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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_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 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: 2026-04-30 07:57:56 UTC
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.12.0’
* 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 6.153  0.411   6.568
* 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 ‘1.12.0’
** 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...
1f18b1605bffcc_GRCh38.primary_assembly.genome.fa.1.bt2 added
1f18b17c24710f_GRCh38.primary_assembly.genome.fa.2.bt2 added
1f18b15d74032b_GRCh38.primary_assembly.genome.fa.3.bt2 added
1f18b1213cd334_GRCh38.primary_assembly.genome.fa.4.bt2 added
1f18b17419140_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1f18b156df649a_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1f18b1238a737e_outfile.txt added
1f18b11b654829_GRCh37_to_GRCh38.chain added
1f18b179a1e8f7_GRCh37_to_NCBI34.chain added
1f18b11925ff7c_GRCh37_to_NCBI35.chain added
1f18b170f28ce1_GRCh37_to_NCBI36.chain added
1f18b14247082_GRCh38_to_GRCh37.chain added
1f18b11653fc7c_GRCh38_to_NCBI34.chain added
1f18b141ec0513_GRCh38_to_NCBI35.chain added
1f18b12360e651_GRCh38_to_NCBI36.chain added
1f18b15fcf7bcc_NCBI34_to_GRCh37.chain added
1f18b15d3b934f_NCBI34_to_GRCh38.chain added
1f18b166471bbe_NCBI35_to_GRCh37.chain added
1f18b118c162c0_NCBI35_to_GRCh38.chain added
1f18b16622b19b_NCBI36_to_GRCh37.chain added
1f18b1736bf2b0_NCBI36_to_GRCh38.chain added
1f18b152665ff2_GRCm38_to_NCBIM36.chain added
1f18b168bcc859_GRCm38_to_NCBIM37.chain added
1f18b12cbbad9_NCBIM36_to_GRCm38.chain added
1f18b1669807f9_NCBIM37_to_GRCm38.chain added
1f18b12802ae89_1000G_omni2.5.b37.vcf.gz added
1f18b1bc01076_1000G_omni2.5.b37.vcf.gz.tbi added
1f18b1601eca88_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1f18b11a8a6af7_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1f18b124523b1a_1000G_omni2.5.hg38.vcf.gz added
1f18b159e0f08_1000G_omni2.5.hg38.vcf.gz.tbi added
1f18b17ae66ac3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1f18b12076ac29_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1f18b163121233_af-only-gnomad.raw.sites.vcf added
1f18b11c233df8_af-only-gnomad.raw.sites.vcf.idx added
1f18b127b83d6a_Mutect2-exome-panel.vcf.idx added
1f18b139f176cd_Mutect2-WGS-panel-b37.vcf added
1f18b13fadb176_Mutect2-WGS-panel-b37.vcf.idx added
1f18b1431d8593_small_exac_common_3.vcf added
1f18b133935fc4_small_exac_common_3.vcf.idx added
1f18b158d3b0f2_1000g_pon.hg38.vcf.gz added
1f18b134101274_1000g_pon.hg38.vcf.gz.tbi added
1f18b137b7d046_af-only-gnomad.hg38.vcf.gz added
1f18b16f27ad6e_af-only-gnomad.hg38.vcf.gz.tbi added
1f18b175fc1788_small_exac_common_3.hg38.vcf.gz added
1f18b15b18b697_small_exac_common_3.hg38.vcf.gz.tbi added
1f18b14ef7293a_gencode.v41.annotation.gtf added
1f18b15337aad7_gencode.v42.annotation.gtf added
1f18b1415fd255_gencode.vM30.annotation.gtf added
1f18b167b88bfa_gencode.vM31.annotation.gtf added
1f18b1395a5c72_gencode.v41.transcripts.fa added
1f18b134cbc506_gencode.v41.transcripts.fa.fai added
1f18b13a1eebed_gencode.v42.transcripts.fa added
1f18b1221724cb_gencode.v42.transcripts.fa.fai added
1f18b137977fdf_gencode.vM30.pc_transcripts.fa added
1f18b120b6f3e6_gencode.vM30.pc_transcripts.fa.fai added
