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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: 2026-05-19 07:43:36 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 6.063  0.261   6.326
* 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...
1553ba67213531_GRCh38.primary_assembly.genome.fa.1.bt2 added
1553ba312bd19c_GRCh38.primary_assembly.genome.fa.2.bt2 added
1553ba151c7d3_GRCh38.primary_assembly.genome.fa.3.bt2 added
1553ba4d11a9d2_GRCh38.primary_assembly.genome.fa.4.bt2 added
1553ba45b726cd_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1553ba3010a703_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1553ba73780b9_outfile.txt added
1553ba5d2c5d3e_GRCh37_to_GRCh38.chain added
1553ba56f20ccb_GRCh37_to_NCBI34.chain added
1553ba1d356e2a_GRCh37_to_NCBI35.chain added
1553ba6c5eb3f5_GRCh37_to_NCBI36.chain added
1553ba5e0aa81a_GRCh38_to_GRCh37.chain added
1553ba6e842059_GRCh38_to_NCBI34.chain added
1553ba3e638ea7_GRCh38_to_NCBI35.chain added
1553ba6dff1a55_GRCh38_to_NCBI36.chain added
1553ba4a62e2f0_NCBI34_to_GRCh37.chain added
1553bad19be2c_NCBI34_to_GRCh38.chain added
1553ba4bf888d6_NCBI35_to_GRCh37.chain added
1553ba49e7a722_NCBI35_to_GRCh38.chain added
1553ba6939a0b3_NCBI36_to_GRCh37.chain added
1553ba6c2465c_NCBI36_to_GRCh38.chain added
1553ba440074e_GRCm38_to_NCBIM36.chain added
1553ba2d86d25e_GRCm38_to_NCBIM37.chain added
1553ba2b655ed1_NCBIM36_to_GRCm38.chain added
1553ba6aea9ed_NCBIM37_to_GRCm38.chain added
1553ba1e843af8_1000G_omni2.5.b37.vcf.gz added
1553ba5d54cfc3_1000G_omni2.5.b37.vcf.gz.tbi added
1553ba3b0ca577_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1553ba49fa4743_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1553ba6aed9be5_1000G_omni2.5.hg38.vcf.gz added
1553ba47e58b7_1000G_omni2.5.hg38.vcf.gz.tbi added
1553ba311b7c74_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1553ba1c196d81_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1553ba5d0208a_af-only-gnomad.raw.sites.vcf added
1553ba7e2d2647_af-only-gnomad.raw.sites.vcf.idx added
1553ba61d0944f_Mutect2-exome-panel.vcf.idx added
1553ba35e0c78d_Mutect2-WGS-panel-b37.vcf added
1553ba564a700_Mutect2-WGS-panel-b37.vcf.idx added
1553ba3efcf18d_small_exac_common_3.vcf added
1553bacd2d459_small_exac_common_3.vcf.idx added
1553ba229a152b_1000g_pon.hg38.vcf.gz added
1553ba2b5ba582_1000g_pon.hg38.vcf.gz.tbi added
1553ba6add7c73_af-only-gnomad.hg38.vcf.gz added
1553ba111e3584_af-only-gnomad.hg38.vcf.gz.tbi added
1553ba69bf3429_small_exac_common_3.hg38.vcf.gz added
1553ba58dc96c8_small_exac_common_3.hg38.vcf.gz.tbi added
1553ba5b811875_gencode.v41.annotation.gtf added
1553ba76d8f256_gencode.v42.annotation.gtf added
1553ba24d51f9f_gencode.vM30.annotation.gtf added
1553ba2568bf97_gencode.vM31.annotation.gtf added
1553ba60129309_gencode.v41.transcripts.fa added
1553ba2b9765fb_gencode.v41.transcripts.fa.fai added
1553ba29a8c6e5_gencode.v42.transcripts.fa added
1553bad996567_gencode.v42.transcripts.fa.fai added
1553ba56fcc4cc_gencode.vM30.pc_transcripts.fa added
1553ba305770d2_gencode.vM30.pc_transcripts.fa.fai added
1553ba2c1da05f_gencode.vM31.pc_transcripts.fa added
1553ba3451948f_gencode.vM31.pc_transcripts.fa.fai added
