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This page was generated on 2024-04-17 11:36:24 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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

Package 2004/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sparseMatrixStats 1.14.0  (landing page)
Constantin Ahlmann-Eltze
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/sparseMatrixStats
git_branch: RELEASE_3_18
git_last_commit: 2923a3b
git_last_commit_date: 2023-10-24 11:20:53 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for sparseMatrixStats on nebbiolo2


To the developers/maintainers of the sparseMatrixStats package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sparseMatrixStats.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: sparseMatrixStats
Version: 1.14.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:sparseMatrixStats.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings sparseMatrixStats_1.14.0.tar.gz
StartedAt: 2024-04-16 04:11:33 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 04:12:35 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 61.7 seconds
RetCode: 0
Status:   OK  
CheckDir: sparseMatrixStats.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:sparseMatrixStats.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings sparseMatrixStats_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/sparseMatrixStats.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘sparseMatrixStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sparseMatrixStats’ version ‘1.14.0’
* 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
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
* 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 loading without being on the library search path ... 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 ...
  ‘sparseMatrixStats.Rmd’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/sparseMatrixStats.Rcheck/00check.log’
for details.



Installation output

sparseMatrixStats.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL sparseMatrixStats
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘sparseMatrixStats’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SparseMatrixView.cpp -o SparseMatrixView.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c methods.cpp -o methods.o
In file included from methods.cpp:6:
quantile.h: In instantiation of ‘double quantile_sparse_impl(T, int, double) [with T = VectorSubsetView<14>]’:
quantile.h:85:58:   required from here
quantile.h:35:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   35 |   for(int i = 0; i < sorted_values.size() + number_of_zeros; i++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
methods.cpp: In instantiation of ‘double colOrderStats::operator()(V&, R&, int) const [with V = SkipNAVectorSubsetView<14>; R = SkipNAVectorSubsetView<13>]’:
methods.cpp:25:18:   required from ‘Rcpp::NumericVector reduce_matrix_double(Rcpp::S4, bool, Functor) [with Functor = colOrderStats; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::S4 = Rcpp::S4_Impl<Rcpp::PreserveStorage>]’
methods.cpp:510:30:   required from here
methods.cpp:475:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  475 |     for(int i = 0; i < sorted_values.size() + number_of_zeros; i++){
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
methods.cpp: In instantiation of ‘double colOrderStats::operator()(V&, R&, int) const [with V = VectorSubsetView<14>; R = VectorSubsetView<13>]’:
methods.cpp:30:18:   required from ‘Rcpp::NumericVector reduce_matrix_double(Rcpp::S4, bool, Functor) [with Functor = colOrderStats; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::S4 = Rcpp::S4_Impl<Rcpp::PreserveStorage>]’
methods.cpp:510:30:   required from here
methods.cpp:475:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from methods.cpp:6:
quantile.h: In instantiation of ‘double quantile_sparse_impl(T, int, double) [with T = SkipNAVectorSubsetView<14>]’:
methods.cpp:269:32:   required from ‘double colMedians::operator()(V&, R&, int) const [with V = SkipNAVectorSubsetView<14>; R = SkipNAVectorSubsetView<13>]’
methods.cpp:25:18:   required from ‘Rcpp::NumericVector reduce_matrix_double(Rcpp::S4, bool, Functor) [with Functor = colMedians; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::S4 = Rcpp::S4_Impl<Rcpp::PreserveStorage>]’
methods.cpp:277:30:   required from here
quantile.h:35:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   35 |   for(int i = 0; i < sorted_values.size() + number_of_zeros; i++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c row_methods.cpp -o row_methods.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o sparseMatrixStats.so RcppExports.o SparseMatrixView.o methods.o row_methods.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-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

sparseMatrixStats.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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")
[ FAIL 0 | WARN 1 | SKIP 22 | PASS 1749 ]

══ Skipped tests (22) ══════════════════════════════════════════════════════════
• MatrixGenerics::xxxOrderStats() does not support missing values (10):
  'test-functions.R:284:5', 'test-functions.R:284:5', 'test-functions.R:284:5',
  'test-functions.R:284:5', 'test-functions.R:284:5', 'test-functions.R:284:5',
  'test-functions.R:284:5', 'test-functions.R:284:5', 'test-functions.R:284:5',
  'test-row_functions.R:170:3'
• With R 4.3 (?) 'colQuantiles' on logical data suddenly produces an error. I
  am unsure why. (1): 'test-logicals.R:88:3'
• different result than matrixStats version, because sparseMatrixStats uses
  `interpolate=FALSE`. (10): 'test-functions.R:373:5',
  'test-functions.R:373:5', 'test-functions.R:373:5', 'test-functions.R:373:5',
  'test-functions.R:373:5', 'test-functions.R:373:5', 'test-functions.R:373:5',
  'test-functions.R:373:5', 'test-functions.R:373:5',
  'test-row_functions.R:236:3'
• matrixStats doesn't convert values to logical if mat is logical?! (1):
  'test-logicals.R:102:3'

[ FAIL 0 | WARN 1 | SKIP 22 | PASS 1749 ]
> 
> proc.time()
   user  system elapsed 
  8.011   0.343   8.345 

Example timings

sparseMatrixStats.Rcheck/sparseMatrixStats-Ex.timings

nameusersystemelapsed
colAlls-xgCMatrix-method0.0020.0000.001
colAnyNAs-xgCMatrix-method0.0010.0010.001
colAnys-xgCMatrix-method0.0010.0000.001
colAvgsPerRowSet-xgCMatrix-method0.0020.0000.002
colCollapse-xgCMatrix-method0.0010.0000.001
colCounts-xgCMatrix-method0.0010.0000.001
colCummaxs-dgCMatrix-method0.0010.0000.001
colCummins-dgCMatrix-method0.0010.0000.000
colCumprods-xgCMatrix-method0.0010.0000.001
colCumsums-xgCMatrix-method0.0010.0000.001
colDiffs-dgCMatrix-method0.0010.0000.001
colIQRDiffs-dgCMatrix-method0.0030.0000.002
colIQRs-xgCMatrix-method0.0030.0000.002
colLogSumExps-xgCMatrix-method0.0010.0000.000
colMadDiffs-dgCMatrix-method0.0020.0000.002
colMads-dgCMatrix-method0.0000.0000.001
colMaxs-dgCMatrix-method0.0010.0000.001
colMeans2-xgCMatrix-method0.0010.0000.001
colMedians-dgCMatrix-method0.0010.0000.000
colMins-dgCMatrix-method0.0010.0000.001
colOrderStats-dgCMatrix-method0.0010.0000.001
colProds-xgCMatrix-method0.0010.0000.001
colQuantiles-xgCMatrix-method0.0030.0000.003
colRanges-dgCMatrix-method0.0010.0000.001
colRanks-dgCMatrix-method0.0010.0000.001
colSdDiffs-dgCMatrix-method0.0020.0000.002
colSds-xgCMatrix-method0.0010.0000.001
colSums2-xgCMatrix-method0.0010.0000.001
colTabulates-xgCMatrix-method0.0010.0000.002
colVarDiffs-dgCMatrix-method0.0010.0000.002
colVars-xgCMatrix-method0.0010.0000.000
colWeightedMads-dgCMatrix-method0.0010.0000.001
colWeightedMeans-xgCMatrix-method0.0010.0000.001
colWeightedMedians-dgCMatrix-method0.0010.0000.001
colWeightedSds-xgCMatrix-method0.0010.0000.002
colWeightedVars-xgCMatrix-method0.0010.0000.001