##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:recount3.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings recount3_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/recount3.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recount3/DESCRIPTION’ ... OK
* this is package ‘recount3’ version ‘1.20.0’
* 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 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 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: create_rse_manual
> ### Title: Internal function for creating a recount3
> ###   RangedSummarizedExperiment object
> ### Aliases: create_rse_manual
> 
> ### ** Examples
> 
> 
> ## Unlike create_rse(), here we create an RSE object by
> ## fully specifying all the arguments for locating this study
> rse_gene_SRP009615_manual <- create_rse_manual(
+     "SRP009615",
+     "data_sources/sra"
+ )
2025-11-11 13:53:06.392284 downloading and reading the metadata.
2025-11-11 13:53:08.933956 caching file sra.sra.SRP009615.MD.gz.
2025-11-11 13:53:10.105048 caching file sra.recount_project.SRP009615.MD.gz.
2025-11-11 13:53:11.34146 caching file sra.recount_qc.SRP009615.MD.gz.
2025-11-11 13:53:13.603503 caching file sra.recount_seq_qc.SRP009615.MD.gz.
2025-11-11 13:53:15.118007 caching file sra.recount_pred.SRP009615.MD.gz.
2025-11-11 13:53:15.465046 downloading and reading the feature information.
2025-11-11 13:53:16.365165 caching file human.gene_sums.G026.gtf.gz.
2025-11-11 13:53:17.660601 downloading and reading the counts: 12 samples across 63856 features.
2025-11-11 13:53:18.691006 caching file sra.gene_sums.SRP009615.G026.gz.
2025-11-11 13:53:20.395686 constructing the RangedSummarizedExperiment (rse) object.
> rse_gene_SRP009615_manual
class: RangedSummarizedExperiment 
dim: 63856 12 
metadata(8): time_created recount3_version ... annotation recount3_url
assays(1): raw_counts
rownames(63856): ENSG00000278704.1 ENSG00000277400.1 ...
  ENSG00000182484.15_PAR_Y ENSG00000227159.8_PAR_Y
rowData names(10): source type ... havana_gene tag
colnames(12): SRR387777 SRR387778 ... SRR389077 SRR389078
colData names(175): rail_id external_id ...
  recount_pred.curated.cell_line BigWigURL
> 
> ## Check how much memory this RSE object uses
> pryr::object_size(rse_gene_SRP009615_manual)
24.81 MB
> 
> ## Test with a collection that has a single sample
> ## NOTE: this requires loading the full data for this study when
> ## creating the RSE object
> rse_gene_ERP110066_collection_manual <- create_rse_manual(
+     "ERP110066",
+     "collections/geuvadis_smartseq",
+     recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3"
+ )
2025-11-11 13:53:20.73255 downloading and reading the metadata.
2025-11-11 13:53:22.043016 caching file geuvadis_smartseq.recount_project.gz.
2025-11-11 13:53:22.792223 caching file sra.sra.ERP110066.MD.gz.
2025-11-11 13:53:23.646651 caching file sra.recount_project.ERP110066.MD.gz.
2025-11-11 13:53:24.409492 caching file sra.recount_qc.ERP110066.MD.gz.
Warning: The 'url' <http://snaptron.cs.jhu.edu/data/temp/recount3/human/data_sources/sra/metadata/66/ERP110066/sra.recount_seq_qc.ERP110066.MD.gz> does not exist or is not available.
2025-11-11 13:53:25.676218 caching file sra.recount_pred.ERP110066.MD.gz.
2025-11-11 13:53:26.44616 caching file geuvadis_smartseq.custom.gz.
2025-11-11 13:53:27.109656 downloading and reading the feature information.
2025-11-11 13:53:27.609219 caching file human.gene_sums.G026.gtf.gz.
2025-11-11 13:53:29.176485 downloading and reading the counts: 1 sample across 63856 features.
2025-11-11 13:53:29.691471 caching file sra.gene_sums.ERP110066.G026.gz.
2025-11-11 13:53:34.565322 constructing the RangedSummarizedExperiment (rse) object.
> rse_gene_ERP110066_collection_manual
class: RangedSummarizedExperiment 
dim: 63856 1 
metadata(8): time_created recount3_version ... annotation recount3_url
assays(1): raw_counts
rownames(63856): ENSG00000278704.1 ENSG00000277400.1 ...
  ENSG00000182484.15_PAR_Y ENSG00000227159.8_PAR_Y
rowData names(10): source type ... havana_gene tag
colnames(1): ERR2713106
colData names(162): rail_id external_id ... custom.sequencing_type
  BigWigURL
> 
> ## Check how much memory this RSE object uses
> pryr::object_size(rse_gene_ERP110066_collection_manual)
19.16 MB
> 
> ## Mouse example
> rse_gene_DRP002367_manual <- create_rse_manual(
+     "DRP002367",
+     "data_sources/sra",
+     organism = "mouse"
+ )
2025-11-11 13:53:34.873162 downloading and reading the metadata.
2025-11-11 13:53:37.59222 caching file sra.sra.DRP002367.MD.gz.
2025-11-11 13:53:39.568233 caching file sra.recount_project.DRP002367.MD.gz.
2025-11-11 13:53:43.879771 caching file sra.recount_qc.DRP002367.MD.gz.
2025-11-11 13:53:46.242479 caching file sra.recount_seq_qc.DRP002367.MD.gz.
2025-11-11 13:53:47.954324 caching file sra.recount_pred.DRP002367.MD.gz.
2025-11-11 13:53:48.242178 downloading and reading the feature information.
2025-11-11 13:53:50.642752 caching file mouse.gene_sums.M023.gtf.gz.
2025-11-11 13:53:51.844938 downloading and reading the counts: 4 samples across 50733 features.
2025-11-11 13:53:54.034956 caching file sra.gene_sums.DRP002367.M023.gz.
adding rname 'http://duffel.rail.bio/recount3/mouse/data_sources/sra/gene_sums/67/DRP002367/sra.gene_sums.DRP002367.M023.gz'

2025-11-11 13:53:58.02144 constructing the RangedSummarizedExperiment (rse) object.
Error in create_rse_manual("DRP002367", "data_sources/sra", organism = "mouse") : 
  Gene names and count rownames are not matching.
Calls: create_rse_manual -> stopifnot
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
create_rse            79.920  1.540 257.537
available_projects    12.755  0.476  42.856
compute_read_counts   10.845  0.247  70.567
available_samples      6.751  0.132  14.872
create_hub             3.063  0.066   5.268
compute_scale_factors  1.486  0.107  16.944
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/recount3.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL recount3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘recount3’ ...
** this is package ‘recount3’ version ‘1.20.0’
** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(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
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

> 
> test_check("recount3")




















[ FAIL 0 | WARN 0 | SKIP 0 | PASS 63 ]
> 
> proc.time()
   user  system elapsed 
 59.585   1.352 293.623