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 12:08 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
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 2010/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SparseArray 1.6.0 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | 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 SparseArray package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SparseArray.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: SparseArray |
Version: 1.6.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SparseArray.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SparseArray_1.6.0.tar.gz |
StartedAt: 2024-12-21 10:06:38 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 10:10:52 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 253.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SparseArray.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SparseArray.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SparseArray_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SparseArray.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SparseArray/DESCRIPTION’ ... OK * this is package ‘SparseArray’ version ‘1.6.0’ * 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 ‘SparseArray’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 whether startup messages can be suppressed ... 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘SparseArray/libs/SparseArray.so’: Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’, ‘Rf_StringFalse’, ‘Rf_StringTrue’, ‘Rf_isBlankString’ Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed SVT_SparseArray-class 13.225 1.100 14.545 rowsum-methods 8.091 0.502 8.650 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/SparseArray.Rcheck/00check.log’ for details.
SparseArray.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SparseArray ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘SparseArray’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c OPBufTree.c -o OPBufTree.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_SparseArray.c -o R_init_SparseArray.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rvector_summarization.c -o Rvector_summarization.o Rvector_summarization.c:1360:12: warning: unused function 'any_NA_list_elt' [-Wunused-function] static int any_NA_list_elt(SEXP x) ^ Rvector_summarization.c:1370:12: warning: unused function 'count_NA_list_elts' [-Wunused-function] static int count_NA_list_elts(SEXP x) ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rvector_utils.c -o Rvector_utils.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SBT_utils.c -o SBT_utils.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_abind.c -o SparseArray_abind.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_aperm.c -o SparseArray_aperm.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_subassignment.c -o SparseArray_subassignment.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_subassignment_OLD.c -o SparseArray_subassignment_OLD.o SparseArray_subassignment_OLD.c:245:19: warning: unused function 'descend_to_bottom_by_coords0' [-Wunused-function] static inline int descend_to_bottom_by_coords0(SEXP SVT, SEXP SVT0, ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_subsetting.c -o SparseArray_subsetting.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseArray_summarization.c -o SparseArray_summarization.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseMatrix_mult.c -o SparseMatrix_mult.o SparseMatrix_mult.c:306:13: warning: unused function 'crossprod2_doubleSV_doublemat' [-Wunused-function] static void crossprod2_doubleSV_doublemat( ^ SparseMatrix_mult.c:346:13: warning: unused function 'crossprod2_doublemat_doubleSV' [-Wunused-function] static void crossprod2_doublemat_doubleSV( ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec.c -o SparseVec.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec_Arith.c -o SparseVec_Arith.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec_Compare.c -o SparseVec_Compare.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec_Logic.c -o SparseVec_Logic.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec_Math.c -o SparseVec_Math.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SparseVec_dotprod.c -o SparseVec_dotprod.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c argcheck_utils.c -o argcheck_utils.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c coerceVector2.c -o coerceVector2.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c leaf_utils.c -o leaf_utils.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c randomSparseArray.c -o randomSparseArray.o randomSparseArray.c:42:19: warning: unused function 'binary_find_interval' [-Wunused-function] static inline int binary_find_interval(double u, ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c readSparseCSV.c -o readSparseCSV.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rowsum_methods.c -o rowsum_methods.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sparseMatrix_utils.c -o sparseMatrix_utils.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test.c -o test.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c thread_control.c -o thread_control.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o SparseArray.so ExtendableJaggedArray.o IRanges_stubs.o OPBufTree.o R_init_SparseArray.o Rvector_summarization.o Rvector_utils.o S4Vectors_stubs.o SBT_utils.o SVT_SparseArray_class.o SparseArray_Arith_methods.o SparseArray_Compare_methods.o SparseArray_Complex_methods.o SparseArray_Logic_methods.o SparseArray_Math_methods.o SparseArray_abind.o SparseArray_aperm.o SparseArray_dim_tuning.o SparseArray_matrixStats.o SparseArray_misc_methods.o SparseArray_subassignment.o SparseArray_subassignment_OLD.o SparseArray_subsetting.o SparseArray_summarization.o SparseMatrix_mult.o SparseVec.o SparseVec_Arith.o SparseVec_Compare.o SparseVec_Logic.o SparseVec_Math.o SparseVec_dotprod.o XVector_stubs.o argcheck_utils.o coerceVector2.o leaf_utils.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o thread_control.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-SparseArray/00new/SparseArray/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (SparseArray)
SparseArray.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: aarch64-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(SparseArray) Loading required package: Matrix Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min 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 Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:Matrix': expand, unname The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: S4Arrays Loading required package: abind Loading required package: IRanges Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum > > test_check("SparseArray") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 26846 ] > > proc.time() user system elapsed 85.178 8.199 94.241
SparseArray.Rcheck/SparseArray-Ex.timings
name | user | system | elapsed | |
COO_SparseArray-class | 1.965 | 0.088 | 2.065 | |
NaArray-Arith-methods | 0.088 | 0.009 | 0.098 | |
NaArray-Compare-methods | 0.021 | 0.002 | 0.024 | |
NaArray-Logic-methods | 0.030 | 0.003 | 0.034 | |
NaArray-Math-methods | 0.013 | 0.001 | 0.015 | |
NaArray-abind | 0 | 0 | 0 | |
NaArray-aperm | 0.000 | 0.001 | 0.000 | |
NaArray-class | 0.273 | 0.028 | 0.303 | |
NaArray-matrixStats | 0.000 | 0.000 | 0.001 | |
NaArray-misc-methods | 0.077 | 0.003 | 0.081 | |
NaArray-subsetting | 0.148 | 0.006 | 0.155 | |
NaArray-summarization | 0.024 | 0.002 | 0.025 | |
SVT_SparseArray-class | 13.225 | 1.100 | 14.545 | |
SparseArray-Arith-methods | 0.072 | 0.007 | 0.080 | |
SparseArray-Compare-methods | 0.009 | 0.002 | 0.010 | |
SparseArray-Complex-methods | 0 | 0 | 0 | |
SparseArray-Logic-methods | 0.018 | 0.002 | 0.021 | |
SparseArray-Math-methods | 0.006 | 0.000 | 0.006 | |
SparseArray-abind | 0.085 | 0.005 | 0.091 | |
SparseArray-aperm | 0.000 | 0.001 | 0.000 | |
SparseArray-class | 2.689 | 0.281 | 2.995 | |
SparseArray-matrixStats | 0.053 | 0.004 | 0.057 | |
SparseArray-misc-methods | 0.111 | 0.006 | 0.118 | |
SparseArray-subassignment | 0.042 | 0.002 | 0.045 | |
SparseArray-subsetting | 0.178 | 0.010 | 0.188 | |
SparseArray-summarization | 0.037 | 0.005 | 0.042 | |
SparseMatrix-mult | 0.041 | 0.008 | 0.050 | |
extract_sparse_array | 0.084 | 0.006 | 0.091 | |
is_nonna | 0.004 | 0.002 | 0.005 | |
is_nonzero | 0.004 | 0.003 | 0.005 | |
randomSparseArray | 3.371 | 0.191 | 3.575 | |
readSparseCSV | 0.023 | 0.006 | 0.029 | |
rowsum-methods | 8.091 | 0.502 | 8.650 | |
thread-control | 0.001 | 0.000 | 0.002 | |