Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-05 11:41 -0400 (Fri, 05 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4593 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4399 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3688 |
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 44/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
alabaster.matrix 1.5.4 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the alabaster.matrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/alabaster.matrix.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: alabaster.matrix |
Version: 1.5.4 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:alabaster.matrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings alabaster.matrix_1.5.4.tar.gz |
StartedAt: 2024-07-04 18:41:33 -0400 (Thu, 04 Jul 2024) |
EndedAt: 2024-07-04 18:45:07 -0400 (Thu, 04 Jul 2024) |
EllapsedTime: 213.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: alabaster.matrix.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:alabaster.matrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings alabaster.matrix_1.5.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/alabaster.matrix.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘alabaster.matrix/DESCRIPTION’ ... OK * this is package ‘alabaster.matrix’ version ‘1.5.4’ * 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 ‘alabaster.matrix’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘alabaster.matrix-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: saveDelayedArray > ### Title: Save DelayedArrays to disk > ### Aliases: saveDelayedArray stageObject,DelayedArray-method > ### stageObject,DelayedMatrix-method saveObject,DelayedArray-method > > ### ** Examples > > mat <- Matrix::rsparsematrix(100, 200, density=0.2) > rownames(mat) <- paste0("GENE_", seq_len(nrow(mat))) > dmat <- DelayedArray::DelayedArray(mat) * 1 > > dir <- tempfile() > saveObject(dmat, dir, delayed.preserve.ops=TRUE) Error: unable to find an inherited method for function ‘nzdata’ for signature ‘x = "SVT_SparseMatrix"’ 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: 9. └─alabaster.matrix:::.extract_sparse_details(mat) 10. └─DelayedArray::blockApply(...) 11. └─DelayedArray::gridApply(...) 12. └─S4Arrays:::bplapply2(...) 13. ├─BiocGenerics::lapply(X, FUN, ...) 14. └─base::lapply(X, FUN, ...) 15. └─DelayedArray (local) FUN(X[[i]], ...) 16. └─DelayedArray (local) FUN(viewport, ...) 17. └─alabaster.matrix (local) FUN(block, ...) 18. └─SparseArray::nzdata(sparse) 19. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) [ FAIL 13 | WARN 90 | SKIP 0 | PASS 560 ] 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, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/alabaster.matrix.Rcheck/00check.log’ for details.
alabaster.matrix.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL alabaster.matrix ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘alabaster.matrix’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -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++17 -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 collect_attributes.cpp -o collect_attributes.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o alabaster.matrix.so RcppExports.o collect_attributes.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-alabaster.matrix/00new/alabaster.matrix/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 (alabaster.matrix)
