##############################################################################
##############################################################################
###
### 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 6.149  0.283   6.434
* 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.

##############################################################################
##############################################################################
###
### 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...
393bb31f3e51f0_GRCh38.primary_assembly.genome.fa.1.bt2 added
393bb311f4b0af_GRCh38.primary_assembly.genome.fa.2.bt2 added
393bb3bf14e4a_GRCh38.primary_assembly.genome.fa.3.bt2 added
393bb35e8f5885_GRCh38.primary_assembly.genome.fa.4.bt2 added
393bb3315d028e_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
393bb31af6d9c5_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
393bb338dc56bc_outfile.txt added
393bb343e23f51_GRCh37_to_GRCh38.chain added
393bb365c54533_GRCh37_to_NCBI34.chain added
393bb335fcdab5_GRCh37_to_NCBI35.chain added
393bb367c8e793_GRCh37_to_NCBI36.chain added
393bb35b61d243_GRCh38_to_GRCh37.chain added
393bb3746debf6_GRCh38_to_NCBI34.chain added
393bb32cdc4221_GRCh38_to_NCBI35.chain added
393bb359d9e39c_GRCh38_to_NCBI36.chain added
393bb315ed0536_NCBI34_to_GRCh37.chain added
393bb3534300d8_NCBI34_to_GRCh38.chain added
393bb332c542e4_NCBI35_to_GRCh37.chain added
393bb31bc000f2_NCBI35_to_GRCh38.chain added
393bb31a5398cd_NCBI36_to_GRCh37.chain added
393bb368c4104_NCBI36_to_GRCh38.chain added
393bb330d57173_GRCm38_to_NCBIM36.chain added
393bb35063677c_GRCm38_to_NCBIM37.chain added
393bb3495a88f5_NCBIM36_to_GRCm38.chain added
393bb3a90c42f_NCBIM37_to_GRCm38.chain added
393bb37218a2a9_1000G_omni2.5.b37.vcf.gz added
393bb352d78bb5_1000G_omni2.5.b37.vcf.gz.tbi added
393bb3221f4e7a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
393bb332530f4b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
393bb314f90b30_1000G_omni2.5.hg38.vcf.gz added
393bb33cc7ed05_1000G_omni2.5.hg38.vcf.gz.tbi added
393bb35191613b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
393bb326edbbe0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
393bb348b93b50_af-only-gnomad.raw.sites.vcf added
393bb33020b9c1_af-only-gnomad.raw.sites.vcf.idx added
393bb3584abe6e_Mutect2-exome-panel.vcf.idx added
393bb363b01515_Mutect2-WGS-panel-b37.vcf added
393bb368fd107d_Mutect2-WGS-panel-b37.vcf.idx added
393bb31c2cfdbf_small_exac_common_3.vcf added
393bb349755a48_small_exac_common_3.vcf.idx added
393bb31ef9eb32_1000g_pon.hg38.vcf.gz added
393bb33f5e552_1000g_pon.hg38.vcf.gz.tbi added
393bb324d72c8b_af-only-gnomad.hg38.vcf.gz added
393bb31367d729_af-only-gnomad.hg38.vcf.gz.tbi added
393bb330d22773_small_exac_common_3.hg38.vcf.gz added
393bb37eb11027_small_exac_common_3.hg38.vcf.gz.tbi added
393bb32954dc5f_gencode.v41.annotation.gtf added
393bb3415284b_gencode.v42.annotation.gtf added
393bb33176530b_gencode.vM30.annotation.gtf added
393bb34514dd52_gencode.vM31.annotation.gtf added
393bb31e68c119_gencode.v41.transcripts.fa added
393bb33802940f_gencode.v41.transcripts.fa.fai added
393bb375ea4ec5_gencode.v42.transcripts.fa added
393bb36ecc2895_gencode.v42.transcripts.fa.fai added
393bb315d1d05_gencode.vM30.pc_transcripts.fa added
393bb37b12f4_gencode.vM30.pc_transcripts.fa.fai added
