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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:TumourMethData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings TumourMethData_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/TumourMethData.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘TumourMethData/DESCRIPTION’ ... OK
* this is package ‘TumourMethData’ version ‘1.4.0’
* 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 ‘TumourMethData’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘HDF5Array::h5ls’ by ‘rhdf5::h5ls’ when loading ‘TumourMethData’
See ‘/home/biocbuild/bbs-3.20-data-experiment/meat/TumourMethData.Rcheck/00install.out’ for details.
* 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘BSgenome.Hsapiens.UCSC.hg19’ ‘ExperimentHubData’ ‘R.utils’
  ‘TCGAutils’ ‘dplyr’ ‘knitr’ ‘methrix’ ‘openxlsx’ ‘readr’ ‘rmarkdown’
  ‘stringr’ ‘tibble’ ‘usethis’ ‘xlsx’
  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 ... NOTE
download_meth_dataset: no visible global function definition for ‘data’
download_meth_dataset: no visible binding for global variable
  ‘TumourMethDatasets’
download_meth_dataset: no visible global function definition for ‘slot’
download_meth_dataset: no visible global function definition for
  ‘slot<-’
download_rnaseq_dataset: no visible global function definition for
  ‘data’
Undefined global functions or variables:
  TumourMethDatasets data slot slot<-
Consider adding
  importFrom("methods", "slot", "slot<-")
  importFrom("utils", "data")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-data-experiment/meat/TumourMethData.Rcheck/00check.log’
for details.