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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.10.0.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.10.0’
* 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 5.857  0.234   6.093
* 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-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ReUseData
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.10.0’
** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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...
1851c4560eba3a_GRCh38.primary_assembly.genome.fa.1.bt2 added
1851c433ee340c_GRCh38.primary_assembly.genome.fa.2.bt2 added
1851c47d948a43_GRCh38.primary_assembly.genome.fa.3.bt2 added
1851c46d647385_GRCh38.primary_assembly.genome.fa.4.bt2 added
1851c4a3d5c87_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1851c416347a14_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1851c4282e5e3b_outfile.txt added
1851c45683c8e_GRCh37_to_GRCh38.chain added
1851c44622b790_GRCh37_to_NCBI34.chain added
1851c411ea607_GRCh37_to_NCBI35.chain added
1851c4e609cde_GRCh37_to_NCBI36.chain added
1851c428b0693f_GRCh38_to_GRCh37.chain added
1851c47956ab00_GRCh38_to_NCBI34.chain added
1851c43a37051_GRCh38_to_NCBI35.chain added
1851c47e95064b_GRCh38_to_NCBI36.chain added
1851c46e5adc77_NCBI34_to_GRCh37.chain added
1851c444ab4b8_NCBI34_to_GRCh38.chain added
1851c4e3c3867_NCBI35_to_GRCh37.chain added
1851c41aee1bde_NCBI35_to_GRCh38.chain added
1851c47055ca4f_NCBI36_to_GRCh37.chain added
1851c4a2c2b1d_NCBI36_to_GRCh38.chain added
1851c45fca2730_GRCm38_to_NCBIM36.chain added
1851c44a8b7ba9_GRCm38_to_NCBIM37.chain added
1851c43c23e931_NCBIM36_to_GRCm38.chain added
1851c438104a19_NCBIM37_to_GRCm38.chain added
1851c4352d5931_1000G_omni2.5.b37.vcf.gz added
1851c452885046_1000G_omni2.5.b37.vcf.gz.tbi added
1851c44a93ce81_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1851c41f26d869_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1851c43e4983b5_1000G_omni2.5.hg38.vcf.gz added
1851c41edcca00_1000G_omni2.5.hg38.vcf.gz.tbi added
1851c4753592a3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1851c47237b7c1_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1851c41c715443_af-only-gnomad.raw.sites.vcf added
1851c4629a0628_af-only-gnomad.raw.sites.vcf.idx added
1851c47c751448_Mutect2-exome-panel.vcf.idx added
1851c432a5ce58_Mutect2-WGS-panel-b37.vcf added
1851c4ac86463_Mutect2-WGS-panel-b37.vcf.idx added
1851c41dd50d7_small_exac_common_3.vcf added
1851c478c885e8_small_exac_common_3.vcf.idx added
1851c4be70a6b_1000g_pon.hg38.vcf.gz added
1851c4103dedb5_1000g_pon.hg38.vcf.gz.tbi added
1851c42178ef27_af-only-gnomad.hg38.vcf.gz added
1851c453db56b_af-only-gnomad.hg38.vcf.gz.tbi added
1851c413e15e06_small_exac_common_3.hg38.vcf.gz added
1851c4200df573_small_exac_common_3.hg38.vcf.gz.tbi added
1851c4739891e2_gencode.v41.annotation.gtf added
1851c4182c12bf_gencode.v42.annotation.gtf added
1851c42e4a2dda_gencode.vM30.annotation.gtf added
1851c4e86adc0_gencode.vM31.annotation.gtf added
1851c4881dd0e_gencode.v41.transcripts.fa added
1851c4387658f8_gencode.v41.transcripts.fa.fai added
1851c46e50d4f1_gencode.v42.transcripts.fa added
1851c4530d58b7_gencode.v42.transcripts.fa.fai added
1851c4749a4229_gencode.vM30.pc_transcripts.fa added
1851c426611f0a_gencode.vM30.pc_transcripts.fa.fai added
1851c483ab1e9_gencode.vM31.pc_transcripts.fa added
