* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/seqgendiff.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 ‘seqgendiff/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqgendiff’ version ‘1.2.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘airway’
* 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 ‘seqgendiff’ can be installed ... 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 ... [8s/10s] OK
* checking Rd files ... NOTE
checkRd: (-1) poisthin.Rd:82-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) poisthin.Rd:84-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) poisthin.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) poisthin.Rd:87-88: Lost braces in \itemize; \value handles \item{}{} directly
* 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’ [50s/65s]
 [50s/66s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(seqgendiff)
  > 
  > test_check("seqgendiff")
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 53 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test_genthin.R:60:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_genthin.R:22:3'): general thinning works ───────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])`: there is no package called 'GenomeInfoDbData'
  Backtrace:
       ▆
    1. ├─seqgendiff::thin_diff(...) at test_genthin.R:22:3
    2. │ └─seqgendiff:::est_sv(...)
    3. │   └─utils::capture.output(...)
    4. │     └─base::withVisible(...elt(i))
    5. └─base::loadNamespace(x)
    6.   ├─base::namespaceImport(...)
    7.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    8.     ├─base::namespaceImportFrom(...)
    9.     │ └─base::asNamespace(ns)
   10.     └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11.       ├─base::namespaceImportClasses(...)
   12.       │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   13.       │ │ └─base::asNamespace(ns)
   14.       │ └─base::asNamespace(ns)
   15.       └─base::loadNamespace(...)
   16.         ├─base::namespaceImportFrom(...)
   17.         │ └─base::asNamespace(ns)
   18.         └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   19.           ├─base::namespaceImportFrom(...)
   20.           │ └─base::asNamespace(ns)
   21.           └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   22.             ├─base::namespaceImport(...)
   23.             └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   24.               ├─base::namespaceImport(...)
   25.               └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   26.                 └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   27.                   └─base (local) withOneRestart(expr, restarts[[1L]])
   28.                     └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test_group_assign.R:13:3'): length of corvec and nfac are 0 ─────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])`: there is no package called 'GenomeInfoDbData'
  Backtrace:
       ▆
    1. ├─testthat::expect_message(...) at test_group_assign.R:13:3
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─seqgendiff::corassign(mat = Y, corvec = c(0.2, 0.2, 0.2))
    7. └─base::loadNamespace(x)
    8.   ├─base::namespaceImport(...)
    9.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   10.     ├─base::namespaceImport(...)
   11.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12.       ├─base::namespaceImportFrom(...)
   13.       │ └─base::asNamespace(ns)
   14.       └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   15.         ├─base::namespaceImportClasses(...)
   16.         │ ├─base::namespaceImportFrom(self, asNamespace(ns), vars, from = from)
   17.         │ │ └─base::asNamespace(ns)
   18.         │ └─base::asNamespace(ns)
   19.         └─base::loadNamespace(...)
   20.           ├─base::namespaceImportFrom(...)
   21.           │ └─base::asNamespace(ns)
   22.           └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   23.             ├─base::namespaceImportFrom(...)
   24.             │ └─base::asNamespace(ns)
   25.             └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   26.               ├─base::namespaceImport(...)
   27.               └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   28.                 ├─base::namespaceImport(...)
   29.                 └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   30.                   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   31.                     └─base (local) withOneRestart(expr, restarts[[1L]])
   32.                       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 53 ]
  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 ... [10s/15s] 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, 2 NOTEs
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/seqgendiff.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:44.55, 110.74 + 11.37