Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:12 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for batchelor on tokay2


To the developers/maintainers of the batchelor package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/batchelor.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 122/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
batchelor 1.10.0  (landing page)
Aaron Lun
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/batchelor
git_branch: RELEASE_3_14
git_last_commit: fbbcf91
git_last_commit_date: 2021-10-26 12:50:33 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: batchelor
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:batchelor.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings batchelor_1.10.0.tar.gz
StartedAt: 2022-04-12 15:58:01 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 16:12:47 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 886.4 seconds
RetCode: 0
Status:   OK  
CheckDir: batchelor.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:batchelor.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings batchelor_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/batchelor.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'batchelor/DESCRIPTION' ... OK
* this is package 'batchelor' version '1.10.0'
* 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 whether package 'batchelor' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/batchelor/libs/i386/batchelor.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/batchelor/libs/x64/batchelor.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
applyMultiSCE      15.04   0.27   15.31
correctExperiments  8.99   0.18    9.17
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
applyMultiSCE      14.57   0.20   14.79
correctExperiments  7.15   0.09    7.23
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/batchelor.Rcheck/00check.log'
for details.



Installation output

batchelor.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/batchelor_1.10.0.tar.gz && rm -rf batchelor.buildbin-libdir && mkdir batchelor.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=batchelor.buildbin-libdir batchelor_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL batchelor_1.10.0.zip && rm batchelor_1.10.0.tar.gz batchelor_1.10.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  132k  100  132k    0     0   389k      0 --:--:-- --:--:-- --:--:--  390k

install for i386

* installing *source* package 'batchelor' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c adjust_shift_variance.cpp -o adjust_shift_variance.o
adjust_shift_variance.cpp: In function 'Rcpp::NumericVector adjust_shift_variance(Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, double, Rcpp::IntegerVector, Rcpp::IntegerVector)':
adjust_shift_variance.cpp:34:16: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'int' [-Wsign-compare]
     if (ngenes != data2.nrow() || ngenes != vect.ncol()) {
         ~~~~~~~^~~~~~~~~~~~~~~
adjust_shift_variance.cpp:34:42: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'int' [-Wsign-compare]
     if (ngenes != data2.nrow() || ngenes != vect.ncol()) {
                                   ~~~~~~~^~~~~~~~~~~~~~
adjust_shift_variance.cpp:39:16: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'int' [-Wsign-compare]
     if (ncells != vect.nrow()) {
         ~~~~~~~^~~~~~~~~~~~~~
adjust_shift_variance.cpp:118:39: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
             for (size_t other=0; other<restrict1.size(); ++other) {
                                  ~~~~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c find_mutual_nns.cpp -o find_mutual_nns.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c smooth_gaussian_kernel.cpp -o smooth_gaussian_kernel.o
smooth_gaussian_kernel.cpp: In function 'SEXPREC* smooth_gaussian_kernel(Rcpp::NumericMatrix, Rcpp::IntegerVector, Rcpp::NumericMatrix, double)':
smooth_gaussian_kernel.cpp:18:13: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     if (nmnn!=index.size()) {
         ~~~~^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o batchelor.dll tmp.def RcppExports.o adjust_shift_variance.o find_mutual_nns.o smooth_gaussian_kernel.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/batchelor.buildbin-libdir/00LOCK-batchelor/00new/batchelor/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'batchelor'
    finding HTML links ... done
    BatchelorParam                          html  
    finding level-2 HTML links ... done