alabaster.matrix.Rcheck/tests/testthat.Rout.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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(alabaster.matrix) Loading required package: alabaster.base > test_check("alabaster.matrix") [ FAIL 13 | WARN 90 | SKIP 0 | PASS 560 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-AmalgamatedArray.R:52:5'): Amalgamated staging and loading works when the inner arrays are delayed wrappers ── Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"' Backtrace: ▆ 1. ├─alabaster.base::stageObject(mat, temp, "amalgam") at test-AmalgamatedArray.R:52:5 2. └─alabaster.matrix::stageObject(mat, temp, "amalgam") 3. └─alabaster.matrix (local) .local(x, dir, path, child, ...) 4. └─alabaster.base::.stageObject(...) 5. └─alabaster.base::altStageObject(...) 6. ├─alabaster.base (local) FUN(...) 7. └─alabaster.matrix (local) FUN(...) 8. └─alabaster.matrix (local) .local(x, dir, path, child, ...) 9. └─alabaster.matrix:::.stage_delayed(...) 10. └─alabaster.matrix (local) fallback(x, dir, path, child = child) 11. └─alabaster.matrix:::.stage_sparse_matrix(x, dir, path, child = child) 12. └─alabaster.matrix::writeSparseMatrix(...) 13. └─alabaster.matrix:::.write_CS_matrix(...) 14. ├─alabaster.matrix:::.extract_sparse_details(mat) 15. └─alabaster.matrix:::.extract_sparse_details(mat) 16. ├─alabaster.matrix:::.extract_sparse_details(x@seed) 17. └─alabaster.matrix:::.extract_sparse_details(x@seed) 18. └─DelayedArray::blockApply(...) 19. └─DelayedArray::gridApply(...) 20. └─S4Arrays:::bplapply2(...) 21. ├─BiocGenerics::lapply(X, FUN, ...) 22. └─base::lapply(X, FUN, ...) 23. └─DelayedArray (local) FUN(X[[i]], ...) 24. └─DelayedArray (local) FUN(viewport, ...) 25. └─alabaster.matrix (local) FUN(block, ...) 26. └─SparseArray::nzdata(sparse) 27. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) ── Error ('test-SparseMatrix.R:53:13'): writing to a sparse matrix works as expected for numeric data ── Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"' Backtrace: ▆ 1. ├─alabaster.base::saveObject(x, tmp) at test-SparseMatrix.R:53:13 2. └─alabaster.matrix::saveObject(x, tmp) 3. └─alabaster.matrix (local) .local(x, path, ...) 4. └─alabaster.matrix:::.save_compressed_sparse_matrix(x, path, ...) 5. └─alabaster.matrix:::optimize_storage(x) 6. └─alabaster.matrix:::optimize_float_storage(x) 7. ├─alabaster.matrix:::collect_float_attributes(x) 8. └─alabaster.matrix:::collect_float_attributes(x) 9. └─DelayedArray::blockApply(...) 10. └─DelayedArray::gridApply(...) 11. └─S4Arrays:::bplapply2(...) 12. ├─BiocGenerics::lapply(X, FUN, ...) 13. └─base::lapply(X, FUN, ...) 14. └─DelayedArray (local) FUN(X[[i]], ...) 15. └─DelayedArray (local) FUN(viewport, ...) 16. └─alabaster.matrix (local) FUN(block, ...) 17. └─SparseArray::nzdata(y) 18. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) ── Error ('test-SparseMatrix.R:77:13'): writing to a sparse matrix works as expected for logical data ── Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"' Backtrace: ▆ 1. ├─alabaster.base::saveObject(x, tmp) at test-SparseMatrix.R:77:13 2. └─alabaster.matrix::saveObject(x, tmp) 3. └─alabaster.matrix (local) .local(x, path, ...) 