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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:RUVSeq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings RUVSeq_1.41.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RUVSeq.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘RUVSeq/DESCRIPTION’ ... OK
* this is package ‘RUVSeq’ version ‘1.41.0’
* 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 ‘RUVSeq’ 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 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
residuals.DGEGLM : <anonymous>: no visible global function definition
  for ‘poisson’
Undefined global functions or variables:
  poisson
Consider adding
  importFrom("stats", "poisson")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) RUVs.Rd:95: Lost braces; missing escapes or markup?
    95 | {(1,11,21),(2,3),(4,5),(6,7,8)}, then \code{scIdx} should be
       | ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RUVg.Rd: SeqExpressionSet-class
  RUVr.Rd: SeqExpressionSet-class, edgeR
  RUVs.Rd: SeqExpressionSet-class
  residuals.DGEGLM.Rd: edgeR, glmFit, DGEGLM-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘RUVg.R’
  Running ‘RUVr.R’
  Running ‘RUVs.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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/RUVSeq.Rcheck/00check.log’
for details.