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This page was generated on 2025-03-17 11:38 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 1489/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Organism.dplyr 1.35.0  (landing page)
Martin Morgan
Snapshot Date: 2025-03-16 13:40 -0400 (Sun, 16 Mar 2025)
git_url: https://git.bioconductor.org/packages/Organism.dplyr
git_branch: devel
git_last_commit: 0892992
git_last_commit_date: 2024-10-29 10:17:41 -0400 (Tue, 29 Oct 2024)
palomino7Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  

CHECK results for Organism.dplyr on palomino7

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: 1.35.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Organism.dplyr.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Organism.dplyr_1.35.0.tar.gz
StartedAt: 2025-03-17 03:52:31 -0400 (Mon, 17 Mar 2025)
EndedAt: 2025-03-17 04:01:56 -0400 (Mon, 17 Mar 2025)
EllapsedTime: 564.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: Organism.dplyr.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Organism.dplyr.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Organism.dplyr_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/Organism.dplyr.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Organism.dplyr/DESCRIPTION' ... OK
* this is package 'Organism.dplyr' version '1.35.0'
* 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 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 6.73   0.22    7.59
select             4.49   0.14    5.67
* 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: 20588)
  [1] 61440 - 82028 == -20588
  [2] 61441 - 82029 == -20588
  [3] 61442 - 82030 == -20588
  [4] 61444 - 82032 == -20588
  [5] 61445 - 82033 == -20588
  [6] 61446 - 82034 == -20588
  
  [ FAIL 47 | WARN 10 | SKIP 1 | PASS 147 ]
  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
  'E:/biocbuild/bbs-3.21-bioc/meat/Organism.dplyr.Rcheck/00check.log'
for details.

Installation output

Organism.dplyr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL Organism.dplyr
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'Organism.dplyr' ...
** this is package 'Organism.dplyr' version '1.35.0'
** 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 Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 47 | WARN 10 | SKIP 1 | PASS 147 ]