4. └─alabaster.matrix:::.save_compressed_sparse_matrix(x, path, ...) 5. └─alabaster.matrix:::optimize_storage(x) 6. └─alabaster.matrix:::optimize_boolean_storage(x) 7. ├─alabaster.matrix:::collect_boolean_attributes(x) 8. └─alabaster.matrix:::collect_boolean_attributes(x) 9. └─DelayedArray::blockApply(...) 10. └─DelayedArray::gridApply(...) 11. └─S4Arrays:::bplapply2(...) 12. ├─BiocGenerics::lapply(X, FUN, ...) 13. └─base::lapply(X, FUN, ...) 14. └─DelayedArray (local) FUN(X[[i]], ...) 15. └─DelayedArray (local) FUN(viewport, ...) 16. └─alabaster.matrix (local) FUN(block, ...) 17. └─SparseArray::nzdata(x) 18. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) ── Error ('test-SparseMatrix.R:100:13'): writing to a sparse matrix works as expected for integer data ── Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"' Backtrace: ▆ 1. ├─alabaster.base::saveObject(x, tmp) at test-SparseMatrix.R:100:13 2. └─alabaster.matrix::saveObject(x, tmp) 3. └─alabaster.matrix (local) .local(x, path, ...) 4. └─alabaster.matrix:::.save_compressed_sparse_matrix(x, path, ...) 5. └─alabaster.matrix:::optimize_storage(x) 6. └─alabaster.matrix:::optimize_integer_storage(x) 7. ├─alabaster.matrix:::collect_integer_attributes(x) 8. └─alabaster.matrix:::collect_integer_attributes(x) 9. └─DelayedArray::blockApply(...) 10. └─DelayedArray::gridApply(...) 11. └─S4Arrays:::bplapply2(...) 12. ├─BiocGenerics::lapply(X, FUN, ...) 13. └─base::lapply(X, FUN, ...) 14. └─DelayedArray (local) FUN(X[[i]], ...) 15. └─DelayedArray (local) FUN(viewport, ...) 16. └─alabaster.matrix (local) FUN(block, ...) 17. ├─alabaster.matrix:::.simple_integer_collector(nzdata(y)) 18. │ └─base::suppressWarnings(range(x, na.rm = TRUE)) 19. │ └─base::withCallingHandlers(...) 20. └─SparseArray::nzdata(y) 21. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) ── Error ('test-SparseMatrix.R:138:9'): depositing small chunks works correctly ── Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"' Backtrace: ▆ 1. └─base::eval(...) 2. └─base::eval(...) 3. ├─alabaster.base::saveObject(y, tmp) at test-SparseMatrix.R:138:9 4. └─alabaster.matrix::saveObject(y, tmp) 5. └─alabaster.matrix (local) .local(x, path, ...) 6. └─alabaster.matrix:::.save_compressed_sparse_matrix(x, path, ...) 7. └─alabaster.matrix:::optimize_storage(x) 8. └─alabaster.matrix:::optimize_float_storage(x) 9. ├─alabaster.matrix:::collect_float_attributes(x) 10. └─alabaster.matrix:::collect_float_attributes(x) 11. └─DelayedArray::blockApply(...) 12. └─DelayedArray::gridApply(...) 13. └─S4Arrays:::bplapply2(...) 14. ├─BiocGenerics::lapply(X, FUN, ...) 15. └─base::lapply(X, FUN, ...) 16. └─DelayedArray (local) FUN(X[[i]], ...) 17. └─DelayedArray (local) FUN(viewport, ...) 18. └─alabaster.matrix (local) FUN(block, ...) 19. └─SparseArray::nzdata(y) 20. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) ── Error ('test-SparseMatrix.R:174:9'): fallback to large integer types for indices works correctly ── Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"' Backtrace: ▆ 1. ├─alabaster.base::saveObject(x, tmp) at test-SparseMatrix.R:174:9 2. └─alabaster.matrix::saveObject(x, tmp) 3. └─alabaster.matrix (local) .local(x, path, ...) 4. └─alabaster.matrix:::.save_compressed_sparse_matrix(x, path, ...) 