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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
###
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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: 2026-04-22 07:54:37 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 6.187  0.409   6.599
* 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 ‘1.11.0’
** 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 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...
1bb4604593af69_GRCh38.primary_assembly.genome.fa.1.bt2 added
1bb4603486c830_GRCh38.primary_assembly.genome.fa.2.bt2 added
1bb4606ed6bea3_GRCh38.primary_assembly.genome.fa.3.bt2 added
1bb46022df416c_GRCh38.primary_assembly.genome.fa.4.bt2 added
1bb46070ca0cea_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1bb46064a86471_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1bb460262b84ac_outfile.txt added
1bb46074e09dc2_GRCh37_to_GRCh38.chain added
1bb46041b82d5e_GRCh37_to_NCBI34.chain added
1bb460195b4e68_GRCh37_to_NCBI35.chain added
1bb46072aba9e3_GRCh37_to_NCBI36.chain added
1bb4602e278d04_GRCh38_to_GRCh37.chain added
1bb460354697a0_GRCh38_to_NCBI34.chain added
1bb4604d6650f9_GRCh38_to_NCBI35.chain added
1bb460445dfdff_GRCh38_to_NCBI36.chain added
1bb4605c9e448a_NCBI34_to_GRCh37.chain added
1bb46018403370_NCBI34_to_GRCh38.chain added
1bb46036bc8fbc_NCBI35_to_GRCh37.chain added
1bb46060582778_NCBI35_to_GRCh38.chain added
1bb460cdcccb1_NCBI36_to_GRCh37.chain added
1bb460547b885_NCBI36_to_GRCh38.chain added
1bb4602fd98a97_GRCm38_to_NCBIM36.chain added
1bb460589197a6_GRCm38_to_NCBIM37.chain added
1bb460411c88f5_NCBIM36_to_GRCm38.chain added
1bb46070341548_NCBIM37_to_GRCm38.chain added
1bb4605929459d_1000G_omni2.5.b37.vcf.gz added
1bb46060c3ed82_1000G_omni2.5.b37.vcf.gz.tbi added
1bb46010893f4a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1bb46070df4b44_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1bb46066f9e23f_1000G_omni2.5.hg38.vcf.gz added
1bb46044a4944d_1000G_omni2.5.hg38.vcf.gz.tbi added
1bb4603672faae_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1bb4601b80aa70_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1bb460337b52f0_af-only-gnomad.raw.sites.vcf added
1bb46059523c1a_af-only-gnomad.raw.sites.vcf.idx added
1bb460c4ab75a_Mutect2-exome-panel.vcf.idx added
1bb4601823b761_Mutect2-WGS-panel-b37.vcf added
1bb4607f7dc0c6_Mutect2-WGS-panel-b37.vcf.idx added
1bb46012b551c_small_exac_common_3.vcf added
1bb46059dbe4bf_small_exac_common_3.vcf.idx added
1bb46018d90f2f_1000g_pon.hg38.vcf.gz added
1bb46073d6feff_1000g_pon.hg38.vcf.gz.tbi added
1bb46080371c3_af-only-gnomad.hg38.vcf.gz added
1bb4604e1fa6cf_af-only-gnomad.hg38.vcf.gz.tbi added
1bb460413d4ff8_small_exac_common_3.hg38.vcf.gz added
1bb4604c616fc2_small_exac_common_3.hg38.vcf.gz.tbi added
1bb4602abdeb59_gencode.v41.annotation.gtf added
1bb460597d8369_gencode.v42.annotation.gtf added
1bb46031dff7e_gencode.vM30.annotation.gtf added
1bb460b1612d1_gencode.vM31.annotation.gtf added
1bb460665a501a_gencode.v41.transcripts.fa added
1bb460865b804_gencode.v41.transcripts.fa.fai added
1bb4603aef9d69_gencode.v42.transcripts.fa added
1bb4603eebe7c1_gencode.v42.transcripts.fa.fai added
1bb460498240f9_gencode.vM30.pc_transcripts.fa added
1bb4602b23b2b1_gencode.vM30.pc_transcripts.fa.fai added
