Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-13 12:04 -0400 (Mon, 13 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
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 1952/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scviR 1.9.11 (landing page) Vincent Carey
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the scviR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scviR.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: scviR |
Version: 1.9.11 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scviR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scviR_1.9.11.tar.gz |
StartedAt: 2025-10-13 04:07:33 -0400 (Mon, 13 Oct 2025) |
EndedAt: 2025-10-13 04:17:57 -0400 (Mon, 13 Oct 2025) |
EllapsedTime: 624.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: scviR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scviR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scviR_1.9.11.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scviR.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘scviR/DESCRIPTION’ ... OK * this is package ‘scviR’ version ‘1.9.11’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘scviR’ 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘scviR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getCh12Sce > ### Title: get SCE for 10k PBMC annotated as in OSCA book chapter 12 > ### Aliases: getCh12Sce > > ### ** Examples > > ch12sce <- getCh12Sce() > ch12sce class: SingleCellExperiment dim: 33538 7472 metadata(2): Samples se.averaged assays(2): counts logcounts rownames(33538): ENSG00000243485 ENSG00000237613 ... ENSG00000277475 ENSG00000268674 rowData names(3): ID Symbol Type colnames(7472): AAACCCAAGATTGTGA-1 AAACCCACATCGGTTA-1 ... TTTGTTGTCGAGTGAG-1 TTTGTTGTCGTTCAGA-1 colData names(3): Sample Barcode sizeFactor Loading required namespace: GenomeInfoDb Failed with error: ‘there is no package called ‘GenomeInfoDb’’ Error in .requirePackage(package) : unable to load required package ‘GenomeInfoDb’ Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘citeseq_tut.Rmd’ using rmarkdown --- finished re-building ‘citeseq_tut.Rmd’ --- re-building ‘compch12.Rmd’ using rmarkdown Failed with error: 'there is no package called 'GenomeInfoDb'' Quitting from compch12.Rmd:44-47 [getdat] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `.requirePackage()`: ! unable to load required package 'GenomeInfoDb' --- Backtrace: ▆ 1. ├─tools:::.buildOneVignette(...) 2. │ ├─base::tryCatch(...) 3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 6. │ └─engine$weave(file, quiet = quiet, encoding = enc) 7. │ └─knitr:::vweave_rmarkdown(...) 8. │ └─rmarkdown::render(...) 9. │ └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 10. │ └─knitr:::process_file(text, output) 11. │ ├─xfun:::handle_error(...) 12. │ ├─base::withCallingHandlers(...) 13. │ └─knitr:::process_group(group) 14. │ └─knitr:::call_block(x) 15. │ └─knitr:::block_exec(params) 16. │ └─knitr:::eng_r(options) 17. │ ├─knitr:::in_input_dir(...) 18. │ │ └─knitr:::in_dir(input_dir(), expr) 19. │ └─knitr (local) evaluate(...) 20. │ └─evaluate::evaluate(...) 21. │ ├─base::withRestarts(...) 22. │ │ └─base (local) withRestartList(expr, restarts) 23. │ │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 24. │ │ │ └─base (local) doWithOneRestart(return(expr), restart) 25. │ │ └─base (local) withRestartList(expr, restarts[-nr]) 26. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 27. │ │ └─base (local) doWithOneRestart(return(expr), restart) 28. │ ├─evaluate:::with_handlers(...) 29. │ │ ├─base::eval(call) 30. │ │ │ └─base::eval(call) 31. │ │ └─base::withCallingHandlers(...) 32. │ └─watcher$print_value(ev$value, ev$visible, envir) 33. │ ├─base::withVisible(handle_value(handler, value, visible, envir)) 34. │ └─evaluate:::handle_value(handler, value, visible, envir) 35. │ └─handler$value(value, visible) 36. │ └─knitr (local) fun(x, options = options) 37. │ ├─base::withVisible(knit_print(x, ...)) 38. │ ├─knitr::knit_print(x, ...) 39. │ └─knitr:::knit_print.default(x, ...) 40. │ └─knitr::normal_print(x) 41. │ ├─methods::show(x) 42. │ └─methods::show(x) 43. │ ├─S4Vectors::coolcat("reducedDimNames(%d): %s\n", reducedDimNames(object)) 44. │ │ └─base::ifelse(nzchar(vals), vals, "''") 45. │ ├─SingleCellExperiment::reducedDimNames(object) 46. │ └─SingleCellExperiment::reducedDimNames(object) 47. │ └─SingleCellExperiment:::.get_internal_names(...) 48. │ ├─BiocGenerics::updateObject(x) 49. │ └─SingleCellExperiment::updateObject(x) 50. │ ├─methods::callNextMethod() 51. │ └─SummarizedExperiment (local) .nextMethod(object = object) 52. │ ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose) 53. │ └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose) 54. │ ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose) 55. │ └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose) 56. │ └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose) 57. └─methods:::.extendsForS3(`<chr>`) 58. └─methods::extends(Class, maybe = FALSE) 59. └─methods::getClassDef(class1) 60. └─methods:::.requirePackage(package) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'compch12.Rmd' failed with diagnostics: unable to load required package 'GenomeInfoDb' --- failed re-building ‘compch12.Rmd’ --- re-building ‘new_citeseq.Rmd’ using rmarkdown /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/anndata/_core/anndata.py:1758: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`. utils.warn_names_duplicates("var") /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/anndata/_core/anndata.py:1758: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`. utils.warn_names_duplicates("var") /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/mudata/_core/mudata.py:1531: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility. self._update_attr("var", axis=0, join_common=join_common) /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/mudata/_core/mudata.py:915: UserWarning: var_names are not