Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2011/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sparseMatrixStats 1.18.0 (landing page) Constantin Ahlmann-Eltze
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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. |
Package: sparseMatrixStats |
Version: 1.18.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sparseMatrixStats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sparseMatrixStats_1.18.0.tar.gz |
StartedAt: 2024-12-20 09:59:33 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 10:01:33 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 119.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sparseMatrixStats.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sparseMatrixStats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sparseMatrixStats_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sparseMatrixStats.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sparseMatrixStats/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sparseMatrixStats’ version ‘1.18.0’ * 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * 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 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 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/sparseMatrixStats.Rcheck/00check.log’ for details.
sparseMatrixStats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sparseMatrixStats ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘sparseMatrixStats’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseMatrixView.cpp -o SparseMatrixView.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c methods.cpp -o methods.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c row_methods.cpp -o row_methods.o clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o sparseMatrixStats.so RcppExports.o SparseMatrixView.o methods.o row_methods.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 0 | SKIP 22 | PASS 1763 ] ══ 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:208:3' • 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:274:3' • matrixStats doesn't convert values to logical if mat is logical?! (1): 'test-logicals.R:102:3' [ FAIL 0 | WARN 0 | SKIP 22 | PASS 1763 ] > > proc.time() user system elapsed 18.163 1.067 19.338
sparseMatrixStats.Rcheck/sparseMatrixStats-Ex.timings
name | user | system | elapsed | |
colAlls-xgCMatrix-method | 0.002 | 0.002 | 0.005 | |
colAnyNAs-xgCMatrix-method | 0.003 | 0.001 | 0.004 | |
colAnys-xgCMatrix-method | 0.003 | 0.001 | 0.004 | |
colAvgsPerRowSet-xgCMatrix-method | 0.004 | 0.002 | 0.006 | |
colCollapse-xgCMatrix-method | 0.003 | 0.002 | 0.005 | |
colCounts-xgCMatrix-method | 0.002 | 0.001 | 0.004 | |
colCummaxs-dgCMatrix-method | 0.002 | 0.002 | 0.004 | |
colCummins-dgCMatrix-method | 0.003 | 0.002 | 0.005 | |
colCumprods-xgCMatrix-method | 0.003 | 0.002 | 0.005 | |
colCumsums-xgCMatrix-method | 0.002 | 0.001 | 0.004 | |
colDiffs-dgCMatrix-method | 0.002 | 0.002 | 0.004 | |
colIQRDiffs-dgCMatrix-method | 0.006 | 0.002 | 0.009 | |
colIQRs-xgCMatrix-method | 0.006 | 0.002 | 0.009 | |
colLogSumExps-xgCMatrix-method | 0.003 | 0.001 | 0.004 | |
colMadDiffs-dgCMatrix-method | 0.005 | 0.002 | 0.007 | |
colMads-dgCMatrix-method | 0.002 | 0.001 | 0.004 | |
colMaxs-dgCMatrix-method | 0.002 | 0.001 | 0.004 | |
colMeans2-xgCMatrix-method | 0.003 | 0.001 | 0.004 | |
colMedians-dgCMatrix-method | 0.002 | 0.002 | 0.003 | |
colMins-dgCMatrix-method | 0.002 | 0.001 | 0.004 | |
colOrderStats-dgCMatrix-method | 0.002 | 0.001 | 0.004 | |
colProds-xgCMatrix-method | 0.002 | 0.002 | 0.004 | |
colQuantiles-xgCMatrix-method | 0.007 | 0.002 | 0.009 | |
colRanges-dgCMatrix-method | 0.002 | 0.001 | 0.004 | |
colRanks-dgCMatrix-method | 0.003 | 0.003 | 0.006 | |
colSdDiffs-dgCMatrix-method | 0.003 | 0.001 | 0.005 | |
colSds-xgCMatrix-method | 0.003 | 0.001 | 0.003 | |
colSums2-xgCMatrix-method | 0.002 | 0.002 | 0.003 | |
colTabulates-xgCMatrix-method | 0.004 | 0.003 | 0.008 | |
colVarDiffs-dgCMatrix-method | 0.027 | 0.002 | 0.029 | |
colVars-xgCMatrix-method | 0.001 | 0.001 | 0.002 | |
colWeightedMads-dgCMatrix-method | 0.003 | 0.001 | 0.004 | |
colWeightedMeans-xgCMatrix-method | 0.003 | 0.002 | 0.004 | |
colWeightedMedians-dgCMatrix-method | 0.002 | 0.002 | 0.003 | |
colWeightedSds-xgCMatrix-method | 0.003 | 0.001 | 0.004 | |
colWeightedVars-xgCMatrix-method | 0.003 | 0.002 | 0.005 | |