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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DESeq2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DESeq2_1.48.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/DESeq2.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DESeq2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DESeq2’ version ‘1.48.2’
* 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 ‘DESeq2’ can be installed ... WARNING
Found the following significant warnings:
  DESeq2.cpp:501:16: warning: 'max' is deprecated: use .index_max() instead [-Wdeprecated-declarations]
  DESeq2.cpp:508:16: warning: 'max' is deprecated: use .index_max() instead [-Wdeprecated-declarations]
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/DESeq2.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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:
  DESeq.Rd: estimateSizeFactors, estimateDispersions, bplapply,
    register, counts
  counts.Rd: sizeFactors
  dispersionFunction.Rd: estimateDispersions
  dispersions.Rd: estimateDispersions
  estimateDispersionsGeneEst.Rd: estimateDispersions
  estimateSizeFactors.Rd: sizeFactors, sizeFactors<-
  estimateSizeFactorsForMatrix.Rd: estimateSizeFactors
  fpkm.Rd: estimateSizeFactors
  nbinomLRT.Rd: sizeFactors
  nbinomWaldTest.Rd: sizeFactors
  normalizationFactors.Rd: sizeFactors
  replaceOutliers.Rd: counts
  results.Rd: bplapply, register
  rlog.Rd: RangedSummarizedExperiment, estimateDispersions
  sizeFactors.Rd: estimateSizeFactors
  varianceStabilizingTransformation.Rd: estimateDispersions
  vst.Rd: estimateDispersions
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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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
results   16.688  0.304  17.798
DESeq     10.820  0.074  11.370
lfcShrink  7.135  0.041   7.213
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/DESeq2.Rcheck/00check.log’
for details.