unique. To make them unique, call `.var_names_make_unique`. warnings.warn( /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/mudata/_core/mudata.py:1429: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility. self._update_attr("obs", axis=1, join_common=join_common) /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/mudata/_core/mudata.py:1531: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility. self._update_attr("var", axis=0, join_common=join_common) /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/mudata/_core/mudata.py:931: UserWarning: Cannot join columns with the same name because var_names are intersecting. warnings.warn( /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/mudata/_core/mudata.py:1429: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility. self._update_attr("obs", axis=1, join_common=join_common) /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/mudata/_core/mudata.py:1531: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility. self._update_attr("var", axis=0, join_common=join_common) /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/mudata/_core/mudata.py:1429: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility. self._update_attr("obs", axis=1, join_common=join_common) /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/docrep/decorators.py:43: SyntaxWarning: 'param_categorical_covariate_keys' is not a valid key! doc = func(self, args[0].__doc__, *args[1:], **kwargs) /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/docrep/decorators.py:43: SyntaxWarning: 'param_continuous_covariate_keys' is not a valid key! doc = func(self, args[0].__doc__, *args[1:], **kwargs) GPU available: False, used: False TPU available: False, using: 0 TPU cores HPU available: False, using: 0 HPUs /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/torch/optim/lr_scheduler.py:62: UserWarning: The verbose parameter is deprecated. Please use get_last_lr() to access the learning rate. warnings.warn( /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/lightning/pytorch/core/optimizer.py:317: The lr scheduler dict contains the key(s) ['monitor'], but the keys will be ignored. You need to call `lr_scheduler.step()` manually in manual optimization. /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/lightning/pytorch/trainer/connectors/data_connector.py:425: The 'train_dataloader' does not have many workers which may be a bottleneck. Consider increasing the value of the `num_workers` argument` to `num_workers=71` in the `DataLoader` to improve performance. /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/lightning/pytorch/trainer/connectors/data_connector.py:425: The 'val_dataloader' does not have many workers which may be a bottleneck. Consider increasing the value of the `num_workers` argument` to `num_workers=71` in the `DataLoader` to improve performance. `Trainer.fit` stopped: `max_epochs=5` reached. GPU available: False, used: False TPU available: False, using: 0 TPU cores HPU available: False, using: 0 HPUs /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/torch/optim/lr_scheduler.py:62: UserWarning: The verbose parameter is deprecated. Please use get_last_lr() to access the learning rate. warnings.warn( /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/lightning/pytorch/core/optimizer.py:317: The lr scheduler dict contains the key(s) ['monitor'], but the keys will be ignored. You need to call `lr_scheduler.step()` manually in manual optimization. /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/lightning/pytorch/trainer/connectors/data_connector.py:425: The 'train_dataloader' does not have many workers which may be a bottleneck. Consider increasing the value of the `num_workers` argument` to `num_workers=71` in the `DataLoader` to improve performance. /var/cache/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/lightning/pytorch/trainer/connectors/data_connector.py:425: The 'val_dataloader' does not have many workers which may be a bottleneck. Consider increasing the value of the `num_workers` argument` to `num_workers=71` in the `DataLoader` to improve performance. `Trainer.fit` stopped: `max_epochs=50` reached. The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/scviR.Rcheck/vign_test/scviR/vignettes/new_citeseq_files/figure-html/lkelb-1.png" but not available. --- finished re-building ‘new_citeseq.Rmd’ --- re-building ‘scviR.Rmd’ using rmarkdown --- finished re-building ‘scviR.Rmd’ SUMMARY: processing the following file failed: ‘compch12.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/scviR.Rcheck/00check.log’ for details.
scviR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scviR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘scviR’ ... ** this is package ‘scviR’ version ‘1.9.11’ ** using staged installation ** R ** data ** 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 (scviR)
scviR.Rcheck/tests/test.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" Copyright (C) 2025 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. > library(testthat) > library(scviR) Loading required package: basilisk Loading required package: reticulate Loading required package: shiny Loading required package: SingleCellExperiment 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: 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: 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: Seqinfo 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 > > test_check("scviR") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ] > > proc.time() user system elapsed 17.632 1.032 18.653
scviR.Rcheck/scviR-Ex.timings
name | user | system | elapsed | |
MuDataR | 3.882 | 0.621 | 4.359 | |
adtProfiles | 4.288 | 0.535 | 4.824 | |
anndataR | 0.004 | 0.000 | 0.004 | |
cacheCiteseq5k10kPbmcs | 0.267 | 0.026 | 0.295 | |
cacheCiteseq5k10kTutvae | 0.000 | 0.000 | 0.001 | |
cacheCiteseqHDPmodel | 0.361 | 0.017 | 0.381 | |
exploreSubcl | 0 | 0 | 0 | |
getCh12AllSce | 4.518 | 0.435 | 4.953 | |