Back to Build/check report for BioC 3.20 experimental data |
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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 |
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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 350/425 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
scRNAseq 2.19.1 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||
To the developers/maintainers of the scRNAseq 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: scRNAseq |
Version: 2.19.1 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scRNAseq_2.19.1.tar.gz |
StartedAt: 2024-07-25 12:00:18 -0400 (Thu, 25 Jul 2024) |
EndedAt: 2024-07-25 12:09:43 -0400 (Thu, 25 Jul 2024) |
EllapsedTime: 564.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: scRNAseq.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scRNAseq_2.19.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/scRNAseq.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 ‘scRNAseq/DESCRIPTION’ ... OK * this is package ‘scRNAseq’ version ‘2.19.1’ * 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 ... 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 ‘scRNAseq’ 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 ... ERROR Running examples in ‘scRNAseq-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: BachMammaryData > ### Title: Obtain the Bach mammary data > ### Aliases: BachMammaryData > > ### ** Examples > > sce <- BachMammaryData(samples="NP_1") see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache loading from cache require("ensembldb") Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! 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: 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) [ FAIL 28 | WARN 10 | SKIP 1 | PASS 67 ] Error: Test failures In addition: Warning message: call dbDisconnect() when finished working with a connection 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: 2 ERRORs, 1 NOTE See ‘/home/biocbuild/bbs-3.20-data-experiment/meat/scRNAseq.Rcheck/00check.log’ for details.
scRNAseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL scRNAseq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘scRNAseq’ ... ** 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 (scRNAseq)
scRNAseq.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. > library(testthat) > library(scRNAseq) 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 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: 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 > test_check("scRNAseq") [ FAIL 28 | WARN 10 | SKIP 1 | PASS 67 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • is.null(gh_token) is TRUE (1): 'test-uploadDirectory.R:59:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-loading.R:11:5'): BaronPancreasData works ────────────────────── Error: failed to load resource name: AH73881 title: Ensembl 97 EnsDb for Homo sapiens reason: file is not a database Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(BaronPancreasData(ensembl = TRUE)) at test-loading.R:11:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::BaronPancreasData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:16:5'): BuettnerESCData works ──────────────────────── Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! Backtrace: ▆ 1. └─scRNAseq::BuettnerESCData() at test-loading.R:16:5 2. └─scRNAseq:::.define_location_from_ensembl(...) 3. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 4. ├─AnnotationHub()[[ahub.id]] 5. └─AnnotationHub()[[ahub.id]] 6. └─AnnotationHub (local) .local(x, i, j = j, ...) 7. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 8. └─base::tryCatch(...) 9. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. └─value[[3L]](cond) ── Error ('test-loading.R:29:5'): CampbellBrainData works ────────────────────── Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(CampbellBrainData(ensembl = TRUE)) at test-loading.R:29:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::CampbellBrainData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:33:5'): ChenBrainData works ────────────────────────── Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(ChenBrainData(ensembl = TRUE)) at test-loading.R:33:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::ChenBrainData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:37:5'): GrunHSCData works ──────────────────────────── Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(GrunHSCData(ensembl = TRUE)) at test-loading.R:37:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::GrunHSCData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:41:5'): GrunPancreasData works ─────────────────────── Error: failed to load resource name: AH73881 title: Ensembl 97 EnsDb for Homo sapiens reason: file is not a database Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(GrunPancreasData(ensembl = TRUE)) at test-loading.R:41:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::GrunPancreasData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:49:5'): KolodziejczykESCData works ─────────────────── Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! Backtrace: ▆ 1. └─scRNAseq::KolodziejczykESCData() at test-loading.R:49:5 2. └─scRNAseq:::.define_location_from_ensembl(...) 3. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 4. ├─AnnotationHub()[[ahub.id]] 5. └─AnnotationHub()[[ahub.id]] 6. └─AnnotationHub (local) .local(x, i, j = j, ...) 7. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 8. └─base::tryCatch(...) 9. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. └─value[[3L]](cond) ── Error ('test-loading.R:58:5'): LaMannoBrainData works ─────────────────────── Error: failed to load resource name: AH73881 title: Ensembl 97 EnsDb for Homo sapiens reason: file is not a database Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(LaMannoBrainData(ensembl = TRUE, "human-es")) at test-loading.R:58:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::LaMannoBrainData(ensembl = TRUE, "human-es") 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:66:5'): LunSpikeInData works ───────────────────────── Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! Backtrace: ▆ 1. └─scRNAseq::LunSpikeInData() at test-loading.R:66:5 2. └─scRNAseq:::.define_location_from_ensembl(...) 3. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 4. ├─AnnotationHub()[[ahub.id]] 5. └─AnnotationHub()[[ahub.id]] 6. └─AnnotationHub (local) .local(x, i, j = j, ...) 7. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 8. └─base::tryCatch(...) 9. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. └─value[[3L]](cond) ── Error ('test-loading.R:78:5'): MacoskoRetinaData works ────────────────────── Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(MacoskoRetinaData(ensembl = TRUE)) at test-loading.R:78:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::MacoskoRetinaData(ensembl = TRUE) 6. ├─AnnotationHub()[[tag]] 7. └─AnnotationHub()[[tag]] 8. └─AnnotationHub (local) .local(x, i, j = j, ...) 9. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 10. └─base::tryCatch(...) 11. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 12. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 13. └─value[[3L]](cond) ── Error ('test-loading.R:82:5'): MarquesBrainData works ─────────────────────── Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(MarquesBrainData(ensembl = TRUE)) at test-loading.R:82:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::MarquesBrainData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:86:5'): MuraroPancreasData works ───────────────────── Error: failed to load resource name: AH73881 title: Ensembl 97 EnsDb for Homo sapiens reason: file is not a database Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(MuraroPancreasData(ensembl = TRUE)) at test-loading.R:86:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::MuraroPancreasData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:90:5'): NestorowaHSCData works ─────────────────────── Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(NestorowaHSCData(remove.htseq = FALSE)) at test-loading.R:90:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::NestorowaHSCData(remove.htseq = FALSE) 6. └─scRNAseq:::.define_location_from_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:94:5'): PaulHSCData works ──────────────────────────── Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(PaulHSCData(ensembl = TRUE)) at test-loading.R:94:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::PaulHSCData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:99:5'): Reprocessed*Data works ─────────────────────── Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(ReprocessedAllenData(assays = "tophat_counts", ensembl = TRUE)) at test-loading.R:99:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::ReprocessedAllenData(assays = "tophat_counts", ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:105:5'): RomanovBrainData works ────────────────────── Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(RomanovBrainData(ensembl = TRUE)) at test-loading.R:105:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::RomanovBrainData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:109:5'): SegerstolpePancreasData works ─────────────── Error: failed to load resource name: AH73881 title: Ensembl 97 EnsDb for Homo sapiens reason: file is not a database Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(SegerstolpePancreasData(ensembl = TRUE)) at test-loading.R:109:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::SegerstolpePancreasData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:113:5'): ShekharRetinaData works ───────────────────── Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(ShekharRetinaData(ensembl = TRUE)) at test-loading.R:113:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::ShekharRetinaData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:117:5'): TasicBrainData works ──────────────────────── Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(TasicBrainData(ensembl = TRUE)) at test-loading.R:117:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::TasicBrainData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:121:5'): UsoskinBrainData works ────────────────────── Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(UsoskinBrainData(ensembl = TRUE)) at test-loading.R:121:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::UsoskinBrainData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:125:5'): XinPancreasData works ─────────────────────── Error: failed to load resource name: AH73881 title: Ensembl 97 EnsDb for Homo sapiens reason: file is not a database Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(XinPancreasData(ensembl = TRUE)) at test-loading.R:125:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::XinPancreasData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:129:5'): ZeiselBrainData works ─────────────────────── Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(ZeiselBrainData(ensembl = TRUE)) at test-loading.R:129:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::ZeiselBrainData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:133:5'): ZilionisBrianData works ───────────────────── Error: failed to load resource name: AH73881 title: Ensembl 97 EnsDb for Homo sapiens reason: file is not a database Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(ZilionisLungData(ensembl = TRUE)) at test-loading.R:133:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::ZilionisLungData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:143:5'): StoeckiusHashingData works ────────────────── Error: failed to load resource name: AH73881 title: Ensembl 97 EnsDb for Homo sapiens reason: file is not a database Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(StoeckiusHashingData(ensembl = TRUE)) at test-loading.R:143:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::StoeckiusHashingData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:166:5'): MairPBMCData works ────────────────────────── Error: failed to load resource name: AH73881 title: Ensembl 97 EnsDb for Homo sapiens reason: file is not a database Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(MairPBMCData(mode = c("adt", "rna"), ensembl = TRUE)) at test-loading.R:166:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::MairPBMCData(mode = c("adt", "rna"), ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:174:5'): KotliarovPBMCData works ───────────────────── Error: failed to load resource name: AH73881 title: Ensembl 97 EnsDb for Homo sapiens reason: file is not a database Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(KotliarovPBMCData(mode = c("adt", "rna"), ensembl = TRUE)) at test-loading.R:174:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::KotliarovPBMCData(mode = c("adt", "rna"), ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:182:5'): HuCortexData works ────────────────────────── Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(HuCortexData(ensembl = TRUE)) at test-loading.R:182:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::HuCortexData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) ── Error ('test-loading.R:190:5'): WuKidneyData works ────────────────────────── Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: Required tables gene, tx, tx2exon, exon, chromosome are not present in the database! Backtrace: ▆ 1. ├─scRNAseq (local) CHECK(WuKidneyData(ensembl = TRUE)) at test-loading.R:190:5 2. │ └─testthat::expect_true(all(dim(sce) > 0)) at test-loading.R:6:5 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 5. └─scRNAseq::WuKidneyData(ensembl = TRUE) 6. └─scRNAseq:::.convert_to_ensembl(...) 7. └─scRNAseq:::.pull_down_ensdb(species, ahub.id = ahub.id) 8. ├─AnnotationHub()[[ahub.id]] 9. └─AnnotationHub()[[ahub.id]] 10. └─AnnotationHub (local) .local(x, i, j = j, ...) 11. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 12. └─base::tryCatch(...) 13. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15. └─value[[3L]](cond) [ FAIL 28 | WARN 10 | SKIP 1 | PASS 67 ] Error: Test failures In addition: Warning message: call dbDisconnect() when finished working with a connection Execution halted
scRNAseq.Rcheck/scRNAseq-Ex.timings
name | user | system | elapsed | |
AztekinTailData | 9.306 | 0.952 | 10.287 | |