1f18b14a19d354_gencode.vM31.pc_transcripts.fa added
1f18b143579055_gencode.vM31.pc_transcripts.fa.fai added
1f18b1d5be6e_GRCh38.primary_assembly.genome.fa.1.ht2 added
1f18b164a43e4c_GRCh38.primary_assembly.genome.fa.2.ht2 added
1f18b167a9cb70_GRCh38.primary_assembly.genome.fa.3.ht2 added
1f18b1673cd76_GRCh38.primary_assembly.genome.fa.4.ht2 added
1f18b15f8aa90f_GRCh38.primary_assembly.genome.fa.5.ht2 added
1f18b18207799_GRCh38.primary_assembly.genome.fa.6.ht2 added
1f18b16985dfa9_GRCh38.primary_assembly.genome.fa.7.ht2 added
1f18b17bade707_GRCh38.primary_assembly.genome.fa.8.ht2 added
1f18b12fd8b503_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1f18b123775676_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1f18b13b5b987d_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1f18b172f63a96_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1f18b1570ab63a_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1f18b1142f496f_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1f18b127064d0b_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1f18b1ec28681_GRCh38.primary_assembly.genome.fa.fai added
1f18b1356f6dd_GRCh38.primary_assembly.genome.fa.amb added
1f18b11d026493_GRCh38.primary_assembly.genome.fa.ann added
1f18b169db3d18_GRCh38.primary_assembly.genome.fa.bwt added
1f18b1524e2017_GRCh38.primary_assembly.genome.fa.pac added
1f18b1703a0f6a_GRCh38.primary_assembly.genome.fa.sa added
1f18b12b3b0f6e_GRCh38.primary_assembly.genome.fa added
1f18b13a06ac12_hs37d5.fa.fai added
1f18b129946bdc_hs37d5.fa.amb added
1f18b16006d474_hs37d5.fa.ann added
1f18b1742597ff_hs37d5.fa.bwt added
1f18b14bab90a7_hs37d5.fa.pac added
1f18b1179e5453_hs37d5.fa.sa added
1f18b114dc8be5_hs37d5.fa added
1f18b115c563fb_complete_ref_lens.bin added
1f18b15af5e4a9_ctable.bin added
1f18b115b24a54_ctg_offsets.bin added
1f18b17a69a247_duplicate_clusters.tsv added
1f18b1429fb019_info.json added
1f18b11c2617ca_mphf.bin added
1f18b159f44b57_pos.bin added
1f18b14ac027b2_pre_indexing.log added
1f18b15abf774_rank.bin added
1f18b155a2325e_ref_indexing.log added
1f18b17a98dcb6_refAccumLengths.bin added
1f18b129234dea_reflengths.bin added
1f18b110fdcadc_refseq.bin added
1f18b16d8f174c_seq.bin added
1f18b12e0425_versionInfo.json added
1f18b1252d144b_salmon_index added
1f18b114956457_chrLength.txt added
1f18b1ef08aa6_chrName.txt added
1f18b128840b29_chrNameLength.txt added
1f18b13197c8ea_chrStart.txt added
1f18b178cbc7be_exonGeTrInfo.tab added
1f18b17ad22b40_exonInfo.tab added
1f18b121d1d854_geneInfo.tab added
1f18b12406d72c_Genome added
1f18b134d8d752_genomeParameters.txt added
1f18b14b664430_Log.out added
1f18b140daba0_SA added
1f18b128fe6f51_SAindex added
1f18b11711d4d7_sjdbInfo.txt added
1f18b11babfff4_sjdbList.fromGTF.out.tab added
1f18b13ddafb37_sjdbList.out.tab added
1f18b12cd738d3_transcriptInfo.tab added
1f18b176a1e49d_GRCh38.GENCODE.v42_100 added
1f18b1538d458b_knownGene_hg38.sql added
1f18b12740db1a_knownGene_hg38.txt added
1f18b1394194b6_refGene_hg38.sql added
1f18b16fb35d55_refGene_hg38.txt added
1f18b11352671_knownGene_mm39.sql added
1f18b1401bc68_knownGene_mm39.txt added
1f18b1755f54c9_refGene_mm39.sql added
1f18b156d758d0_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/RtmpBD3DJn/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 
 19.211   1.821  21.209