5. └─alabaster.matrix:::optimize_storage(x) 6. └─alabaster.matrix:::optimize_float_storage(x) 7. ├─alabaster.matrix:::collect_float_attributes(x) 8. └─alabaster.matrix:::collect_float_attributes(x) 9. └─DelayedArray::blockApply(...) 10. └─DelayedArray::gridApply(...) 11. └─S4Arrays:::bplapply2(...) 12. ├─BiocGenerics::lapply(X, FUN, ...) 13. └─base::lapply(X, FUN, ...) 14. └─DelayedArray (local) FUN(X[[i]], ...) 15. └─DelayedArray (local) FUN(viewport, ...) 16. └─alabaster.matrix (local) FUN(block, ...) 17. └─SparseArray::nzdata(y) 18. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) ── Error ('test-SparseMatrix.R:224:5'): writing a DelayedMatrixworks with row-major storage ── Error in `.Call2(.NAME, ..., PACKAGE = "SparseArray")`: 'x' must be a [d|l|n]gCMatrix object Backtrace: ▆ 1. ├─alabaster.base::saveObject(y, tmp) at test-SparseMatrix.R:224:5 2. └─alabaster.matrix::saveObject(y, tmp) 3. └─alabaster.matrix (local) .local(x, path, ...) 4. └─alabaster.matrix:::.save_compressed_sparse_matrix(x, path, ...) 5. └─alabaster.matrix:::optimize_storage(x) 6. └─alabaster.matrix:::optimize_float_storage(x) 7. ├─alabaster.matrix:::collect_float_attributes(x) 8. └─alabaster.matrix:::collect_float_attributes(x) 9. └─DelayedArray::blockApply(...) 10. └─DelayedArray::gridApply(...) 11. └─S4Arrays:::bplapply2(...) 12. ├─BiocGenerics::lapply(X, FUN, ...) 13. └─base::lapply(X, FUN, ...) 14. └─DelayedArray (local) FUN(X[[i]], ...) 15. └─DelayedArray (local) FUN(viewport, ...) 16. └─S4Arrays::read_block(x, viewport, as.sparse = as.sparse) 17. └─S4Arrays:::.NEW_read_block(x, viewport, as.sparse = as.sparse) 18. ├─SparseArray::read_block_as_sparse(x, viewport) 19. └─SparseArray::read_block_as_sparse(x, viewport) 20. ├─SparseArray::extract_sparse_array(x, Nindex) 21. └─DelayedArray::extract_sparse_array(x, Nindex) 22. ├─SparseArray::extract_sparse_array(x@seed, index) 23. └─DelayedArray::extract_sparse_array(x@seed, index) 24. ├─SparseArray::extract_sparse_array(x@seed, index) 25. └─SparseArray::extract_sparse_array(x@seed, index) 26. └─methods::as(slice, "SparseArray") 27. └─SparseArray (local) asMethod(object) 28. └─methods::as(from, "SVT_SparseArray") 29. └─SparseArray (local) asMethod(object) 30. └─methods::as(from, "SVT_SparseMatrix") 31. └─SparseArray (local) asMethod(object) 32. └─SparseArray:::.build_SVT_SparseMatrix_from_CsparseMatrix(from) 33. └─SparseArray:::SparseArray.Call(...) 34. └─S4Vectors::.Call2(.NAME, ..., PACKAGE = "SparseArray") ── Error ('test-optimize_storage.R:422:14'): storage optimization works for sparse objects ── <notSubsettableError/error/condition> Error in `.Primitive("[")(new("SparseArraySeed", dim = c(100L, 10L), nzindex = structure(c(1L, 24L, 57L, 67L, 76L, 82L, 98L, 10L, 34L, 37L, 41L, 42L, 55L, 64L, 72L, 80L, 84L, 89L, 90L, 91L, 7L, 10L, 18L, 33L, 39L, 41L, 54L, 55L, 56L, 59L, 96L, 99L, 8L, 19L, 29L, 32L, 43L, 44L, 45L, 60L, 65L, 67L, 81L, 82L, 86L, 3L, 17L, 19L, 28L, 31L, 48L, 64L, 65L, 94L, 99L, 7L, 21L, 47L, 58L, 65L, 68L, 76L, 77L, 100L, 8L, 12L, 28L, 32L, 39L, 57L, 59L, 69L, 75L, 77L, 87L, 10L, 39L, 46L, 54L, 68L, 74L, 100L, 5L, 15L, 29L, 34L, 61L, 66L, 73L, 75L, 97L, 100L, 6L, 15L, 19L, 27L, 32L, 40L, 77L, 85L, 94L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L), dim = c(101L, 2L)), nzdata = c(NA, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L, 10000L), dimnames = list(NULL, NULL)), 1:10, , drop = FALSE)`: object of type 'S4' is not subsettable Backtrace: ▆ 1. └─alabaster.matrix:::optimize_storage(fun(y)) at test-optimize_storage.R:422:14 2. └─alabaster.matrix:::optimize_integer_storage(x) 3. ├─alabaster.matrix:::collect_integer_attributes(x) 4. └─alabaster.matrix:::collect_integer_attributes(x) 5. └─DelayedArray::blockApply(...) 