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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 6.062   0.26   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-3.22-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...
e5821301afa9b_GRCh38.primary_assembly.genome.fa.1.bt2 added
e5821572a3441_GRCh38.primary_assembly.genome.fa.2.bt2 added
e58216b55acbc_GRCh38.primary_assembly.genome.fa.3.bt2 added
e5821ed4559a_GRCh38.primary_assembly.genome.fa.4.bt2 added
e582135663535_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
e58212115c39b_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
e58213aac0105_outfile.txt added
e58214f61219b_GRCh37_to_GRCh38.chain added
e58211dc8a2d2_GRCh37_to_NCBI34.chain added
e582129e8444f_GRCh37_to_NCBI35.chain added
e582154dd81f1_GRCh37_to_NCBI36.chain added
e582157287d22_GRCh38_to_GRCh37.chain added
e5821663aa5d2_GRCh38_to_NCBI34.chain added
e5821664dddbe_GRCh38_to_NCBI35.chain added
e582163accdb0_GRCh38_to_NCBI36.chain added
e582117c2c8bf_NCBI34_to_GRCh37.chain added
e58213399377c_NCBI34_to_GRCh38.chain added
e58214aaafe6e_NCBI35_to_GRCh37.chain added
e58213c1f2d9c_NCBI35_to_GRCh38.chain added
e58217d2cfb0c_NCBI36_to_GRCh37.chain added
e58215709b7af_NCBI36_to_GRCh38.chain added
e582147303fa8_GRCm38_to_NCBIM36.chain added
e582132cba9d8_GRCm38_to_NCBIM37.chain added
e5821311bd1a3_NCBIM36_to_GRCm38.chain added
e58217039c873_NCBIM37_to_GRCm38.chain added
e58217b7ef51b_1000G_omni2.5.b37.vcf.gz added
e5821726dcf5d_1000G_omni2.5.b37.vcf.gz.tbi added
e582172224493_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
e582138914b5f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
e582113bf7ca9_1000G_omni2.5.hg38.vcf.gz added
e58212f7d5bc2_1000G_omni2.5.hg38.vcf.gz.tbi added
e582168ac45fb_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
e58216ae9b0ea_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
e58211ad3087e_af-only-gnomad.raw.sites.vcf added
e582177809b95_af-only-gnomad.raw.sites.vcf.idx added
e5821204fe620_Mutect2-exome-panel.vcf.idx added
e58213be8cc19_Mutect2-WGS-panel-b37.vcf added
e5821322c9c9a_Mutect2-WGS-panel-b37.vcf.idx added
e58216fb107bb_small_exac_common_3.vcf added
e582159b16eec_small_exac_common_3.vcf.idx added
e58215c14e0ea_1000g_pon.hg38.vcf.gz added
e5821448e89ac_1000g_pon.hg38.vcf.gz.tbi added
e582130d9ec0e_af-only-gnomad.hg38.vcf.gz added
e5821424f86bc_af-only-gnomad.hg38.vcf.gz.tbi added
e58212adc676a_small_exac_common_3.hg38.vcf.gz added
e58211486b9be_small_exac_common_3.hg38.vcf.gz.tbi added
e58215a124f7b_gencode.v41.annotation.gtf added
e58215e759ee7_gencode.v42.annotation.gtf added
e58215f31b82c_gencode.vM30.annotation.gtf added
e582116317d17_gencode.vM31.annotation.gtf added
e58215ba299f3_gencode.v41.transcripts.fa added
e5821363b6fdb_gencode.v41.transcripts.fa.fai added
e58215d61bcbf_gencode.v42.transcripts.fa added
e5821e6e43cb_gencode.v42.transcripts.fa.fai added
e58216757417e_gencode.vM30.pc_transcripts.fa added
e58214d9b8533_gencode.vM30.pc_transcripts.fa.fai added
e58219ed38e6_gencode.vM31.pc_transcripts.fa added
e582159c510db_gencode.vM31.pc_transcripts.fa.fai added
