Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-17 11:38 -0400 (Mon, 17 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
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 2024/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SparseArray 1.7.6 (landing page) Hervé Pagès
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
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: 1.7.6 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SparseArray.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings SparseArray_1.7.6.tar.gz |
StartedAt: 2025-03-17 05:44:26 -0400 (Mon, 17 Mar 2025) |
EndedAt: 2025-03-17 05:49:08 -0400 (Mon, 17 Mar 2025) |
EllapsedTime: 281.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: SparseArray.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SparseArray.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings SparseArray_1.7.6.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/SparseArray.Rcheck' * using R Under development (unstable) (2025-03-01 r87860 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'SparseArray/DESCRIPTION' ... OK * this is package 'SparseArray' version '1.7.6' * 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 whether package 'SparseArray' can be installed ... WARNING Found the following significant warnings: OPBufTree.c:271:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] SVT_SparseArray_class.c:645:23: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] See 'E:/biocbuild/bbs-3.21-bioc/meat/SparseArray.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 14.2.0' * 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: rowsum-methods.Rd: dgCMatrix-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 for x64 is not available * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'SparseArray-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: NaArray-Math-methods > ### Title: 'Math' and 'Math2' methods for NaArray objects > ### Aliases: NaArray-Math-methods NaArray_Math_methods NaArray-Math > ### NaArray_Math NaArray-math-methods NaArray_math_methods NaArray-math > ### NaArray_math NaArray-Math2-methods NaArray_Math2_methods > ### NaArray-Math2 NaArray_Math2 NaArray-math2-methods > ### NaArray_math2_methods NaArray-math2 NaArray_math2 Math,NaArray-method > ### Math2,NaArray-method round,NaArray-method signif,NaArray-method > ### Keywords: array methods arith > > ### ** Examples > > nam <- NaArray(dim=c(15, 6)) > nam[c(2, 6, 12:17, 22:33, 55, 59:62, 90)] <- + c(runif(22)*1e4, Inf, -Inf, NA, NaN) > > log(nam) Warning in .Call2(.NAME, ..., PACKAGE = "SparseArray") : NaNs produced <15 x 6 NaMatrix> of type "double" [nnacount=25 (28%)]: [,1] [,2] [,3] [,4] [,5] [,6] [1,] NA 9.153426 9.202214 NA NaN NA [2,] 7.884233 8.796033 8.242849 NA NA NA [3,] NA NA 8.958598 NA NA NA [4,] NA NA NA NA NA NA [5,] NA NA NA NA NA NA ... . . . . . . [11,] NA 8.834953 NA NA NA NA [12,] 8.653215 8.253498 NA NA NA NA [13,] 9.114058 8.948770 NA NA NA NA [14,] 7.609277 8.512581 NA 7.659843 NA NA [15,] 9.103189 8.878523 NA Inf NA NaN > exp(nam) <15 x 6 NaMatrix> of type "double" [nnacount=25 (28%)]: [,1] [,2] [,3] [,4] [,5] [,6] [1,] NA Inf Inf NA 0 NA [2,] Inf Inf Inf NA NA NA [3,] NA NA Inf NA NA NA [4,] NA NA NA NA NA NA [5,] NA NA NA NA NA NA ... . . . . . . [11,] NA Inf NA NA NA NA [12,] Inf Inf NA NA NA NA [13,] Inf Inf NA NA NA NA [14,] Inf Inf NA Inf NA NA [15,] Inf Inf NA Inf NA NaN > cos(nam) Warning in .Call2(.NAME, ..., PACKAGE = "SparseArray") : NaNs produced <15 x 6 NaMatrix> of type "double" [nnacount=25 (28%)]: [,1] [,2] [,3] [,4] [,5] [,6] [1,] NA -0.9998651 -0.4950179 NA NaN NA [2,] -0.9043939 -0.3543529 0.5609061 NA NA NA [3,] NA NA -0.5490205 NA NA NA [4,] NA NA NA NA NA NA [5,] NA NA NA NA NA NA ... . . . . . . [11,] NA -0.90701040 NA NA NA NA [12,] -0.15988120 -0.42608705 NA NA NA NA [13,] -0.96470867 0.05856411 NA NA NA NA [14,] 0.99654310 0.75858504 NA -0.65985418 NA NA [15,] 0.49049417 0.70564603 NA NaN NA NaN > lgamma(nam) <15 x 6 NaMatrix> of type "double" [nnacount=25 (28%)]: [,1] [,2] [,3] [,4] [,5] [,6] [1,] NA 77019.74 81354.57 NA Inf NA [2,] 18275.21 51512.53 27522.17 NA NA NA [3,] NA NA 61870.18 NA NA NA [4,] NA NA NA NA NA NA [5,] NA NA NA NA NA NA ... . . . . . . [11,] NA 53824.42 NA NA NA NA [12,] 43838.29 27857.75 NA NA NA NA [13,] 73688.87 61189.37 NA NA NA NA [14,] 13326.83 37386.72 NA 14125.45 NA NA [15,] 72794.58 56534.22 NA Inf NA NaN > > ## Sanity checks: > m <- as.matrix(nam) > stopifnot( + suppressWarnings(identical(as.matrix(log(nam)), log(m))), + identical(as.matrix(exp(nam)), exp(m)), + suppressWarnings(identical(as.matrix(cos(nam)), cos(m))), + suppressWarnings(identical(as.matrix(lgamma(nam)), lgamma(m))) + ) Error: identical(as.matrix(exp(nam)), exp(m)) is not TRUE Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' ERROR Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: Backtrace: ▆ 1. └─SparseArray (local) .test_Math_op(m, svt2, op) at test-SparseArray-Math-methods.R:48:9 2. └─testthat::expect_identical(as.array(current), expected) at test-SparseArray-Math-methods.R:30:9 ── Failure ('test-SparseArray-Math-methods.R:49:9'): 'Math' ops on SVT_SparseArray objects ── as.array(current) not identical to `expected`. Objects equal but not identical Backtrace: ▆ 1. └─SparseArray (local) .test_Math_op(a, svt3, op) at test-SparseArray-Math-methods.R:49:9 2. └─testthat::expect_identical(as.array(current), expected) at test-SparseArray-Math-methods.R:30:9 [ FAIL 9 | WARN 0 | SKIP 0 | PASS 28567 ] Error: Test failures Execution halted * 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 ERRORs, 1 WARNING, 2 NOTEs See 'E:/biocbuild/bbs-3.21-bioc/meat/SparseArray.Rcheck/00check.log' for details.
SparseArray.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL SparseArray ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'SparseArray' ... ** this is package 'SparseArray' version '1.7.6' ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 14.2.0' gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o ExtendableJaggedArray.c: In function '_move_ExtendableJaggedArrays_to_SVT': ExtendableJaggedArray.c:129:25: warning: 'nzvals_p' may be used uninitialized [-Wmaybe-uninitialized] 129 | free(nzvals_p); | ^~~~~~~~~~~~~~ ExtendableJaggedArray.c:111:22: note: 'nzvals_p' was declared here 111 | int *nzvals_p, *nzoffs_p; | ^~~~~~~~ ExtendableJaggedArray.c:125:25: warning: 'nzoffs_p' may be used uninitialized [-Wmaybe-uninitialized] 125 | free(nzoffs_p); | ^~~~~~~~~~~~~~ ExtendableJaggedArray.c:111:33: note: 'nzoffs_p' was declared here 111 | int *nzvals_p, *nzoffs_p; | ^~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c OPBufTree.c -o OPBufTree.o OPBufTree.c: In function 'print_OPBuf': OPBufTree.c:271:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 271 | Rprintf("%4lu", opbuf->xLoffs[k]); | ~~~^ ~~~~~~~~~~~~~~~~ | | | | | R_xlen_t {aka long long int} | long unsigned int | %4llu gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c R_init_SparseArray.c -o R_init_SparseArray.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c Rvector_summarization.c -o Rvector_summarization.o Rvector_summarization.c:1370:12: warning: 'count_NA_list_elts' defined but not used [-Wunused-function] 1370 | static int count_NA_list_elts(SEXP x) | ^~~~~~~~~~~~~~~~~~ Rvector_summarization.c:1360:12: warning: 'any_NA_list_elt' defined but not used [-Wunused-function] 1360 | static int any_NA_list_elt(SEXP x) | ^~~~~~~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c Rvector_utils.c -o Rvector_utils.