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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:recount3.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings recount3_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/recount3.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recount3/DESCRIPTION’ ... OK
* this is package ‘recount3’ version ‘1.8.0’
* 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 ‘recount3’ 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 R 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 ... 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 ... ERROR
Running examples in ‘recount3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: available_projects
> ### Title: List available projects in recount3
> ### Aliases: available_projects
> 
> ### ** Examples
> 
> 
> ## Find all the human projects
> human_projects <- available_projects()
2023-04-10 22:12:22 caching file sra.recount_project.MD.gz.
2023-04-10 22:12:23 caching file gtex.recount_project.MD.gz.
2023-04-10 22:12:23 caching file tcga.recount_project.MD.gz.
> 
> ## Explore the results
> dim(human_projects)
[1] 8742    6
> head(human_projects)
    project organism file_source     project_home project_type n_samples
1 SRP107565    human         sra data_sources/sra data_sources       216
2 SRP149665    human         sra data_sources/sra data_sources         4
3 SRP017465    human         sra data_sources/sra data_sources        23
4 SRP119165    human         sra data_sources/sra data_sources         6
5 SRP133965    human         sra data_sources/sra data_sources        12
6 SRP096765    human         sra data_sources/sra data_sources         7
> 
> ## How many are from a data source vs a compilation?
> table(human_projects$project_type, useNA = "ifany")

data_sources 
        8742 
> 
> ## What are the unique file sources?
> table(
+     human_projects$file_source[human_projects$project_type == "data_sources"]
+ )

gtex  sra tcga 
  32 8677   33 
> 
> ## Note that big projects are broken up to make them easier to access
> ## For example, GTEx and TCGA are broken up by tissue
> head(subset(human_projects, file_source == "gtex"))
            project organism file_source      project_home project_type
8678 ADIPOSE_TISSUE    human        gtex data_sources/gtex data_sources
8679         MUSCLE    human        gtex data_sources/gtex data_sources
8680   BLOOD_VESSEL    human        gtex data_sources/gtex data_sources
8681          HEART    human        gtex data_sources/gtex data_sources
8682          OVARY    human        gtex data_sources/gtex data_sources
8683         UTERUS    human        gtex data_sources/gtex data_sources
     n_samples
8678      1293
8679       881
8680      1398
8681       942
8682       195
8683       159
> head(subset(human_projects, file_source == "tcga"))
     project organism file_source      project_home project_type n_samples
8710     ACC    human        tcga data_sources/tcga data_sources        79
8711    BLCA    human        tcga data_sources/tcga data_sources       433
8712    BRCA    human        tcga data_sources/tcga data_sources      1256
8713    CESC    human        tcga data_sources/tcga data_sources       309
8714    CHOL    human        tcga data_sources/tcga data_sources        45
8715    COAD    human        tcga data_sources/tcga data_sources       546
> 
> ## Find all the mouse projects
> mouse_projects <- available_projects(organism = "mouse")
2023-04-10 22:12:29 caching file sra.recount_project.MD.gz.
> 
> ## Explore the results
> dim(mouse_projects)
[1] 10088     6
> head(mouse_projects)
    project organism file_source     project_home project_type n_samples
1 SRP170963    mouse         sra data_sources/sra data_sources       368
2 SRP045763    mouse         sra data_sources/sra data_sources        22
3 DRP005463    mouse         sra data_sources/sra data_sources        12
4 SRP172863    mouse         sra data_sources/sra data_sources         8
5 SRP186363    mouse         sra data_sources/sra data_sources        13
6 SRP101363    mouse         sra data_sources/sra data_sources        22
> 
> ## How many are from a data source vs a compilation?
> table(mouse_projects$project_type, useNA = "ifany")

data_sources 
       10088 
> 
> ## What are the unique file sources?
> table(
+     mouse_projects$file_source[mouse_projects$project_type == "data_sources"]
+ )

  sra 
10088 
> 
> ## Use with a custom recount3_url:
> available_projects(
+     recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3test",
+     available_homes = "data_sources/sra"
+ )
Warning: The 'url' <http://snaptron.cs.jhu.edu/data/temp/recount3test/human/data_sources/sra/metadata/sra.recount_project.MD.gz> does not exist or is not available.
Error in file(file, "rt") : invalid 'description' argument
Calls: available_projects ... available_samples -> lapply -> FUN -> read.table -> file
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   4. └─recount3::locate_url(...)
   5.   ├─base::match.arg(project_home)
   6.   │ └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
   7.   │   └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
   8.   └─recount3::project_homes(organism = organism, recount3_url = recount3_url)
  ── Error ('test-recount3_cache_rm.R:4:1'): (code run outside of `test_that()`) ──
  Error in `BiocFileCache::bfcrpath(temp_bfc_rm, test_url)`: not all 'rnames' found or unique.
  Backtrace:
      ▆
   1. ├─BiocFileCache::bfcrpath(temp_bfc_rm, test_url) at test-recount3_cache_rm.R:4:0
   2. └─BiocFileCache::bfcrpath(temp_bfc_rm, test_url)
  
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 50 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/recount3.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL recount3
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘recount3’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (recount3)

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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(recount3)
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: 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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

> 
> test_check("recount3")
[ FAIL 2 | WARN 3 | SKIP 0 | PASS 50 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-locate_url.R:29:5'): Locating URLs works ───────────────────────
Error: 'recount3_url' is not a valid supported URL since it's missing the URL/<organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.
Backtrace:
    ▆
 1. ├─testthat::expect_equivalent(...) at test-locate_url.R:29:4
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─recount3::locate_url(...)
 5.   ├─base::match.arg(project_home)
 6.   │ └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
 7.   │   └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
 8.   └─recount3::project_homes(organism = organism, recount3_url = recount3_url)
── Error ('test-recount3_cache_rm.R:4:1'): (code run outside of `test_that()`) ──
Error in `BiocFileCache::bfcrpath(temp_bfc_rm, test_url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. ├─BiocFileCache::bfcrpath(temp_bfc_rm, test_url) at test-recount3_cache_rm.R:4:0
 2. └─BiocFileCache::bfcrpath(temp_bfc_rm, test_url)

[ FAIL 2 | WARN 3 | SKIP 0 | PASS 50 ]
Error: Test failures
Execution halted