##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:recount.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings recount_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/recount.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘recount/DESCRIPTION’ ... OK
* this is package ‘recount’ version ‘1.37.0’
* 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 ‘recount’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
* 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘recount-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: all_metadata
> ### Title: This function downloads the metadata for all projects.
> ### Aliases: all_metadata
> 
> ### ** Examples
> 
> 
> metadata <- all_metadata()
2025-12-20 02:45:28.764034 downloading the metadata to /tmp/Rtmp0sCfwu/metadata_clean_sra.Rdata
trying URL 'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true'
Warning in download.file(url, method = method, ...) :
  downloaded length 0 != reported length 54894
Warning in download.file(url, method = method, ...) :
  cannot open URL 'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true': HTTP status was '503 Service Unavailable'
trying URL 'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true'
Warning in download.file(url, method = method, ...) :
  URL 'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true': status was 'Failure when receiving data from the peer'
trying URL 'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true'
Warning in download.file(url, method = method, ...) :
  URL 'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true': status was 'Failure when receiving data from the peer'
Error in download_retry(url = url, destfile = destfile, mode = "wb") : 
  'download_retry()' failed:
  URL: https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true
  error: cannot open URL 'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true'
Calls: all_metadata -> download_retry
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
add_metadata    1.855  0.300  38.335
add_predictions 0.660  0.086  22.689
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-data.R:152:1'): (code run outside of `test_that()`) ────────────
  Error in `download_retry(url = url, destfile = destfile, mode = "wb")`: 'download_retry()' failed:
    URL: https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true
    error: cannot open URL 'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true'
  Backtrace:
      ▆
   1. └─recount::all_metadata() at test-data.R:152:1
   2.   └─recount::download_retry(url = url, destfile = destfile, mode = "wb")
  
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 38 ]
  Error:
  ! Test failures.
  Execution halted
* 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: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/recount.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL recount
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘recount’ ...
** this is package ‘recount’ version ‘1.37.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (recount)

R Under development (unstable) (2025-10-20 r88955) -- "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.

> ## Disable the tests if the system variable 'R_DISABLE_TESTS' is set to TRUE
> 
> flag <- as.logical(Sys.getenv("R_DISABLE_TESTS"))
> if (is.na(flag) | flag == FALSE) {
+     library("testthat")
+     test_check("recount")
+ }
Loading required package: recount
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
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

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
Content type 'binary/octet-stream' length 3130229 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/rse_gene.Rdata'
Content type 'binary/octet-stream' length 1753074 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/rse_exon.Rdata'
Content type 'binary/octet-stream' length 3973986 bytes (3.8 MB)
==================================================
downloaded 3.8 MB

trying URL 'http://duffel.rail.bio/recount/SRP002001/rse_jx.Rdata'
Content type 'binary/octet-stream' length 1257137 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/rse_tx.RData'
Content type 'binary/octet-stream' length 14016087 bytes (13.4 MB)
==================================================
downloaded 13.4 MB

trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/counts_gene.tsv.gz'
Content type 'text/tab-separated-values' length 258000 bytes (251 KB)
==================================================
downloaded 251 KB

trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/counts_exon.tsv.gz'
Content type 'text/tab-separated-values' length 435233 bytes (425 KB)
==================================================
downloaded 425 KB

trying URL 'http://duffel.rail.bio/recount/SRP002001/counts_jx.tsv.gz'
Content type 'text/tab-separated-values' length 8833 bytes
==================================================
downloaded 8833 bytes

trying URL 'http://duffel.rail.bio/recount/SRP002001/SRP002001.tsv'
Content type 'text/tab-separated-values' length 629 bytes
==================================================
downloaded 629 bytes

trying URL 'http://duffel.rail.bio/recount/v2/SRP002001/files_info.tsv'
Content type 'text/tab-separated-values' length 705 bytes
==================================================
downloaded 705 bytes

trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/SRR036661.bw'
Content type 'binary/octet-stream' length 19539759 bytes (18.6 MB)
==================================================
downloaded 18.6 MB

trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw'
Content type 'binary/octet-stream' length 50936703 bytes (48.6 MB)
==================================================
downloaded 48.6 MB

trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/mean_SRP002001.bw'
Content type 'binary/octet-stream' length 50936703 bytes (48.6 MB)
==================================================
downloaded 48.6 MB

trying URL 'http://duffel.rail.bio/recount/SRP002001/bw/SRR036661.bw'
Content type 'binary/octet-stream' length 19539759 bytes (18.6 MB)
==================================================
downloaded 18.6 MB

trying URL 'http://duffel.rail.bio/recount/SRP002001/SRP002001.tsv'
Content type 'text/tab-separated-values' length 629 bytes
==================================================
downloaded 629 bytes

trying URL 'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true'
trying URL 'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true'
trying URL 'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true'
Saving _problems/test-data-152.R
trying URL 'http://duffel.rail.bio/recount/v2/DRP000366/files_info.tsv_fake'
[ FAIL 1 | WARN 7 | SKIP 0 | PASS 38 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-data.R:152:1'): (code run outside of `test_that()`) ────────────
Error in `download_retry(url = url, destfile = destfile, mode = "wb")`: 'download_retry()' failed:
  URL: https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true
  error: cannot open URL 'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true'
Backtrace:
    ▆
 1. └─recount::all_metadata() at test-data.R:152:1
 2.   └─recount::download_retry(url = url, destfile = destfile, mode = "wb")

[ FAIL 1 | WARN 7 | SKIP 0 | PASS 38 ]
Error:
! Test failures.
Execution halted