* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/eclust.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 ‘eclust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘eclust’ version ‘0.1.0’
* 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 ‘eclust’ can be installed ... [11s/14s] 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 whether startup messages can be suppressed ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [15s/18s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘eclust-Ex.R’ failed
The error most likely occurred in:

> ### Name: s_generate_data
> ### Title: Generate linear response data and test and training sets for
> ###   simulation study
> ### Aliases: s_generate_data
> 
> ### ** Examples
> 
> library(magrittr)
> 
> # simulation parameters
> rho = 0.90; p = 500 ;SNR = 1 ; n = 200; n0 = n1 = 100 ; nActive = p*0.10 ; cluster_distance = "tom";
> Ecluster_distance = "difftom"; rhoOther = 0.6; betaMean = 2;
> alphaMean = 1; betaE = 3; distanceMethod = "euclidean"; clustMethod = "hclust";
> cutMethod = "dynamic"; agglomerationMethod = "average"
> 
> #in this simulation its blocks 3 and 4 that are important
> #leaveOut:  optional specification of modules that should be left out
> #of the simulation, that is their genes will be simulated as unrelated
> #("grey"). This can be useful when simulating several sets, in some which a module
> #is present while in others it is absent.
> d0 <- s_modules(n = n0, p = p, rho = 0, exposed = FALSE,
+                 modProportions = c(0.15,0.15,0.15,0.15,0.15,0.25),
+                 minCor = 0.01,
+                 maxCor = 1,
+                 corPower = 1,
+                 propNegativeCor = 0.3,
+                 backgroundNoise = 0.5,
+                 signed = FALSE,
+                 leaveOut = 1:4)
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘GO.db’
Calls: s_modules ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [10s/12s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘eclust.Rmd’ using rmarkdown

Quitting from lines  at lines 142-168 [unnamed-chunk-6] (eclust.Rmd)
Error: processing vignette 'eclust.Rmd' failed with diagnostics:
there is no package called 'GO.db'
--- failed re-building ‘eclust.Rmd’

SUMMARY: processing the following file failed:
  ‘eclust.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [13s/18s] 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, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/eclust.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:16.09, 92.95 + 12.26