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This page was generated on 2025-10-25 12:05 -0400 (Sat, 25 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4658
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 1525/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Organism.dplyr 1.37.1  (landing page)
Martin Morgan
Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 Oct 2025)
git_url: https://git.bioconductor.org/packages/Organism.dplyr
git_branch: devel
git_last_commit: 93d938b
git_last_commit_date: 2025-06-23 19:11:11 -0400 (Mon, 23 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    NA    NA  

CHECK results for Organism.dplyr on lconway

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.

raw results


Summary

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: 2025-10-24 23:05:28 -0400 (Fri, 24 Oct 2025)
EndedAt: 2025-10-24 23:15:24 -0400 (Fri, 24 Oct 2025)
EllapsedTime: 596.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: Organism.dplyr.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
Genomic-Extractors 5.261  0.150   5.513
select             4.363  0.081   7.446
* 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.

Installation output

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-x86_64/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)

Tests output

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: x86_64-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

Example timings

Organism.dplyr.Rcheck/Organism.dplyr-Ex.timings

nameusersystemelapsed
Genomic-Extractors5.2610.1505.513
filter0.3510.0080.365
select4.3630.0817.446
src0.5880.0091.077
utils0.0020.0010.004