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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings ReUseData_1.13.0.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* 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: 2026-05-06 07:30:15 UTC
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.13.0’
* 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 5.898  0.239    6.14
* 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-3.24-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL ReUseData
###
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* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.13.0’
** 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 RC (2026-04-17 r89917) -- "Because it was There"
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...
2df1671354231c_GRCh38.primary_assembly.genome.fa.1.bt2 added
2df1676de810e0_GRCh38.primary_assembly.genome.fa.2.bt2 added
2df1672af23bec_GRCh38.primary_assembly.genome.fa.3.bt2 added
2df167354eb8c_GRCh38.primary_assembly.genome.fa.4.bt2 added
2df167972d926_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2df167649be793_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2df1673a3eb299_outfile.txt added
2df1676822e7da_GRCh37_to_GRCh38.chain added
2df1675b6f638e_GRCh37_to_NCBI34.chain added
2df1674398f2f5_GRCh37_to_NCBI35.chain added
2df1673acbae22_GRCh37_to_NCBI36.chain added
2df1675675a6b2_GRCh38_to_GRCh37.chain added
2df1672f2fd0b_GRCh38_to_NCBI34.chain added
2df16717b24bff_GRCh38_to_NCBI35.chain added
2df167611515f0_GRCh38_to_NCBI36.chain added
2df1671c20ee95_NCBI34_to_GRCh37.chain added
2df16768f3bd47_NCBI34_to_GRCh38.chain added
2df16726ebf5a0_NCBI35_to_GRCh37.chain added
2df1672c4d7a92_NCBI35_to_GRCh38.chain added
2df167184a6f2d_NCBI36_to_GRCh37.chain added
2df1673c62c180_NCBI36_to_GRCh38.chain added
2df16711173427_GRCm38_to_NCBIM36.chain added
2df1673b720d7_GRCm38_to_NCBIM37.chain added
2df167290deaeb_NCBIM36_to_GRCm38.chain added
2df16739f9206c_NCBIM37_to_GRCm38.chain added
2df1673164ea1e_1000G_omni2.5.b37.vcf.gz added
2df16715d0bd8a_1000G_omni2.5.b37.vcf.gz.tbi added
2df167f02ac9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2df1673ecdd89_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2df1671b08cb74_1000G_omni2.5.hg38.vcf.gz added
2df1673c40b669_1000G_omni2.5.hg38.vcf.gz.tbi added
2df167174100a5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2df1678f0dc55_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2df1676732f256_af-only-gnomad.raw.sites.vcf added
2df1671a95ec31_af-only-gnomad.raw.sites.vcf.idx added
2df1671263b57b_Mutect2-exome-panel.vcf.idx added
2df1674bced9e9_Mutect2-WGS-panel-b37.vcf added
2df16754d49ecb_Mutect2-WGS-panel-b37.vcf.idx added
2df1677a869d55_small_exac_common_3.vcf added
2df167273e3d77_small_exac_common_3.vcf.idx added
2df167186d91c0_1000g_pon.hg38.vcf.gz added
2df16735524b77_1000g_pon.hg38.vcf.gz.tbi added
2df1677db3e42a_af-only-gnomad.hg38.vcf.gz added
2df1671b608ecb_af-only-gnomad.hg38.vcf.gz.tbi added
2df1674d049776_small_exac_common_3.hg38.vcf.gz added
2df1675ec8fa1a_small_exac_common_3.hg38.vcf.gz.tbi added
2df16737817d61_gencode.v41.annotation.gtf added
2df16735f854bd_gencode.v42.annotation.gtf added
2df1675b4efba_gencode.vM30.annotation.gtf added
2df16763cef7f3_gencode.vM31.annotation.gtf added
2df1674e42c3ea_gencode.v41.transcripts.fa added
2df1674217b13b_gencode.v41.transcripts.fa.fai added
2df16774e62c1b_gencode.v42.transcripts.fa added