    applyMultiSCE                           html  
    batchCorrect                            html  
    batchelor-restrict                      html  
    checkInputs                             html  
    clusterMNN                              html  
    convertPCsToSCE                         html  
    correctExperiments                      html  
    cosineNorm                              html  
    diagnostics-cluster                     html  
    divideIntoBatches                       html  
    fastMNN                                 html  
    intersectRows                           html  
    mnnCorrect                              html  
    mnnDeltaVariance                        html  
    multiBatchNorm                          html  
    multiBatchPCA                           html  
    noCorrect                               html  
    quickCorrect                            html  
    reducedMNN                              html  
    reexports                               html  
    regressBatches                          html  
    rescaleBatches                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'batchelor' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c adjust_shift_variance.cpp -o adjust_shift_variance.o
adjust_shift_variance.cpp: In function 'Rcpp::NumericVector adjust_shift_variance(Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, double, Rcpp::IntegerVector, Rcpp::IntegerVector)':
adjust_shift_variance.cpp:34:16: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'int' [-Wsign-compare]
     if (ngenes != data2.nrow() || ngenes != vect.ncol()) {
         ~~~~~~~^~~~~~~~~~~~~~~
adjust_shift_variance.cpp:34:42: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'int' [-Wsign-compare]
     if (ngenes != data2.nrow() || ngenes != vect.ncol()) {
                                   ~~~~~~~^~~~~~~~~~~~~~
adjust_shift_variance.cpp:39:16: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'int' [-Wsign-compare]
     if (ncells != vect.nrow()) {
         ~~~~~~~^~~~~~~~~~~~~~
adjust_shift_variance.cpp:118:39: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
             for (size_t other=0; other<restrict1.size(); ++other) {
                                  ~~~~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c find_mutual_nns.cpp -o find_mutual_nns.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c smooth_gaussian_kernel.cpp -o smooth_gaussian_kernel.o
smooth_gaussian_kernel.cpp: In function 'SEXPREC* smooth_gaussian_kernel(Rcpp::NumericMatrix, Rcpp::IntegerVector, Rcpp::NumericMatrix, double)':
smooth_gaussian_kernel.cpp:18:13: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
     if (nmnn!=index.size()) {
         ~~~~^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o batchelor.dll tmp.def RcppExports.o adjust_shift_variance.o find_mutual_nns.o smooth_gaussian_kernel.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/batchelor.buildbin-libdir/batchelor/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'batchelor' as batchelor_1.10.0.zip
* DONE (batchelor)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'batchelor' successfully unpacked and MD5 sums checked

Tests output

batchelor.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.

> library(testthat)
> library(batchelor)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

> test_check("batchelor")
Loading required package: Matrix

Attaching package: 'Matrix'

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

    expand


Attaching package: 'DelayedArray'

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

    aperm, apply, rowsum, scale, sweep

[ FAIL 0 | WARN 21 | SKIP 0 | PASS 1016 ]

[ FAIL 0 | WARN 21 | SKIP 0 | PASS 1016 ]
> 
> proc.time()
   user  system elapsed 
 251.93    2.10  254.07 

batchelor.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> library(testthat)
> library(batchelor)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

> test_check("batchelor")
Loading required package: Matrix

Attaching package: 'Matrix'

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

    expand


Attaching package: 'DelayedArray'

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

    aperm, apply, rowsum, scale, sweep

[ FAIL 0 | WARN 21 | SKIP 0 | PASS 1016 ]

[ FAIL 0 | WARN 21 | SKIP 0 | PASS 1016 ]
> 
> proc.time()
   user  system elapsed 
 299.54    1.68  301.28 

Example timings

batchelor.Rcheck/examples_i386/batchelor-Ex.timings

nameusersystemelapsed
BatchelorParam0.070.000.06
applyMultiSCE15.04 0.2715.31
batchCorrect1.750.041.80
batchelor-restrict0.460.000.45
checkInputs000
clusterMNN3.920.043.95
convertPCsToSCE0.890.000.89
correctExperiments8.990.189.17
cosineNorm0.010.000.02
diagnostics-cluster1.930.071.98
divideIntoBatches000
fastMNN1.840.001.85
intersectRows0.000.010.01
mnnCorrect0.610.000.61
mnnDeltaVariance2.670.032.70
multiBatchNorm1.390.001.39
multiBatchPCA1.220.001.22
noCorrect0.220.000.22
quickCorrect3.530.023.78
reducedMNN0.550.000.55
regressBatches0.230.000.24
rescaleBatches0.220.000.22

batchelor.Rcheck/examples_x64/batchelor-Ex.timings

nameusersystemelapsed
BatchelorParam0.100.000.09
applyMultiSCE14.57 0.2014.79
batchCorrect2.130.032.91
batchelor-restrict0.430.030.47
checkInputs000
clusterMNN4.220.054.26
convertPCsToSCE0.950.000.96
correctExperiments7.150.097.23
cosineNorm0.010.000.02
diagnostics-cluster1.130.001.12
divideIntoBatches000
fastMNN1.230.001.23
intersectRows000
mnnCorrect0.360.000.36
mnnDeltaVariance2.060.052.11
multiBatchNorm1.240.001.24
multiBatchPCA1.110.001.11
noCorrect0.180.000.18
quickCorrect2.940.012.95
reducedMNN0.50.00.5
regressBatches0.190.000.19
rescaleBatches0.220.000.22