══ 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: 166, 163
Attributes: < Component "elementMetadata": Attributes: < Component "nrows": Mean relative difference: 0.01807229 > >
Attributes: < Component "ranges": Lengths: 166, 163 >
Attributes: < Component "ranges": Attributes: < Component "start": Numeric: lengths (166, 163) differ > >
Attributes: < Component "ranges": Attributes: < Component "width": Numeric: lengths (166, 163) differ > >
Attributes: < Component "seqnames": Lengths: 166, 163 >
Attributes: < Component "seqnames": Attributes: < Component "lengths": Numeric: lengths (15, 14) differ > >
Attributes: < Component "seqnames": Attributes: < Component "values": Lengths: 15, 14 > >
Attributes: < Component "seqnames": Attributes: < Component "values": Lengths (15, 14) differ (string compare on first 14) > >
...
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 (166, 163) differ >
Attributes: < Component "listData": Component "tx_name": Lengths (166, 163) differ (string compare on first 163) >
Attributes: < Component "listData": Component "tx_name": 140 string mismatches >
Attributes: < Component "nrows": Mean relative difference: 0.01807229 >
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 ──
length(src) not equal to length(txdb).
1/1 mismatches
[1] 64 - 67 == -3
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, transcripts, "tx_id") at test-GenomicFeatures-extractors.R:151:5
 2.   └─testthat::expect_equal(length(src), length(txdb)) at test-GenomicFeatures-extractors.R:36:5
── 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 ──
length(src) not equal to length(txdb).
1/1 mismatches
[1] 64 - 67 == -3
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, transcripts, "tx_id") at test-GenomicFeatures-extractors.R:151:5
 2.   └─testthat::expect_equal(length(src), length(txdb)) at test-GenomicFeatures-extractors.R:42:5
── 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 ──
length(src) not equal to length(txdb).
1/1 mismatches
[1] 64 - 67 == -3
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, transcripts, "tx_id") at test-GenomicFeatures-extractors.R:151:5
 2.   └─testthat::expect_equal(length(src), length(txdb)) at test-GenomicFeatures-extractors.R:48:5
── 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 ──
length(src) not equal to length(txdb).
1/1 mismatches
[1] 64 - 67 == -3
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, transcripts, "tx_id") at test-GenomicFeatures-extractors.R:151:5
 2.   └─testthat::expect_equal(length(src), length(txdb)) at test-GenomicFeatures-extractors.R:54:5
── 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: 0.5192183 > >
Attributes: < Component "ranges": Attributes: < Component "width": Mean relative difference: 1.078164 > >
Attributes: < Component "seqnames": Attributes: < Component "lengths": Numeric: lengths (15, 12) differ > >
Attributes: < Component "seqnames": Attributes: < Component "values": Lengths: 15, 12 > >
Attributes: < Component "seqnames": Attributes: < Component "values": Lengths (15, 12) differ (string compare on first 12) > >
Attributes: < Component "seqnames": Attributes: < Component "values": 11 string mismatches > >
Attributes: < Component "strand": Attributes: < Component "lengths": Numeric: lengths (10, 9) differ > >
Attributes: < Component "strand": Attributes: < Component "values": Lengths: 10, 9 > >
Attributes: < Component "strand": Attributes: < Component "values": Lengths (10, 9) differ (string compare on first 9) > >
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 ────────
length(src) not equal to length(txdb).
1/1 mismatches
[1] 104 - 109 == -5
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, exons, "exon_id") at test-GenomicFeatures-extractors.R:156:5
 2.   └─testthat::expect_equal(length(src), length(txdb)) at test-GenomicFeatures-extractors.R:36:5
── 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 ────────
length(src) not equal to length(txdb).
1/1 mismatches
[1] 104 - 109 == -5
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, exons, "exon_id") at test-GenomicFeatures-extractors.R:156:5
 2.   └─testthat::expect_equal(length(src), length(txdb)) at test-GenomicFeatures-extractors.R:42:5
── 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 ────────
length(src) not equal to length(txdb).
1/1 mismatches
[1] 104 - 109 == -5
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, exons, "exon_id") at test-GenomicFeatures-extractors.R:156:5
 2.   └─testthat::expect_equal(length(src), length(txdb)) at test-GenomicFeatures-extractors.R:48:5
── 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 ────────
length(src) not equal to length(txdb).
1/1 mismatches
[1] 104 - 109 == -5
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, exons, "exon_id") at test-GenomicFeatures-extractors.R:156:5
 2.   └─testthat::expect_equal(length(src), length(txdb)) at test-GenomicFeatures-extractors.R:54:5
── 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: 0.04829451 > >
Attributes: < Component "ranges": Attributes: < Component "width": Mean relative difference: 0.9561115 > >
Attributes: < Component "seqnames": Attributes: < Component "lengths": Numeric: lengths (12, 14) differ > >
Attributes: < Component "seqnames": Attributes: < Component "values": Lengths: 12, 14 > >
Attributes: < Component "seqnames": Attributes: < Component "values": Lengths (12, 14) 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: 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: 0.7364896 > >
Attributes: < Component "seqnames": Attributes: < Component "lengths": Numeric: lengths (15, 12) differ > >
Attributes: < Component "seqnames": Attributes: < Component "values": Lengths: 15, 12 > >
Attributes: < Component "seqnames": Attributes: < Component "values": Lengths (15, 12) differ (string compare on first 12) > >
Attributes: < Component "seqnames": Attributes: < Component "values": 11 string mismatches > >
Attributes: < Component "strand": Attributes: < Component "lengths": Numeric: lengths (10, 12) differ > >
