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: 2017-10-18 02:21:22 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:25:43 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 261.2 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 3.4.2 (2017-09-28)
* 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 7.504  0.004   7.611
plotPCA        5.944  0.008   5.957
plotReducedDim 5.836  0.004   5.856
plotRLE        5.736  0.020   5.763
* 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	0.828	0.000	0.830
arrange	0.46	0.00	0.46
bootstraps	0.244	0.000	0.247
calcAverage	0.304	0.000	0.305
calcIsExprs	0.300	0.000	0.301
calculateCPM	0.320	0.000	0.317
calculateFPKM	0.672	0.000	0.673
calculateQCMetrics	0.488	0.016	0.504
calculateTPM	0.460	0.008	0.470
cellNames	0.496	0.012	0.508
cellPairwiseDistances	0.224	0.000	0.226
counts	0.288	0.076	0.368
cpm	0.212	0.004	0.217
fData	0	0	0
featureControlInfo	0.256	0.000	0.255
featurePairwiseDistances	0.232	0.000	0.230
filter	0.316	0.000	0.317
findImportantPCs	2.284	0.000	2.283
fpkm	0.256	0.000	0.255
fromCellDataSet	0.512	0.004	0.515
getBMFeatureAnnos	0	0	0
get_exprs	0.640	0.120	0.761
isOutlier	0.436	0.000	0.434
isSpike	0.272	0.004	0.278
is_exprs	0.256	0.004	0.263
mergeSCESet	2.792	0.000	2.795
multiplot	2.192	0.000	2.194
mutate	0.236	0.000	0.237
newSCESet	0.232	0.000	0.231
nexprs	0.240	0.000	0.242
norm_counts	0.240	0.000	0.237
norm_cpm	0.224	0.000	0.226
norm_exprs	0.232	0.000	0.234
norm_fpkm	0.232	0.000	0.230
norm_tpm	0.228	0.000	0.226
normaliseExprs	1.06	0.00	1.06
normalize	1.000	0.004	1.006
pData	0	0	0
plot	3.908	0.020	3.930
plotDiffusionMap	4.336	0.012	4.364
plotExplanatoryVariables	0.944	0.008	0.955
plotExpression	7.504	0.004	7.611
plotExprsFreqVsMean	3.024	0.000	3.027
plotExprsVsTxLength	1.828	0.004	1.833
plotFeatureData	1.008	0.000	1.009
plotHighestExprs	1.192	0.000	1.194
plotMDS	1.956	0.004	1.963
plotMetadata	0.540	0.000	0.544
plotPCA	5.944	0.008	5.957
plotPhenoData	1.248	0.000	1.251
plotPlatePosition	0.952	0.000	0.952
plotQC	2.424	0.004	2.432
plotRLE	5.736	0.020	5.763
plotReducedDim	5.836	0.004	5.856
plotTSNE	4.064	0.004	4.072
read10XResults	0.000	0.000	0.001
readKallistoResults	0.000	0.000	0.001
readKallistoResultsOneSample	0	0	0
readSalmonResults	0	0	0
readSalmonResultsOneSample	0	0	0
readTxResults	0.000	0.000	0.001
reducedDimension	0.412	0.000	0.413
rename	0.316	0.000	0.318
runKallisto	0	0	0
runSalmon	0	0	0
scater_gui	0.572	0.000	0.571
setSpike	0.304	0.000	0.303
set_exprs	0.416	0.000	0.418
sizeFactors	0.472	0.000	0.475
spikes	0.300	0.000	0.302
stand_exprs	0.244	0.000	0.244
summariseExprsAcrossFeatures	2.508	0.000	2.510
toCellDataSet	0.660	0.004	0.666
tpm	0.352	0.000	0.348
updateSCESet	0.556	0.000	0.557
whichSpike	0.392	0.000	0.392
writeSCESet	0.352	0.000	0.352