BioC 3.5: CHECK report for scater on veracruz2

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scater_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/scater.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.4.0’
* 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 11.1Mb
  sub-directories of 1Mb or more:
    doc   8.4Mb
* 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 ... NOTE
S3 methods shown with full name in documentation object 'arrange':
  ‘arrange.SCESet’

S3 methods shown with full name in documentation object 'filter':
  ‘filter.SCESet’

S3 methods shown with full name in documentation object 'mutate':
  ‘mutate.SCESet’

S3 methods shown with full name in documentation object 'rename':
  ‘rename.SCESet’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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   10.889  0.088  11.297
plotPCA           8.091  0.047   9.926
plotDiffusionMap  6.453  0.070   6.733
plotRLE           5.688  0.186   7.489
plotReducedDim    5.548  0.036   7.158
plot              4.992  0.112   5.264
plotTSNE          4.706  0.020   6.000
* 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: 2 NOTEs
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   -fPIC  -Wall -g -O2  -c calc_exprs.cpp -o calc_exprs.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix_info.cpp -o matrix_info.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -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	1.021	0.004	1.057
arrange	0.612	0.004	0.631
bootstraps	0.314	0.002	0.333
calcAverage	0.274	0.002	0.284
calcIsExprs	0.390	0.002	0.402
calculateCPM	0.380	0.003	0.387
calculateFPKM	0.464	0.004	0.488
calculateQCMetrics	0.695	0.004	0.733
calculateTPM	0.798	0.026	0.851
cellNames	0.655	0.006	0.691
cellPairwiseDistances	0.287	0.002	0.297
counts	0.473	0.202	0.688
cpm	0.296	0.002	0.313
fData	0.001	0.000	0.000
featureControlInfo	0.309	0.003	0.321
featurePairwiseDistances	0.308	0.002	0.330
filter	0.419	0.005	0.436
findImportantPCs	3.024	0.022	3.152
fpkm	0.314	0.002	0.317
fromCellDataSet	0.581	0.013	0.606
getBMFeatureAnnos	0.001	0.000	0.001
get_exprs	0.577	0.200	0.790
isOutlier	0.353	0.003	0.366
isSpike	0.355	0.003	0.363
is_exprs	0.339	0.003	0.351
mergeSCESet	2.820	0.008	2.901
multiplot	2.901	0.012	2.955
mutate	0.285	0.002	0.304
newSCESet	0.298	0.002	0.320
nexprs	0.318	0.002	0.323
norm_counts	0.295	0.002	0.307
norm_cpm	0.309	0.004	0.338
norm_exprs	0.277	0.002	0.281
norm_fpkm	0.287	0.001	0.293
norm_tpm	0.317	0.002	0.328
normaliseExprs	1.345	0.010	1.373
normalize	1.257	0.011	1.296
pData	0.001	0.000	0.001
plot	4.992	0.112	5.264
plotDiffusionMap	6.453	0.070	6.733
plotExplanatoryVariables	1.581	0.030	1.668
plotExpression	10.889	0.088	11.297
plotExprsFreqVsMean	3.850	0.024	4.003
plotExprsVsTxLength	2.468	0.032	2.557
plotFeatureData	1.249	0.010	1.271
plotHighestExprs	1.459	0.007	1.515
plotMDS	2.083	0.011	2.168
plotMetadata	0.669	0.003	0.727
plotPCA	8.091	0.047	9.926
plotPhenoData	0.676	0.005	0.775
plotPlatePosition	1.242	0.008	1.436
plotQC	3.051	0.033	3.679
plotRLE	5.688	0.186	7.489
plotReducedDim	5.548	0.036	7.158
plotTSNE	4.706	0.020	6.000
read10XResults	0.001	0.000	0.000
readKallistoResults	0	0	0
readKallistoResultsOneSample	0	0	0
readSalmonResults	0.000	0.000	0.001
readSalmonResultsOneSample	0.000	0.001	0.000
readTxResults	0.001	0.000	0.001
reducedDimension	0.337	0.004	0.423
rename	0.338	0.004	0.434
runKallisto	0.001	0.000	0.001
runSalmon	0.001	0.000	0.001
scater_gui	0.591	0.003	0.798
setSpike	0.399	0.004	0.518
set_exprs	0.554	0.004	0.717
sizeFactors	0.584	0.003	0.742
spikes	0.373	0.003	0.479
stand_exprs	0.344	0.004	0.450
summariseExprsAcrossFeatures	2.979	0.086	3.714
toCellDataSet	0.590	0.007	0.675
tpm	0.328	0.002	0.374
updateSCESet	0.549	0.006	0.630
whichSpike	0.376	0.003	0.431
writeSCESet	0.332	0.003	0.380

BioC 3.5: CHECK report for scater on veracruz2

Summary

Command output