Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-09 12:06 -0400 (Thu, 09 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" | 4854 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4642 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4587 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4584 |
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 1510/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Organism.dplyr 1.37.1 (landing page) Martin Morgan
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the Organism.dplyr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Organism.dplyr.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: Organism.dplyr |
Version: 1.37.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Organism.dplyr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Organism.dplyr_1.37.1.tar.gz |
StartedAt: 2025-10-08 20:58:03 -0400 (Wed, 08 Oct 2025) |
EndedAt: 2025-10-08 21:00:49 -0400 (Wed, 08 Oct 2025) |
EllapsedTime: 165.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: Organism.dplyr.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Organism.dplyr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Organism.dplyr_1.37.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Organism.dplyr.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Organism.dplyr/DESCRIPTION’ ... OK * this is package ‘Organism.dplyr’ version ‘1.37.1’ * 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 ‘Organism.dplyr’ 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘AnnotationDbi:::smartKeys’ ‘GenomicFeatures:::.exons_with_3utr’ ‘GenomicFeatures:::.exons_with_5utr’ ‘GenomicFeatures:::get_TxDb_seqinfo0’ ‘S4Vectors:::extract_data_frame_rows’ See the note in ?`:::` about the use of this operator. * 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: Genomic-Extractors.Rd: GRanges, GRangesList select.Rd: AnnotationDb-class src.Rd: dplyr 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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: ── Failure ('test-src_organism-select.R:51:5'): mapIds ───────────────────────── `rs_src` not equal to `rs_txdb`. 6/6 mismatches (average diff: 15) [1] 82028 - 82013 == 15 [2] 82029 - 82014 == 15 [3] 82030 - 82015 == 15 [4] 82032 - 82017 == 15 [5] 82033 - 82018 == 15 [6] 82034 - 82019 == 15 [ FAIL 34 | WARN 7 | SKIP 1 | PASS 160 ] 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/Organism.dplyr.Rcheck/00check.log’ for details.
Organism.dplyr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Organism.dplyr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘Organism.dplyr’ ... ** this is package ‘Organism.dplyr’ version ‘1.37.1’ ** 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 (Organism.dplyr)
Organism.dplyr.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(Organism.dplyr) Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: AnnotationFilter Attaching package: 'AnnotationFilter' The following object is masked from 'package:testthat': not > > test_check("Organism.dplyr") [ FAIL 34 | WARN 7 | SKIP 1 | PASS 160 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-GenomicFeatures-extractors.R:201:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-GenomicFeatures-extractors.R:150:5'): transcripts-extractor ── all(mcols(src)[[subset]] %in% mcols(txdb)[[subset]]) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor(src, txdb, transcripts, "tx_name") at test-GenomicFeatures-extractors.R:150:5 2. └─testthat::expect_true(all(mcols(src)[[subset]] %in% mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:16:5 ── Failure ('test-GenomicFeatures-extractors.R:150:5'): transcripts-extractor ── granges(src)[o_src] not identical to granges(txdb)[o_txdb]. Lengths: 182, 181 Attributes: < Component "elementMetadata": Attributes: < Component "nrows": Mean relative difference: 0.005494505 > > Attributes: < Component "ranges": Lengths: 182, 181 > Attributes: < Component "ranges": Attributes: < Component "start": Numeric: lengths (182, 181) differ > > Attributes: < Component "ranges": Attributes: < Component "width": Numeric: lengths (182, 181) differ > > Attributes: < Component "seqnames": Lengths: 182, 181 > Attributes: < Component "seqnames": Attributes: < Component "lengths": Mean relative difference: 0.0625 > > Attributes: < Component "strand": Lengths: 182, 181 > Attributes: < Component "strand": Attributes: < Component "lengths": Mean relative difference: 0.01123596 > > Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor(src, txdb, transcripts, "tx_name") at test-GenomicFeatures-extractors.R:150:5 2. └─testthat::expect_identical(granges(src)[o_src], granges(txdb)[o_txdb]) at test-GenomicFeatures-extractors.R:25:5 ── Failure ('test-GenomicFeatures-extractors.R:150:5'): transcripts-extractor ── mcols(src)[o_src, ] not identical to mcols(txdb)[o_txdb, ]. Attributes: < Component "listData": Component "tx_id": Numeric: lengths (182, 181) differ > Attributes: < Component "listData": Component "tx_name": Lengths (182, 181) differ (string compare on first 181) > Attributes: < Component "listData": Component "tx_name": 84 string mismatches > Attributes: < Component "nrows": Mean relative difference: 0.005494505 > Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor(src, txdb, transcripts, "tx_name") at test-GenomicFeatures-extractors.R:150:5 2. └─testthat::expect_identical(...) at test-GenomicFeatures-extractors.R:26:5 ── Failure ('test-GenomicFeatures-extractors.R:151:5'): transcripts-extractor ── setequal(mcols(src)[[subset]], mcols(txdb)[[subset]]) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, transcripts, "tx_id") at test-GenomicFeatures-extractors.R:151:5 2. └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:38:5 ── Failure ('test-GenomicFeatures-extractors.R:151:5'): transcripts-extractor ── setequal(mcols(src)[[subset]], mcols(txdb)[[subset]]) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, transcripts, "tx_id") at test-GenomicFeatures-extractors.R:151:5 2. └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:44:5 ── Failure ('test-GenomicFeatures-extractors.R:151:5'): transcripts-extractor ── setequal(mcols(src)[[subset]], mcols(txdb)[[subset]]) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, transcripts, "tx_id") at test-GenomicFeatures-extractors.R:151:5 2. └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:50:5 ── Failure ('test-GenomicFeatures-extractors.R:151:5'): transcripts-extractor ── setequal(mcols(src)[[subset]], mcols(txdb)[[subset]]) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, transcripts, "tx_id") at test-GenomicFeatures-extractors.R:151:5 2. └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:56:5 ── Failure ('test-GenomicFeatures-extractors.R:155:5'): exons-extractor ──────── granges(src)[o_src] not identical to granges(txdb)[o_txdb]. Attributes: < Component "ranges": Attributes: < Component "start": Mean relative difference: 0.001973834 > > Attributes: < Component "ranges": Attributes: < Component "width": Mean relative difference: 1.36292 > > Attributes: < Component "seqnames": Attributes: < Component "lengths": Numeric: lengths (15, 16) differ > > Attributes: < Component "seqnames": Attributes: < Component "values": Lengths: 15, 16 > > Attributes: < Component "seqnames": Attributes: < Component "values": Lengths (15, 16) differ (string compare on first 15) > > Attributes: < Component "seqnames": Attributes: < Component "values": 2 string mismatches > > Attributes: < Component "strand": Attributes: < Component "lengths": Mean relative difference: 0.2857143 > > Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor(src, txdb, exons, "exon_id") at test-GenomicFeatures-extractors.R:155:5 