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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:restfulSE.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings restfulSE_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/restfulSE.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘restfulSE/DESCRIPTION’ ... OK
* this is package ‘restfulSE’ version ‘1.20.0’
* 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 ‘restfulSE’ 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
  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
BQ3_ArraySeed: no visible global function definition for ‘is’
BQ3_ArraySeed: no visible global function definition for ‘new’
BQ3_Source: no visible global function definition for ‘slot’
BQ3_Source: no visible binding for global variable
  ‘SampleTypeLetterCode’
BQ3_Source: no visible global function definition for ‘new’
BQ3m2: no visible binding for global variable ‘SampleTypeLetterCode’
BQM_ArraySeed: no visible global function definition for ‘is’
BQM_ArraySeed: no visible global function definition for ‘new’
BQM_Source: no visible global function definition for ‘new’
TCGA_tablerefs: no visible global function definition for ‘new’
newDA: no visible global function definition for ‘new’
replaceSlots: no visible global function definition for ‘validObject’
seByTumor: no visible global function definition for ‘new’
unsafe_replaceSlots: no visible global function definition for ‘slot’
unsafe_replaceSlots: no visible global function definition for ‘slot<-’
coerce,BQ3_Array-BQ3_Matrix: no visible global function definition for
  ‘new’
coerce,BQM_Array-BQM_Matrix: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  SampleTypeLetterCode is new slot slot<- validObject
Consider adding
  importFrom("methods", "is", "new", "slot", "slot<-", "validObject")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
gtexTiss 4.314  0.405   5.875
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘restfulSE.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/restfulSE.Rcheck/00check.log’
for details.