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### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:DESeq2.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings DESeq2_1.51.3.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/DESeq2.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘DESeq2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DESeq2’ version ‘1.51.3’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Michael Love <michaelisaiahlove@gmail.com>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

The Title field should be in title case. Current version is:
  ‘Differential gene expression analysis based on the negative binomial distribution’
In title case that is:
  ‘Differential Gene Expression Analysis Based on the Negative Binomial Distribution’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘DESeq.Rd’:
    https://doi.org/10.1186/s13059-014-0550-8
    https://doi.org/10.1093/bioinformatics/btaa1009
  File ‘DESeq2-package.Rd’:
    https://doi.org/10.1186/s13059-014-0550-8
  File ‘estimateDispersions.Rd’:
    http://dx.doi.org/10.1186/gb-2010-11-10-r106
    http://dx.doi.org/10.1093/nar/gks042
    http://dx.doi.org/10.1093/biostatistics/kxs033
    https://doi.org/10.1093/bioinformatics/btaa1009
  File ‘estimateSizeFactors.Rd’:
    http://dx.doi.org/10.1186/gb-2010-11-10-r106
  File ‘lfcShrink.Rd’:
    https://doi.org/10.1093/bioinformatics/bty895
    https://doi.org/10.1093/biostatistics/kxw041
    https://doi.org/10.1186/s13059-014-0550-8
  File ‘results.Rd’:
    http://dx.doi.org/10.1073/pnas.0914005107
  File ‘rlog.Rd’:
    http://dx.doi.org/10.1186/s13059-014-0550-8
  File ‘varianceStabilizingTransformation.Rd’:
    http://dx.doi.org/10.1186/gb-2010-11-10-r106
* 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 ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
* 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 use of S3 registration ... 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
DESeq: no visible global function definition for ‘error’
plotPCA.DESeqTransform: no visible binding for global variable ‘.data’
results: multiple local function definitions for ‘pfunc_lfc’ with
  different formal arguments
plotPCA,DESeqTransform: no visible binding for global variable ‘.data’
Undefined global functions or variables:
  .data error
* 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 ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NOTE
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
results 5.122  0.005   5.127
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/DESeq2.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL DESeq2
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘DESeq2’ ...
** this is package ‘DESeq2’ version ‘1.51.3’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c DESeq2.cpp -o DESeq2.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -llapack -L/home/rapidbuild/bbs-3.23-bioc-rapid/R/lib -lRblas -lgfortran -lm -lquadmath
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/00LOCK-DESeq2/00new/DESeq2/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DESeq2)

R Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("testthat")
> library("DESeq2")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Seqinfo
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> test_check("DESeq2")
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 242 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test_LRT.R:14:1', 'test_results.R:151:1',
  'test_weights.R:101:1'

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 242 ]
> 
> proc.time()
   user  system elapsed 
127.443   1.459 128.291