2. └─testthat::expect_identical(granges(src)[o_src], granges(txdb)[o_txdb]) at test-GenomicFeatures-extractors.R:25:5 ── Failure ('test-GenomicFeatures-extractors.R:156:5'): exons-extractor ──────── setequal(mcols(src)[[subset]], mcols(txdb)[[subset]]) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, exons, "exon_id") at test-GenomicFeatures-extractors.R:156:5 2. └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:38:5 ── Failure ('test-GenomicFeatures-extractors.R:156:5'): exons-extractor ──────── setequal(mcols(src)[[subset]], mcols(txdb)[[subset]]) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, exons, "exon_id") at test-GenomicFeatures-extractors.R:156:5 2. └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:44:5 ── Failure ('test-GenomicFeatures-extractors.R:156:5'): exons-extractor ──────── setequal(mcols(src)[[subset]], mcols(txdb)[[subset]]) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, exons, "exon_id") at test-GenomicFeatures-extractors.R:156:5 2. └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:50:5 ── Failure ('test-GenomicFeatures-extractors.R:156:5'): exons-extractor ──────── setequal(mcols(src)[[subset]], mcols(txdb)[[subset]]) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, exons, "exon_id") at test-GenomicFeatures-extractors.R:156:5 2. └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:56:5 ── Failure ('test-GenomicFeatures-extractors.R:160:5'): cds-extractor ────────── granges(src)[o_src] not identical to granges(txdb)[o_txdb]. Attributes: < Component "ranges": Attributes: < Component "start": Mean relative difference: 0.01668973 > > Attributes: < Component "ranges": Attributes: < Component "width": Mean relative difference: 1.417904 > > Attributes: < Component "seqnames": Attributes: < Component "lengths": Numeric: lengths (12, 13) differ > > Attributes: < Component "seqnames": Attributes: < Component "values": Lengths: 12, 13 > > Attributes: < Component "seqnames": Attributes: < Component "values": Lengths (12, 13) differ (string compare on first 12) > > Attributes: < Component "seqnames": Attributes: < Component "values": 2 string mismatches > > Attributes: < Component "strand": Attributes: < Component "lengths": Numeric: lengths (8, 9) differ > > Attributes: < Component "strand": Attributes: < Component "values": Lengths: 8, 9 > > Attributes: < Component "strand": Attributes: < Component "values": Lengths (8, 9) differ (string compare on first 8) > > Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor(src, txdb, cds, "cds_id") at test-GenomicFeatures-extractors.R:160:5 2. └─testthat::expect_identical(granges(src)[o_src], granges(txdb)[o_txdb]) at test-GenomicFeatures-extractors.R:25:5 ── Failure ('test-GenomicFeatures-extractors.R:161:5'): cds-extractor ────────── setequal(mcols(src)[[subset]], mcols(txdb)[[subset]]) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, cds, "cds_id") at test-GenomicFeatures-extractors.R:161:5 2. └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:38:5 ── Failure ('test-GenomicFeatures-extractors.R:161:5'): cds-extractor ────────── setequal(mcols(src)[[subset]], mcols(txdb)[[subset]]) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, cds, "cds_id") at test-GenomicFeatures-extractors.R:161:5 2. └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:44:5 ── Failure ('test-GenomicFeatures-extractors.R:161:5'): cds-extractor ────────── setequal(mcols(src)[[subset]], mcols(txdb)[[subset]]) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, cds, "cds_id") at test-GenomicFeatures-extractors.R:161:5 2. └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:50:5 ── Failure ('test-GenomicFeatures-extractors.R:161:5'): cds-extractor ────────── setequal(mcols(src)[[subset]], mcols(txdb)[[subset]]) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, cds, "cds_id") at test-GenomicFeatures-extractors.R:161:5 