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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 Under development (unstable) (2025-12-22 r89219)
* 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 ‘1.11.0’
* 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 6.084  0.366   6.452
* 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) (2025-12-22 r89219) -- "Unsuffered Consequences"
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...
18c9bd34c91a46_GRCh38.primary_assembly.genome.fa.1.bt2 added
18c9bd1be96ea0_GRCh38.primary_assembly.genome.fa.2.bt2 added
18c9bd482c5a4b_GRCh38.primary_assembly.genome.fa.3.bt2 added
18c9bddc3f4d4_GRCh38.primary_assembly.genome.fa.4.bt2 added
18c9bd31445c8c_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
18c9bd378e3fd4_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
18c9bd412a290c_outfile.txt added
18c9bd77fd06d8_GRCh37_to_GRCh38.chain added
18c9bd22ecd208_GRCh37_to_NCBI34.chain added
18c9bd5993bfc6_GRCh37_to_NCBI35.chain added
18c9bd80b7177_GRCh37_to_NCBI36.chain added
18c9bd2f4f0f92_GRCh38_to_GRCh37.chain added
18c9bd2417ea90_GRCh38_to_NCBI34.chain added
18c9bd2b76d51f_GRCh38_to_NCBI35.chain added
18c9bd44ef2e16_GRCh38_to_NCBI36.chain added
18c9bd50feb5a5_NCBI34_to_GRCh37.chain added
18c9bd76cea92b_NCBI34_to_GRCh38.chain added
18c9bd459597f2_NCBI35_to_GRCh37.chain added
18c9bd5ea6430c_NCBI35_to_GRCh38.chain added
18c9bd4dfd1017_NCBI36_to_GRCh37.chain added
18c9bd31c6bc6c_NCBI36_to_GRCh38.chain added
18c9bd181edc4d_GRCm38_to_NCBIM36.chain added
18c9bd127c7cd5_GRCm38_to_NCBIM37.chain added
18c9bd1c1768c8_NCBIM36_to_GRCm38.chain added
18c9bd3a073dbb_NCBIM37_to_GRCm38.chain added
18c9bd39503376_1000G_omni2.5.b37.vcf.gz added
18c9bd6e690bf2_1000G_omni2.5.b37.vcf.gz.tbi added
18c9bde7a2277_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
18c9bd20969704_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
18c9bd15afd974_1000G_omni2.5.hg38.vcf.gz added
18c9bd17404468_1000G_omni2.5.hg38.vcf.gz.tbi added
18c9bd555fb14a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
18c9bd31994814_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
18c9bd5f6c9eb3_af-only-gnomad.raw.sites.vcf added
18c9bd6323a61e_af-only-gnomad.raw.sites.vcf.idx added
18c9bd62dda4a0_Mutect2-exome-panel.vcf.idx added
18c9bd16fade87_Mutect2-WGS-panel-b37.vcf added
18c9bd244dcf2b_Mutect2-WGS-panel-b37.vcf.idx added
18c9bd5adaab78_small_exac_common_3.vcf added
18c9bd39e7b08f_small_exac_common_3.vcf.idx added
18c9bd7de18ef1_1000g_pon.hg38.vcf.gz added
18c9bd62e61cef_1000g_pon.hg38.vcf.gz.tbi added
18c9bd6936c022_af-only-gnomad.hg38.vcf.gz added
18c9bd21f97981_af-only-gnomad.hg38.vcf.gz.tbi added
18c9bde5cf20f_small_exac_common_3.hg38.vcf.gz added
18c9bd2e25ee38_small_exac_common_3.hg38.vcf.gz.tbi added
18c9bd72f82f26_gencode.v41.annotation.gtf added
18c9bd52b9b3a_gencode.v42.annotation.gtf added
18c9bd73bb862a_gencode.vM30.annotation.gtf added
18c9bd519e7232_gencode.vM31.annotation.gtf added
18c9bd5328ab52_gencode.v41.transcripts.fa added
18c9bd25824296_gencode.v41.transcripts.fa.fai added
18c9bd69bd4e7f_gencode.v42.transcripts.fa added
18c9bd65a52827_gencode.v42.transcripts.fa.fai added
18c9bd4199ab5e_gencode.vM30.pc_transcripts.fa added
18c9bd23c48c3a_gencode.vM30.pc_transcripts.fa.fai added
