BioC 3.5: CHECK report for scater on malbec2

Package: scater

Version: 1.4.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings scater_1.4.0.tar.gz

StartedAt: 2017-08-16 02:08:43 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:12:51 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 248.2 seconds

RetCode: 0

Status:  OK

CheckDir: scater.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings scater_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/scater.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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  8.6Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
* 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 7.512  0.020   7.556
plotPCA        6.356  0.016   6.376
plotRLE        5.848  0.016   5.870
* 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/scater.Rcheck/00check.log’
for details.

* installing *source* package ‘scater’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c calc_exprs.cpp -o calc_exprs.o
calc_exprs.cpp: In instantiation of ‘SEXPREC* calc_exprs_internal(const T*, const matrix_info&, SEXP, SEXP, SEXP, SEXP, SEXP) [with T = int; SEXP = SEXPREC*]’:
calc_exprs.cpp:78:95:   required from here
calc_exprs.cpp:5:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (!isReal(size_fac) || LENGTH(size_fac)!=MAT.ncol) { 
                                              ^
calc_exprs.cpp: In instantiation of ‘SEXPREC* calc_exprs_internal(const T*, const matrix_info&, SEXP, SEXP, SEXP, SEXP, SEXP) [with T = double; SEXP = SEXPREC*]’:
calc_exprs.cpp:80:98:   required from here
calc_exprs.cpp:5:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c matrix_info.cpp -o matrix_info.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
utils.cpp: In function ‘subset_info process_subset_vector(SEXP, const matrix_info&, bool)’:
utils.cpp:20:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (sptr[s] < 0 || sptr[s] >= upper) { 
                                    ^
utils.cpp: In instantiation of ‘SEXPREC* rowsum_subset_internal(const T*, const matrix_info&, SEXP) [with T = int; SEXP = SEXPREC*]’:
utils.cpp:106:65:   required from here
utils.cpp:86:13: warning: unused variable ‘s’ [-Wunused-variable]
         int s;
             ^
utils.cpp: In instantiation of ‘SEXPREC* rowsum_subset_internal(const T*, const matrix_info&, SEXP) [with T = double; SEXP = SEXPREC*]’:
utils.cpp:108:68:   required from here
utils.cpp:86:13: warning: unused variable ‘s’ [-Wunused-variable]
utils.cpp: In instantiation of ‘SEXPREC* calc_top_features_internal(const T*, const matrix_info&, SEXP, SEXP) [with T = int; SEXP = SEXPREC*]’:
utils.cpp:336:74:   required from here
utils.cpp:263:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t t=1; t<ntop; ++t) {
                       ^
utils.cpp:292:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (t=1; t<ntop; ++t) {
                    ^
utils.cpp:303:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (r=0; r<itercycles; ++r) {
                        ^
utils.cpp:313:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (t=0; t<ntop; ++t) {
                        ^
utils.cpp: In instantiation of ‘SEXPREC* calc_top_features_internal(const T*, const matrix_info&, SEXP, SEXP) [with T = double; SEXP = SEXPREC*]’:
utils.cpp:338:77:   required from here
utils.cpp:263:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t t=1; t<ntop; ++t) {
                       ^
utils.cpp:292:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (t=1; t<ntop; ++t) {
                    ^
utils.cpp:303:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (r=0; r<itercycles; ++r) {
                        ^
utils.cpp:313:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (t=0; t<ntop; ++t) {
                        ^
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o scater.so calc_exprs.o init.o matrix_info.o utils.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/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	0.824	0.004	0.829
arrange	0.452	0.000	0.450
bootstraps	0.244	0.004	0.247
calcAverage	0.244	0.000	0.241
calcIsExprs	0.552	0.000	0.552
calculateCPM	0.276	0.016	0.291
calculateFPKM	0.312	0.008	0.320
calculateQCMetrics	0.480	0.000	0.482
calculateTPM	0.436	0.000	0.438
cellNames	0.528	0.000	0.528
cellPairwiseDistances	0.220	0.004	0.226
counts	0.264	0.100	0.363
cpm	0.212	0.004	0.215
fData	0.000	0.000	0.001
featureControlInfo	0.256	0.000	0.256
featurePairwiseDistances	0.212	0.004	0.219
filter	0.384	0.000	0.386
findImportantPCs	2.296	0.004	2.301
fpkm	0.248	0.000	0.248
fromCellDataSet	0.540	0.008	0.552
getBMFeatureAnnos	0	0	0
get_exprs	0.400	0.100	0.501
isOutlier	0.304	0.000	0.304
isSpike	0.292	0.000	0.291
is_exprs	0.248	0.000	0.247
mergeSCESet	2.620	0.000	2.624
multiplot	1.848	0.004	1.855
mutate	0.228	0.000	0.228
newSCESet	0.228	0.000	0.225
nexprs	0.220	0.000	0.221
norm_counts	0.224	0.000	0.222
norm_cpm	0.244	0.000	0.242
norm_exprs	0.22	0.00	0.22
norm_fpkm	0.208	0.000	0.209
norm_tpm	0.224	0.000	0.225
normaliseExprs	1.008	0.000	1.009
normalize	0.972	0.004	0.977
pData	0.000	0.000	0.001
plot	3.852	0.004	3.858
plotDiffusionMap	4.460	0.052	4.531
plotExplanatoryVariables	1.040	0.004	1.048
plotExpression	7.512	0.020	7.556
plotExprsFreqVsMean	2.648	0.000	2.648
plotExprsVsTxLength	2.364	0.000	2.366
plotFeatureData	0.924	0.024	0.945
plotHighestExprs	1.060	0.000	1.061
plotMDS	1.404	0.008	1.411
plotMetadata	0.472	0.000	0.472
plotPCA	6.356	0.016	6.376
plotPhenoData	0.516	0.000	0.516
plotPlatePosition	0.900	0.000	0.898
plotQC	2.664	0.008	2.673
plotRLE	5.848	0.016	5.870
plotReducedDim	4.832	0.004	4.847
plotTSNE	3.712	0.000	3.726
read10XResults	0	0	0
readKallistoResults	0	0	0
readKallistoResultsOneSample	0	0	0
readSalmonResults	0.000	0.000	0.001
readSalmonResultsOneSample	0.000	0.000	0.001
readTxResults	0.000	0.004	0.002
reducedDimension	0.392	0.000	0.392
rename	0.396	0.000	0.398
runKallisto	0.000	0.000	0.001
runSalmon	0	0	0
scater_gui	0.668	0.000	0.670
setSpike	0.796	0.000	0.800
set_exprs	0.368	0.000	0.369
sizeFactors	0.432	0.000	0.432
spikes	0.320	0.000	0.318
stand_exprs	0.344	0.000	0.346
summariseExprsAcrossFeatures	2.532	0.008	2.545
toCellDataSet	0.512	0.000	0.514
tpm	0.264	0.000	0.264
updateSCESet	0.480	0.000	0.479
whichSpike	0.284	0.000	0.283
writeSCESet	0.268	0.000	0.269