6. └─DelayedArray::gridApply(...) 7. └─S4Arrays:::bplapply2(...) 8. ├─BiocGenerics::lapply(X, FUN, ...) 9. └─base::lapply(X, FUN, ...) 10. └─DelayedArray (local) FUN(X[[i]], ...) 11. └─DelayedArray (local) FUN(viewport, ...) 12. └─S4Arrays::read_block(x, viewport, as.sparse = as.sparse) 13. └─S4Arrays:::.NEW_read_block(x, viewport, as.sparse = as.sparse) 14. ├─SparseArray::read_block_as_sparse(x, viewport) 15. └─SparseArray::read_block_as_sparse(x, viewport) 16. ├─SparseArray::extract_sparse_array(x, Nindex) 17. └─DelayedArray::extract_sparse_array(x, Nindex) 18. ├─SparseArray::extract_sparse_array(x@seed, index) 19. └─SparseArray::extract_sparse_array(x@seed, index) 20. └─S4Arrays:::subset_by_Nindex(x, index) 21. ├─BiocGenerics::do.call(`[`, c(list(x), subscripts, list(drop = drop))) 22. └─base::do.call(`[`, c(list(x), subscripts, list(drop = drop))) ── Error ('test-sparse.R:21:9'): writing to a sparse matrix works as expected ── Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"' Backtrace: ▆ 1. └─alabaster.matrix::writeSparseMatrix(x, tmp, "csc_matrix") at test-sparse.R:21:9 2. └─alabaster.matrix:::.write_CS_matrix(...) 3. ├─alabaster.matrix:::.extract_sparse_details(mat) 4. └─alabaster.matrix:::.extract_sparse_details(mat) 5. ├─alabaster.matrix:::.extract_sparse_details(x@seed) 6. └─alabaster.matrix:::.extract_sparse_details(x@seed) 7. └─DelayedArray::blockApply(...) 8. └─DelayedArray::gridApply(...) 9. └─S4Arrays:::bplapply2(...) 10. ├─BiocGenerics::lapply(X, FUN, ...) 11. └─base::lapply(X, FUN, ...) 12. └─DelayedArray (local) FUN(X[[i]], ...) 13. └─DelayedArray (local) FUN(viewport, ...) 14. └─alabaster.matrix (local) FUN(block, ...) 15. └─SparseArray::nzdata(sparse) 16. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) ── Error ('test-sparse.R:47:9'): writing to a sparse matrix works with tiny chunks ── Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"' Backtrace: ▆ 1. └─alabaster.matrix::writeSparseMatrix(x, tmp, "csc_matrix") at test-sparse.R:47:9 2. └─alabaster.matrix:::.write_CS_matrix(...) 3. ├─alabaster.matrix:::.extract_sparse_details(mat) 4. └─alabaster.matrix:::.extract_sparse_details(mat) 5. ├─alabaster.matrix:::.extract_sparse_details(x@seed) 6. └─alabaster.matrix:::.extract_sparse_details(x@seed) 7. └─DelayedArray::blockApply(...) 8. └─DelayedArray::gridApply(...) 9. └─S4Arrays:::bplapply2(...) 10. ├─BiocGenerics::lapply(X, FUN, ...) 11. └─base::lapply(X, FUN, ...) 12. └─DelayedArray (local) FUN(X[[i]], ...) 13. └─DelayedArray (local) FUN(viewport, ...) 14. └─alabaster.matrix (local) FUN(block, ...) 15. └─SparseArray::nzdata(sparse) 16. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) ── Error ('test-sparse.R:87:9'): writing to a sparse matrix works with guessed type ── Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"' Backtrace: ▆ 1. └─alabaster.matrix::writeSparseMatrix(y, tmp, "csc_matrix") at test-sparse.R:87:9 2. └─alabaster.matrix:::.write_CS_matrix(...) 