* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/seeker.Rcheck’
* using R Under development (unstable) (2024-04-19 r86451)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘seeker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seeker’ version ‘1.1.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘org.Mm.eg.db’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘seeker’ can be installed ... [11s/13s] OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [17s/20s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [15s/19s]
 [15s/20s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(seeker)
  > 
  > test_check('seeker')
  qs 0.26.1
  reading in files with read_tsv
  1 2 
  transcripts missing from tx2gene: 116471
  summarizing abundance
  summarizing counts
  summarizing length
  [ FAIL 1 | WARN 0 | SKIP 15 | PASS 30 ]
  
  ══ Skipped tests (15) ══════════════════════════════════════════════════════════
  • On CRAN (15): 'test-array-utils.R:33:3', 'test-array-utils.R:154:3',
    'test-array-utils.R:166:3', 'test-array-utils.R:175:3', 'test-array.R:39:3',
    'test-array.R:77:3', 'test-fetch.R:33:3', 'test-qc.R:2:3', 'test-qc.R:21:3',
    'test-qc.R:40:3', 'test-salmon.R:2:3', 'test-seeker.R:2:3',
    'test-seeker.R:22:3', 'test-seeker.R:43:3', 'test-seeker.R:51:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-tximport.R:10:3'): getTx2gene ──────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])`: there is no package called 'GenomeInfoDbData'
  Backtrace:
       ▆
    1. ├─base::do.call(getTx2gene, c(list(outputDir = outputDir), paramsNow$tx2gene)) at test-tximport.R:10:3
    2. ├─seeker (local) `<fn>`(outputDir = "data/staging/GSE143524", checkArgsOnly = TRUE)
    3. │ └─data.table::setDT(biomaRt::listEnsemblArchives())
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImportFrom(...)
    6.   │ └─base::asNamespace(ns)
    7.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
    8.     ├─base::namespaceImportFrom(...)
    9.     │ └─base::asNamespace(ns)
   10.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11.       ├─base::namespaceImportFrom(...)
   12.       │ └─base::asNamespace(ns)
   13.       └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   14.         ├─base::namespaceImport(...)
   15.         └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   16.           ├─base::namespaceImport(...)
   17.           └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   18.             └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   19.               └─base (local) withOneRestart(expr, restarts[[1L]])
   20.                 └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 15 | PASS 30 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [11s/16s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/seeker.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:27.11, 102.26 + 13.10