BioC 3.4: CHECK report for scater on morelia

Package: scater

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scater_1.2.0.tar.gz

StartedAt: 2017-04-15 07:51:17 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 07:55:51 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 273.5 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/scater.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.2.0’
* 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  5.8Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
* 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   11.648  0.124  11.830
plotPCA           8.566  0.040   8.823
plotDiffusionMap  5.380  0.069   5.568
* 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’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scater)

name	user	system	elapsed
arrange	0.667	0.003	0.671
bootstraps	0.403	0.016	0.419
calcIsExprs	0.633	0.008	0.641
calculateFPKM	0.508	0.008	0.516
calculateQCMetrics	0.459	0.003	0.462
calculateTPM	0.819	0.005	0.825
cellNames	0.892	0.005	0.898
cellPairwiseDistances	0.470	0.005	0.475
counts	0.641	0.234	0.877
cpm	0.394	0.002	0.396
fData	0.000	0.000	0.001
featurePairwiseDistances	0.322	0.001	0.325
filter	0.460	0.007	0.467
findImportantPCs	1.652	0.013	1.666
fpkm	0.420	0.002	0.423
fromCellDataSet	2.169	0.034	2.205
getBMFeatureAnnos	0.001	0.000	0.001
getExprs	0.916	0.021	0.937
get_exprs	0.779	0.201	0.982
isOutlier	0.730	0.003	0.733
is_exprs	0.400	0.024	0.424
mergeSCESet	2.898	0.029	2.930
multiplot	1.710	0.009	1.756
mutate	0.341	0.002	0.343
newSCESet	0.372	0.002	0.374
nexprs	0.384	0.002	0.386
norm_counts	0.439	0.003	0.442
norm_cpm	0.431	0.008	0.439
norm_exprs	0.423	0.005	0.429
norm_fpkm	0.378	0.001	0.380
norm_tpm	0.437	0.002	0.439
normaliseExprs	1.564	0.016	1.597
normalize	1.930	0.013	1.945
pData	0	0	0
plot	4.373	0.131	4.580
plotDiffusionMap	5.380	0.069	5.568
plotExplanatoryVariables	1.431	0.038	1.478
plotExpression	11.648	0.124	11.830
plotExprsFreqVsMean	2.425	0.039	2.470
plotExprsVsTxLength	3.400	0.047	3.465
plotFeatureData	1.604	0.019	1.629
plotHighestExprs	1.737	0.016	1.758
plotMDS	2.295	0.012	2.310
plotMetadata	0.894	0.004	0.899
plotPCA	8.566	0.040	8.823
plotPhenoData	0.796	0.005	0.802
plotPlatePosition	1.092	0.010	1.104
plotQC	2.686	0.021	2.710
plotReducedDim	4.324	0.023	4.351
plotTSNE	4.671	0.020	4.776
readKallistoResults	0.001	0.000	0.001
readKallistoResultsOneSample	0	0	0
readSalmonResults	0.000	0.000	0.001
readSalmonResultsOneSample	0	0	0
readTxResults	0.001	0.000	0.001
reducedDimension	0.411	0.003	0.413
rename	0.438	0.003	0.441
runKallisto	0.000	0.001	0.001
runSalmon	0.001	0.000	0.001
scater_gui	0.745	0.004	0.749
set_exprs	0.774	0.004	0.781
sizeFactors	0.785	0.010	0.795
stand_exprs	0.412	0.001	0.414
summariseExprsAcrossFeatures	4.015	0.047	4.067
toCellDataSet	0.765	0.005	0.772
tpm	0.390	0.002	0.393
updateSCESet	0.689	0.003	0.694
writeSCESet	0.330	0.001	0.331