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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.10.0’
* 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 5.85  0.197    6.05
* 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-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.10.0’
** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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.

> 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...
3a435847763b2a_GRCh38.primary_assembly.genome.fa.1.bt2 added
3a43581f6a6567_GRCh38.primary_assembly.genome.fa.2.bt2 added
3a4358250f358c_GRCh38.primary_assembly.genome.fa.3.bt2 added
3a43581f4010c4_GRCh38.primary_assembly.genome.fa.4.bt2 added
3a43585eea4593_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3a435819714aee_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3a43582e6b77b8_outfile.txt added
3a43585bac0e11_GRCh37_to_GRCh38.chain added
3a43587bf6c345_GRCh37_to_NCBI34.chain added
3a435869049b01_GRCh37_to_NCBI35.chain added
3a435862321cb8_GRCh37_to_NCBI36.chain added
3a43584b5d07b7_GRCh38_to_GRCh37.chain added
3a4358f186a0b_GRCh38_to_NCBI34.chain added
3a43581d329d4a_GRCh38_to_NCBI35.chain added
3a43585c19b078_GRCh38_to_NCBI36.chain added
3a435858b06518_NCBI34_to_GRCh37.chain added
3a4358448c4e68_NCBI34_to_GRCh38.chain added
3a43584ecc047e_NCBI35_to_GRCh37.chain added
3a435825992181_NCBI35_to_GRCh38.chain added
3a43581fe7c2a5_NCBI36_to_GRCh37.chain added
3a4358212449d9_NCBI36_to_GRCh38.chain added
3a43583632bec1_GRCm38_to_NCBIM36.chain added
3a43583ac65bee_GRCm38_to_NCBIM37.chain added
3a43583e89a2c5_NCBIM36_to_GRCm38.chain added
3a43581168d6b3_NCBIM37_to_GRCm38.chain added
3a43582294592a_1000G_omni2.5.b37.vcf.gz added
3a4358562c42de_1000G_omni2.5.b37.vcf.gz.tbi added
3a435815d5b415_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3a4358f8b7a9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3a435829d0f566_1000G_omni2.5.hg38.vcf.gz added
3a43585c05ef92_1000G_omni2.5.hg38.vcf.gz.tbi added
3a4358486ef2d3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3a4358493b5acd_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3a4358115251e_af-only-gnomad.raw.sites.vcf added
3a435867af0397_af-only-gnomad.raw.sites.vcf.idx added
3a43582825a060_Mutect2-exome-panel.vcf.idx added
3a43581a86700c_Mutect2-WGS-panel-b37.vcf added
3a4358161a7b4f_Mutect2-WGS-panel-b37.vcf.idx added
3a43583d1ae71_small_exac_common_3.vcf added
3a4358167d3352_small_exac_common_3.vcf.idx added
3a43587f1f1651_1000g_pon.hg38.vcf.gz added
3a43586603cb2a_1000g_pon.hg38.vcf.gz.tbi added
3a435861da3b09_af-only-gnomad.hg38.vcf.gz added
3a4358e37805c_af-only-gnomad.hg38.vcf.gz.tbi added
3a43583366874_small_exac_common_3.hg38.vcf.gz added
3a43583df3eb81_small_exac_common_3.hg38.vcf.gz.tbi added
3a435866e7e575_gencode.v41.annotation.gtf added
3a435847c2b6dc_gencode.v42.annotation.gtf added
3a4358cbff000_gencode.vM30.annotation.gtf added
3a4358c8106f6_gencode.vM31.annotation.gtf added
3a435867aa7981_gencode.v41.transcripts.fa added
3a43582de439d9_gencode.v41.transcripts.fa.fai added
3a435842b3c5b7_gencode.v42.transcripts.fa added
3a43582270d56f_gencode.v42.transcripts.fa.fai added
3a43586c6ddc9e_gencode.vM30.pc_transcripts.fa added
3a4358541c9c6a_gencode.vM30.pc_transcripts.fa.fai added
3a435845052e99_gencode.vM31.pc_transcripts.fa added
