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This page was generated on 2025-10-16 15:41 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4867 |
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 382/434 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
spatialLIBD 1.21.6 (landing page) Leonardo Collado-Torres
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||
To the developers/maintainers of the spatialLIBD 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: spatialLIBD |
Version: 1.21.6 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:spatialLIBD.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings spatialLIBD_1.21.6.tar.gz |
StartedAt: 2025-10-16 13:05:24 -0400 (Thu, 16 Oct 2025) |
EndedAt: 2025-10-16 13:19:05 -0400 (Thu, 16 Oct 2025) |
EllapsedTime: 821.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: spatialLIBD.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:spatialLIBD.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings spatialLIBD_1.21.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/spatialLIBD.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 ‘spatialLIBD/DESCRIPTION’ ... OK * this is package ‘spatialLIBD’ version ‘1.21.6’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 36 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘spatialLIBD’ 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: check_sce.Rd: SingleCellExperiment-class check_sce_layer.Rd: SingleCellExperiment-class fetch_data.Rd: SingleCellExperiment-class layer_boxplot.Rd: SingleCellExperiment-class run_app.Rd: SingleCellExperiment-class sce_to_spe.Rd: SingleCellExperiment-class sig_genes_extract.Rd: SingleCellExperiment-class sig_genes_extract_all.Rd: SingleCellExperiment-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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘spatialLIBD-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: add_key > ### Title: Create a unique spot identifier > ### Aliases: add_key > > ### ** Examples > > if (enough_ram()) { + ## Obtain the necessary data + if (!exists("spe")) spe <- fetch_data("spe") + + ## This object already has a 'key' + head(spe$key) + + ## We can clean it + spe$key_original <- spe$key + spe$key <- NULL + + ## and then add it back + spe <- add_key(spe) + head(spe$key) + + ## Note that the original 'key' order was 'sample_id'_'barcode' and we' + ## have since changed it to 'barcode'_'sample_id'. + + ## Below we restore the original 'key' + spe$key <- spe$key_original + spe$key_original <- NULL + head(spe$key) + } 2025-10-16 13:10:33.257936 loading file /home/biocbuild/.cache/R/BiocFileCache/3f9c9a512e589f_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 Warning in open.connection(con, "rb") : URL 'https://raw.githubusercontent.com/LieberInstitute/HumanPilot/master/10X/151507/scalefactors_json.json': status was 'SSL connect error' Error in open.connection(con, "rb") : cannot open the connection to 'https://raw.githubusercontent.com/LieberInstitute/HumanPilot/master/10X/151507/scalefactors_json.json' Calls: fetch_data ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed add_images 21.415 2.65 24.712 * 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: ▆ 1. └─spatialLIBD::fetch_data("spe") at test-vis_gene.R:2:5 2. └─spatialLIBD::sce_to_spe(...) 