000	0.000	0.001
readSalmonResultsOneSample	0	0	0
readTxResults	0.001	0.000	0.001
reducedDimension	0.416	0.004	0.442
rename	0.377	0.005	0.381
runKallisto	0.001	0.000	0.000
runSalmon	0.001	0.000	0.001
scater_gui	0.594	0.004	0.598
setSpike	0.485	0.003	0.487
set_exprs	0.582	0.003	0.585
sizeFactors	0.631	0.002	0.633
spikes	0.366	0.004	0.370
stand_exprs	0.358	0.001	0.359
summariseExprsAcrossFeatures	4.386	0.089	4.874
toCellDataSet	0.755	0.009	0.836
tpm	0.410	0.002	0.440
updateSCESet	0.696	0.003	0.817
whichSpike	0.470	0.002	0.533
writeSCESet	0.403	0.003	0.456