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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:getDEE2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings getDEE2_1.21.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/getDEE2.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* 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 Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘getDEE2/DESCRIPTION’ ... OK
* this is package ‘getDEE2’ version ‘1.21.0’
* 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 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 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  2.874  0.205  19.156
getDEE2         0.982  0.163  31.253
Tx2Gene         1.003  0.113  26.184
query_bundles   0.490  0.021   5.013
loadGeneInfo    0.215  0.054  12.366
se              0.218  0.045  13.321
loadTxInfo      0.209  0.053  13.113
loadGeneCounts  0.204  0.054  12.896
loadTxCounts    0.199  0.054  13.087
loadSummaryMeta 0.190  0.057  13.065
loadFullMeta    0.198  0.048  12.026
loadQcMx        0.183  0.049  12.683
srx_agg         0.178  0.049  12.929
queryDEE2       0.108  0.025   8.645
getDEE2Metadata 0.107  0.024   8.930
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/getDEE2.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL getDEE2
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’
* installing *source* package ‘getDEE2’ ...
** this is package ‘getDEE2’ version ‘1.21.0’
** using staged installation
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (getDEE2)

R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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("getDEE2")
> library("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: GenomicRanges
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

Loading required package: S4Vectors

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: Seqinfo
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

> library("testthat")
> 
> # E. coli 
> x<-getDEE2("ecoli",c("SRR1613487","SRR1613488"),legacy=TRUE)
trying URL 'http://dee2.io/metadata/ecoli_metadata.tsv.cut'
Content type 'text/tab-separated-values' length 2078249 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

trying URL 'http://dee2.io/cgi-bin/request.sh?org=ecoli&x=SRR1613487&x=SRR1613488'
downloaded 154 KB

For more information about DEE2 QC metrics, visit
    https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
> 
> test_that("eco works", {
+     expect_equal( sum(x$GeneCounts) , 20624168 )
+ })
Test passed with 1 success 😀.
> 
> 
> # A. thaliana bundle
> x <- getDEE2_bundle("athaliana", "SRP058781",col="SRP_accession")
trying URL 'http://dee2.io/huge/athaliana/'
downloaded 860 KB

trying URL 'http://dee2.io/huge/athaliana/SRP058781_NA.zip'
Content type 'application/zip' length 4214382 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

For more information about DEE2 QC metrics, visit
    https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
> 
> test_that("ath bundles work", {
+     expect_equal( nrow(assays(x)[[1]]) , 32833 )
+     expect_equal( ncol(assays(x)[[1]]) , 32 )
+ })
Test passed with 2 successes 😀.
> 
> 
> # check absent present
> dat <- query_bundles("drerio",c("SRP131781","SRP055996","SRXXX"),col="SRP_accession")
trying URL 'http://dee2.io/huge/drerio/'
downloaded 170 KB

> 
> test_that("dre bundle query", {
+     expect_equal( length(dat$absent) , 1 )
+     expect_equal( length(dat$present) , 2 )
+ })
Test passed with 2 successes 🌈.
> 
> proc.time()
   user  system elapsed 
 14.341   0.871  50.102