3. └─base::lapply(url_scaleFactors, jsonlite::read_json) 4. └─jsonlite (local) FUN(X[[i]], ...) 5. └─jsonlite::parse_json(...) 6. └─jsonlite:::parse_and_simplify(...) 7. └─jsonlite:::parseJSON(txt, bigint_as_char) 8. └─jsonlite:::parse_con(txt, bigint_as_char) 9. ├─base::open(con, "rb") 10. └─base::open.connection(con, "rb") [ FAIL 4 | WARN 25 | SKIP 0 | PASS 33 ] Error: Test failures Execution halted * 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 ‘TenX_data_download.Rmd’ using rmarkdown --- finished re-building ‘TenX_data_download.Rmd’ --- re-building ‘guide_to_spatial_registration.Rmd’ using rmarkdown --- finished re-building ‘guide_to_spatial_registration.Rmd’ --- re-building ‘multi_gene_plots.Rmd’ using rmarkdown Failed with error: 'there is no package called 'GenomeInfoDb'' Quitting from multi_gene_plots.Rmd:81-85 [setup] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <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. │ ├─methods::callNextMethod() 44. │ └─SingleCellExperiment (local) .nextMethod(object = object) 45. │ ├─S4Vectors::coolcat("reducedDimNames(%d): %s\n", reducedDimNames(object)) 46. │ │ └─base::ifelse(nzchar(vals), vals, "''") 47. │ ├─SingleCellExperiment::reducedDimNames(object) 48. │ └─SingleCellExperiment::reducedDimNames(object) 49. │ └─SingleCellExperiment:::.get_internal_names(...) 50. │ ├─BiocGenerics::updateObject(x) 51. │ └─SingleCellExperiment::updateObject(x) 52. │ ├─methods::callNextMethod() 53. │ └─SummarizedExperiment (local) .nextMethod(object = object) 54. │ ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose) 55. │ └─GenomicRanges::updateObject(object@rowRanges, ..., 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 'multi_gene_plots.Rmd' failed with diagnostics: unable to load required package 'GenomeInfoDb' --- failed re-building ‘multi_gene_plots.Rmd’ --- re-building ‘spatialLIBD.Rmd’ using rmarkdown --- finished re-building ‘spatialLIBD.Rmd’ SUMMARY: processing the following file failed: ‘multi_gene_plots.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 3 ERRORs, 1 NOTE See ‘/home/biocbuild/bbs-3.22-data-experiment/meat/spatialLIBD.Rcheck/00check.log’ for details.
spatialLIBD.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL spatialLIBD ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘spatialLIBD’ ... ** this is package ‘spatialLIBD’ version ‘1.21.6’ ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (spatialLIBD)
spatialLIBD.Rcheck/tests/testthat.Rout.fail
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(spatialLIBD) Loading required package: SpatialExperiment 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("spatialLIBD") rgstr_> ## Ensure reproducibility of example data rgstr_> set.seed(20220907) rgstr_> ## Generate example data rgstr_> sce <- scuttle::mockSCE() rgstr_> ## Add some sample IDs rgstr_> sce$sample_id <- sample(LETTERS[1:5], ncol(sce), replace = TRUE) rgstr_> ## Add a sample-level covariate: age rgstr_> ages <- rnorm(5, mean = 20, sd = 4) rgstr_> names(ages) <- LETTERS[1:5] rgstr_> sce$age <- ages[sce$sample_id] rgstr_> ## Add