1bb46018152d5e_gencode.vM31.pc_transcripts.fa added
1bb4602a462e7b_gencode.vM31.pc_transcripts.fa.fai added
1bb4603bacf1fb_GRCh38.primary_assembly.genome.fa.1.ht2 added
1bb4608f478a2_GRCh38.primary_assembly.genome.fa.2.ht2 added
1bb460114010bb_GRCh38.primary_assembly.genome.fa.3.ht2 added
1bb460518648_GRCh38.primary_assembly.genome.fa.4.ht2 added
1bb4603f677350_GRCh38.primary_assembly.genome.fa.5.ht2 added
1bb4602cc0bb2b_GRCh38.primary_assembly.genome.fa.6.ht2 added
1bb46033ccd938_GRCh38.primary_assembly.genome.fa.7.ht2 added
1bb46018b9af6a_GRCh38.primary_assembly.genome.fa.8.ht2 added
1bb460390b7285_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1bb4604bf09099_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1bb46018377031_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1bb4603a36c7a1_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1bb46025cc7559_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1bb46031107f60_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1bb4602e0dc6a1_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1bb4602dcfe71c_GRCh38.primary_assembly.genome.fa.fai added
1bb4607f30262f_GRCh38.primary_assembly.genome.fa.amb added
1bb4606f4b1699_GRCh38.primary_assembly.genome.fa.ann added
1bb4607a3156df_GRCh38.primary_assembly.genome.fa.bwt added
1bb46029ee1188_GRCh38.primary_assembly.genome.fa.pac added
1bb46048c89a02_GRCh38.primary_assembly.genome.fa.sa added
1bb4607d4f565d_GRCh38.primary_assembly.genome.fa added
1bb4603504245a_hs37d5.fa.fai added
1bb4602f22ea1d_hs37d5.fa.amb added
1bb4605b50e61_hs37d5.fa.ann added
1bb4606ff3c1c3_hs37d5.fa.bwt added
1bb4606e0ed1de_hs37d5.fa.pac added
1bb4604f374f5a_hs37d5.fa.sa added
1bb4601b177474_hs37d5.fa added
1bb460623ff3c_complete_ref_lens.bin added
1bb460797d7dd6_ctable.bin added
1bb46056c4666f_ctg_offsets.bin added
1bb460f1877de_duplicate_clusters.tsv added
1bb460abd8e91_info.json added
1bb4605715ecb8_mphf.bin added
1bb4604e7feb2f_pos.bin added
1bb460377e49bc_pre_indexing.log added
1bb460ae2c5f0_rank.bin added
1bb46067399a99_ref_indexing.log added
1bb4607089bc41_refAccumLengths.bin added
1bb46056d3568a_reflengths.bin added
1bb4607f710aca_refseq.bin added
1bb4602ac083e2_seq.bin added
1bb4607c9fcbe3_versionInfo.json added
1bb46030818a2a_salmon_index added
1bb46058ce4a83_chrLength.txt added
1bb4602a6fb2ff_chrName.txt added
1bb4602fb1b059_chrNameLength.txt added
1bb4604819611d_chrStart.txt added
1bb46024a109de_exonGeTrInfo.tab added
1bb460599fc1e2_exonInfo.tab added
1bb46010e1fb1f_geneInfo.tab added
1bb46021f0603c_Genome added
1bb460ea3e63c_genomeParameters.txt added
1bb4604004e53c_Log.out added
1bb46027a56e9d_SA added
1bb4607e97a7ff_SAindex added
1bb4602e13b71a_sjdbInfo.txt added
1bb46076dcbdf8_sjdbList.fromGTF.out.tab added
1bb46019af1c73_sjdbList.out.tab added
1bb4603437b656_transcriptInfo.tab added
1bb460705a3bce_GRCh38.GENCODE.v42_100 added
1bb460707382e2_knownGene_hg38.sql added
1bb46043502e35_knownGene_hg38.txt added
1bb4607b17ca5f_refGene_hg38.sql added
1bb46047896f9a_refGene_hg38.txt added
1bb46011d01964_knownGene_mm39.sql added
1bb4603296141b_knownGene_mm39.txt added
1bb460526c358b_refGene_mm39.sql added
1bb4607909b3fd_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/Rtmp66vAyC/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 
 21.210   1.981  24.098