e58213fbdc9c6_GRCh38.primary_assembly.genome.fa.1.ht2 added
e5821427e8446_GRCh38.primary_assembly.genome.fa.2.ht2 added
e58216d848d84_GRCh38.primary_assembly.genome.fa.3.ht2 added
e58216f3b2588_GRCh38.primary_assembly.genome.fa.4.ht2 added
e58212b2aca41_GRCh38.primary_assembly.genome.fa.5.ht2 added
e5821586e3e6f_GRCh38.primary_assembly.genome.fa.6.ht2 added
e5821a0e2e06_GRCh38.primary_assembly.genome.fa.7.ht2 added
e582122ab65d6_GRCh38.primary_assembly.genome.fa.8.ht2 added
e582178be248f_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
e582145f6fa20_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
e582154d80271_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
e5821686f2c4a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
e58211fa8690c_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
e582130ece35b_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
e58212cfdb5f7_GRCh38_full_analysis_set_plus_decoy_hla.fa added
e58215082551a_GRCh38.primary_assembly.genome.fa.fai added
e5821733c6a17_GRCh38.primary_assembly.genome.fa.amb added
e582157da1d61_GRCh38.primary_assembly.genome.fa.ann added
e582165090ed8_GRCh38.primary_assembly.genome.fa.bwt added
e58214d4eb992_GRCh38.primary_assembly.genome.fa.pac added
e5821364fbc48_GRCh38.primary_assembly.genome.fa.sa added
e5821443ac704_GRCh38.primary_assembly.genome.fa added
e5821638036a9_hs37d5.fa.fai added
e582111f2563b_hs37d5.fa.amb added
e58217a7636e0_hs37d5.fa.ann added
e582140e1f368_hs37d5.fa.bwt added
e582120609a07_hs37d5.fa.pac added
e582161cd785e_hs37d5.fa.sa added
e5821e7d789b_hs37d5.fa added
e58212a4dd2ed_complete_ref_lens.bin added
e58213b92893a_ctable.bin added
e58214e3b4261_ctg_offsets.bin added
e58216ccc5733_duplicate_clusters.tsv added
e5821291716be_info.json added
e58213d7667e9_mphf.bin added
e582117f72174_pos.bin added
e5821185552d_pre_indexing.log added
e5821478495f0_rank.bin added
e58213aa2874b_ref_indexing.log added
e58217a4379bc_refAccumLengths.bin added
e5821d7b9010_reflengths.bin added
e5821f7a89bc_refseq.bin added
e582162b2a607_seq.bin added
e58212d23f91c_versionInfo.json added
e582140676d17_salmon_index added
e5821fb05bfe_chrLength.txt added
e58217da64e36_chrName.txt added
e582133a3d72e_chrNameLength.txt added
e5821678a795f_chrStart.txt added
e582162af5d0e_exonGeTrInfo.tab added
e5821f290c0_exonInfo.tab added
e58211dda35a8_geneInfo.tab added
e582126ea2412_Genome added
e58216472c769_genomeParameters.txt added
e58212fcc8be3_Log.out added
e582121605af2_SA added
e58212554bad1_SAindex added
e5821502d25ea_sjdbInfo.txt added
e582132dd351_sjdbList.fromGTF.out.tab added
e582133d2336d_sjdbList.out.tab added
e58217a7af8d8_transcriptInfo.tab added
e58213ec05c8b_GRCh38.GENCODE.v42_100 added
e582120d75ce_knownGene_hg38.sql added
e58216747500b_knownGene_hg38.txt added
e582167d77349_refGene_hg38.sql added
e58213f83ddb8_refGene_hg38.txt added
e58217f3e7180_knownGene_mm39.sql added
e5821695cc877_knownGene_mm39.txt added
e582170873a8_refGene_mm39.sql added
e582139e0f8cb_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/RtmpAJQ0nt/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 
 17.995   0.989  19.699