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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_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-07 08:42:44 UTC
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.11.0’
* 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 5.958  0.387   6.347
* 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
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.11.0’
** 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 Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
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...
161fb84657b676_GRCh38.primary_assembly.genome.fa.1.bt2 added
161fb848119c6f_GRCh38.primary_assembly.genome.fa.2.bt2 added
161fb82b308087_GRCh38.primary_assembly.genome.fa.3.bt2 added
161fb842e4282_GRCh38.primary_assembly.genome.fa.4.bt2 added
161fb8af299e7_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
161fb87b9a9896_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
161fb8550b7bf4_outfile.txt added
161fb85c2fa1f1_GRCh37_to_GRCh38.chain added
161fb8385b4b1b_GRCh37_to_NCBI34.chain added
161fb878e0bc96_GRCh37_to_NCBI35.chain added
161fb8302ecd86_GRCh37_to_NCBI36.chain added
161fb852d36f18_GRCh38_to_GRCh37.chain added
161fb8703e87e1_GRCh38_to_NCBI34.chain added
161fb8606ceec0_GRCh38_to_NCBI35.chain added
161fb81b9e1899_GRCh38_to_NCBI36.chain added
161fb86c79cea0_NCBI34_to_GRCh37.chain added
161fb810580b48_NCBI34_to_GRCh38.chain added
161fb82e828daa_NCBI35_to_GRCh37.chain added
161fb83f5932d6_NCBI35_to_GRCh38.chain added
161fb838894ce0_NCBI36_to_GRCh37.chain added
161fb868d634e0_NCBI36_to_GRCh38.chain added
161fb85a8aefec_GRCm38_to_NCBIM36.chain added
161fb81def1d7a_GRCm38_to_NCBIM37.chain added
161fb81e374c17_NCBIM36_to_GRCm38.chain added
161fb82e4c611c_NCBIM37_to_GRCm38.chain added
161fb831ec07fa_1000G_omni2.5.b37.vcf.gz added
161fb84147f50e_1000G_omni2.5.b37.vcf.gz.tbi added
161fb823326c89_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
161fb831e181c1_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
161fb8538e06a3_1000G_omni2.5.hg38.vcf.gz added
161fb820b470cc_1000G_omni2.5.hg38.vcf.gz.tbi added
161fb878393837_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
161fb81b9fa312_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
161fb84be4f153_af-only-gnomad.raw.sites.vcf added
161fb87c677ab9_af-only-gnomad.raw.sites.vcf.idx added
161fb826923cfa_Mutect2-exome-panel.vcf.idx added
161fb8477f89e9_Mutect2-WGS-panel-b37.vcf added
161fb85172f6ad_Mutect2-WGS-panel-b37.vcf.idx added
161fb82c1deeb_small_exac_common_3.vcf added
161fb87fdad504_small_exac_common_3.vcf.idx added
161fb84a53b344_1000g_pon.hg38.vcf.gz added
161fb832f0ac72_1000g_pon.hg38.vcf.gz.tbi added
161fb852ae441d_af-only-gnomad.hg38.vcf.gz added
161fb83a923b25_af-only-gnomad.hg38.vcf.gz.tbi added
161fb8135d9b32_small_exac_common_3.hg38.vcf.gz added
161fb86e4c5cb6_small_exac_common_3.hg38.vcf.gz.tbi added
161fb8270c09c5_gencode.v41.annotation.gtf added
161fb823b5a67a_gencode.v42.annotation.gtf added
161fb81cceea60_gencode.vM30.annotation.gtf added
161fb866653c9b_gencode.vM31.annotation.gtf added
161fb85c3ef35b_gencode.v41.transcripts.fa added
161fb85a51f40_gencode.v41.transcripts.fa.fai added
161fb840f02c88_gencode.v42.transcripts.fa added
161fb87a2e10d5_gencode.v42.transcripts.fa.fai added
161fb823dc6b57_gencode.vM30.pc_transcripts.fa added
