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This page was generated on 2024-07-25 14:51 -0400 (Thu, 25 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" | 4690 |
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 348/425 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
scMultiome 1.5.1 (landing page) Xiaosai Yao
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||
To the developers/maintainers of the scMultiome package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: scMultiome |
Version: 1.5.1 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scMultiome.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scMultiome_1.5.1.tar.gz |
StartedAt: 2024-07-25 12:00:02 -0400 (Thu, 25 Jul 2024) |
EndedAt: 2024-07-25 12:04:25 -0400 (Thu, 25 Jul 2024) |
EllapsedTime: 263.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: scMultiome.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scMultiome.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scMultiome_1.5.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/scMultiome.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘scMultiome/DESCRIPTION’ ... OK * this is package ‘scMultiome’ version ‘1.5.1’ * 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 ‘scMultiome’ can be installed ... OK * 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed fileOperations 7.134 0.232 7.366 * 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: 3. └─scMultiome:::.guess_integer_type(mat) 4. └─DelayedArray::blockApply(...) 5. └─DelayedArray::gridApply(...) 6. └─S4Arrays:::bplapply2(...) 7. ├─BiocGenerics::lapply(X, FUN, ...) 8. └─base::lapply(X, FUN, ...) 9. └─DelayedArray (local) FUN(X[[i]], ...) 10. └─DelayedArray (local) FUN(viewport, ...) 11. └─scMultiome (local) FUN(block, ...) 12. └─DelayedArray::nzdata(sparse) 13. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) [ FAIL 4 | WARN 3 | SKIP 0 | PASS 67 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.20-data-experiment/meat/scMultiome.Rcheck/00check.log’ for details.
scMultiome.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL scMultiome ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘scMultiome’ ... ** using staged installation ** 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 (scMultiome)
scMultiome.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-pc-linux-gnu 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(scMultiome) Loading required package: AnnotationHub 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, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: BiocFileCache Loading required package: dbplyr Loading required package: ExperimentHub Loading required package: MultiAssayExperiment Loading required package: SummarizedExperiment 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: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians The following object is masked from 'package:ExperimentHub': cache The following object is masked from 'package:AnnotationHub': cache Loading required package: SingleCellExperiment > > test_check("scMultiome") see ?scMultiome and browseVignettes('scMultiome') for documentation loading from cache see ?scMultiome and browseVignettes('scMultiome') for documentation loading from cache Loading required package: SparseArray Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Loading required package: S4Arrays Loading required package: abind Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: DelayedArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Loading required package: rhdf5 Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls automatic block size set to 800 bytes (was 1e+08) /home/biocbuild/bbs-3.20-bioc/R/site-library/scMultiome/scripts/make-data-fictitiousDataset.Rmd created /home/biocbuild/bbs-3.20-bioc/R/site-library/scMultiome/scripts/make-metadata-fictitiousDataset.R created /home/biocbuild/bbs-3.20-bioc/R/site-library/scMultiome/R/fictitiousDataset.R created [ FAIL 4 | WARN 3 | SKIP 0 | PASS 67 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-sparse.R:14:9'): 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. └─scMultiome:::writeSparseMatrix(x, tmp, "csc_matrix") at test-sparse.R:14:9 2. └─scMultiome:::.write_CS_matrix(...) 3. └─scMultiome:::.guess_integer_type(mat) 4. └─DelayedArray::blockApply(...) 5. └─DelayedArray::gridApply(...) 6. └─S4Arrays:::bplapply2(...) 7. ├─BiocGenerics::lapply(X, FUN, ...) 8. └─base::lapply(X, FUN, ...) 9. └─DelayedArray (local) FUN(X[[i]], ...) 10. └─DelayedArray (local) FUN(viewport, ...) 11. └─scMultiome (local) FUN(block, ...) 12. └─DelayedArray::nzdata(sparse) 13. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) ── Error ('test-sparse.R:31:5'): 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. └─scMultiome:::writeSparseMatrix(x, tmp, "csc_matrix") at test-sparse.R:31:5 2. └─scMultiome:::.write_CS_matrix(...) 3. └─scMultiome:::.guess_integer_type(mat) 4. └─DelayedArray::blockApply(...) 5. └─DelayedArray::gridApply(...) 6. └─S4Arrays:::bplapply2(...) 7. ├─BiocGenerics::lapply(X, FUN, ...) 8. └─base::lapply(X, FUN, ...) 9. └─DelayedArray (local) FUN(X[[i]], ...) 10. └─DelayedArray (local) FUN(viewport, ...) 11. └─scMultiome (local) FUN(block, ...) 12. └─DelayedArray::nzdata(sparse) 13. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) ── Error ('test-sparse.R:65:9'): 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. └─scMultiome:::writeSparseMatrix(y, tmp, "csc_matrix") at test-sparse.R:65:9 2. └─scMultiome:::.write_CS_matrix(...) 3. └─scMultiome:::.guess_integer_type(mat) 4. └─DelayedArray::blockApply(...) 5. └─DelayedArray::gridApply(...) 6. └─S4Arrays:::bplapply2(...) 7. ├─BiocGenerics::lapply(X, FUN, ...) 8. └─base::lapply(X, FUN, ...) 9. └─DelayedArray (local) FUN(X[[i]], ...) 10. └─DelayedArray (local) FUN(viewport, ...) 11. └─scMultiome (local) FUN(block, ...) 12. └─DelayedArray::nzdata(sparse) 13. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) ── Error ('test-sparse.R:102:9'): 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. └─scMultiome:::writeSparseMatrix(x, tmp, "csc_matrix") at test-sparse.R:102:9 2. └─scMultiome:::.write_CS_matrix(...) 3. └─scMultiome:::.guess_integer_type(mat) 4. └─DelayedArray::blockApply(...) 5. └─DelayedArray::gridApply(...) 6. └─S4Arrays:::bplapply2(...) 7. ├─BiocGenerics::lapply(X, FUN, ...) 8. └─base::lapply(X, FUN, ...) 9. └─DelayedArray (local) FUN(X[[i]], ...) 10. └─DelayedArray (local) FUN(viewport, ...) 11. └─scMultiome (local) FUN(block, ...) 12. └─DelayedArray::nzdata(sparse) 13. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`) [ FAIL 4 | WARN 3 | SKIP 0 | PASS 67 ] Error: Test failures Execution halted
scMultiome.Rcheck/scMultiome-Ex.timings
name | user | system | elapsed | |
assertHDF5 | 0.049 | 0.012 | 0.061 | |
colonHealthy | 0.953 | 0.112 | 1.295 | |
dummies | 3.226 | 0.232 | 3.458 | |
fileOperations | 7.134 | 0.232 | 7.366 | |
hematopoiesis | 0.752 | 0.048 | 0.925 | |
listDatasets | 0.028 | 0.000 | 0.029 | |
prostateENZ | 0.722 | 0.019 | 0.870 | |
reprogramSeq | 0.728 | 0.056 | 0.861 | |
tfBinding | 0.843 | 0.043 | 0.963 | |
tfMotifs | 0.796 | 0.051 | 0.926 | |
writeSparseMatrix | 0.340 | 0.024 | 0.364 | |