##############################################################################
##############################################################################
###
### 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"
+ )
2025-12-05 14:43:30.181034 downloading and reading the metadata.
2025-12-05 14:43:30.861644 caching file sra.sra.SRP009615.MD.gz.
2025-12-05 14:43:31.615115 caching file sra.recount_project.SRP009615.MD.gz.
2025-12-05 14:43:32.365783 caching file sra.recount_qc.SRP009615.MD.gz.
2025-12-05 14:43:33.156839 caching file sra.recount_seq_qc.SRP009615.MD.gz.
2025-12-05 14:43:33.931077 caching file sra.recount_pred.SRP009615.MD.gz.
2025-12-05 14:43:34.092763 downloading and reading the feature information.
2025-12-05 14:43:35.046777 caching file human.gene_sums.G026.gtf.gz.
2025-12-05 14:43:35.771889 downloading and reading the counts: 12 samples across 63856 features.
2025-12-05 14:43:38.588797 caching file sra.gene_sums.SRP009615.G026.gz.
2025-12-05 14:43:39.619671 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"
+ )
2025-12-05 14:43:39.887006 downloading and reading the metadata.
2025-12-05 14:43:43.684547 caching file geuvadis_smartseq.recount_project.gz.
2025-12-05 14:43:44.332187 caching file sra.sra.ERP110066.MD.gz.
2025-12-05 14:43:45.67971 caching file sra.recount_project.ERP110066.MD.gz.
2025-12-05 14:43:46.305532 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.
2025-12-05 14:43:47.442208 caching file sra.recount_pred.ERP110066.MD.gz.
2025-12-05 14:43:48.072195 caching file geuvadis_smartseq.custom.gz.
2025-12-05 14:43:48.501059 downloading and reading the feature information.
2025-12-05 14:43:49.012692 caching file human.gene_sums.G026.gtf.gz.
2025-12-05 14:43:49.731396 downloading and reading the counts: 1 sample across 63856 features.
2025-12-05 14:43:50.24426 caching file sra.gene_sums.ERP110066.G026.gz.
2025-12-05 14:43:54.292435 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"
+ )
2025-12-05 14:43:54.542362 downloading and reading the metadata.
2025-12-05 14:43:59.018292 caching file sra.sra.DRP002367.MD.gz.
2025-12-05 14:44:00.297881 caching file sra.recount_project.DRP002367.MD.gz.
2025-12-05 14:44:01.603173 caching file sra.recount_qc.DRP002367.MD.gz.
2025-12-05 14:44:02.899323 caching file sra.recount_seq_qc.DRP002367.MD.gz.
2025-12-05 14:44:04.183741 caching file sra.recount_pred.DRP002367.MD.gz.
2025-12-05 14:44:04.35178 downloading and reading the feature information.
2025-12-05 14:44:05.538778 caching file mouse.gene_sums.M023.gtf.gz.
2025-12-05 14:44:06.19867 downloading and reading the counts: 4 samples across 50733 features.
2025-12-05 14:44:08.281241 caching file sra.gene_sums.DRP002367.M023.gz.
2025-12-05 14:44:08.559918 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            80.576  4.946 175.407
available_projects    11.883  1.022  25.601
compute_read_counts   10.881  1.603  37.160
available_samples      7.540  0.590  10.859
compute_scale_factors  2.617  0.449  11.020
* 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.