1553ba6b64164a_GRCh38.primary_assembly.genome.fa.1.ht2 added
1553ba7617e7a3_GRCh38.primary_assembly.genome.fa.2.ht2 added
1553ba1f3f3074_GRCh38.primary_assembly.genome.fa.3.ht2 added
1553ba6fe26f01_GRCh38.primary_assembly.genome.fa.4.ht2 added
1553ba27336417_GRCh38.primary_assembly.genome.fa.5.ht2 added
1553ba3b589df6_GRCh38.primary_assembly.genome.fa.6.ht2 added
1553ba75b28f8b_GRCh38.primary_assembly.genome.fa.7.ht2 added
1553ba25608a5e_GRCh38.primary_assembly.genome.fa.8.ht2 added
1553ba1d293245_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1553ba2b935718_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1553ba2ac5315f_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1553ba5c2623d2_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1553ba38662b71_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1553ba4d5f468a_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1553ba781c954_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1553ba2343a7e4_GRCh38.primary_assembly.genome.fa.fai added
1553ba5e7d7c0e_GRCh38.primary_assembly.genome.fa.amb added
1553ba7140fd7e_GRCh38.primary_assembly.genome.fa.ann added
1553ba7c203ead_GRCh38.primary_assembly.genome.fa.bwt added
1553ba39fe9483_GRCh38.primary_assembly.genome.fa.pac added
1553ba6819efd4_GRCh38.primary_assembly.genome.fa.sa added
1553ba20f55e4c_GRCh38.primary_assembly.genome.fa added
1553ba5f67541a_hs37d5.fa.fai added
1553ba482c82dd_hs37d5.fa.amb added
1553ba4c8cc447_hs37d5.fa.ann added
1553ba9101b00_hs37d5.fa.bwt added
1553ba55c5e844_hs37d5.fa.pac added
1553ba23898913_hs37d5.fa.sa added
1553ba39678bd2_hs37d5.fa added
1553ba1e388a4_complete_ref_lens.bin added
1553ba57db1da3_ctable.bin added
1553ba24cba21c_ctg_offsets.bin added
1553ba77fb7047_duplicate_clusters.tsv added
1553ba771a4e17_info.json added
1553ba14ae111d_mphf.bin added
1553ba1f2ed45e_pos.bin added
1553ba3272ec0d_pre_indexing.log added
1553baa60a0a8_rank.bin added
1553ba448f5ebd_ref_indexing.log added
1553ba4f9c1e52_refAccumLengths.bin added
1553ba35f3f7c1_reflengths.bin added
1553ba6f54901c_refseq.bin added
1553ba2bc24224_seq.bin added
1553ba6e5a2332_versionInfo.json added
1553ba3cb3d6a6_salmon_index added
1553ba33440b79_chrLength.txt added
1553ba119dcb17_chrName.txt added
1553ba1b3152b4_chrNameLength.txt added
1553ba248508f7_chrStart.txt added
1553badbe09c4_exonGeTrInfo.tab added
1553ba552fe738_exonInfo.tab added
1553bac9ef8cb_geneInfo.tab added
1553ba2eb36810_Genome added
1553ba34973b52_genomeParameters.txt added
1553ba54cb7ba8_Log.out added
1553ba7b402c57_SA added
1553ba3da75652_SAindex added
1553ba2a9163ec_sjdbInfo.txt added
1553ba1ec9b56a_sjdbList.fromGTF.out.tab added
1553ba770ee225_sjdbList.out.tab added
1553ba2c74ec90_transcriptInfo.tab added
1553ba76a4d30d_GRCh38.GENCODE.v42_100 added
1553ba1bda8441_knownGene_hg38.sql added
1553ba24705cd7_knownGene_hg38.txt added
1553ba6dbf2125_refGene_hg38.sql added
1553ba3088955f_refGene_hg38.txt added
1553ba439f3136_knownGene_mm39.sql added
1553ba20320d32_knownGene_mm39.txt added
1553ba3ae93607_refGene_mm39.sql added
1553ba82e8ff3_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/RtmpG5Ca6G/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 
 18.566   1.065  20.269