Package: scater

Version: 1.11.15

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:scater.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings scater_1.11.15.tar.gz

StartedAt: 2019-04-09 03:28:37 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:36:04 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 447.0 seconds

RetCode: 0

Status:  OK

CheckDir: scater.Rcheck

Warnings: 0

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:scater.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings scater_1.11.15.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/scater.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.11.15’
* 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 11.2Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
* 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 ... 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
plot_reddim 5.916   0.02   5.947
* 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-3.9-bioc/meat/scater.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL scater
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘scater’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c calc_exprs.cpp -o calc_exprs.o
calc_exprs.cpp: In instantiation of ‘normalizer<M>::normalizer(M*, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
calc_exprs.cpp:105:19:   required from ‘Rcpp::RObject norm_exprs_internal(Rcpp::RObject, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]’
calc_exprs.cpp:144:112:   required from here
calc_exprs.cpp:24:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (i < 0 || i >= nsets) {
                          ˜˜^˜˜˜˜˜˜˜
calc_exprs.cpp:39:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (current.size() != ncells) {
                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
calc_exprs.cpp:51:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (set_id.size()!=ptr->get_nrow()) {
calc_exprs.cpp: In instantiation of ‘normalizer<M>::normalizer(M*, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
calc_exprs.cpp:105:19:   required from ‘Rcpp::RObject norm_exprs_internal(Rcpp::RObject, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]’
calc_exprs.cpp:146:112:   required from here
calc_exprs.cpp:24:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (i < 0 || i >= nsets) {
                          ˜˜^˜˜˜˜˜˜˜
calc_exprs.cpp:39:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (current.size() != ncells) {
                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
calc_exprs.cpp:51:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (set_id.size()!=ptr->get_nrow()) {
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c combined_qc.cpp -o combined_qc.o
combined_qc.cpp: In function ‘void check_topset(const IntegerVector&)’:
combined_qc.cpp:15:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t t=1; t<top.size(); ++t) {
                      ˜^˜˜˜˜˜˜˜˜˜˜
combined_qc.cpp: In instantiation of ‘void compute_cumsum(typename V::iterator, size_t, const IntegerVector&, IT) [with T = int; V = Rcpp::Vector<13>; IT = double*; typename V::iterator = int*; size_t = long unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]’:
combined_qc.cpp:274:61:   required from ‘SEXPREC* top_cumprop_internal(Rcpp::RObject, Rcpp::IntegerVector) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; SEXP = SEXPREC*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>]’
combined_qc.cpp:285:74:   required from here
combined_qc.cpp:35:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         while (x<target_index && x<ngenes) { // '<' as top contains 1-based indices.
                                  ˜^˜˜˜˜˜˜
combined_qc.cpp: In instantiation of ‘void compute_cumsum(typename V::iterator, size_t, const IntegerVector&, IT) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; IT = double*; typename V::iterator = double*; size_t = long unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]’:
combined_qc.cpp:274:61:   required from ‘SEXPREC* top_cumprop_internal(Rcpp::RObject, Rcpp::IntegerVector) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; SEXP = SEXPREC*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>]’
combined_qc.cpp:287:74:   required from here
combined_qc.cpp:35:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c num_exprs.cpp -o num_exprs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c sum_counts.cpp -o sum_counts.o
sum_counts.cpp: In function ‘SEXPREC* sum_row_counts(SEXP, SEXP, SEXP, SEXP)’:
sum_counts.cpp:72:18: warning: unused variable ‘ncells’ [-Wunused-variable]
     const size_t ncells=end_index - start_index;
                  ^˜˜˜˜˜
sum_counts.cpp: In instantiation of ‘Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector<Rcpp::Vector<13> >&, size_t, size_t) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; O = beachmat::lin_output<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’:
sum_counts.cpp:150:83:   required from here
sum_counts.cpp:96:18: warning: unused variable ‘ncells’ [-Wunused-variable]
     const size_t ncells=mat->get_ncol();
                  ^˜˜˜˜˜
sum_counts.cpp: In instantiation of ‘Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector<Rcpp::Vector<13> >&, size_t, size_t) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; O = beachmat::lin_output<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’:
sum_counts.cpp:154:83:   required from here
sum_counts.cpp:96:18: warning: unused variable ‘ncells’ [-Wunused-variable]
In file included from sum_counts.cpp:5:0:
/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of ‘Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’:
sum_counts.cpp:120:22:   required from ‘Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector<Rcpp::Vector<13> >&, size_t, size_t) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >; O = beachmat::lin_output<int, Rcpp::Vector<13> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’
sum_counts.cpp:150:83:   required from here
/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (ref->get_nrow() > indices.size()) {
/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of ‘Rcpp::traits::storage_type<13>::type* beachmat::const_column<M>::get_indices() [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]’:
sum_counts.cpp:120:22:   required from ‘Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector<Rcpp::Vector<13> >&, size_t, size_t) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; O = beachmat::lin_output<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; size_t = long unsigned int]’
sum_counts.cpp:154:83:   required from here
/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o scater.so calc_exprs.o combined_qc.o init.o num_exprs.o sum_counts.o utils.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-scater/00new/scater/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scater)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(scater)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: ggplot2

Attaching package: 'scater'

The following object is masked from 'package:S4Vectors':

    rename

The following object is masked from 'package:stats':

    filter

> 
> test_check("scater")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 1227 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
165.126   3.884 219.263 

name	user	system	elapsed
accessors	0.730	0.052	0.782
arrange	0.062	0.004	0.066
bootstraps	0.046	0.000	0.045
calculateAverage	0.060	0.000	0.061
calculateCPM	0.053	0.004	0.058
calculateFPKM	0.046	0.004	0.050
calculateQCMetrics	0.28	0.00	0.28
calculateTPM	0.084	0.000	0.084
centreSizeFactors	0.057	0.000	0.056
filter	0.066	0.000	0.065
getBMFeatureAnnos	0	0	0
getExplanatoryPCs	0.272	0.094	0.361
getVarianceExplained	0.143	0.016	0.158
isOutlier	0.300	0.012	0.313
librarySizeFactors	0.012	0.000	0.011
multiplot	2.133	0.036	2.170
mutate	0.037	0.004	0.041
nexprs	0.047	0.000	0.047
normalize	0.115	0.008	0.123
normalizeCounts	0.008	0.000	0.007
plotColData	1.907	0.004	1.987
plotExplanatoryPCs	0.708	0.004	0.712
plotExplanatoryVariables	0.621	0.008	0.629
plotExpression	4.64	0.06	4.70
plotExprsFreqVsMean	1.411	0.016	1.427
plotExprsVsTxLength	2.252	0.012	2.264
plotHeatmap	0.982	0.000	1.002
plotHighestExprs	1.34	0.00	1.34
plotPlatePosition	0.946	0.000	0.947
plotRLE	2.234	0.020	2.254
plotReducedDim	4.043	0.008	4.051
plotRowData	1.435	0.004	1.439
plotScater	3.428	0.012	3.440
plot_reddim	5.916	0.020	5.947
readSparseCounts	0.025	0.000	0.025
rename	0.073	0.004	0.076
runDiffusionMap	0.235	0.000	0.236
runMDS	0.123	0.004	0.127
runPCA	0.162	0.000	0.161
runTSNE	0.233	0.004	0.238
runUMAP	3.020	0.003	3.096
sumCountsAcrossCells	0.061	0.012	0.073
sumCountsAcrossFeatures	0.055	0.004	0.058
toSingleCellExperiment	0	0	0
uniquifyFeatureNames	0.000	0.000	0.001