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CHECK report for scater on malbec1

This page was generated on 2019-04-16 11:51:51 -0400 (Tue, 16 Apr 2019).

Package 1391/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scater 1.10.1
Davis McCarthy
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/scater
Branch: RELEASE_3_8
Last Commit: 2e6694a
Last Changed Date: 2019-01-04 13:48:22 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: scater
Version: 1.10.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:scater.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings scater_1.10.1.tar.gz
StartedAt: 2019-04-16 02:53:36 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:59:53 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 376.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: scater.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:scater.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings scater_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/scater.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.10.1’
* 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 ... OK
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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: 'calcIsExprs' is deprecated.
  Warning: 'plotQC' is deprecated.
  Warning: 'add_ticks' is deprecated.
  Warning: 'add_ticks' is deprecated.
  Warning: 'add_ticks' is deprecated.
  Warning: 'add_ticks' is deprecated.
  Warning: 'add_ticks' is deprecated.
  Warning: 'add_ticks' is deprecated.
  Warning: 'add_ticks' is deprecated.
  Warning: 'add_ticks' is deprecated.
  Warning: 'add_ticks' is deprecated.
  Warning: 'add_ticks' is deprecated.
  Warning: 'add_ticks' is deprecated.
  Warning: 'readTxResults' is deprecated.
  Warning: 'summariseExprsAcrossFeatures' is deprecated.
  Warning: 'summariseExprsAcrossFeatures' 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
readTxResults 13.064  0.328  13.574
plot_reddim    5.440  0.024   5.469
* 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/scater.Rcheck/00check.log’
for details.

Installation output

scater.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL scater
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘scater’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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<V, M>::normalizer(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with V = Rcpp::Vector<13>; 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:86:64:   required from ‘Rcpp::RObject norm_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with V = Rcpp::Vector<13>; 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:126:110:   required from here
calc_exprs.cpp:14:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (i < 0 || i >= nsets) {
                            ^
calc_exprs.cpp:29:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (current.size() != ncells) { 
                                ^
calc_exprs.cpp:41:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (set_id.size()!=ptr->get_nrow()) { 
                          ^
calc_exprs.cpp: In instantiation of ‘normalizer<V, M>::normalizer(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; 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:86:64:   required from ‘Rcpp::RObject norm_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; 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:129:110:   required from here
calc_exprs.cpp:14:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (i < 0 || i >= nsets) {
                            ^
calc_exprs.cpp:29:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (current.size() != ncells) { 
                                ^
calc_exprs.cpp:41:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (set_id.size()!=ptr->get_nrow()) { 
                          ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from calc_exprs.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
calc_exprs.cpp:172:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
calc_exprs.cpp:172:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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:6:23: 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:257:29:   required from ‘SEXPREC* top_cumprop_internal(M, Rcpp::IntegerVector) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]’
combined_qc.cpp:269:77:   required from here
combined_qc.cpp:26:35: 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:257:29:   required from ‘SEXPREC* top_cumprop_internal(M, Rcpp::IntegerVector) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*; Rcpp::IntegerVector = Rcpp::Vector<13>]’
combined_qc.cpp:272:80:   required from here
combined_qc.cpp:26:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from combined_qc.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
combined_qc.cpp:277:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
combined_qc.cpp:277:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c num_exprs.cpp -o num_exprs.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from num_exprs.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
num_exprs.cpp:137:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
num_exprs.cpp:137:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c sum_counts.cpp -o sum_counts.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
                 from scater.h:5,
                 from sum_counts.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long unsigned int; typename V::iterator = double*]’:
sum_counts.cpp:61:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (indices.size()!=this->get_nrow()) {
                       ^
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of ‘beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long unsigned int; typename V::iterator = int*]’:
sum_counts.cpp:61:1:   required from here
/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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-3.8-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-3.8-bioc/R/library/beachmat/lib -Wl,-rpath,/home/biocbuild/bbs-3.8-bioc/R/library/beachmat/lib -lbeachmat -pthread -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/scater/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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)

Tests output

scater.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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, lengths, 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

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: 1210 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 88.792   4.520 149.963

Example timings

scater.Rcheck/scater-Ex.timings

nameusersystemelapsed
accessors1.2680.0121.283
arrange0.0760.0040.079
bootstraps0.0720.0000.070
calcIsExprs0.0640.0000.063
calculateAverage0.0640.0000.065
calculateCPM0.0960.0040.100
calculateFPKM0.0800.0120.093
calculateQCMetrics0.5400.0000.551
calculateTPM0.1480.0000.146
centreSizeFactors0.0960.0000.094
filter0.1120.0120.126
getBMFeatureAnnos000
getExplanatoryPCs0.2600.0040.266
getVarianceExplained0.1360.0040.141
isOutlier0.3280.0080.339
librarySizeFactors0.0160.0000.012
multiplot1.9840.0001.988
mutate0.0720.0000.072
nexprs0.0960.0000.095
normalize0.1040.0000.103
normalizeCounts0.0080.0040.012
plotColData1.7560.0121.770
plotExplanatoryPCs0.4160.0000.417
plotExplanatoryVariables0.6160.0080.623
plotExpression3.0040.0043.012
plotExprsFreqVsMean0.9640.0040.967
plotExprsVsTxLength2.5480.0202.568
plotHeatmap0.2960.0040.337
plotHighestExprs0.9880.0000.988
plotPlatePosition1.4000.0041.412
plotQC0.5480.0000.548
plotRLE1.9120.0321.947
plotReducedDim3.4320.0083.444
plotRowData1.1040.0081.112
plotScater2.9640.0082.981
plot_reddim5.4400.0245.469
readSparseCounts0.0240.0000.025
readTxResults13.064 0.32813.574
rename0.0760.0040.080
runDiffusionMap0.2200.0000.217
runMDS0.1280.0040.130
runPCA0.1320.0040.135
runTSNE0.2200.0040.225
runUMAP1.4721.1401.877
sumCountsAcrossFeatures0.0720.0000.071
summariseExprsAcrossFeatures1.1040.0361.144
toSingleCellExperiment0.0040.0000.001
uniquifyFeatureNames0.0000.0000.001