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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:pcaExplorer.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings pcaExplorer_3.1.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/pcaExplorer.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'pcaExplorer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pcaExplorer' version '3.1.0'
* 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 whether package 'pcaExplorer' 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 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 ... NOTE
pcaExplorer: no visible binding for '<<-' assignment to
  'pcaexplorer_env'
pcaExplorer : <anonymous>: no visible binding for global variable
  'pcaexplorer_env'
Undefined global functions or variables:
  pcaexplorer_env
* 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:
  distro_expr.Rd: DESeqTransform
  geneprofiler.Rd: DESeqDataSet, DESeqTransform
  genespca.Rd: DESeqTransform, rlog, varianceStabilizingTransformation
  get_annotation.Rd: DESeqDataSet, getBM
  get_annotation_orgdb.Rd: DESeqDataSet, mapIds
  hi_loadings.Rd: DESeqDataSet
  limmaquickpca2go.Rd: DESeqTransform, rlog,
    varianceStabilizingTransformation
  makeExampleDESeqDataSet_multifac.Rd: makeExampleDESeqDataSet,
    DESeqDataSet
  pca2go.Rd: DESeqTransform, rlog, varianceStabilizingTransformation
  pcaExplorer.Rd: DESeqDataSet, DESeqTransform
  pcaplot.Rd: DESeqTransform, rlog, varianceStabilizingTransformation,
    vst
  pcaplot3d.Rd: DESeqTransform, rlog, varianceStabilizingTransformation
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
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
get_annotation_orgdb 5.08    0.1    5.22
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/pcaExplorer.Rcheck/00check.log'
for details.