gene-level information rgstr_> rowData(sce)$gene_id <- paste0("ENSG", seq_len(nrow(sce))) rgstr_> rowData(sce)$gene_name <- paste0("gene", seq_len(nrow(sce))) rgstr_> ## Pseudo-bulk by Cell Cycle rgstr_> sce_pseudo <- registration_pseudobulk( rgstr_+ sce, rgstr_+ var_registration = "Cell_Cycle", rgstr_+ var_sample_id = "sample_id", rgstr_+ covars = c("age"), rgstr_+ min_ncells = NULL rgstr_+ ) rgstr_> colData(sce_pseudo) DataFrame with 20 rows and 9 columns Mutation_Status Cell_Cycle Treatment sample_id age <character> <character> <character> <character> <numeric> A_G0 NA G0 NA A 19.1872 B_G0 NA G0 NA B 25.3496 C_G0 NA G0 NA C 24.1802 D_G0 NA G0 NA D 15.5211 E_G0 NA G0 NA E 20.9701 ... ... ... ... ... ... A_S NA S NA A 19.1872 B_S NA S NA B 25.3496 C_S NA S NA C 24.1802 D_S NA S NA D 15.5211 E_S NA S NA E 20.9701 registration_variable registration_sample_id ncells pseudo_sum_umi <character> <character> <integer> <numeric> A_G0 G0 A 8 2946915 B_G0 G0 B 13 4922867 C_G0 G0 C 9 3398888 D_G0 G0 D 7 2630651 E_G0 G0 E 10 3761710 ... ... ... ... ... A_S S A 12 4516334 B_S S B 8 2960685 C_S S C 7 2595774 D_S S D 14 5233560 E_S S E 11 4151818 rgstr_> rowData(sce_pseudo) DataFrame with 2000 rows and 3 columns gene_id gene_name gene_search <character> <character> <character> Gene_0001 ENSG1 gene1 gene1; ENSG1 Gene_0002 ENSG2 gene2 gene2; ENSG2 Gene_0003 ENSG3 gene3 gene3; ENSG3 Gene_0004 ENSG4 gene4 gene4; ENSG4 Gene_0005 ENSG5 gene5 gene5; ENSG5 ... ... ... ... Gene_1996 ENSG1996 gene1996 gene1996; ENSG1996 Gene_1997 ENSG1997 gene1997 gene1997; ENSG1997 Gene_1998 ENSG1998 gene1998 gene1998; ENSG1998 Gene_1999 ENSG1999 gene1999 gene1999; ENSG1999 Gene_2000 ENSG2000 gene2000 gene2000; ENSG2000 rgstr_> ## Ensure reproducibility of example data rgstr_> set.seed(20220907) rgstr_> ## Generate example data rgstr_> sce <- scuttle::mockSCE() rgstr_> ## Add some sample IDs rgstr_> sce$sample_id <- sample(LETTERS[1:5], ncol(sce), replace = TRUE) rgstr_> ## Add a sample-level covariate: age rgstr_> ages <- rnorm(5, mean = 20, sd = 4) rgstr_> names(ages) <- LETTERS[1:5] rgstr_> sce$age <- ages[sce$sample_id] rgstr_> ## Add gene-level information rgstr_> rowData(sce)$gene_id <- paste0("ENSG", seq_len(nrow(sce))) rgstr_> rowData(sce)$gene_name <- paste0("gene", seq_len(nrow(sce))) rgstr_> ## Pseudo-bulk by Cell Cycle rgstr_> sce_pseudo <- registration_pseudobulk( rgstr_+ sce, rgstr_+ var_registration = "Cell_Cycle", rgstr_+ var_sample_id = "sample_id", rgstr_+ covars = c("age"), rgstr_+ min_ncells = NULL rgstr_+ ) rgstr_> colData(sce_pseudo) DataFrame with 20 rows and 9 columns Mutation_Status Cell_Cycle Treatment sample_id age <character> <character> <character> <character> <numeric> A_G0 NA G0 NA A 19.1872 B_G0 NA G0 NA B 25.3496 C_G0 NA G0 NA C 24.1802 D_G0 NA G0 NA D 15.5211 E_G0 NA G0 NA E 20.9701 ... ... ... ... ... ... A_S NA S NA A 19.1872 B_S NA S NA B 25.3496 C_S NA S NA C 24.1802 D_S NA S NA D 15.5211 E_S NA S NA E 20.9701 registration_variable registration_sample_id ncells pseudo_sum_umi <character> <character> <integer> <numeric> A_G0 G0 A 8 2946915 B_G0 G0 B 13 4922867 C_G0 G0 C 9 3398888 D_G0 G0 D 7 2630651 E_G0 G0 E 10 3761710 ... ... ... ... ... A_S S A 12 