2df16751f9e4c1_gencode.v42.transcripts.fa.fai added
2df1676b259c26_gencode.vM30.pc_transcripts.fa added
2df1672edf4c87_gencode.vM30.pc_transcripts.fa.fai added
2df16735ecedf_gencode.vM31.pc_transcripts.fa added
2df167f659b0_gencode.vM31.pc_transcripts.fa.fai added
2df1672fcf7751_GRCh38.primary_assembly.genome.fa.1.ht2 added
2df16774bac69_GRCh38.primary_assembly.genome.fa.2.ht2 added
2df1671bff2524_GRCh38.primary_assembly.genome.fa.3.ht2 added
2df1676c102dba_GRCh38.primary_assembly.genome.fa.4.ht2 added
2df1671e8cad0e_GRCh38.primary_assembly.genome.fa.5.ht2 added
2df16724f00179_GRCh38.primary_assembly.genome.fa.6.ht2 added
2df16753432010_GRCh38.primary_assembly.genome.fa.7.ht2 added
2df16739229940_GRCh38.primary_assembly.genome.fa.8.ht2 added
2df1673753b6f4_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2df1671f11f9fa_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2df167df7380b_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2df16731da5449_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2df16746503771_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2df1672664c9cb_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2df167672c9fc0_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2df16744041b9b_GRCh38.primary_assembly.genome.fa.fai added
2df16741c55896_GRCh38.primary_assembly.genome.fa.amb added
2df16734313736_GRCh38.primary_assembly.genome.fa.ann added
2df16722cd15b6_GRCh38.primary_assembly.genome.fa.bwt added
2df1677946d5f7_GRCh38.primary_assembly.genome.fa.pac added
2df1676a298bf3_GRCh38.primary_assembly.genome.fa.sa added
2df16728820570_GRCh38.primary_assembly.genome.fa added
2df1675d15cdeb_hs37d5.fa.fai added
2df167386c4fdd_hs37d5.fa.amb added
2df1676a99b6ab_hs37d5.fa.ann added
2df16751fbfa06_hs37d5.fa.bwt added
2df167a66349f_hs37d5.fa.pac added
2df16755bf52d1_hs37d5.fa.sa added
2df167db468d_hs37d5.fa added
2df167dc5037e_complete_ref_lens.bin added
2df16756b5ac81_ctable.bin added
2df16730aabdde_ctg_offsets.bin added
2df1671510afe7_duplicate_clusters.tsv added
2df16772b4d1a6_info.json added
2df1671cbaeb99_mphf.bin added
2df167339d5cf6_pos.bin added
2df16717a4d31f_pre_indexing.log added
2df1676ffe0ba9_rank.bin added
2df1676cbff636_ref_indexing.log added
2df1674ef88a14_refAccumLengths.bin added
2df167f1005a3_reflengths.bin added
2df1677ab72e41_refseq.bin added
2df167d2de5d_seq.bin added
2df16755603d15_versionInfo.json added
2df167211bf80c_salmon_index added
2df16767ff7e1e_chrLength.txt added
2df167196458b0_chrName.txt added
2df16762e150a2_chrNameLength.txt added
2df1671c30b554_chrStart.txt added
2df1673c316e66_exonGeTrInfo.tab added
2df1675c28269a_exonInfo.tab added
2df16765a4148_geneInfo.tab added
2df16764b373d7_Genome added
2df167393df485_genomeParameters.txt added
2df1673ec69125_Log.out added
2df1674f4d2a82_SA added
2df167b39ee8b_SAindex added
2df167492cc5c4_sjdbInfo.txt added
2df167250c7d54_sjdbList.fromGTF.out.tab added
2df167c153518_sjdbList.out.tab added
2df16756f1c943_transcriptInfo.tab added
2df1677bc229d5_GRCh38.GENCODE.v42_100 added
2df1673cbff2f7_knownGene_hg38.sql added
2df1676c02792a_knownGene_hg38.txt added
2df1676e76fb7b_refGene_hg38.sql added
2df167597ade90_refGene_hg38.txt added
2df1671f9fd620_knownGene_mm39.sql added
2df16761bce9b_knownGene_mm39.txt added
2df1674978ea39_refGene_mm39.sql added
2df167c5fcc56_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/RtmpEw2pmL/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 
 19.171   1.304  21.182