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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:iterClust.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings iterClust_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/iterClust.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘iterClust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iterClust’ version ‘1.26.0’
* 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 ‘iterClust’ 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 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 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 ... 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
iterClust 14.288   0.14  14.428
* 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 ‘introduction.rnw’ using Sweave
Warning in fun(libname, pkgname) :
  Package 'iterClust' is deprecated and will be removed from Bioconductor
  version 3.20
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")'.

Initialize iteration 1
Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...
Heterogenous cluster detected, iterClust proceeding...
Removing outlier samples...
Iteration 1 done, giving 5 clusters in total


Initialize iteration 2, for each cluster given by the previous iteration:
Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Heterogenous cluster detected, iterClust proceeding...
Removing outlier samples...
Iteration 2 done, giving 7 clusters in total


Initialize iteration 3, for each cluster given by the previous iteration:
Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

iterClust finished, giving 7 clusters in total

Error: processing vignette 'introduction.rnw' failed with diagnostics:
 chunk 10 (label = consensusclust) 
Error in library(ConsensusClusterPlus) : 
  there is no package called ‘ConsensusClusterPlus’

--- failed re-building ‘introduction.rnw’

SUMMARY: processing the following file failed:
  ‘introduction.rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/iterClust.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL iterClust
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘iterClust’ ...
** 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
Warning in fun(libname, pkgname) :
  Package 'iterClust' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'iterClust' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (iterClust)