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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-07 08:01:26 UTC
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.11.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ReUseData’ 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
dataHub-class 6.041   0.37   6.413
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ReUseData
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.11.0’
** 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 (ReUseData)

R version 4.6.0 alpha (2026-04-05 r89794)
Copyright (C) 2026 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(testthat)
> library(ReUseData)
> 
> test_check("ReUseData")
Note: you need to assign a name for the recipe: rcpName <- recipeLoad('xx')
Data recipe loaded!
Use inputs() to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/echo_out.html
for user instructions (e.g., eligible input values, data source, etc.)

}INFO Final process status is success

Updating data record...
outfile.txt added

Updating data record...
c085f5a677e99_GRCh38.primary_assembly.genome.fa.1.bt2 added
c085f2219ea17_GRCh38.primary_assembly.genome.fa.2.bt2 added
c085f6d2f05e3_GRCh38.primary_assembly.genome.fa.3.bt2 added
c085f67f7a0dc_GRCh38.primary_assembly.genome.fa.4.bt2 added
c085f7ed71b0f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
c085fe69bb1_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
c085f64b1a5b8_outfile.txt added
c085f2d903812_GRCh37_to_GRCh38.chain added
c085f4b19c656_GRCh37_to_NCBI34.chain added
c085f28be6a10_GRCh37_to_NCBI35.chain added
c085f7a732ef8_GRCh37_to_NCBI36.chain added
c085f7c515296_GRCh38_to_GRCh37.chain added
c085f50b38257_GRCh38_to_NCBI34.chain added
c085f6b55fd48_GRCh38_to_NCBI35.chain added
c085f42deb91a_GRCh38_to_NCBI36.chain added
c085f2df8b5fd_NCBI34_to_GRCh37.chain added
c085f1950cf3d_NCBI34_to_GRCh38.chain added
c085f284d9d98_NCBI35_to_GRCh37.chain added
c085f31333795_NCBI35_to_GRCh38.chain added
c085f7673d212_NCBI36_to_GRCh37.chain added
c085f7e828e6e_NCBI36_to_GRCh38.chain added
c085f4cea4727_GRCm38_to_NCBIM36.chain added
c085f432a881a_GRCm38_to_NCBIM37.chain added
c085f3dda93bf_NCBIM36_to_GRCm38.chain added
c085f49a2f614_NCBIM37_to_GRCm38.chain added
c085f60dad360_1000G_omni2.5.b37.vcf.gz added
c085f248e4ff0_1000G_omni2.5.b37.vcf.gz.tbi added
c085f14527770_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
c085f75a28fe5_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
c085f14c9ff2d_1000G_omni2.5.hg38.vcf.gz added
c085f4e08a32f_1000G_omni2.5.hg38.vcf.gz.tbi added
c085f500a0e7e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
c085f36e3e945_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
c085f3b37a912_af-only-gnomad.raw.sites.vcf added
c085f3801af5b_af-only-gnomad.raw.sites.vcf.idx added
c085f35bb0454_Mutect2-exome-panel.vcf.idx added
c085f3c1e44c4_Mutect2-WGS-panel-b37.vcf added
c085f1cb35513_Mutect2-WGS-panel-b37.vcf.idx added
c085f634b3c66_small_exac_common_3.vcf added
c085f7380b1a_small_exac_common_3.vcf.idx added
c085f4571bf23_1000g_pon.hg38.vcf.gz added
c085f5dbe6b5e_1000g_pon.hg38.vcf.gz.tbi added
c085f3895db0_af-only-gnomad.hg38.vcf.gz added
c085f1625417b_af-only-gnomad.hg38.vcf.gz.tbi added
c085f491468a6_small_exac_common_3.hg38.vcf.gz added
c085f466816ca_small_exac_common_3.hg38.vcf.gz.tbi added
c085f441df778_gencode.v41.annotation.gtf added
c085f626537e3_gencode.v42.annotation.gtf added
c085f6eb5b463_gencode.vM30.annotation.gtf added
c085f75512f0d_gencode.vM31.annotation.gtf added
c085f58d909f5_gencode.v41.transcripts.fa added
c085f6d3842d1_gencode.v41.transcripts.fa.fai added
c085f423b7634_gencode.v42.transcripts.fa added
c085f1c039210_gencode.v42.transcripts.fa.fai added
c085f2b12d690_gencode.vM30.pc_transcripts.fa added
c085fbde6c49_gencode.vM30.pc_transcripts.fa.fai added
c085f7cde6570_gencode.vM31.pc_transcripts.fa added
c085f4fa12680_gencode.vM31.pc_transcripts.fa.fai added
c085f2030e3b9_GRCh38.primary_assembly.genome.fa.1.ht2 added
c085f7280f555_GRCh38.primary_assembly.genome.fa.2.ht2 added
c085f646b25ad_GRCh38.primary_assembly.genome.fa.3.ht2 added
c085f6e3986e8_GRCh38.primary_assembly.genome.fa.4.ht2 added
c085f428b03d4_GRCh38.primary_assembly.genome.fa.5.ht2 added
c085f1b4f0ef2_GRCh38.primary_assembly.genome.fa.6.ht2 added
c085f29712ffa_GRCh38.primary_assembly.genome.fa.7.ht2 added
c085f7a8cb32f_GRCh38.primary_assembly.genome.fa.8.ht2 added
c085f510a1346_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
c085f658f74be_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
c085f17400842_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
c085f34554fac_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
c085f6cc77fd8_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
c085f5cb1c765_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
c085f1213bb0a_GRCh38_full_analysis_set_plus_decoy_hla.fa added
c085f7050dd89_GRCh38.primary_assembly.genome.fa.fai added
c085f72d708e0_GRCh38.primary_assembly.genome.fa.amb added
c085f5b2823b1_GRCh38.primary_assembly.genome.fa.ann added
c085f36b8f453_GRCh38.primary_assembly.genome.fa.bwt added
c085f36f50058_GRCh38.primary_assembly.genome.fa.pac added
c085f3d8d5b94_GRCh38.primary_assembly.genome.fa.sa added
c085f256ea8b6_GRCh38.primary_assembly.genome.fa added
c085f2c462f65_hs37d5.fa.fai added
c085f1666658a_hs37d5.fa.amb added
c085f12a6eb87_hs37d5.fa.ann added
c085f6e81a59a_hs37d5.fa.bwt added
c085f3269f79a_hs37d5.fa.pac added
c085f3db9c217_hs37d5.fa.sa added
c085f7a6011e3_hs37d5.fa added
c085f2f485d0a_complete_ref_lens.bin added
c085fd5ae897_ctable.bin added
c085f1a90f59c_ctg_offsets.bin added
c085f21c9525f_duplicate_clusters.tsv added
c085f71c60e45_info.json added
c085f8ca7c84_mphf.bin added
c085f64545633_pos.bin added
c085fd151d37_pre_indexing.log added
c085f323bac7e_rank.bin added
c085f5ee10962_ref_indexing.log added
c085f5e1f307e_refAccumLengths.bin added
c085f17cb213d_reflengths.bin added
c085f762111a4_refseq.bin added
c085f1274802a_seq.bin added
c085f492a115_versionInfo.json added
c085f52d2d90a_salmon_index added
c085f24883b35_chrLength.txt added
c085f74e37e9e_chrName.txt added
c085f45a9e1ea_chrNameLength.txt added
c085f7fb05ee6_chrStart.txt added
c085f2b9c72f2_exonGeTrInfo.tab added
c085f7c9ee243_exonInfo.tab added
c085f3d3dba7a_geneInfo.tab added
c085f510b1ba8_Genome added
c085f28e511a8_genomeParameters.txt added
c085f53a42004_Log.out added
c085f63b20730_SA added
c085f1766b742_SAindex added
c085f60e179e_sjdbInfo.txt added
c085f216bc947_sjdbList.fromGTF.out.tab added
c085f11c6c925_sjdbList.out.tab added
c085f355674a8_transcriptInfo.tab added
c085f2ec6b1df_GRCh38.GENCODE.v42_100 added
c085f2c57bec1_knownGene_hg38.sql added
c085f571fc708_knownGene_hg38.txt added
c085f208cc024_refGene_hg38.sql added
c085f35223b45_refGene_hg38.txt added
c085f3b741d3b_knownGene_mm39.sql added
c085f2da1dd5b_knownGene_mm39.txt added
c085f675de7c4_refGene_mm39.sql added
c085f1a55269e_refGene_mm39.txt added
trying URL 'https://storage.googleapis.com/reusedata/echo/outfile.txt'
Content type 'text/plain' length 30 bytes
==================================================
downloaded 30 bytes

trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.yml'
Content type 'application/x-yaml' length 151 bytes
==================================================
downloaded 151 bytes

trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.cwl'
Content type 'application/octet-stream' length 1152 bytes
==================================================
downloaded 1152 bytes

trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.md5'
Content type 'application/octet-stream' length 45 bytes
==================================================
downloaded 45 bytes

trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.sh'
Content type 'application/x-shellscript' length 68 bytes
==================================================
downloaded 68 bytes

Data is downloaded: 
/tmp/RtmpBiA6gB/test_gcpData/outfile.txt
}INFO Final process status is success
NOTE: existing caches will be removed and regenerated!
Updating recipes...
STAR_index.R added
bowtie2_index.R added
echo_out.R added
ensembl_liftover.R added
gcp_broad_gatk_hg19.R added
gcp_broad_gatk_hg38.R added
gcp_gatk_mutect2_b37.R added
gcp_gatk_mutect2_hg38.R added
gencode_annotation.R added
gencode_genome_grch38.R added
gencode_transcripts.R added
hisat2_index.R added
reference_genome.R added
salmon_index.R added
ucsc_database.R added

Data recipe loaded!
Use inputs(ensembl_liftover) to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/ensembl_liftover.html
for user instructions (e.g., eligible input values, data source, etc.)

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 44 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
> 
> 
> 
> proc.time()
   user  system elapsed 
 18.130   1.674  20.221