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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:getDEE2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings getDEE2_1.19.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/getDEE2.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘getDEE2/DESCRIPTION’ ... OK
* this is package ‘getDEE2’ version ‘1.19.3’
* 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 ‘getDEE2’ 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
srx_agg: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
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
getDEE2_bundle  1.821  0.092  18.813
getDEE2         1.196  0.065  34.080
getDEE2Metadata 0.961  0.019   9.560
Tx2Gene         0.639  0.055  22.101
query_bundles   0.557  0.022   5.538
list_bundles    0.568  0.001   5.043
loadSummaryMeta 0.472  0.021  15.751
loadTxInfo      0.410  0.015  15.539
se              0.359  0.054  16.093
loadFullMeta    0.376  0.019  15.342
loadGeneInfo    0.368  0.020  14.777
loadTxCounts    0.362  0.018  14.585
loadGeneCounts  0.342  0.028  17.140
srx_agg         0.342  0.019  14.631
loadQcMx        0.284  0.022  15.302
queryDEE2       0.193  0.021  12.417
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-getDEE2.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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/getDEE2.Rcheck/00check.log’
for details.