Package: scater

Version: 1.14.6

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:scater.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings scater_1.14.6.tar.gz

StartedAt: 2020-04-15 03:34:05 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:43:46 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 581.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: scater.Rcheck

Warnings: 2

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:scater.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings scater_1.14.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/scater.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.14.6’
* 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 11.6Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
* 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 ... WARNING
Output for data("sc_example_cell_info", package = "scater"):
  Warning message:
  'data(sc_example_cell_info)' is deprecated.
  Use mockSCE() instead. 
Output for data("sc_example_counts", package = "scater"):
  Warning message:
  'data(sc_example_counts)' is deprecated.
  Use mockSCE() instead. 
* 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 ... WARNING
Found the following significant warnings:

  Warning: 'calculateQCMetrics' is deprecated.
  Warning: 'calculateQCMetrics' is deprecated.
  Warning: 'calculateQCMetrics' is deprecated.
  Warning: 'type=' is deprecated.
  Warning: 'type=' is deprecated.
  Warning: 'centreSizeFactors' is deprecated.
  Warning: 'type=' is deprecated.
  Warning: 'normalizeSCE' is deprecated.
  Warning: 'centreSizeFactors' is deprecated.
  Warning: 'ncomponents' is deprecated.
  Warning: 'calculateQCMetrics' is deprecated.
  Warning: 'plotExprsFreqVsMean' is deprecated.
  Warning: 'plotExprsFreqVsMean' is deprecated.
  Warning: 'plotExprsVsTxLength' is deprecated.
  Warning: 'plotExprsVsTxLength' is deprecated.
  Warning: 'plotExprsVsTxLength' is deprecated.
  Warning: 'plotExprsVsTxLength' is deprecated.
  Warning: 'plotExprsVsTxLength' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotRLE        11.612  0.048  11.677
plot_reddim     9.208  0.020   9.337
plotScater      8.852  0.064   8.984
plotReducedDim  5.648  0.004   5.723
* 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 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/scater.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL scater
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘scater’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-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 instantiation of ‘Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const List&, 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>; Rcpp::List = Rcpp::Vector<19>; size_t = long unsigned int]’:
sum_counts.cpp:154:76:   required from here
sum_counts.cpp:114:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i_summed=0; i_summed!=summable_set.size(); ++i_summed) {
                             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
sum_counts.cpp:94:18: 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 List&, 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>; Rcpp::List = Rcpp::Vector<19>; size_t = long unsigned int]’:
sum_counts.cpp:158:76:   required from here
sum_counts.cpp:114:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i_summed=0; i_summed!=summable_set.size(); ++i_summed) {
                             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
sum_counts.cpp:94:18: warning: unused variable ‘ncells’ [-Wunused-variable]
     const size_t ncells=mat->get_ncol();
                  ^~~~~~
In file included from sum_counts.cpp:5:0:
/home/biocbuild/bbs-3.10-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:125:22:   required from ‘Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const List&, 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>; Rcpp::List = Rcpp::Vector<19>; size_t = long unsigned int]’
sum_counts.cpp:154:76:   required from here
/home/biocbuild/bbs-3.10-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-3.10-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:125:22:   required from ‘Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const List&, 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>; Rcpp::List = Rcpp::Vector<19>; size_t = long unsigned int]’
sum_counts.cpp:158:76:   required from here
/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-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-3.10-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-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-scater/00new/scater/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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, 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
> 
> test_check("scater")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 1649 | SKIPPED: 0 | WARNINGS: 26 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
260.740  15.456 290.256 

name	user	system	elapsed
accessors	1.576	0.004	1.580
addPerCellQC	0.904	0.000	0.904
annotateBMFeatures	0	0	0
bootstraps	0.300	0.016	0.315
calculateAverage	0.244	0.020	0.264
calculateCPM	0.320	0.000	0.319
calculateFPKM	0.908	0.000	0.909
calculateQCMetrics	0.900	0.000	0.901
calculateTPM	0.252	0.000	0.253
centreSizeFactors	0.236	0.000	0.235
getExplanatoryPCs	0.940	0.008	1.023
getVarianceExplained	1.016	0.008	1.023
isOutlier	0.436	0.000	0.434
librarySizeFactors	0.288	0.000	0.287
logNormCounts	0.416	0.000	0.418
medianSizeFactors	0.348	0.004	0.377
mockSCE	0.360	0.008	0.370
multiplot	2.032	0.000	2.033
nexprs	0.384	0.000	0.385
normalize	0.404	0.000	0.405
normalizeCounts	0.364	0.008	0.373
numDetectedAcrossCells	0.356	0.004	0.362
numDetectedAcrossFeatures	0.420	0.000	0.455
perCellQCMetrics	1.46	0.00	1.46
perFeatureQCMetrics	0.396	0.000	0.395
plotColData	2.436	0.000	2.458
plotDots	0.616	0.000	0.616
plotExplanatoryPCs	1.144	0.000	1.146
plotExplanatoryVariables	0.616	0.004	0.618
plotExpression	4.144	0.008	4.168
plotExprsFreqVsMean	1.148	0.016	1.165
plotExprsVsTxLength	3.820	0.024	3.853
plotHeatmap	0.580	0.000	0.582
plotHighestExprs	1.688	0.008	1.700
plotPlatePosition	1.368	0.004	1.385
plotRLE	11.612	0.048	11.677
plotReducedDim	5.648	0.004	5.723
plotRowData	0.772	0.004	0.778
plotScater	8.852	0.064	8.984
plot_reddim	9.208	0.020	9.337
quickPerCellQC	0.800	0.004	0.805
readSparseCounts	0.024	0.000	0.026
retrieveCellInfo	0.464	0.000	0.468
retrieveFeatureInfo	0.524	0.000	0.524
runColDataPCA	0.892	0.000	0.893
runDiffusionMap	0.820	0.000	0.822
runMDS	0.480	0.000	0.483
runMultiUMAP	4.408	0.012	4.439
runPCA	0.800	0.000	0.803
runTSNE	1.536	0.000	1.546
runUMAP	4.660	0.000	4.675
sumCountsAcrossCells	0.712	0.004	0.717
sumCountsAcrossFeatures	0.340	0.000	0.341
toSingleCellExperiment	0	0	0
uniquifyFeatureNames	0.004	0.000	0.001