3a4358429a1f7c_gencode.vM31.pc_transcripts.fa.fai added
3a435869f25080_GRCh38.primary_assembly.genome.fa.1.ht2 added
3a435845fde642_GRCh38.primary_assembly.genome.fa.2.ht2 added
3a43586c6b14e2_GRCh38.primary_assembly.genome.fa.3.ht2 added
3a435845f84012_GRCh38.primary_assembly.genome.fa.4.ht2 added
3a4358e6cd915_GRCh38.primary_assembly.genome.fa.5.ht2 added
3a435835a66faf_GRCh38.primary_assembly.genome.fa.6.ht2 added
3a4358470d6530_GRCh38.primary_assembly.genome.fa.7.ht2 added
3a4358761bdcad_GRCh38.primary_assembly.genome.fa.8.ht2 added
3a43585dcc100f_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3a43586193d53d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3a4358c3657fc_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3a4358619dbe81_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3a43587811088f_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3a4358b556e4d_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3a435847a189ab_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3a435859eb4398_GRCh38.primary_assembly.genome.fa.fai added
3a4358198ceeaa_GRCh38.primary_assembly.genome.fa.amb added
3a43584ad7f21f_GRCh38.primary_assembly.genome.fa.ann added
3a435817df2f1a_GRCh38.primary_assembly.genome.fa.bwt added
3a435874d41f_GRCh38.primary_assembly.genome.fa.pac added
3a4358129aa8fb_GRCh38.primary_assembly.genome.fa.sa added
3a4358249f1f1a_GRCh38.primary_assembly.genome.fa added
3a4358cf5db15_hs37d5.fa.fai added
3a43587a45227c_hs37d5.fa.amb added
3a4358528358f3_hs37d5.fa.ann added
3a43584fa9a0cc_hs37d5.fa.bwt added
3a43581cb5f7ec_hs37d5.fa.pac added
3a43583ef13592_hs37d5.fa.sa added
3a435823c63d37_hs37d5.fa added
3a435861bb2685_complete_ref_lens.bin added
3a435818b550e_ctable.bin added
3a4358db88db7_ctg_offsets.bin added
3a435827b90cc8_duplicate_clusters.tsv added
3a43586df669f1_info.json added
3a435853b0cdc9_mphf.bin added
3a43583625e5dd_pos.bin added
3a4358239cd9a0_pre_indexing.log added
3a43581abe32f9_rank.bin added
3a43582c41c28a_ref_indexing.log added
3a4358168e9b0_refAccumLengths.bin added
3a43587c520836_reflengths.bin added
3a435838781a87_refseq.bin added
3a43586306a831_seq.bin added
3a4358746310c5_versionInfo.json added
3a435843cd88d4_salmon_index added
3a43582aa831dc_chrLength.txt added
3a43584e4e545e_chrName.txt added
3a43585d5a777e_chrNameLength.txt added
3a4358758023fb_chrStart.txt added
3a4358662d8378_exonGeTrInfo.tab added
3a43585dcf4b9d_exonInfo.tab added
3a435881accf6_geneInfo.tab added
3a4358acca292_Genome added
3a43586ac526b2_genomeParameters.txt added
3a435825fef72_Log.out added
3a43585d4ffb85_SA added
3a43583a6ec77f_SAindex added
3a43581f15e75e_sjdbInfo.txt added
3a43581c413117_sjdbList.fromGTF.out.tab added
3a43585e3504b6_sjdbList.out.tab added
3a4358d10de4_transcriptInfo.tab added
3a43581dcc8626_GRCh38.GENCODE.v42_100 added
3a43586bed926d_knownGene_hg38.sql added
3a4358288a1aac_knownGene_hg38.txt added
3a4358bc2f017_refGene_hg38.sql added
3a43583f9e6036_refGene_hg38.txt added
3a43585eb00089_knownGene_mm39.sql added
3a43582f5fc9b7_knownGene_mm39.txt added
3a43585a5c932f_refGene_mm39.sql added
3a4358af1c314_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/Rtmpt8DwlV/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 0 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
> 
> 
> 
> proc.time()
   user  system elapsed 
 18.172   1.143  20.057