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###
### 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_1.29.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/Organism.dplyr.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Organism.dplyr/DESCRIPTION’ ... OK
* this is package ‘Organism.dplyr’ version ‘1.29.0’
* 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 R 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 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
Genomic-Extractors 6.221  0.615  10.954
* 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: 66)
  [1] 61144 - 61078 == 66
  [2] 61145 - 61079 == 66
  [3] 61146 - 61080 == 66
  [4] 61148 - 61082 == 66
  [5] 61149 - 61083 == 66
  [6] 61150 - 61084 == 66
  
  [ FAIL 32 | WARN 8 | SKIP 1 | PASS 146 ]
  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 in ‘inst/doc’ ... 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/Organism.dplyr.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Organism.dplyr
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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)

R version 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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 32 | WARN 8 | SKIP 1 | PASS 146 ]

══ 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: 0.001007524 >
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractor(src, txdb, transcripts, "tx_name") at test-GenomicFeatures-extractors.R:150:4
 2.   └─testthat::expect_identical(...) at test-GenomicFeatures-extractors.R:26:4
── 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:151:4
 2.   └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:38:4
── 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:151:4
 2.   └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:44:4
── 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:151:4
 2.   └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:50:4
── 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:151:4
 2.   └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:56:4
── 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: 0.08546369 > >
Attributes: < Component "ranges": Attributes: < Component "width": Mean relative difference: 1.460089 > >
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": 6 string mismatches > >
Attributes: < Component "strand": Attributes: < Component "lengths": Numeric: lengths (10, 16) differ > >
Attributes: < Component "strand": Attributes: < Component "values": Lengths: 10, 16 > >
Attributes: < Component "strand": Attributes: < Component "values": Lengths (10, 16) differ (string compare on first 10) > >
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractor(src, txdb, exons, "exon_id") at test-GenomicFeatures-extractors.R:155:4
 2.   └─testthat::expect_identical(granges(src)[o_src], granges(txdb)[o_txdb]) at test-GenomicFeatures-extractors.R:25:4
── 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:156:4
 2.   └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:38:4
── 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:156:4
 2.   └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:44:4
── 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:156:4
 2.   └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:50:4
── 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:156:4
 2.   └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:56:4
── 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: 0.1343047 > >
Attributes: < Component "ranges": Attributes: < Component "width": Mean relative difference: 1.138247 > >
Attributes: < Component "seqnames": Attributes: < Component "lengths": Mean relative difference: 1.022727 > >
Attributes: < Component "seqnames": Attributes: < Component "values": 5 string mismatches > >
Attributes: < Component "strand": Attributes: < Component "lengths": Numeric: lengths (8, 11) differ > >
Attributes: < Component "strand": Attributes: < Component "values": Lengths: 8, 11 > >
Attributes: < Component "strand": Attributes: < Component "values": Lengths (8, 11) differ (string compare on first 8) > >
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractor(src, txdb, cds, "cds_id") at test-GenomicFeatures-extractors.R:160:4
 2.   └─testthat::expect_identical(granges(src)[o_src], granges(txdb)[o_txdb]) at test-GenomicFeatures-extractors.R:25:4
── 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:161:4
 2.   └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:38:4
── 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:161:4
 2.   └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:44:4
── 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:161:4
 2.   └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:50:4
── 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:161:4
 2.   └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:56:4
── Failure ('test-GenomicFeatures-extractors.R:165:5'): promoters-extractor ────
granges(src)[o_src] not identical to granges(txdb)[o_txdb].
Names: 165 string mismatches
Attributes: < Component "ranges": Names: 165 string mismatches >
Attributes: < Component "ranges": Attributes: < Component "NAMES": 165 string mismatches > >
Attributes: < Component "ranges": Attributes: < Component "start": Mean relative difference: 0.00966609 > >
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": 3 string mismatches > >
Attributes: < Component "strand": Attributes: < Component "lengths": Numeric: lengths (10, 8) differ > >
...