...
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: 5.612234e-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 ────
length(src) not equal to length(txdb).
1/1 mismatches
[1] 64 - 67 == -3
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, promoters, "tx_id") at test-GenomicFeatures-extractors.R:166:5
 2.   └─testthat::expect_equal(length(src), length(txdb)) at test-GenomicFeatures-extractors.R:36:5
── 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 ────
length(src) not equal to length(txdb).
1/1 mismatches
[1] 64 - 67 == -3
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, promoters, "tx_id") at test-GenomicFeatures-extractors.R:166:5
 2.   └─testthat::expect_equal(length(src), length(txdb)) at test-GenomicFeatures-extractors.R:42:5
── 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 ────
length(src) not equal to length(txdb).
1/1 mismatches
[1] 64 - 67 == -3
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, promoters, "tx_id") at test-GenomicFeatures-extractors.R:166:5
 2.   └─testthat::expect_equal(length(src), length(txdb)) at test-GenomicFeatures-extractors.R:48:5
── 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 ────
length(src) not equal to length(txdb).
1/1 mismatches
[1] 64 - 67 == -3
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractor_egfilter(src, txdb, promoters, "tx_id") at test-GenomicFeatures-extractors.R:166:5
 2.   └─testthat::expect_equal(length(src), length(txdb)) at test-GenomicFeatures-extractors.R:54:5
── 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: 166, 182
Names: Lengths (166, 182) differ (string compare on first 166)
Names: 81 string mismatches
Attributes: < Component "elementMetadata": Attributes: < Component "nrows": Mean relative difference: 0.09638554 > >
Attributes: < Component "ranges": Lengths: 166, 182 >
Attributes: < Component "ranges": Names: Lengths (166, 182) differ (string compare on first 166) >
Attributes: < Component "ranges": Names: 81 string mismatches >
Attributes: < Component "ranges": Attributes: < Component "NAMES": Lengths (166, 182) differ (string compare on first 166) > >
Attributes: < Component "ranges": Attributes: < Component "NAMES": 81 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 (166, 182) differ >
Attributes: < Component "listData": Component "tx_name": Lengths (166, 182) differ (string compare on first 166) >
Attributes: < Component "listData": Component "tx_name": 143 string mismatches >
Attributes: < Component "nrows": Mean relative difference: 0.09638554 >
Attributes: < Component "rownames": Lengths (166, 182) differ (string compare on first 166) >
Attributes: < Component "rownames": 81 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:178:5'): transcriptsBy-extractor ──
length(tx_src) not equal to length(tx_txdb).
1/1 mismatches
[1] 64 - 67 == -3
── Failure ('test-GenomicFeatures-extractors.R:180:5'): transcriptsBy-extractor ──
tx_src$tx_id not equal to tx_txdb$tx_id.
Lengths differ: 64 is not 67
── Failure ('test-GenomicFeatures-extractors.R:185:5'): exonsBy-extractor ──────
granges(unlist(src))[o_src] not identical to granges(unlist(txdb)[o_txdb]).
Lengths: 1297, 817
Names: Lengths (1297, 817) differ (string compare on first 817)
Names: 810 string mismatches
Attributes: < Component "elementMetadata": Attributes: < Component "nrows": Mean relative difference: 0.3700848 > >
Attributes: < Component "ranges": Lengths: 1297, 817 >
Attributes: < Component "ranges": Names: Lengths (1297, 817) differ (string compare on first 817) >
Attributes: < Component "ranges": Names: 810 string mismatches >
Attributes: < Component "ranges": Attributes: < Component "NAMES": Lengths (1297, 817) differ (string compare on first 817) > >
Attributes: < Component "ranges": Attributes: < Component "NAMES": 810 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, 817) differ >
Attributes: < Component "listData": Component "exon_name": Lengths (1297, 817) differ (string compare on first 817) >
Attributes: < Component "listData": Component "exon_rank": Numeric: lengths (1297, 817) differ >
Attributes: < Component "nrows": Mean relative difference: 0.3700848 >
Attributes: < Component "rownames": Lengths (1297, 817) differ (string compare on first 817) >
Attributes: < Component "rownames": 810 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, 651
Names: Lengths (1131, 651) differ (string compare on first 651)
Names: 651 string mismatches
Attributes: < Component "elementMetadata": Attributes: < Component "nrows": Mean relative difference: 0.4244032 > >
Attributes: < Component "ranges": Lengths: 1131, 651 >
Attributes: < Component "ranges": Names: Lengths (1131, 651) differ (string compare on first 651) >
Attributes: < Component "ranges": Names: 651 string mismatches >
Attributes: < Component "ranges": Attributes: < Component "NAMES": Lengths (1131, 651) differ (string compare on first 651) > >
Attributes: < Component "ranges": Attributes: < Component "NAMES": 651 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: 0.4244032 >
Attributes: < Component "rownames": Lengths (1131, 651) differ (string compare on first 651) >
Attributes: < Component "rownames": 651 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: 12316)
[1] 22450 - 34766 == -12316
[2] 22450 - 34766 == -12316
[3] 22450 - 34766 == -12316
[4] 22450 - 34766 == -12316
[5] 22450 - 34766 == -12316
[6] 22450 - 34766 == -12316
[7] 22450 - 34766 == -12316
[8] 22450 - 34766 == -12316
[9] 22450 - 34766 == -12316
...
── Failure ('test-src_organism-select.R:51:5'): mapIds ─────────────────────────
`rs_src` not equal to `rs_txdb`.
6/6 mismatches (average diff: 20588)
[1] 61440 - 82028 == -20588
[2] 61441 - 82029 == -20588
[3] 61442 - 82030 == -20588
[4] 61444 - 82032 == -20588
[5] 61445 - 82033 == -20588
[6] 61446 - 82034 == -20588

[ FAIL 47 | WARN 10 | SKIP 1 | PASS 147 ]
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-Extractors6.730.227.59
filter0.360.000.56
select4.490.145.67
src0.590.050.80
utils000