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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings easyRNASeq_2.36.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/easyRNASeq.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘easyRNASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘easyRNASeq’ version ‘2.36.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/01-Introduction.Rmd’
   ‘inst/doc/02-AnnotParam.Rmd’
   ‘inst/doc/03-SyntheticTranscripts.Rmd’
   ‘inst/doc/04-BamParam.Rmd’
   ‘inst/doc/05-RnaSeqParam.Rmd’
   ‘inst/doc/06-simpleRNASeq.Rmd’
   ‘inst/doc/07-cleanUp.Rmd’
   ‘inst/doc/08-Session-Info.Rmd’
   ‘inst/doc/09-Acknowledgments.Rmd’
   ‘inst/doc/10-Foonotes.Rmd’
   ‘inst/doc/11-Images.Rmd’
   ‘inst/doc/12-Appendix.Rmd’
(Is a VignetteBuilder field missing?)
* 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 ‘easyRNASeq’ 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 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 startup messages can be suppressed ... NOTE
No methods found in package ‘BiocGenerics’ for request: ‘clusterApply’ when loading ‘easyRNASeq’

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘locfit’
  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
.parallelize: no visible global function definition for ‘clusterApply’
Undefined global functions or variables:
  clusterApply
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
easyRNASeq-simpleRNASeq          67.514  2.363  70.678
easyRNASeq-package               47.680  3.087  51.204
easyRNASeq-synthetic-transcripts 34.649  1.576  36.392
BiocFileCache-methods             8.858  1.400  25.079
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘simpleRNASeq.Rmd’ using ‘UTF-8’... OK
  ‘easyRNASeq.Rnw’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/easyRNASeq.Rcheck/00check.log’
for details.