Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-03 11:42 -0400 (Thu, 03 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4716 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
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 1461/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Organism.dplyr 1.33.0 (landing page) Martin Morgan
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
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: 1.33.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Organism.dplyr.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Organism.dplyr_1.33.0.tar.gz |
StartedAt: 2024-10-02 23:56:42 -0400 (Wed, 02 Oct 2024) |
EndedAt: 2024-10-03 00:07:01 -0400 (Thu, 03 Oct 2024) |
EllapsedTime: 619.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: Organism.dplyr.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Organism.dplyr.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Organism.dplyr_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Organism.dplyr.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘Organism.dplyr/DESCRIPTION’ ... OK * this is package ‘Organism.dplyr’ version ‘1.33.0’ * 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 loading without being on the library search path ... 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 ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed select 6.164 0.073 6.710 Genomic-Extractors 5.970 0.106 6.087 * 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: 362) [1] 61078 - 61440 == -362 [2] 61079 - 61441 == -362 [3] 61080 - 61442 == -362 [4] 61082 - 61444 == -362 [5] 61083 - 61445 == -362 [6] 61084 - 61446 == -362 [ FAIL 31 | WARN 5 | SKIP 1 | PASS 163 ] 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: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/Organism.dplyr.Rcheck/00check.log’ for details.
Organism.dplyr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Organism.dplyr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘Organism.dplyr’ ... ** 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 4.4.1 (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(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 31 | WARN 5 | SKIP 1 | PASS 163 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-GenomicFeatures-extractors.R:201:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── 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": Mean relative difference: 0.005090428 > 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: 0.1772058 > > Attributes: < Component "ranges": Attributes: < Component "width": Mean relative difference: 1.290761 > > Attributes: < Component "seqnames": Attributes: < Component "lengths": Mean relative difference: 0.3018868 > > Attributes: < Component "seqnames": Attributes: < Component "values": 3 string mismatches > > Attributes: < Component "strand": Attributes: < Component "lengths": Mean relative difference: 0.2758621 > > 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: 0.1297377 > > Attributes: < Component "ranges": Attributes: < Component "width": Mean relative difference: 0.8034751 > > Attributes: < Component "seqnames": Attributes: < Component "values": 2 string mismatches > > Attributes: < Component "strand": Attributes: < Component "lengths": Numeric: lengths (8, 7) differ > > Attributes: < Component "strand": Attributes: < Component "values": Lengths: 8, 7 > > Attributes: < Component "strand": Attributes: < Component "values": Lengths (8, 7) differ (string compare on first 7) > > 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: 166 string mismatches Attributes: < Component "ranges": Names: 166 string mismatches > Attributes: < Component "ranges": Attributes: < Component "NAMES": 166 string mismatches > > Attributes: < Component "ranges": Attributes: < Component "start": Mean relative difference: 0.2901882 > > Attributes: < Component "seqnames": Attributes: < Component "lengths": Mean relative difference: 0.6666667 > > Attributes: < Component "seqnames": Attributes: < Component "values": 3 string mismatches > > Attributes: < Component "strand": Attributes: < Component "lengths": Numeric: lengths (10, 11) differ > > Attributes: < Component "strand": Attributes: < Component "values": Lengths: 10, 11 > > Attributes: < Component "strand": Attributes: < Component "values": Lengths (10, 11) differ (string compare on first 10) > > 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: 5.733843e-05 > Attributes: < Component "listData": Component "tx_name": 166 string mismatches > Attributes: < Component "rownames": 166 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 ── mcols(unlist(src))[o_src, ] not identical to mcols(unlist(txdb))[o_txdb, ]. Attributes: < Component "listData": Component "tx_id": Mean relative difference: 0.005090428 > 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. 64/64 mismatches (average diff: 1177) [1] 104459 - 104998 == -539 [2] 104461 - 105000 == -539 [3] 104462 - 105001 == -539 [4] 234115 - 235323 == -1208 [5] 234116 - 235324 == -1208 [6] 234117 - 235325 == -1208 [7] 234118 - 235326 == -1208 [8] 234119 - 235327 == -1208 [9] 234120 - 235328 == -1208 ... ── Failure ('test-GenomicFeatures-extractors.R:185:5'): exonsBy-extractor ────── granges(unlist(src))[o_src] not identical to granges(unlist(txdb)[o_txdb]). Lengths: 1297, 755 Names: Lengths (1297, 755) differ (string compare on first 755) Names: 726 string mismatches Attributes: < Component "elementMetadata": Attributes: < Component "nrows": Mean relative difference: 0.4178874 > > Attributes: < Component "ranges": Lengths: 1297, 755 > Attributes: < Component "ranges": Names: Lengths (1297, 755) differ (string compare on first 755) > Attributes: < Component "ranges": Names: 726 string mismatches > Attributes: < Component "ranges": Attributes: < Component "NAMES": Lengths (1297, 755) differ (string compare on first 755) > > Attributes: < Component "ranges": Attributes: < Component "NAMES": 726 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 (1297, 755) differ > Attributes: < Component "listData": Component "exon_name": Lengths (1297, 755) differ (string compare on first 755) > Attributes: < Component "listData": Component "exon_rank": Numeric: lengths (1297, 755) differ > Attributes: < Component "nrows": Mean relative difference: 0.4178874 > Attributes: < Component "rownames": Lengths (1297, 755) differ (string compare on first 755) > Attributes: < Component "rownames": 726 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: 1131, 589 Names: Lengths (1131, 589) differ (string compare on first 589) Names: 577 string mismatches Attributes: < Component "elementMetadata": Attributes: < Component "nrows": Mean relative difference: 0.4792219 > > Attributes: < Component "ranges": Lengths: 1131, 589 > Attributes: < Component "ranges": Names: Lengths (1131, 589) differ (string compare on first 589) > Attributes: < Component "ranges": Names: 577 string mismatches > Attributes: < Component "ranges": Attributes: < Component "NAMES": Lengths (1131, 589) differ (string compare on first 589) > > Attributes: < Component "ranges": Attributes: < Component "NAMES": 577 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: 0.4792219 > Attributes: < Component "rownames": Lengths (1131, 589) differ (string compare on first 589) > Attributes: < Component "rownames": 577 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: 225) [1] 22225 - 22450 == -225 [2] 22225 - 22450 == -225 [3] 22225 - 22450 == -225 [4] 22225 - 22450 == -225 [5] 22225 - 22450 == -225 [6] 22225 - 22450 == -225 [7] 22225 - 22450 == -225 [8] 22225 - 22450 == -225 [9] 22225 - 22450 == -225 ... ── Failure ('test-src_organism-select.R:51:5'): mapIds ───────────────────────── `rs_src` not equal to `rs_txdb`. 6/6 mismatches (average diff: 362) [1] 61078 - 61440 == -362 [2] 61079 - 61441 == -362 [3] 61080 - 61442 == -362 [4] 61082 - 61444 == -362 [5] 61083 - 61445 == -362 [6] 61084 - 61446 == -362 [ FAIL 31 | WARN 5 | SKIP 1 | PASS 163 ] 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 | 5.970 | 0.106 | 6.087 | |
filter | 0.610 | 0.005 | 0.723 | |
select | 6.164 | 0.073 | 6.710 | |
src | 0.846 | 0.006 | 0.868 | |
utils | 0.003 | 0.000 | 0.003 | |