* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/snplinkage.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 ‘snplinkage/DESCRIPTION’ ... OK
* this is package ‘snplinkage’ version ‘1.0.0’
* 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 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 ‘snplinkage’ can be installed ... [37s/56s] 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 ... [9s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/14s] OK
* checking whether the package can be unloaded cleanly ... [10s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/12s] OK
* checking loading without being on the library search path ... [10s/11s] 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 ... [46s/52s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [27s/28s]
 [27s/28s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(snplinkage)
  Loading required package: GWASTools
  Loading required package: Biobase
  Loading required package: BiocGenerics
  
  Attaching package: 'BiocGenerics'
  
  The following objects are masked from 'package:stats':
  
      IQR, mad, sd, var, xtabs
  
  The following objects are masked from 'package:base':
  
      Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
      as.data.frame, basename, cbind, colnames, dirname, do.call,
      duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
      lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
      pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
      union, unique, unsplit, which.max, which.min
  
  Welcome to Bioconductor
  
      Vignettes contain introductory material; view with
      'browseVignettes()'. To cite Bioconductor, see
      'citation("Biobase")', and for packages 'citation("pkgname")'.
  
  > 
  > test_check("snplinkage")
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 4 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ggplots_ld.R:6:1'): (code run outside of `test_that()`) ────────
  <packageNotFoundError/error/condition>
  Error in `Library(SNPRelate)`: there is no package called 'SNPRelate'
  Backtrace:
      ▆
   1. └─snplinkage::save_hgdp_as_gds() at test-ggplots_ld.R:6:1
   2.   └─snplinkage:::save_genotype_data_as_gds(...)
   3.     ├─base::system.time(...)
   4.     └─snplinkage:::snp_gds_open(filename, FALSE)
   5.       └─base (local) Library(SNPRelate)
  ── Error ('test-snprelate_ld.R:3:1'): (code run outside of `test_that()`) ──────
  <packageNotFoundError/error/condition>
  Error in `Library(SNPRelate)`: there is no package called 'SNPRelate'
  Backtrace:
      ▆
   1. └─snplinkage:::save_hgdp_as_gds() at test-snprelate_ld.R:3:1
   2.   └─snplinkage:::save_genotype_data_as_gds(...)
   3.     ├─base::system.time(...)
   4.     └─snplinkage:::snp_gds_open(filename, FALSE)
   5.       └─base (local) Library(SNPRelate)
  ── Error ('test-vignette.R:4:5'): vignette ─────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `Library(SNPRelate)`: there is no package called 'SNPRelate'
  Backtrace:
      ▆
   1. └─snplinkage::save_hgdp_as_gds() at test-vignette.R:4:5
   2.   └─snplinkage:::save_genotype_data_as_gds(...)
   3.     ├─base::system.time(...)
   4.     └─snplinkage:::snp_gds_open(filename, FALSE)
   5.       └─base (local) Library(SNPRelate)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘snplinkage.Rnw’ using Sweave
Loading required package: GWASTools
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm,
    append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rownames, sapply, setdiff, table, tapply, union, unique,
    unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages
    'citation("pkgname")'.

Timing stopped at: 0.001 0 0

Error: processing vignette 'snplinkage.Rnw' failed with diagnostics:
 chunk 2 (label = qc) 
Error in Library(SNPRelate) : there is no package called 'SNPRelate'

--- failed re-building 'snplinkage.Rnw'

SUMMARY: processing the following file failed:
  'snplinkage.Rnw'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... 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: 2 ERRORs
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/snplinkage.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 6:14.38, 276.30 + 26.86