161fb86f3c8da4_gencode.vM30.pc_transcripts.fa.fai added
161fb82c1a18cf_gencode.vM31.pc_transcripts.fa added
161fb865246066_gencode.vM31.pc_transcripts.fa.fai added
161fb8126efa2e_GRCh38.primary_assembly.genome.fa.1.ht2 added
161fb85dfb9a90_GRCh38.primary_assembly.genome.fa.2.ht2 added
161fb838b26709_GRCh38.primary_assembly.genome.fa.3.ht2 added
161fb833236afa_GRCh38.primary_assembly.genome.fa.4.ht2 added
161fb85634d2c8_GRCh38.primary_assembly.genome.fa.5.ht2 added
161fb854520a1c_GRCh38.primary_assembly.genome.fa.6.ht2 added
161fb87f085c4d_GRCh38.primary_assembly.genome.fa.7.ht2 added
161fb8529c4d81_GRCh38.primary_assembly.genome.fa.8.ht2 added
161fb87ae44716_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
161fb84687e636_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
161fb8240f442f_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
161fb87da62601_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
161fb84662bb3b_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
161fb86e62f773_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
161fb83096d273_GRCh38_full_analysis_set_plus_decoy_hla.fa added
161fb81910ff58_GRCh38.primary_assembly.genome.fa.fai added
161fb828f53298_GRCh38.primary_assembly.genome.fa.amb added
161fb843f46da6_GRCh38.primary_assembly.genome.fa.ann added
161fb875d5c0e_GRCh38.primary_assembly.genome.fa.bwt added
161fb850013c5d_GRCh38.primary_assembly.genome.fa.pac added
161fb867aa1420_GRCh38.primary_assembly.genome.fa.sa added
161fb8242c466e_GRCh38.primary_assembly.genome.fa added
161fb8366678f8_hs37d5.fa.fai added
161fb843e9077b_hs37d5.fa.amb added
161fb829d165ae_hs37d5.fa.ann added
161fb87756a580_hs37d5.fa.bwt added
161fb83e171850_hs37d5.fa.pac added
161fb84dadd105_hs37d5.fa.sa added
161fb866933325_hs37d5.fa added
161fb86a31311f_complete_ref_lens.bin added
161fb832d2316b_ctable.bin added
161fb879022d53_ctg_offsets.bin added
161fb8482ccbb0_duplicate_clusters.tsv added
161fb86b849875_info.json added
161fb82c25984d_mphf.bin added
161fb81e619e78_pos.bin added
161fb83fd6a291_pre_indexing.log added
161fb82b2df49a_rank.bin added
161fb870fdebf9_ref_indexing.log added
161fb83abae9a7_refAccumLengths.bin added
161fb871b5dad0_reflengths.bin added
161fb8150d3028_refseq.bin added
161fb838610fa8_seq.bin added
161fb83818960b_versionInfo.json added
161fb8370279b_salmon_index added
161fb868f7e21c_chrLength.txt added
161fb851299563_chrName.txt added
161fb82c655a33_chrNameLength.txt added
161fb82cec4fc2_chrStart.txt added
161fb85886f171_exonGeTrInfo.tab added
161fb87c669690_exonInfo.tab added
161fb8149663e2_geneInfo.tab added
161fb87cb337df_Genome added
161fb832cd0f89_genomeParameters.txt added
161fb8587f6b5e_Log.out added
161fb826849d8d_SA added
161fb82a23b509_SAindex added
161fb8169683ae_sjdbInfo.txt added
161fb874326e93_sjdbList.fromGTF.out.tab added
161fb810b6e82e_sjdbList.out.tab added
161fb8c7b4ce_transcriptInfo.tab added
161fb827049ffe_GRCh38.GENCODE.v42_100 added
161fb89b91581_knownGene_hg38.sql added
161fb848f4807e_knownGene_hg38.txt added
161fb812893873_refGene_hg38.sql added
161fb835deadce_refGene_hg38.txt added
161fb867561ef6_knownGene_mm39.sql added
161fb8525fdb04_knownGene_mm39.txt added
161fb8610ca268_refGene_mm39.sql added
161fb858540aef_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/RtmpQfu7JR/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 
 20.957   2.209  23.777