1851c44722926f_gencode.vM31.pc_transcripts.fa.fai added
1851c470f4ed8b_GRCh38.primary_assembly.genome.fa.1.ht2 added
1851c427618a52_GRCh38.primary_assembly.genome.fa.2.ht2 added
1851c456c1624_GRCh38.primary_assembly.genome.fa.3.ht2 added
1851c4fd1b78b_GRCh38.primary_assembly.genome.fa.4.ht2 added
1851c41c971cf5_GRCh38.primary_assembly.genome.fa.5.ht2 added
1851c477a3cde5_GRCh38.primary_assembly.genome.fa.6.ht2 added
1851c42c430bce_GRCh38.primary_assembly.genome.fa.7.ht2 added
1851c47f31231d_GRCh38.primary_assembly.genome.fa.8.ht2 added
1851c47418e22d_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1851c45ee8da26_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1851c49f98781_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1851c475f63304_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1851c457b1600f_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1851c415e091ec_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1851c463420b9_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1851c4792a4f36_GRCh38.primary_assembly.genome.fa.fai added
1851c41b1e4757_GRCh38.primary_assembly.genome.fa.amb added
1851c41a157ec0_GRCh38.primary_assembly.genome.fa.ann added
1851c4193844a9_GRCh38.primary_assembly.genome.fa.bwt added
1851c4eb6d939_GRCh38.primary_assembly.genome.fa.pac added
1851c43241917f_GRCh38.primary_assembly.genome.fa.sa added
1851c447827284_GRCh38.primary_assembly.genome.fa added
1851c41d3d86fa_hs37d5.fa.fai added
1851c43ac36e8d_hs37d5.fa.amb added
1851c47ff8cb7c_hs37d5.fa.ann added
1851c4b8e5beb_hs37d5.fa.bwt added
1851c4dd0c744_hs37d5.fa.pac added
1851c474930da5_hs37d5.fa.sa added
1851c431ef7af5_hs37d5.fa added
1851c4160b792d_complete_ref_lens.bin added
1851c43bb5a014_ctable.bin added
1851c422e46880_ctg_offsets.bin added
1851c43d6d037f_duplicate_clusters.tsv added
1851c44121b638_info.json added
1851c432b6200b_mphf.bin added
1851c45a042074_pos.bin added
1851c438c5841d_pre_indexing.log added
1851c45ef92bd9_rank.bin added
1851c459354392_ref_indexing.log added
1851c42cde664a_refAccumLengths.bin added
1851c43de20600_reflengths.bin added
1851c4632ecb13_refseq.bin added
1851c422d4994f_seq.bin added
1851c41593660f_versionInfo.json added
1851c4790f5cff_salmon_index added
1851c42908ba08_chrLength.txt added
1851c4ebdb545_chrName.txt added
1851c4142da456_chrNameLength.txt added
1851c4431e38c8_chrStart.txt added
1851c427f5f9ef_exonGeTrInfo.tab added
1851c422e47d8f_exonInfo.tab added
1851c4755fca47_geneInfo.tab added
1851c46f786c73_Genome added
1851c440220489_genomeParameters.txt added
1851c4302338d4_Log.out added
1851c46f7137ef_SA added
1851c44bb06074_SAindex added
1851c43df40019_sjdbInfo.txt added
1851c464044594_sjdbList.fromGTF.out.tab added
1851c47d9fdb69_sjdbList.out.tab added
1851c453ff7946_transcriptInfo.tab added
1851c41fb9e5a8_GRCh38.GENCODE.v42_100 added
1851c4208443e9_knownGene_hg38.sql added
1851c4116c7cc6_knownGene_hg38.txt added
1851c460db9be0_refGene_hg38.sql added
1851c4533a63f4_refGene_hg38.txt added
1851c46b709d3a_knownGene_mm39.sql added
1851c419a11ffd_knownGene_mm39.txt added
1851c432338fce_refGene_mm39.sql added
1851c444a5e0cc_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/RtmpksgrEq/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 0 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
> 
> 
> 
> proc.time()
   user  system elapsed 
 18.718   1.734  21.077