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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:bandle.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings bandle_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/bandle.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘bandle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bandle’ version ‘1.9.0’
* 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  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
* 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 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 ... NOTE
Auto-generated content requiring editing in Rd file 'bandle-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
  \references: ‘~~ Literature or other references for background information ~~’
* 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   22.447  0.660  23.107
bandle-gpfit                      15.316  0.308  15.624
bandle                            10.007  0.056  10.063
bandle-EFDR                        7.913  0.552   8.465
bandle-plots-translocations        7.484  0.040   7.524
bandle-predict                     7.204  0.072   7.276
bandle-process                     6.982  0.036   7.019
bandle-prior                       6.397  0.140   6.537
bandle-plots-translocations-table  6.103  0.100   6.203
bandle-plots-convergence           6.138  0.032   6.170
bandle-plots-prob                  5.261  0.108   5.369
* 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/bandle.Rcheck/00check.log’
for details.