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### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:bandle.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings bandle_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/bandle.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘bandle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bandle’ version ‘1.6.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bandle’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
* 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 R 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘Biobase’ which was already attached by Depends.
  Please remove these calls from your code.
':::' call which should be '::': ‘dplyr:::summarise’
  See the note in ?`:::` about the use of this operator.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
bandle-differentiallocalisation   23.369  0.499  23.870
bandle-gpfit                      17.380  0.212  17.592
bandle                            11.261  0.192  11.454
bandle-EFDR                        9.061  0.708   9.769
bandle-plots-translocations        8.378  0.048   8.425
bandle-predict                     7.869  0.028   7.897
bandle-process                     7.446  0.044   7.489
bandle-prior                       6.532  0.468   7.000
bandle-plots-translocations-table  6.788  0.080   6.869
bandle-plots-convergence           6.630  0.068   6.698
bandle-plots-prob                  5.985  0.036   6.021
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘v01-getting-started.Rmd’ using ‘UTF-8’... OK
  ‘v02-workflow.Rmd’ using ‘UTF-8’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘v02-workflow.Rmd’
  ...
> fData(res_12h[[2]])$bandle.allocation.pred.pred <- res_alloc_12hr

> par(mfrow = c(5, 2))

> plot2D(res_0h[[1]], main = "Unstimulated - replicate 1 \n subcellular markers", 
+     fcol = "markers")

  When sourcing ‘v02-workflow.R’:
Error: figure margins too large
Execution halted

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/bandle.Rcheck/00check.log’
for details.