3. ├─alabaster.matrix:::.extract_sparse_details(mat) 4. └─alabaster.matrix:::.extract_sparse_details(mat) 5. ├─alabaster.matrix:::.extract_sparse_details(x@seed) 6. └─alabaster.matrix:::.extract_sparse_details(x@seed) 7. └─DelayedArray::blockApply(...) 8. └─DelayedArray::gridApply(...) 9. └─S4Arrays:::bplapply2(...) 10. ├─BiocGenerics::lapply(X, FUN, ...) 11. └─base::lapply(X, FUN, ...) 12. └─DelayedArray (local) FUN(X[[i]], ...) 13. └─DelayedArray (local) FUN(viewport, ...) 14. └─alabaster.matrix (local) FUN(block, ...) 15. └─SparseArray::nzdata(sparse) 16. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) ── Error ('test-sparse.R:128:13'): writing to a sparse matrix works with guessed index type for block method ── Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"' Backtrace: ▆ 1. └─alabaster.matrix::writeSparseMatrix(x, tmp, "csc_matrix") at test-sparse.R:128:13 2. └─alabaster.matrix:::.write_CS_matrix(...) 3. ├─alabaster.matrix:::.extract_sparse_details(mat) 4. └─alabaster.matrix:::.extract_sparse_details(mat) 5. ├─alabaster.matrix:::.extract_sparse_details(x@seed) 6. └─alabaster.matrix:::.extract_sparse_details(x@seed) 7. └─DelayedArray::blockApply(...) 8. └─DelayedArray::gridApply(...) 9. └─S4Arrays:::bplapply2(...) 10. ├─BiocGenerics::lapply(X, FUN, ...) 11. └─base::lapply(X, FUN, ...) 12. └─DelayedArray (local) FUN(X[[i]], ...) 13. └─DelayedArray (local) FUN(viewport, ...) 14. └─alabaster.matrix (local) FUN(block, ...) 15. └─SparseArray::nzdata(sparse) 16. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) ── Error ('test-stage-matrix.R:123:5'): stageObject works with logical matrices ── Error: unable to find an inherited method for function 'nzdata' for signature 'x = "SVT_SparseMatrix"' Backtrace: ▆ 1. ├─alabaster.base::stageObject(mat, dir, file.path(experiment, assay2)) at test-stage-matrix.R:123:5 2. └─alabaster.matrix::stageObject(...) 3. └─alabaster.matrix (local) .local(x, dir, path, child, ...) 4. └─alabaster.matrix:::.stage_any_matrix(x, dir, path, child = child) 5. └─alabaster.matrix:::.stage_sparse_matrix(x, dir, path, child = child) 6. └─alabaster.matrix::writeSparseMatrix(...) 7. └─alabaster.matrix:::.write_CS_matrix(...) 8. ├─alabaster.matrix:::.extract_sparse_details(mat) 9. └─alabaster.matrix:::.extract_sparse_details(mat) 10. └─DelayedArray::blockApply(...) 11. └─DelayedArray::gridApply(...) 12. └─S4Arrays:::bplapply2(...) 13. ├─BiocGenerics::lapply(X, FUN, ...) 14. └─base::lapply(X, FUN, ...) 15. └─DelayedArray (local) FUN(X[[i]], ...) 16. └─DelayedArray (local) FUN(viewport, ...) 17. └─alabaster.matrix (local) FUN(block, ...) 18. └─SparseArray::nzdata(sparse) 19. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) [ FAIL 13 | WARN 90 | SKIP 0 | PASS 560 ] Error: Test failures Execution halted
alabaster.matrix.Rcheck/alabaster.matrix-Ex.timings
name | user | system | elapsed | |
AmalgamatedArray | 0.138 | 0.006 | 0.144 | |
DelayedMask | 0.045 | 0.003 | 0.048 | |
ReloadedArraySeed | 0.663 | 0.026 | 0.693 | |
WrapperArraySeed | 0.025 | 0.002 | 0.027 | |
createRawArraySeed | 0.088 | 0.012 | 0.102 | |
preserveDelayedOperations | 0.001 | 0.000 | 0.000 | |
readArray | 0.117 | 0.012 | 0.130 | |
readDelayedArray | 0.116 | 0.019 | 0.136 | |
readSparseMatrix | 0.140 | 0.022 | 0.165 | |
recycleHdf5Files | 0 | 0 | 0 | |
saveArray | 0.020 | 0.004 | 0.025 | |