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SBT_utils.c -o SBT_utils.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o SVT_SparseArray_class.c: In function 'C_from_SVT_SparseMatrix_to_CsparseMatrix': SVT_SparseArray_class.c:645:23: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=] 645 | error("SVT_SparseMatrix object contains too many nonzero " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 646 | "values (%ld) to \"fit\" in a CsparseMatrix derivative", 647 | x_nzcount); | ~~~~~~~~~ | | | R_xlen_t {aka long long int} SVT_SparseArray_class.c:646:34: note: format string is defined here 646 | "values (%ld) to \"fit\" in a CsparseMatrix derivative", | ~~^ | | | long int | %lld gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_abind.c -o SparseArray_abind.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_aperm.c -o SparseArray_aperm.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_subassignment.c -o SparseArray_subassignment.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_subassignment_OLD.c -o SparseArray_subassignment_OLD.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_subsetting.c -o SparseArray_subsetting.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseArray_summarization.c -o SparseArray_summarization.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseMatrix_mult.c -o SparseMatrix_mult.o SparseMatrix_mult.c:346:13: warning: 'crossprod2_doublemat_doubleSV' defined but not used [-Wunused-function] 346 | static void crossprod2_doublemat_doubleSV( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SparseMatrix_mult.c:306:13: warning: 'crossprod2_doubleSV_doublemat' defined but not used [-Wunused-function] 306 | static void crossprod2_doubleSV_doublemat( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseVec.c -o SparseVec.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseVec_Arith.c -o SparseVec_Arith.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseVec_Compare.c -o SparseVec_Compare.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseVec_Logic.c -o SparseVec_Logic.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseVec_Math.c -o SparseVec_Math.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c SparseVec_dotprod.c -o SparseVec_dotprod.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c argcheck_utils.c -o argcheck_utils.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c coerceVector2.c -o coerceVector2.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c leaf_utils.c -o leaf_utils.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c randomSparseArray.c -o randomSparseArray.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c readSparseCSV.c -o readSparseCSV.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c rowsum_methods.c -o rowsum_methods.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c sparseMatrix_utils.c -o sparseMatrix_utils.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c test.c -o test.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -c thread_control.c -o thread_control.o gcc -shared -s -static-libgcc -o SparseArray.dll tmp.def 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 -fopenmp -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-SparseArray/00new/SparseArray/libs/x64 ** 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 ** 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.fail