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractor(src, txdb, promoters, "tx_id") at test-GenomicFeatures-extractors.R:165:4
 2.   └─testthat::expect_identical(granges(src)[o_src], granges(txdb)[o_txdb]) at test-GenomicFeatures-extractors.R:25:4
── 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: 6.265176e-05 >
Attributes: < Component "listData": Component "tx_name": 165 string mismatches >
Attributes: < Component "rownames": 165 string mismatches >
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractor(src, txdb, promoters, "tx_id") at test-GenomicFeatures-extractors.R:165:4
 2.   └─testthat::expect_identical(...) at test-GenomicFeatures-extractors.R:26:4
── 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:166:4
 2.   └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:38:4
── 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:166:4
 2.   └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:44:4
── 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:166:4
 2.   └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:50:4
── 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:166:4
 2.   └─testthat::expect_true(setequal(mcols(src)[[subset]], mcols(txdb)[[subset]])) at test-GenomicFeatures-extractors.R:56:4
── Failure ('test-GenomicFeatures-extractors.R:171:5'): transcriptsBy-extractor ──
granges(unlist(src))[o_src] not identical to granges(unlist(txdb)[o_txdb]).
Lengths: 165, 166
Names: Lengths (165, 166) differ (string compare on first 165)
Names: 2 string mismatches
Attributes: < Component "elementMetadata": Attributes: < Component "nrows": Mean relative difference: 0.006060606 > >
Attributes: < Component "ranges": Lengths: 165, 166 >
Attributes: < Component "ranges": Names: Lengths (165, 166) differ (string compare on first 165) >
Attributes: < Component "ranges": Names: 2 string mismatches >
Attributes: < Component "ranges": Attributes: < Component "NAMES": Lengths (165, 166) differ (string compare on first 165) > >
Attributes: < Component "ranges": Attributes: < Component "NAMES": 2 string mismatches > >
...
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractorBy(src, txdb, transcriptsBy) at test-GenomicFeatures-extractors.R:171:4
 2.   └─testthat::expect_identical(granges(unlist(src))[o_src], granges(unlist(txdb)[o_txdb])) at test-GenomicFeatures-extractors.R:88:4
── 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 (165, 166) differ >
Attributes: < Component "listData": Component "tx_name": Lengths (165, 166) differ (string compare on first 165) >
Attributes: < Component "listData": Component "tx_name": 11 string mismatches >
Attributes: < Component "nrows": Mean relative difference: 0.006060606 >
Attributes: < Component "rownames": Lengths (165, 166) differ (string compare on first 165) >
Attributes: < Component "rownames": 2 string mismatches >
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractorBy(src, txdb, transcriptsBy) at test-GenomicFeatures-extractors.R:171:4
 2.   └─testthat::expect_identical(...) at test-GenomicFeatures-extractors.R:89:4
── 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: 62.8)
[1] 104477 - 104459 == 18
[2] 104479 - 104461 == 18
[3] 104480 - 104462 == 18
[4] 234180 - 234115 == 65
[5] 234181 - 234116 == 65
[6] 234182 - 234117 == 65
[7] 234183 - 234118 == 65
[8] 234184 - 234119 == 65
[9] 234185 - 234120 == 65
...
── Failure ('test-GenomicFeatures-extractors.R:185:5'): exonsBy-extractor ──────
granges(unlist(src))[o_src] not identical to granges(unlist(txdb)[o_txdb]).
Lengths: 1292, 972
Names: Lengths (1292, 972) differ (string compare on first 972)
Names: 953 string mismatches
Attributes: < Component "elementMetadata": Attributes: < Component "nrows": Mean relative difference: 0.247678 > >
Attributes: < Component "ranges": Lengths: 1292, 972 >
Attributes: < Component "ranges": Names: Lengths (1292, 972) differ (string compare on first 972) >
Attributes: < Component "ranges": Names: 953 string mismatches >
Attributes: < Component "ranges": Attributes: < Component "NAMES": Lengths (1292, 972) differ (string compare on first 972) > >
Attributes: < Component "ranges": Attributes: < Component "NAMES": 953 string mismatches > >
...
