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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:GSVA.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings GSVA_2.1.2.tar.gz
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/GSVA.Rcheck’
* using R Under development (unstable) (2024-11-14 r87333)
* 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 ‘GSVA/DESCRIPTION’ ... OK
* this is package ‘GSVA’ version ‘2.1.2’
* 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 ‘GSVA’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GsvaExprData-class.Rd: dgCMatrix-class, ExpressionSet-class,
    SummarizedExperiment-class, SingleCellExperiment-class,
    SpatialExperiment-class
  GsvaGeneSets-class.Rd: GeneSetCollection
  GsvaMethodParam-class.Rd: GeneIdentifierType-class,
    GeneIdentifierType
  geneIdsToGeneSetCollection.Rd: GeneIdentifierType, CollectionType,
    GeneSetCollection, GeneSet, geneIds
  gsva.Rd: BiocParallelParam, dgCMatrix-class, ExpressionSet,
    SingleCellExperiment
  gsvaAnnotation.Rd: ExpressionSet-class, SummarizedExperiment-class,
    GeneIdentifierType
  gsvaParam-class.Rd: GeneIdentifierType-class, GeneIdentifierType,
    ExpressionSet, SummarizedExperiment, SingleCellExperiment
  gsvaRanks.Rd: BiocParallelParam, dgCMatrix-class, ExpressionSet,
    SingleCellExperiment
  guessGeneIdType.Rd: GeneIdentifierType
  plageParam-class.Rd: GeneIdentifierType-class, GeneIdentifierType
  readGMT.Rd: GeneIdentifierType, getGmt, GeneSetCollection, GSEABase
  ssgseaParam-class.Rd: GeneIdentifierType-class, GeneIdentifierType,
    ExpressionSet, SummarizedExperiment, SingleCellExperiment
  zscoreParam-class.Rd: GeneIdentifierType-class, GeneIdentifierType
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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
readGMT 10.284  0.363  11.903
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
  Running ‘test_gsva_newapi.R’
  Comparing ‘test_gsva_newapi.Rout’ to ‘test_gsva_newapi.Rout.save’ ... OK
  Running ‘test_plage_newapi.R’
  Comparing ‘test_plage_newapi.Rout’ to ‘test_plage_newapi.Rout.save’ ... OK
  Running ‘test_ssgsea_newapi.R’
  Comparing ‘test_ssgsea_newapi.Rout’ to ‘test_ssgsea_newapi.Rout.save’ ... OK
  Running ‘test_zscore_newapi.R’
  Comparing ‘test_zscore_newapi.Rout’ to ‘test_zscore_newapi.Rout.save’ ... OK
 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: 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/GSVA.Rcheck/00check.log’
for details.