4516334 B_S S B 8 2960685 C_S S C 7 2595774 D_S S D 14 5233560 E_S S E 11 4151818 rgstr_> rowData(sce_pseudo) DataFrame with 2000 rows and 3 columns gene_id gene_name gene_search <character> <character> <character> Gene_0001 ENSG1 gene1 gene1; ENSG1 Gene_0002 ENSG2 gene2 gene2; ENSG2 Gene_0003 ENSG3 gene3 gene3; ENSG3 Gene_0004 ENSG4 gene4 gene4; ENSG4 Gene_0005 ENSG5 gene5 gene5; ENSG5 ... ... ... ... Gene_1996 ENSG1996 gene1996 gene1996; ENSG1996 Gene_1997 ENSG1997 gene1997 gene1997; ENSG1997 Gene_1998 ENSG1998 gene1998 gene1998; ENSG1998 Gene_1999 ENSG1999 gene1999 gene1999; ENSG1999 Gene_2000 ENSG2000 gene2000 gene2000; ENSG2000 rgst__> example("registration_model", package = "spatialLIBD") rgstr_> example("registration_pseudobulk", package = "spatialLIBD") rgstr_> ## Ensure reproducibility of example data rgstr_> set.seed(20220907) rgstr_> ## Generate example data rgstr_> sce <- scuttle::mockSCE() rgstr_> ## Add some sample IDs rgstr_> sce$sample_id <- sample(LETTERS[1:5], ncol(sce), replace = TRUE) rgstr_> ## Add a sample-level covariate: age rgstr_> ages <- rnorm(5, mean = 20, sd = 4) rgstr_> names(ages) <- LETTERS[1:5] rgstr_> sce$age <- ages[sce$sample_id] rgstr_> ## Add gene-level information rgstr_> rowData(sce)$gene_id <- paste0("ENSG", seq_len(nrow(sce))) rgstr_> rowData(sce)$gene_name <- paste0("gene", seq_len(nrow(sce))) rgstr_> ## Pseudo-bulk by Cell Cycle rgstr_> sce_pseudo <- registration_pseudobulk( rgstr_+ sce, rgstr_+ var_registration = "Cell_Cycle", rgstr_+ var_sample_id = "sample_id", rgstr_+ covars = c("age"), rgstr_+ min_ncells = NULL rgstr_+ ) rgstr_> colData(sce_pseudo) DataFrame with 20 rows and 9 columns Mutation_Status Cell_Cycle Treatment sample_id age <character> <character> <character> <character> <numeric> A_G0 NA G0 NA A 19.1872 B_G0 NA G0 NA B 25.3496 C_G0 NA G0 NA C 24.1802 D_G0 NA G0 NA D 15.5211 E_G0 NA G0 NA E 20.9701 ... ... ... ... ... ... A_S NA S NA A 19.1872 B_S NA S NA B 25.3496 C_S NA S NA C 24.1802 D_S NA S NA D 15.5211 E_S NA S NA E 20.9701 registration_variable registration_sample_id ncells pseudo_sum_umi <character> <character> <integer> <numeric> A_G0 G0 A 8 2946915 B_G0 G0 B 13 4922867 C_G0 G0 C 9 3398888 D_G0 G0 D 7 2630651 E_G0 G0 E 10 3761710 ... ... ... ... ... A_S S A 12 4516334 B_S S B 8 2960685 C_S S C 7 2595774 D_S S D 14 5233560 E_S S E 11 4151818 rgstr_> rowData(sce_pseudo) DataFrame with 2000 rows and 3 columns gene_id gene_name gene_search <character> <character> <character> Gene_0001 ENSG1 gene1 gene1; ENSG1 Gene_0002 ENSG2 gene2 gene2; ENSG2 Gene_0003 ENSG3 gene3 gene3; ENSG3 Gene_0004 ENSG4 gene4 gene4; ENSG4 Gene_0005 ENSG5 gene5 gene5; ENSG5 ... ... ... ... Gene_1996 ENSG1996 gene1996 gene1996; ENSG1996 Gene_1997 ENSG1997 gene1997 gene1997; ENSG1997 Gene_1998 ENSG1998 gene1998 gene1998; ENSG1998 Gene_1999 ENSG1999 gene1999 gene1999; ENSG1999 Gene_2000 ENSG2000 gene2000 gene2000; ENSG2000 rgstr_> registration_mod <- registration_model(sce_pseudo, "age") rgstr_> head(registration_mod) registration_variableG0 registration_variableG1 registration_variableG2M A_G0 1 0 0 B_G0 1 0 0 C_G0 1 0 0 D_G0 1 0 0 E_G0 1 0 0 A_G1 0 1 0 registration_variableS age A_G0 0 19.18719 B_G0 0 25.34965 C_G0 