| Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:12 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1967/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sparseMatrixStats 1.12.2 (landing page) Constantin Ahlmann-Eltze
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the sparseMatrixStats package: - 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: 1.12.2 |
| 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_1.12.2.tar.gz |
| StartedAt: 2023-10-19 02:49:28 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 02:51:35 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 127.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sparseMatrixStats.Rcheck |
| Warnings: 0 |
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###
### 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_1.12.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/sparseMatrixStats.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sparseMatrixStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sparseMatrixStats’ version ‘1.12.2’
* 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 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-arm64/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 arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseMatrixView.cpp -o SparseMatrixView.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c methods.cpp -o methods.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c row_methods.cpp -o row_methods.o clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 0 | SKIP 32 | PASS 1706 ]
══ Skipped tests (32) ══════════════════════════════════════════════════════════
• MatrixGenerics::xxxOrderStats() does not support missing values (10):
'test-functions.R:286:5', 'test-functions.R:286:5', 'test-functions.R:286:5',
'test-functions.R:286:5', 'test-functions.R:286:5', 'test-functions.R:286:5',
'test-functions.R:286:5', 'test-functions.R:286:5', 'test-functions.R:286:5',
'test-row_functions.R:168:3'
• Naming incompatible (10): 'test-functions.R:120:5', 'test-functions.R:139:5',
'test-functions.R:335:5', 'test-functions.R:239:5', 'test-functions.R:120:5',
'test-functions.R:139:5', 'test-functions.R:239:5', 'test-functions.R:335:5',
'test-functions.R:239:5', 'test-row_functions.R:222:3'
• With R 4.3 (?) 'colQuantiles' on logical data suddenly produces an error. I
am unsure why. (1): 'test-logicals.R:87:3'
• different result than matrixStats version, because sparseMatrixStats uses
`interpolate=FALSE`. (10): 'test-functions.R:376:5',
'test-functions.R:376:5', 'test-functions.R:376:5', 'test-functions.R:376:5',
'test-functions.R:376:5', 'test-functions.R:376:5', 'test-functions.R:376:5',
'test-functions.R:376:5', 'test-functions.R:376:5',
'test-row_functions.R:238:3'
• matrixStats doesn't convert values to logical if mat is logical?! (1):
'test-logicals.R:101:3'
[ FAIL 0 | WARN 0 | SKIP 32 | PASS 1706 ]
>
> proc.time()
user system elapsed
9.497 0.291 16.021
sparseMatrixStats.Rcheck/sparseMatrixStats-Ex.timings
| name | user | system | elapsed | |
| colAlls-xgCMatrix-method | 0.001 | 0.001 | 0.002 | |
| colAnyNAs-xgCMatrix-method | 0.002 | 0.001 | 0.011 | |
| colAnys-xgCMatrix-method | 0.001 | 0.000 | 0.001 | |
| colAvgsPerRowSet-xgCMatrix-method | 0.002 | 0.001 | 0.007 | |
| colCollapse-xgCMatrix-method | 0.001 | 0.000 | 0.003 | |
| colCounts-xgCMatrix-method | 0.001 | 0.000 | 0.005 | |
| colCummaxs-dgCMatrix-method | 0.001 | 0.000 | 0.005 | |
| colCummins-dgCMatrix-method | 0.001 | 0.001 | 0.005 | |
| colCumprods-xgCMatrix-method | 0.001 | 0.001 | 0.002 | |
| colCumsums-xgCMatrix-method | 0.002 | 0.001 | 0.002 | |
| colDiffs-dgCMatrix-method | 0.002 | 0.001 | 0.002 | |
| colIQRDiffs-dgCMatrix-method | 0.005 | 0.001 | 0.009 | |
| colIQRs-xgCMatrix-method | 0.002 | 0.001 | 0.006 | |
| colLogSumExps-xgCMatrix-method | 0.001 | 0.001 | 0.001 | |
| colMadDiffs-dgCMatrix-method | 0.002 | 0.001 | 0.006 | |
| colMads-dgCMatrix-method | 0.001 | 0.001 | 0.002 | |
| colMaxs-dgCMatrix-method | 0.001 | 0.001 | 0.003 | |
| colMeans2-xgCMatrix-method | 0.001 | 0.001 | 0.001 | |
| colMedians-dgCMatrix-method | 0.001 | 0.001 | 0.002 | |
| colMins-dgCMatrix-method | 0.001 | 0.001 | 0.003 | |
| colOrderStats-dgCMatrix-method | 0.001 | 0.000 | 0.001 | |
| colProds-xgCMatrix-method | 0.001 | 0.000 | 0.002 | |
| colQuantiles-xgCMatrix-method | 0.004 | 0.001 | 0.009 | |
| colRanges-dgCMatrix-method | 0.001 | 0.001 | 0.002 | |
| colRanks-dgCMatrix-method | 0.002 | 0.001 | 0.002 | |
| colSdDiffs-dgCMatrix-method | 0.002 | 0.001 | 0.005 | |
| colSds-xgCMatrix-method | 0.001 | 0.001 | 0.005 | |
| colSums2-xgCMatrix-method | 0.002 | 0.001 | 0.003 | |
| colTabulates-xgCMatrix-method | 0.002 | 0.001 | 0.003 | |
| colVarDiffs-dgCMatrix-method | 0.002 | 0.000 | 0.002 | |
| colVars-xgCMatrix-method | 0.001 | 0.000 | 0.002 | |
| colWeightedMads-dgCMatrix-method | 0.002 | 0.001 | 0.003 | |
| colWeightedMeans-xgCMatrix-method | 0.002 | 0.000 | 0.006 | |
| colWeightedMedians-dgCMatrix-method | 0.001 | 0.000 | 0.003 | |
| colWeightedSds-xgCMatrix-method | 0.003 | 0.000 | 0.007 | |
| colWeightedVars-xgCMatrix-method | 0.001 | 0.000 | 0.003 | |