2. └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:56:5 ── Failure ('test-GenomicFeatures-extractors.R:165:5'): promoters-extractor ──── granges(src)[o_src] not identical to granges(txdb)[o_txdb]. Names: 175 string mismatches Attributes: < Component "ranges": Names: 175 string mismatches > Attributes: < Component "ranges": Attributes: < Component "NAMES": 175 string mismatches > > Attributes: < Component "ranges": Attributes: < Component "start": Mean relative difference: 0.003308557 > > Attributes: < Component "seqnames": Attributes: < Component "lengths": Numeric: lengths (15, 16) differ > > Attributes: < Component "seqnames": Attributes: < Component "values": Lengths: 15, 16 > > Attributes: < Component "seqnames": Attributes: < Component "values": Lengths (15, 16) differ (string compare on first 15) > > Attributes: < Component "seqnames": Attributes: < Component "values": 2 string mismatches > > Attributes: < Component "strand": Attributes: < Component "lengths": Mean relative difference: 1 > > Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor(src, txdb, promoters, "tx_id") at test-GenomicFeatures-extractors.R:165:5 2. └─testthat::expect_identical(granges(src)[o_src], granges(txdb)[o_txdb]) at test-GenomicFeatures-extractors.R:25:5 ── Failure ('test-GenomicFeatures-extractors.R:165:5'): promoters-extractor ──── mcols(src)[o_src, ] not identical to mcols(txdb)[o_txdb, ]. Attributes: < Component "listData": Component "tx_id": Mean relative difference: 3.625366e-05 > Attributes: < Component "listData": Component "tx_name": 175 string mismatches > Attributes: < Component "rownames": 175 string mismatches > Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor(src, txdb, promoters, "tx_id") at test-GenomicFeatures-extractors.R:165:5 2. └─testthat::expect_identical(...) at test-GenomicFeatures-extractors.R:26:5 ── Failure ('test-GenomicFeatures-extractors.R:166:5'): promoters-extractor ──── setequal(mcols(src)[[subset]], mcols(txdb)[[subset]]) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, promoters, "tx_id") at test-GenomicFeatures-extractors.R:166:5 2. └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:38:5 ── Failure ('test-GenomicFeatures-extractors.R:166:5'): promoters-extractor ──── setequal(mcols(src)[[subset]], mcols(txdb)[[subset]]) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, promoters, "tx_id") at test-GenomicFeatures-extractors.R:166:5 2. └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:44:5 ── Failure ('test-GenomicFeatures-extractors.R:166:5'): promoters-extractor ──── setequal(mcols(src)[[subset]], mcols(txdb)[[subset]]) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, promoters, "tx_id") at test-GenomicFeatures-extractors.R:166:5 2. └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:50:5 ── Failure ('test-GenomicFeatures-extractors.R:166:5'): promoters-extractor ──── setequal(mcols(src)[[subset]], mcols(txdb)[[subset]]) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, promoters, "tx_id") at test-GenomicFeatures-extractors.R:166:5 2. └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:56:5 ── Failure ('test-GenomicFeatures-extractors.R:171:5'): transcriptsBy-extractor ── granges(unlist(src))[o_src] not identical to granges(unlist(txdb)[o_txdb]). Lengths: 182, 184 Names: Lengths (182, 184) differ (string compare on first 182) Names: 9 string mismatches Attributes: < Component "elementMetadata": Attributes: < Component "nrows": Mean relative difference: 0.01098901 > > Attributes: < Component "ranges": Lengths: 182, 184 > Attributes: < Component "ranges": Names: Lengths (182, 184) differ (string compare on first 182) > Attributes: < Component "ranges": Names: 9 string mismatches > Attributes: < Component "ranges": Attributes: < Component "NAMES": Lengths (182, 184) differ (string compare on first 182) > > Attributes: < Component "ranges": Attributes: < Component "NAMES": 9 string mismatches > > ... Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractorBy(src, txdb, transcriptsBy) at test-GenomicFeatures-extractors.R:171:5 2. └─testthat::expect_identical(granges(unlist(src))[o_src], granges(unlist(txdb)[o_txdb])) at test-GenomicFeatures-extractors.R:88:5 ── Failure ('test-GenomicFeatures-extractors.R:171:5'): transcriptsBy-extractor ── mcols(unlist(src))[o_src, ] not identical to mcols(unlist(txdb))[o_txdb, ]. Attributes: < Component "listData": Component "tx_id": Numeric: lengths (182, 184) differ > Attributes: < Component "listData": Component "tx_name": Lengths (182, 184) differ (string compare on first 182) > Attributes: < Component "listData": Component "tx_name": 87 string mismatches > Attributes: < Component "nrows": Mean relative difference: 0.01098901 > Attributes: < Component "rownames": Lengths (182, 184) differ (string compare on first 182) > Attributes: < Component "rownames": 9 string mismatches > Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractorBy(src, txdb, transcriptsBy) at test-GenomicFeatures-extractors.R:171:5 2. └─testthat::expect_identical(...) at test-GenomicFeatures-extractors.R:89:5 ── Failure ('test-GenomicFeatures-extractors.R:180:5'): transcriptsBy-extractor ── tx_src$tx_id not equal to tx_txdb$tx_id. 67/67 mismatches (average diff: 18.3) [1] 166643 - 166654 == -11 [2] 166644 - 166655 == -11 [3] 166645 - 166656 == -11 [4] 166648 - 166659 == -11 [5] 166650 - 166661 == -11 [6] 166651 - 166662 == -11 [7] 357154 - 357173 == -19 [8] 357155 - 357174 == -19 [9] 357156 - 357175 == -19 ... ── Failure ('test-GenomicFeatures-extractors.R:185:5'): exonsBy-extractor ────── granges(unlist(src))[o_src] not identical to granges(unlist(txdb)[o_txdb]). Lengths: 1345, 1043 Names: Lengths (1345, 1043) differ (string compare on first 1043) Names: 1036 string mismatches Attributes: < Component "elementMetadata": Attributes: < Component "nrows": Mean relative difference: 0.2245353 > > Attributes: < Component "ranges": Lengths: 1345, 1043 > Attributes: < Component "ranges": Names: Lengths (1345, 1043) differ (string compare on first 1043) > Attributes: < Component "ranges": Names: 1036 string mismatches > Attributes: < Component "ranges": Attributes: < Component "NAMES": Lengths (1345, 1043) differ (string compare on first 1043) > > Attributes: < Component "ranges": Attributes: < Component "NAMES": 1036 string mismatches > > ... Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractorBy(src, txdb, exonsBy) at test-GenomicFeatures-extractors.R:185:5 2. └─testthat::expect_identical(granges(unlist(src))[o_src], granges(unlist(txdb)[o_txdb])) at test-GenomicFeatures-extractors.R:88:5 ── Failure ('test-GenomicFeatures-extractors.R:185:5'): exonsBy-extractor ────── mcols(unlist(src))[o_src, ] not identical to mcols(unlist(txdb))[o_txdb, ]. Attributes: < Component "listData": Component "exon_id": Numeric: lengths (1345, 1043) differ > Attributes: < Component "listData": Component "exon_name": Lengths (1345, 1043) differ (string compare on first 1043) > Attributes: < Component "listData": Component "exon_rank": Numeric: lengths (1345, 1043) differ > Attributes: < Component "nrows": Mean relative difference: 0.2245353 > Attributes: < Component "rownames": Lengths (1345, 1043) differ (string compare on first 1043) > Attributes: < Component "rownames": 1036 string mismatches > Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractorBy(src, txdb, exonsBy) at test-GenomicFeatures-extractors.R:185:5 2. └─testthat::expect_identical(...) at test-GenomicFeatures-extractors.R:89:5 ── Failure ('test-GenomicFeatures-extractors.R:191:5'): cdsBy-extractor ──────── all(names(src) %in% names(txdb)) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractorBy(src, txdb, cdsBy) at