393bb360e4cb3e_gencode.vM31.pc_transcripts.fa added
393bb35434a8ba_gencode.vM31.pc_transcripts.fa.fai added
393bb3229a616f_GRCh38.primary_assembly.genome.fa.1.ht2 added
393bb31337da89_GRCh38.primary_assembly.genome.fa.2.ht2 added
393bb3692db3eb_GRCh38.primary_assembly.genome.fa.3.ht2 added
393bb35f624e74_GRCh38.primary_assembly.genome.fa.4.ht2 added
393bb364c93bc4_GRCh38.primary_assembly.genome.fa.5.ht2 added
393bb3101b6fcb_GRCh38.primary_assembly.genome.fa.6.ht2 added
393bb3281b89c4_GRCh38.primary_assembly.genome.fa.7.ht2 added
393bb314e9f585_GRCh38.primary_assembly.genome.fa.8.ht2 added
393bb368662e39_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
393bb3bcb9eda_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
393bb37de70603_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
393bb34932bf9_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
393bb35540f922_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
393bb31ce0f135_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
393bb3889114b_GRCh38_full_analysis_set_plus_decoy_hla.fa added
393bb37a1825ae_GRCh38.primary_assembly.genome.fa.fai added
393bb33048c85e_GRCh38.primary_assembly.genome.fa.amb added
393bb3395b38bf_GRCh38.primary_assembly.genome.fa.ann added
393bb378c935d5_GRCh38.primary_assembly.genome.fa.bwt added
393bb3599da4be_GRCh38.primary_assembly.genome.fa.pac added
393bb33d70610a_GRCh38.primary_assembly.genome.fa.sa added
393bb32a3f88e1_GRCh38.primary_assembly.genome.fa added
393bb31eb28210_hs37d5.fa.fai added
393bb35bd92223_hs37d5.fa.amb added
393bb362421cf0_hs37d5.fa.ann added
393bb3149cd0d5_hs37d5.fa.bwt added
393bb34aa54ab8_hs37d5.fa.pac added
393bb3639f39f5_hs37d5.fa.sa added
393bb31517e3ca_hs37d5.fa added
393bb32b8a15f6_complete_ref_lens.bin added
393bb337d3e2b0_ctable.bin added
393bb337b24539_ctg_offsets.bin added
393bb33ec1f07f_duplicate_clusters.tsv added
393bb32101969b_info.json added
393bb3171493ad_mphf.bin added
393bb3238b2c44_pos.bin added
393bb3311d0666_pre_indexing.log added
393bb33f301d72_rank.bin added
393bb3387521c9_ref_indexing.log added
393bb31983349f_refAccumLengths.bin added
393bb34afbbc4c_reflengths.bin added
393bb3365c27cc_refseq.bin added
393bb31e166098_seq.bin added
393bb3203cb56e_versionInfo.json added
393bb3533d1902_salmon_index added
393bb3269f71e4_chrLength.txt added
393bb31a54db1c_chrName.txt added
393bb3385e160_chrNameLength.txt added
393bb35ffaaaa3_chrStart.txt added
393bb3131e10f2_exonGeTrInfo.tab added
393bb35d23861e_exonInfo.tab added
393bb31d6b0bad_geneInfo.tab added
393bb33d5d99d3_Genome added
393bb37bd6082e_genomeParameters.txt added
393bb379442dd1_Log.out added
393bb31f9fb6c3_SA added
393bb31072d904_SAindex added
393bb343e97889_sjdbInfo.txt added
393bb333ef0b9_sjdbList.fromGTF.out.tab added
393bb3258abcce_sjdbList.out.tab added
393bb36f738e80_transcriptInfo.tab added
393bb33b12d369_GRCh38.GENCODE.v42_100 added
393bb35d3d0207_knownGene_hg38.sql added
393bb32e357eff_knownGene_hg38.txt added
393bb35c146a04_refGene_hg38.sql added
393bb3745195b4_refGene_hg38.txt added
393bb351c0ab43_knownGene_mm39.sql added
393bb3d31706a_knownGene_mm39.txt added
393bb33381b326_refGene_mm39.sql added
393bb3a35cd0d_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/RtmpgcZATW/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 
 18.060   0.903  19.525