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractorBy(src, txdb, exonsBy) at test-GenomicFeatures-extractors.R:185:4
 2.   └─testthat::expect_identical(granges(unlist(src))[o_src], granges(unlist(txdb)[o_txdb])) at test-GenomicFeatures-extractors.R:88:4
── 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 (1292, 972) differ >
Attributes: < Component "listData": Component "exon_name": Lengths (1292, 972) differ (string compare on first 972) >
Attributes: < Component "listData": Component "exon_rank": Numeric: lengths (1292, 972) differ >
Attributes: < Component "nrows": Mean relative difference: 0.247678 >
Attributes: < Component "rownames": Lengths (1292, 972) differ (string compare on first 972) >
Attributes: < Component "rownames": 953 string mismatches >
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractorBy(src, txdb, exonsBy) at test-GenomicFeatures-extractors.R:185:4
 2.   └─testthat::expect_identical(...) at test-GenomicFeatures-extractors.R:89:4
── 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:191:4
 2.   └─testthat::expect_true(all(names(src) %in% names(txdb))) at test-GenomicFeatures-extractors.R:81:4
── 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:191:4
  2.   ├─txdb[names(src)] at test-GenomicFeatures-extractors.R:84:4
  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: 1127, 807
Names: Lengths (1127, 807) differ (string compare on first 807)
Names: 787 string mismatches
Attributes: < Component "elementMetadata": Attributes: < Component "nrows": Mean relative difference: 0.2839397 > >
Attributes: < Component "ranges": Lengths: 1127, 807 >
Attributes: < Component "ranges": Names: Lengths (1127, 807) differ (string compare on first 807) >
Attributes: < Component "ranges": Names: 787 string mismatches >
Attributes: < Component "ranges": Attributes: < Component "NAMES": Lengths (1127, 807) differ (string compare on first 807) > >
Attributes: < Component "ranges": Attributes: < Component "NAMES": 787 string mismatches > >
...
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractorBy(src, txdb, intronsByTranscript) at test-GenomicFeatures-extractors.R:197:4
 2.   └─testthat::expect_identical(granges(unlist(src))[o_src], granges(unlist(txdb)[o_txdb])) at test-GenomicFeatures-extractors.R:88:4
── 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: 0.2839397 >
Attributes: < Component "rownames": Lengths (1127, 807) differ (string compare on first 807) >
Attributes: < Component "rownames": 787 string mismatches >
Backtrace:
    ▆
 1. └─Organism.dplyr (local) .test_extractorBy(src, txdb, intronsByTranscript) at test-GenomicFeatures-extractors.R:197:4
 2.   └─testthat::expect_identical(...) at test-GenomicFeatures-extractors.R:89:4
── 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: 13)
[1] 22238 - 22225 == 13
[2] 22238 - 22225 == 13
[3] 22238 - 22225 == 13
[4] 22238 - 22225 == 13
[5] 22238 - 22225 == 13
[6] 22238 - 22225 == 13
[7] 22238 - 22225 == 13
[8] 22238 - 22225 == 13
[9] 22238 - 22225 == 13
...
── Failure ('test-src_organism-select.R:51:5'): mapIds ─────────────────────────
`rs_src` not equal to `rs_txdb`.
6/6 mismatches (average diff: 66)
[1] 61144 - 61078 == 66
[2] 61145 - 61079 == 66
[3] 61146 - 61080 == 66
[4] 61148 - 61082 == 66
[5] 61149 - 61083 == 66
[6] 61150 - 61084 == 66

[ FAIL 32 | WARN 8 | SKIP 1 | PASS 146 ]
Error: Test failures
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
Execution halted