test-GenomicFeatures-extractors.R:191:5 2. └─testthat::expect_true(all(names(src) %in% names(txdb))) at test-GenomicFeatures-extractors.R:81:5 ── Error ('test-GenomicFeatures-extractors.R:191:5'): cdsBy-extractor ────────── Error: subscript contains invalid names Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractorBy(src, txdb, cdsBy) at test-GenomicFeatures-extractors.R:191:5 2. ├─txdb[names(src)] at test-GenomicFeatures-extractors.R:84:5 3. └─txdb[names(src)] 4. ├─methods::callNextMethod(x = x, i = i) 5. │ └─base::eval(call, callEnv) 6. │ └─base::eval(call, callEnv) 7. └─S4Vectors (local) .nextMethod(x = x, i = i) 8. └─S4Vectors:::subset_along_ROWS(x, i, drop = drop) 9. ├─S4Vectors::extractROWS(x, i) 10. └─GenomicRanges (local) extractROWS(x, i) 11. └─IRanges (local) METHOD(x, i) 12. └─S4Vectors::normalizeSingleBracketSubscript(i, x, as.NSBS = TRUE) 13. ├─S4Vectors::NSBS(...) 14. └─S4Vectors::NSBS(...) 15. └─S4Vectors:::.subscript_error("subscript contains invalid ", what) ── Failure ('test-GenomicFeatures-extractors.R:197:5'): intronsByTranscript-extractor ── granges(unlist(src))[o_src] not identical to granges(unlist(txdb)[o_txdb]). Lengths: 1163, 861 Names: Lengths (1163, 861) differ (string compare on first 861) Names: 855 string mismatches Attributes: < Component "elementMetadata": Attributes: < Component "nrows": Mean relative difference: 0.2596733 > > Attributes: < Component "ranges": Lengths: 1163, 861 > Attributes: < Component "ranges": Names: Lengths (1163, 861) differ (string compare on first 861) > Attributes: < Component "ranges": Names: 855 string mismatches > Attributes: < Component "ranges": Attributes: < Component "NAMES": Lengths (1163, 861) differ (string compare on first 861) > > Attributes: < Component "ranges": Attributes: < Component "NAMES": 855 string mismatches > > ... Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractorBy(src, txdb, intronsByTranscript) at test-GenomicFeatures-extractors.R:197:5 2. └─testthat::expect_identical(granges(unlist(src))[o_src], granges(unlist(txdb)[o_txdb])) at test-GenomicFeatures-extractors.R:88:5 ── Failure ('test-GenomicFeatures-extractors.R:197:5'): intronsByTranscript-extractor ── mcols(unlist(src))[o_src, ] not identical to mcols(unlist(txdb))[o_txdb, ]. Attributes: < Component "nrows": Mean relative difference: 0.2596733 > Attributes: < Component "rownames": Lengths (1163, 861) differ (string compare on first 861) > Attributes: < Component "rownames": 855 string mismatches > Backtrace: ▆ 1. └─Organism.dplyr (local) .test_extractorBy(src, txdb, intronsByTranscript) at test-GenomicFeatures-extractors.R:197:5 2. └─testthat::expect_identical(...) at test-GenomicFeatures-extractors.R:89:5 ── Failure ('test-src_organism-select.R:39:5'): select ───────────────────────── rs_src[order(rs_src[, keytype_src]), ]$tx_id not equal to rs_txdb[order(rs_txdb[, keytype_txdb]), ]$TXID. 73/73 mismatches (average diff: 3) [1] 34766 - 34763 == 3 [2] 34766 - 34763 == 3 [3] 34766 - 34763 == 3 [4] 34766 - 34763 == 3 [5] 34766 - 34763 == 3 [6] 34766 - 34763 == 3 [7] 34766 - 34763 == 3 [8] 34766 - 34763 == 3 [9] 34766 - 34763 == 3 ... ── Failure ('test-src_organism-select.R:51:5'): mapIds ───────────────────────── `rs_src` not equal to `rs_txdb`. 6/6 mismatches (average diff: 15) [1] 82028 - 82013 == 15 [2] 82029 - 82014 == 15 [3] 82030 - 82015 == 15 [4] 82032 - 82017 == 15 [5] 82033 - 82018 == 15 [6] 82034 - 82019 == 15 [ FAIL 34 | WARN 7 | SKIP 1 | PASS 160 ] Error: Test failures In addition: Warning message: call dbDisconnect() when finished working with a connection Execution halted
Organism.dplyr.Rcheck/Organism.dplyr-Ex.timings
name | user | system | elapsed | |
Genomic-Extractors | 1.256 | 0.020 | 1.282 | |
filter | 0.070 | 0.002 | 0.072 | |
select | 0.707 | 0.014 | 0.721 | |
src | 0.106 | 0.002 | 0.107 | |
utils | 0.000 | 0.001 | 0.000 | |