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Type 'q()' to quit R. > library(testthat) > library(SparseArray) Loading required package: Matrix Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: 'IRanges' The following object is masked from 'package:grDevices': windows 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 9 | WARN 0 | SKIP 0 | PASS 28567 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-NaArray-Math-methods.R:43:5'): 'Math' ops on NaArray objects ── as.array(current) not identical to `expected`. Objects equal but not identical Backtrace: ▆ 1. └─SparseArray (local) .test_NaMath_op(a, naa, op) at test-NaArray-Math-methods.R:43:5 2. └─testthat::expect_identical(as.array(current), expected) at test-NaArray-Math-methods.R:30:9 ── Failure ('test-NaArray-Math-methods.R:43:5'): 'Math' ops on NaArray objects ── as.array(current) not identical to `expected`. 1/120 mismatches [53] -0.818 - 0.979 == -1.8 Backtrace: ▆ 1. └─SparseArray (local) .test_NaMath_op(a, naa, op) at test-NaArray-Math-methods.R:43:5 2. └─testthat::expect_identical(as.array(current), expected) at test-NaArray-Math-methods.R:30:9 ── Failure ('test-NaArray-Math-methods.R:43:5'): 'Math' ops on NaArray objects ── as.array(current) not identical to `expected`. Objects equal but not identical Backtrace: ▆ 1. └─SparseArray (local) .test_NaMath_op(a, naa, op) at test-NaArray-Math-methods.R:43:5 2. └─testthat::expect_identical(as.array(current), expected) at test-NaArray-Math-methods.R:30:9 ── Failure ('test-NaArray-Math-methods.R:43:5'): 'Math' ops on NaArray objects ── as.array(current) not identical to `expected`. 1/120 mismatches [53] -0.575 - 0.204 == -0.779 Backtrace: ▆ 1. └─SparseArray (local) .test_NaMath_op(a, naa, op) at test-NaArray-Math-methods.R:43:5 2. └─testthat::expect_identical(as.array(current), expected) at test-NaArray-Math-methods.R:30:9 ── Failure ('test-NaArray-Math-methods.R:43:5'): 'Math' ops on NaArray objects ── as.array(current) not identical to `expected`. Objects equal but not identical Backtrace: ▆ 1. └─SparseArray (local) .test_NaMath_op(a, naa, op) at test-NaArray-Math-methods.R:43:5 2. └─testthat::expect_identical(as.array(current), expected) at test-NaArray-Math-methods.R:30:9 ── Failure ('test-SparseArray-Math-methods.R:49:9'): 'Math' ops on SVT_SparseArray objects ── as.array(current) not identical to `expected`. Objects equal but not identical Backtrace: ▆ 1. └─SparseArray (local) .test_Math_op(a, svt3, op) at test-SparseArray-Math-methods.R:49:9 2. └─testthat::expect_identical(as.array(current), expected) at test-SparseArray-Math-methods.R:30:9 ── Failure ('test-SparseArray-Math-methods.R:49:9'): 'Math' ops on SVT_SparseArray objects ── as.array(current) not identical to `expected`. 1/120 mismatches [53] -0.818 - 0.979 == -1.8 Backtrace: ▆ 1. └─SparseArray (local) .test_Math_op(a, svt3, op) at test-SparseArray-Math-methods.R:49:9 2. └─testthat::expect_identical(as.array(current), expected) at test-SparseArray-Math-methods.R:30:9 ── Failure ('test-SparseArray-Math-methods.R:48:9'): 'Math' ops on SVT_SparseArray objects ── as.array(current) not identical to `expected`. Objects equal but not identical Backtrace: ▆ 1. └─SparseArray (local) .test_Math_op(m, svt2, op) at test-SparseArray-Math-methods.R:48:9 2. └─testthat::expect_identical(as.array(current), expected) at test-SparseArray-Math-methods.R:30:9 ── Failure ('test-SparseArray-Math-methods.R:49:9'): 'Math' ops on SVT_SparseArray objects ── as.array(current) not identical to `expected`. Objects equal but not identical Backtrace: ▆ 1. └─SparseArray (local) .test_Math_op(a, svt3, op) at test-SparseArray-Math-methods.R:49:9 2. └─testthat::expect_identical(as.array(current), expected) at test-SparseArray-Math-methods.R:30:9 [ FAIL 9 | WARN 0 | SKIP 0 | PASS 28567 ] Error: Test failures Execution halted
SparseArray.Rcheck/SparseArray-Ex.timings
name | user | system | elapsed | |
COO_SparseArray-class | 1.80 | 0.06 | 1.86 | |
NaArray-Arith-methods | 0.08 | 0.02 | 0.09 | |
NaArray-Compare-methods | 0.03 | 0.00 | 0.04 | |
NaArray-Logic-methods | 0.03 | 0.00 | 0.03 | |