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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:getDEE2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings getDEE2_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/getDEE2.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘getDEE2/DESCRIPTION’ ... OK
* this is package ‘getDEE2’ version ‘1.15.0’
* 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 loading without being on the library search path ... 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  2.439  0.090  19.605
getDEE2         1.649  0.455  32.980
Tx2Gene         0.724  0.075  23.544
se              0.368  0.029  15.367
loadSummaryMeta 0.392  0.001  16.129
loadGeneInfo    0.364  0.012  13.870
srx_agg         0.313  0.011  13.350
loadFullMeta    0.303  0.019  12.914
loadTxInfo      0.301  0.021  14.648
loadQcMx        0.297  0.021  13.813
loadGeneCounts  0.290  0.020  13.084
loadTxCounts    0.286  0.008  14.988
queryDEE2       0.241  0.011   9.295
getDEE2Metadata 0.214  0.014   9.417
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/getDEE2.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL getDEE2
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘getDEE2’ ...
** using staged installation
** 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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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("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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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: GenomeInfoDb
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 2078161 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 😀
> 
> 
> # A. thaliana bundle
> x <- getDEE2_bundle("athaliana", "SRP058781",col="SRP_accession")
trying URL 'http://dee2.io/huge/athaliana/'
downloaded 461 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 🥳
> 
> 
> # check absent present
> dat <- query_bundles("drerio",c("SRP131781","SRP055996","SRXXX"),col="SRP_accession")
trying URL 'http://dee2.io/huge/drerio/'
downloaded 161 KB

> 
> test_that("dre bundle query", {
+     expect_equal( length(dat$absent) , 1 )
+     expect_equal( length(dat$present) , 2 )
+ })
Test passed 🎉
> 
> proc.time()
   user  system elapsed 
 11.527   0.486  48.961