BioC 3.6: CHECK report for scater on malbec1

Package: scater

Version: 1.5.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings scater_1.5.0.tar.gz

StartedAt: 2017-08-16 02:16:06 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:20:11 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 244.9 seconds

RetCode: 0

Status:  OK

CheckDir: scater.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings scater_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-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 ‘1.5.0’
* 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 7.048  0.012   7.240
plotRLE        5.956  0.016   5.983
plotPCA        5.584  0.016   5.606
* 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-3.6-bioc/meat/scater.Rcheck/00check.log’
for details.

* installing *source* package ‘scater’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++  -I/home/biocbuild/bbs-3.6-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-3.6-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-3.6-bioc/R/lib -L/usr/local/lib -o scater.so calc_exprs.o init.o matrix_info.o utils.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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	0.836	0.000	0.839
arrange	0.448	0.000	0.447
bootstraps	0.228	0.000	0.228
calcAverage	0.224	0.000	0.227
calcIsExprs	0.54	0.00	0.54
calculateCPM	0.300	0.004	0.306
calculateFPKM	0.320	0.004	0.324
calculateQCMetrics	0.484	0.004	0.485
calculateTPM	0.484	0.000	0.485
cellNames	0.532	0.000	0.531
cellPairwiseDistances	0.224	0.000	0.225
counts	0.292	0.092	0.383
cpm	0.224	0.000	0.222
fData	0	0	0
featureControlInfo	0.280	0.000	0.277
featurePairwiseDistances	0.224	0.000	0.224
filter	0.328	0.000	0.328
findImportantPCs	2.192	0.004	2.198
fpkm	0.224	0.000	0.224
fromCellDataSet	0.524	0.000	0.523
getBMFeatureAnnos	0.000	0.000	0.001
get_exprs	0.380	0.104	0.487
isOutlier	0.272	0.000	0.273
isSpike	0.260	0.000	0.262
is_exprs	0.228	0.000	0.228
mergeSCESet	3.224	0.008	3.239
multiplot	1.896	0.000	1.898
mutate	0.244	0.000	0.245
newSCESet	0.220	0.000	0.223
nexprs	0.232	0.000	0.235
norm_counts	0.236	0.000	0.239
norm_cpm	0.224	0.000	0.226
norm_exprs	0.24	0.00	0.24
norm_fpkm	0.236	0.000	0.233
norm_tpm	0.240	0.000	0.243
normaliseExprs	1.012	0.000	1.013
normalize	1.020	0.000	1.021
pData	0.000	0.000	0.001
plot	3.808	0.032	3.843
plotDiffusionMap	4.364	0.008	4.375
plotExplanatoryVariables	1.044	0.000	1.045
plotExpression	7.048	0.012	7.240
plotExprsFreqVsMean	2.812	0.016	2.830
plotExprsVsTxLength	1.760	0.008	1.766
plotFeatureData	0.920	0.000	0.922
plotHighestExprs	1.052	0.008	1.058
plotMDS	1.408	0.000	1.408
plotMetadata	0.508	0.004	0.513
plotPCA	5.584	0.016	5.606
plotPhenoData	0.520	0.004	0.528
plotPlatePosition	0.760	0.000	0.761
plotQC	2.152	0.000	2.153
plotRLE	5.956	0.016	5.983
plotReducedDim	3.832	0.004	3.842
plotTSNE	3.112	0.004	3.121
read10XResults	0.004	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	0.004	0.418
rename	0.308	0.004	0.315
runKallisto	0.004	0.000	0.000
runSalmon	0.000	0.000	0.001
scater_gui	0.448	0.000	0.449
setSpike	0.328	0.000	0.328
set_exprs	0.428	0.000	0.427
sizeFactors	0.468	0.000	0.469
spikes	0.312	0.000	0.313
stand_exprs	0.264	0.000	0.267
summariseExprsAcrossFeatures	2.876	0.004	2.886
toCellDataSet	0.540	0.000	0.541
tpm	0.236	0.000	0.236
updateSCESet	0.440	0.004	0.443
whichSpike	0.292	0.000	0.290
writeSCESet	0.260	0.000	0.261