Multiple platform build/check report for BioC 3.12 - CHECK report for sparseMatrixStats on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:sparseMatrixStats.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings sparseMatrixStats_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/sparseMatrixStats.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sparseMatrixStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sparseMatrixStats’ version ‘1.2.1’
* package encoding: UTF-8
* 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 ‘sparseMatrixStats’ 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 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
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/sparseMatrixStats.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL sparseMatrixStats
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘sparseMatrixStats’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c SparseMatrixView.cpp -o SparseMatrixView.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c methods.cpp -o methods.o
In file included from methods.cpp:6:0:
quantile.h: In instantiation of ‘double quantile_sparse(T, int, double) [with T = VectorSubsetView<14>]’:
quantile.h:85:80:   required from here
quantile.h:35:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0; i < sorted_values.size() + number_of_zeros; i++){
                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
methods.cpp: In instantiation of ‘dgCMatrix_colOrderStats(Rcpp::S4, int, bool)::<lambda(auto:15, auto:16, int)> [with auto:15 = SkipNAVectorSubsetView<14>; auto:16 = SkipNAVectorSubsetView<13>]’:
methods.cpp:25:18:   required from ‘reduce_matrix_double(Rcpp::S4, bool, Functor)::<lambda(ColumnView::col_container)> [with Functor = dgCMatrix_colOrderStats(Rcpp::S4, int, bool)::<lambda(auto:15, auto:16, int)>]’
methods.cpp:22:8:   required from ‘struct reduce_matrix_double(Rcpp::S4, bool, Functor) [with Functor = dgCMatrix_colOrderStats(Rcpp::S4, int, bool)::<lambda(auto:15, auto:16, int)>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::S4 = Rcpp::S4_Impl<Rcpp::PreserveStorage>]::<lambda(class ColumnView::col_container)>’
methods.cpp:21:19:   required from ‘Rcpp::NumericVector reduce_matrix_double(Rcpp::S4, bool, Functor) [with Functor = dgCMatrix_colOrderStats(Rcpp::S4, int, bool)::<lambda(auto:15, auto:16, int)>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::S4 = Rcpp::S4_Impl<Rcpp::PreserveStorage>]’
methods.cpp:378:4:   required from here
methods.cpp:351:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0; i < sorted_values.size() + number_of_zeros; i++){
                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
methods.cpp: In instantiation of ‘dgCMatrix_colOrderStats(Rcpp::S4, int, bool)::<lambda(auto:15, auto:16, int)> [with auto:15 = VectorSubsetView<14>; auto:16 = VectorSubsetView<13>]’:
methods.cpp:30:18:   required from ‘reduce_matrix_double(Rcpp::S4, bool, Functor)::<lambda(ColumnView::col_container)> [with Functor = dgCMatrix_colOrderStats(Rcpp::S4, int, bool)::<lambda(auto:15, auto:16, int)>]’
methods.cpp:29:8:   required from ‘struct reduce_matrix_double(Rcpp::S4, bool, Functor) [with Functor = dgCMatrix_colOrderStats(Rcpp::S4, int, bool)::<lambda(auto:15, auto:16, int)>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::S4 = Rcpp::S4_Impl<Rcpp::PreserveStorage>]::<lambda(class ColumnView::col_container)>’
methods.cpp:28:19:   required from ‘Rcpp::NumericVector reduce_matrix_double(Rcpp::S4, bool, Functor) [with Functor = dgCMatrix_colOrderStats(Rcpp::S4, int, bool)::<lambda(auto:15, auto:16, int)>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::S4 = Rcpp::S4_Impl<Rcpp::PreserveStorage>]’
methods.cpp:378:4:   required from here
methods.cpp:351:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from methods.cpp:6:0:
quantile.h: In instantiation of ‘double quantile_sparse(T, int, double) [with T = SkipNAVectorSubsetView<14>]’:
methods.cpp:226:27:   required from ‘dgCMatrix_colMedians(Rcpp::S4, bool)::<lambda(auto:5, auto:6, int)> [with auto:5 = SkipNAVectorSubsetView<14>; auto:6 = SkipNAVectorSubsetView<13>]’
methods.cpp:25:18:   required from ‘reduce_matrix_double(Rcpp::S4, bool, Functor)::<lambda(ColumnView::col_container)> [with Functor = dgCMatrix_colMedians(Rcpp::S4, bool)::<lambda(auto:5, auto:6, int)>]’
methods.cpp:22:8:   required from ‘struct reduce_matrix_double(Rcpp::S4, bool, Functor) [with Functor = dgCMatrix_colMedians(Rcpp::S4, bool)::<lambda(auto:5, auto:6, int)>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::S4 = Rcpp::S4_Impl<Rcpp::PreserveStorage>]::<lambda(class ColumnView::col_container)>’
methods.cpp:21:19:   required from ‘Rcpp::NumericVector reduce_matrix_double(Rcpp::S4, bool, Functor) [with Functor = dgCMatrix_colMedians(Rcpp::S4, bool)::<lambda(auto:5, auto:6, int)>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::S4 = Rcpp::S4_Impl<Rcpp::PreserveStorage>]’
methods.cpp:227:4:   required from here
quantile.h:35:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0; i < sorted_values.size() + number_of_zeros; i++){
                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c row_methods.cpp -o row_methods.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o sparseMatrixStats.so RcppExports.o SparseMatrixView.o methods.o row_methods.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-sparseMatrixStats/00new/sparseMatrixStats/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (sparseMatrixStats)

