| Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:41:21 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 2000/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sparseMatrixStats 1.15.0 (landing page) Constantin Ahlmann-Eltze
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: sparseMatrixStats |
| Version: 1.15.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:sparseMatrixStats.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings sparseMatrixStats_1.15.0.tar.gz |
| StartedAt: 2024-03-28 09:51:23 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 09:52:33 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 70.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sparseMatrixStats.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:sparseMatrixStats.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings sparseMatrixStats_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/sparseMatrixStats.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sparseMatrixStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sparseMatrixStats’ version ‘1.15.0’
* 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++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 6.1Mb
sub-directories of 1Mb or more:
libs 5.0Mb
* 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 code 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/sparseMatrixStats.Rcheck/00check.log’
for details.
sparseMatrixStats.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL sparseMatrixStats
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘sparseMatrixStats’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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:85:85: 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:510:73: 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:510:73: 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:277:63: 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/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o sparseMatrixStats.so RcppExports.o SparseMatrixView.o methods.o row_methods.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/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)
sparseMatrixStats.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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
10.885 0.321 11.215
sparseMatrixStats.Rcheck/sparseMatrixStats-Ex.timings
| name | user | system | elapsed | |
| colAlls-xgCMatrix-method | 0.001 | 0.002 | 0.002 | |
| colAnyNAs-xgCMatrix-method | 0.003 | 0.001 | 0.002 | |
| colAnys-xgCMatrix-method | 0.001 | 0.001 | 0.002 | |
| colAvgsPerRowSet-xgCMatrix-method | 0.003 | 0.000 | 0.004 | |
| colCollapse-xgCMatrix-method | 0.001 | 0.000 | 0.002 | |
| colCounts-xgCMatrix-method | 0.000 | 0.002 | 0.002 | |
| colCummaxs-dgCMatrix-method | 0.001 | 0.000 | 0.002 | |
| colCummins-dgCMatrix-method | 0.001 | 0.001 | 0.002 | |
| colCumprods-xgCMatrix-method | 0.000 | 0.000 | 0.002 | |
| colCumsums-xgCMatrix-method | 0.000 | 0.001 | 0.001 | |
| colDiffs-dgCMatrix-method | 0.001 | 0.000 | 0.001 | |
| colIQRDiffs-dgCMatrix-method | 0.004 | 0.001 | 0.004 | |
| colIQRs-xgCMatrix-method | 0.004 | 0.000 | 0.003 | |
| colLogSumExps-xgCMatrix-method | 0.002 | 0.000 | 0.001 | |
| colMadDiffs-dgCMatrix-method | 0.003 | 0.000 | 0.003 | |
| colMads-dgCMatrix-method | 0.001 | 0.000 | 0.001 | |
| colMaxs-dgCMatrix-method | 0.001 | 0.000 | 0.001 | |
| colMeans2-xgCMatrix-method | 0.000 | 0.001 | 0.001 | |
| colMedians-dgCMatrix-method | 0.000 | 0.002 | 0.002 | |
| colMins-dgCMatrix-method | 0.000 | 0.001 | 0.002 | |
| colOrderStats-dgCMatrix-method | 0.000 | 0.001 | 0.002 | |
| colProds-xgCMatrix-method | 0.000 | 0.001 | 0.002 | |
| colQuantiles-xgCMatrix-method | 0.001 | 0.005 | 0.005 | |
| colRanges-dgCMatrix-method | 0.002 | 0.000 | 0.001 | |
| colRanks-dgCMatrix-method | 0.002 | 0.000 | 0.002 | |
| colSdDiffs-dgCMatrix-method | 0.000 | 0.003 | 0.003 | |
| colSds-xgCMatrix-method | 0.002 | 0.000 | 0.002 | |
| colSums2-xgCMatrix-method | 0.001 | 0.000 | 0.001 | |
| colTabulates-xgCMatrix-method | 0.003 | 0.000 | 0.003 | |
| colVarDiffs-dgCMatrix-method | 0.002 | 0.000 | 0.002 | |
| colVars-xgCMatrix-method | 0.001 | 0.000 | 0.001 | |
| colWeightedMads-dgCMatrix-method | 0.003 | 0.000 | 0.003 | |
| colWeightedMeans-xgCMatrix-method | 0.002 | 0.000 | 0.003 | |
| colWeightedMedians-dgCMatrix-method | 0.000 | 0.002 | 0.001 | |
| colWeightedSds-xgCMatrix-method | 0.002 | 0.000 | 0.002 | |
| colWeightedVars-xgCMatrix-method | 0.001 | 0.001 | 0.002 | |