0 24.18019 D_G0 0 15.52107 E_G0 0 20.97006 A_G1 0 19.18719 rgst__> block_cor <- registration_block_cor(sce_pseudo, registration_mod) [ FAIL 4 | WARN 25 | SKIP 0 | PASS 33 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-add_qc_metrics.R:4:9'): add_qc_metrics returns modified spe ──── Error in `open.connection(con, "rb")`: cannot open the connection to 'https://raw.githubusercontent.com/LieberInstitute/HumanPilot/master/10X/151507/scalefactors_json.json' Backtrace: ▆ 1. └─spatialLIBD::fetch_data("spe") at test-add_qc_metrics.R:4:9 2. └─spatialLIBD::sce_to_spe(...) 3. └─base::lapply(url_scaleFactors, jsonlite::read_json) 4. └─jsonlite (local) FUN(X[[i]], ...) 5. └─jsonlite::parse_json(...) 6. └─jsonlite:::parse_and_simplify(...) 7. └─jsonlite:::parseJSON(txt, bigint_as_char) 8. └─jsonlite:::parse_con(txt, bigint_as_char) 9. ├─base::open(con, "rb") 10. └─base::open.connection(con, "rb") ── Error ('test-prep_stitched_data.R:4:9'): prep_stitched_data ───────────────── Error in `open.connection(con, "rb")`: cannot open the connection to 'https://raw.githubusercontent.com/LieberInstitute/HumanPilot/master/10X/151507/scalefactors_json.json' Backtrace: ▆ 1. └─spatialLIBD::fetch_data("spe") at test-prep_stitched_data.R:4:9 2. └─spatialLIBD::sce_to_spe(...) 3. └─base::lapply(url_scaleFactors, jsonlite::read_json) 4. └─jsonlite (local) FUN(X[[i]], ...) 5. └─jsonlite::parse_json(...) 6. └─jsonlite:::parse_and_simplify(...) 7. └─jsonlite:::parseJSON(txt, bigint_as_char) 8. └─jsonlite:::parse_con(txt, bigint_as_char) 9. ├─base::open(con, "rb") 10. └─base::open.connection(con, "rb") ── Error ('test-vis_clus.R:4:9'): vis_clus ───────────────────────────────────── Error in `open.connection(con, "rb")`: cannot open the connection to 'https://raw.githubusercontent.com/LieberInstitute/HumanPilot/master/10X/151507/scalefactors_json.json' Backtrace: ▆ 1. └─spatialLIBD::fetch_data("spe") at test-vis_clus.R:4:9 2. └─spatialLIBD::sce_to_spe(...) 3. └─base::lapply(url_scaleFactors, jsonlite::read_json) 4. └─jsonlite (local) FUN(X[[i]], ...) 5. └─jsonlite::parse_json(...) 6. └─jsonlite:::parse_and_simplify(...) 7. └─jsonlite:::parseJSON(txt, bigint_as_char) 8. └─jsonlite:::parse_con(txt, bigint_as_char) 9. ├─base::open(con, "rb") 10. └─base::open.connection(con, "rb") ── Error ('test-vis_gene.R:2:5'): vis_gene ───────────────────────────────────── Error in `open.connection(con, "rb")`: cannot open the connection to 'https://raw.githubusercontent.com/LieberInstitute/HumanPilot/master/10X/151507/scalefactors_json.json' Backtrace: ▆ 1. └─spatialLIBD::fetch_data("spe") at test-vis_gene.R:2:5 2. └─spatialLIBD::sce_to_spe(...) 3. └─base::lapply(url_scaleFactors, jsonlite::read_json) 4. └─jsonlite (local) FUN(X[[i]], ...) 5. └─jsonlite::parse_json(...) 6. └─jsonlite:::parse_and_simplify(...) 7. └─jsonlite:::parseJSON(txt, bigint_as_char) 8. └─jsonlite:::parse_con(txt, bigint_as_char) 9. ├─base::open(con, "rb") 10. └─base::open.connection(con, "rb") [ FAIL 4 | WARN 25 | SKIP 0 | PASS 33 ] Error: Test failures Execution halted
spatialLIBD.Rcheck/spatialLIBD-Ex.timings
name | user | system | elapsed | |
add10xVisiumAnalysis | 0 | 0 | 0 | |
add_images | 21.415 | 2.650 | 24.712 | |