Tests output


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> library(testthat)
> library(sparseMatrixStats)
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

> 
> test_check("sparseMatrixStats")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• different result than matrixStats version, because sparseMatrixStats uses `interpolate=FALSE`. (10)
• matrixStats doesn't convert values to logical if mat is logical?! (1)
• matrixStats has a bug if colCollapse is combined with subsetting (9)
• matrixStats has a bug if rowCollapse is combined with subsetting (1)
• matrixStats::xxxOrderStats() does not support missing values (10)

[ FAIL 0 | WARN 0 | SKIP 31 | PASS 1713 ]
> 
> proc.time()
   user  system elapsed 
  9.024   0.076   9.111

Example timings

name	user	system	elapsed
colAlls-xgCMatrix-method	0.004	0.000	0.002
colAnyNAs-xgCMatrix-method	0.004	0.000	0.001
colAnys-xgCMatrix-method	0.000	0.000	0.002
colAvgsPerRowSet-xgCMatrix-method	0.004	0.000	0.005
colCollapse-xgCMatrix-method	0.000	0.000	0.002
colCounts-xgCMatrix-method	0.004	0.000	0.002
colCummaxs-dgCMatrix-method	0.004	0.000	0.003
colCummins-dgCMatrix-method	0.004	0.000	0.002
colCumprods-xgCMatrix-method	0.004	0.000	0.003
colCumsums-xgCMatrix-method	0.000	0.000	0.002
colDiffs-dgCMatrix-method	0.000	0.000	0.003
colIQRDiffs-dgCMatrix-method	0.000	0.004	0.006
colIQRs-xgCMatrix-method	0.028	0.000	0.026
colLogSumExps-xgCMatrix-method	0.004	0.000	0.001
colMadDiffs-dgCMatrix-method	0.000	0.004	0.004
colMads-dgCMatrix-method	0.004	0.000	0.001
colMaxs-dgCMatrix-method	0.000	0.000	0.002
colMeans2-xgCMatrix-method	0.004	0.000	0.001
colMedians-dgCMatrix-method	0.000	0.000	0.002
colMins-dgCMatrix-method	0.000	0.000	0.002
colOrderStats-dgCMatrix-method	0.004	0.000	0.001
colProds-xgCMatrix-method	0.000	0.000	0.002
colQuantiles-xgCMatrix-method	0.008	0.000	0.005
colRanges-dgCMatrix-method	0.000	0.000	0.002
colRanks-dgCMatrix-method	0.000	0.000	0.001
colSdDiffs-dgCMatrix-method	0.004	0.000	0.002
colSds-xgCMatrix-method	0.000	0.004	0.002
colSums2-xgCMatrix-method	0.000	0.000	0.001
colTabulates-xgCMatrix-method	0.000	0.000	0.003
colVarDiffs-dgCMatrix-method	0.000	0.004	0.003
colVars-xgCMatrix-method	0.004	0.000	0.001
colWeightedMads-dgCMatrix-method	0.004	0.000	0.003
colWeightedMeans-xgCMatrix-method	0.000	0.004	0.003
colWeightedMedians-dgCMatrix-method	0.000	0.000	0.002
colWeightedSds-xgCMatrix-method	0.000	0.000	0.002
colWeightedVars-xgCMatrix-method	0.004	0.000	0.002

CHECK report for sparseMatrixStats on malbec1

Summary

Command output

Installation output

Tests output

Example timings