18c9bd1ef55b9d_gencode.vM31.pc_transcripts.fa added
18c9bd3002b750_gencode.vM31.pc_transcripts.fa.fai added
18c9bd323eaeb2_GRCh38.primary_assembly.genome.fa.1.ht2 added
18c9bd3f8bf2a1_GRCh38.primary_assembly.genome.fa.2.ht2 added
18c9bd45b290c4_GRCh38.primary_assembly.genome.fa.3.ht2 added
18c9bd497ef31a_GRCh38.primary_assembly.genome.fa.4.ht2 added
18c9bd14eba3ec_GRCh38.primary_assembly.genome.fa.5.ht2 added
18c9bd774bd8d8_GRCh38.primary_assembly.genome.fa.6.ht2 added
18c9bd28eb91ce_GRCh38.primary_assembly.genome.fa.7.ht2 added
18c9bd780f4a0a_GRCh38.primary_assembly.genome.fa.8.ht2 added
18c9bd5a297d79_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
18c9bd3fe67055_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
18c9bd1c5d1935_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
18c9bd350428f1_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
18c9bd79ce20e5_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
18c9bd1a3ea826_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
18c9bd17ea45e1_GRCh38_full_analysis_set_plus_decoy_hla.fa added
18c9bd6304e107_GRCh38.primary_assembly.genome.fa.fai added
18c9bd3c3821a7_GRCh38.primary_assembly.genome.fa.amb added
18c9bd264737f0_GRCh38.primary_assembly.genome.fa.ann added
18c9bd112acf3f_GRCh38.primary_assembly.genome.fa.bwt added
18c9bd2f3050cd_GRCh38.primary_assembly.genome.fa.pac added
18c9bd2b72d32a_GRCh38.primary_assembly.genome.fa.sa added
18c9bd4e65569_GRCh38.primary_assembly.genome.fa added
18c9bdcec2ff_hs37d5.fa.fai added
18c9bd7e9b7e7c_hs37d5.fa.amb added
18c9bd2a6897ff_hs37d5.fa.ann added
18c9bd6a8c117e_hs37d5.fa.bwt added
18c9bd6440a6a3_hs37d5.fa.pac added
18c9bd6c02435d_hs37d5.fa.sa added
18c9bde509db9_hs37d5.fa added
18c9bd3360241_complete_ref_lens.bin added
18c9bd1c04faae_ctable.bin added
18c9bd408f4c6b_ctg_offsets.bin added
18c9bd42c1f4e2_duplicate_clusters.tsv added
18c9bd61b78b72_info.json added
18c9bda0e3f85_mphf.bin added
18c9bd57ad98ce_pos.bin added
18c9bd5903644b_pre_indexing.log added
18c9bd32f9d153_rank.bin added
18c9bd4fbce2d9_ref_indexing.log added
18c9bd332ce1c4_refAccumLengths.bin added
18c9bd72e041a9_reflengths.bin added
18c9bd6c19fc0e_refseq.bin added
18c9bd68310ab5_seq.bin added
18c9bd6cae628e_versionInfo.json added
18c9bd658a435_salmon_index added
18c9bd1b5096_chrLength.txt added
18c9bd4fb34395_chrName.txt added
18c9bd4290c5dc_chrNameLength.txt added
18c9bd26628886_chrStart.txt added
18c9bd60de12d4_exonGeTrInfo.tab added
18c9bd71c116aa_exonInfo.tab added
18c9bd51d55bb1_geneInfo.tab added
18c9bd65c4683d_Genome added
18c9bd728fd9a9_genomeParameters.txt added
18c9bd5070da2d_Log.out added
18c9bd102d003c_SA added
18c9bd5d1beb28_SAindex added
18c9bd34b180d1_sjdbInfo.txt added
18c9bd7c2f4399_sjdbList.fromGTF.out.tab added
18c9bd6b6c88e1_sjdbList.out.tab added
18c9bd37e78312_transcriptInfo.tab added
18c9bd18343e47_GRCh38.GENCODE.v42_100 added
18c9bd2bfbd54c_knownGene_hg38.sql added
18c9bd7aa977f4_knownGene_hg38.txt added
18c9bd79ebc9ba_refGene_hg38.sql added
18c9bd360a14d1_refGene_hg38.txt added
18c9bd525710c3_knownGene_mm39.sql added
18c9bd52ef2e05_knownGene_mm39.txt added
18c9bd6903e625_refGene_mm39.sql added
18c9bd2213f39c_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/RtmpoODQcG/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 
 18.800   1.298  20.738