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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) (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 5.977  0.356   6.338
* 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...
14bb1414618f8f_GRCh38.primary_assembly.genome.fa.1.bt2 added
14bb14641bbc6f_GRCh38.primary_assembly.genome.fa.2.bt2 added
14bb14547e6710_GRCh38.primary_assembly.genome.fa.3.bt2 added
14bb142e869ec0_GRCh38.primary_assembly.genome.fa.4.bt2 added
14bb142fc5d214_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
14bb143dd69a94_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
14bb1478a68cb0_outfile.txt added
14bb142348f1e7_GRCh37_to_GRCh38.chain added
14bb144a9e7030_GRCh37_to_NCBI34.chain added
14bb1474e5b29b_GRCh37_to_NCBI35.chain added
14bb14421cb1d_GRCh37_to_NCBI36.chain added
14bb143b680c7b_GRCh38_to_GRCh37.chain added
14bb145905f149_GRCh38_to_NCBI34.chain added
14bb1439df4713_GRCh38_to_NCBI35.chain added
14bb144f206e77_GRCh38_to_NCBI36.chain added
14bb143a3cafdc_NCBI34_to_GRCh37.chain added
14bb14621ddcb8_NCBI34_to_GRCh38.chain added
14bb14598396dd_NCBI35_to_GRCh37.chain added
14bb1429d4efd3_NCBI35_to_GRCh38.chain added
14bb144d20c969_NCBI36_to_GRCh37.chain added
14bb146398b4ac_NCBI36_to_GRCh38.chain added
14bb145d566b27_GRCm38_to_NCBIM36.chain added
14bb14392bd73e_GRCm38_to_NCBIM37.chain added
14bb1439eb9047_NCBIM36_to_GRCm38.chain added
14bb1467f12470_NCBIM37_to_GRCm38.chain added
14bb1417801bb_1000G_omni2.5.b37.vcf.gz added
14bb146042b5ee_1000G_omni2.5.b37.vcf.gz.tbi added
14bb1412580fce_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
14bb1458f4144a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
14bb144ba78077_1000G_omni2.5.hg38.vcf.gz added
14bb14766e710_1000G_omni2.5.hg38.vcf.gz.tbi added
14bb146d55a3da_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
14bb142fc33ce6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
14bb145be54e20_af-only-gnomad.raw.sites.vcf added
14bb141bdc429a_af-only-gnomad.raw.sites.vcf.idx added
14bb145f890efb_Mutect2-exome-panel.vcf.idx added
14bb1419bbe8b4_Mutect2-WGS-panel-b37.vcf added
14bb141482cf4a_Mutect2-WGS-panel-b37.vcf.idx added
14bb142d200e2_small_exac_common_3.vcf added
14bb14645a58e4_small_exac_common_3.vcf.idx added
14bb1496881e6_1000g_pon.hg38.vcf.gz added
14bb146f3cc00_1000g_pon.hg38.vcf.gz.tbi added
14bb141fc26560_af-only-gnomad.hg38.vcf.gz added
14bb14626e732f_af-only-gnomad.hg38.vcf.gz.tbi added
14bb1440d31313_small_exac_common_3.hg38.vcf.gz added
14bb146ee2d3d7_small_exac_common_3.hg38.vcf.gz.tbi added
14bb141cab230c_gencode.v41.annotation.gtf added
14bb1422f0efcc_gencode.v42.annotation.gtf added
14bb1448666ab4_gencode.vM30.annotation.gtf added
14bb14468012df_gencode.vM31.annotation.gtf added
14bb147011b935_gencode.v41.transcripts.fa added
14bb142bff1f60_gencode.v41.transcripts.fa.fai added
14bb1423d67e06_gencode.v42.transcripts.fa added
14bb14293d9073_gencode.v42.transcripts.fa.fai added
14bb1465eaafa8_gencode.vM30.pc_transcripts.fa added
14bb14bc7a276_gencode.vM30.pc_transcripts.fa.fai added
14bb142ab5922e_gencode.vM31.pc_transcripts.fa added
14bb14462d6596_gencode.vM31.pc_transcripts.fa.fai added
14bb141e1fb244_GRCh38.primary_assembly.genome.fa.1.ht2 added
14bb143a9a678_GRCh38.primary_assembly.genome.fa.2.ht2 added
14bb1411d4e60d_GRCh38.primary_assembly.genome.fa.3.ht2 added
14bb1425869954_GRCh38.primary_assembly.genome.fa.4.ht2 added
14bb1470ff4a52_GRCh38.primary_assembly.genome.fa.5.ht2 added
14bb14419822f3_GRCh38.primary_assembly.genome.fa.6.ht2 added
14bb1416be774_GRCh38.primary_assembly.genome.fa.7.ht2 added
14bb14cdb8ced_GRCh38.primary_assembly.genome.fa.8.ht2 added
14bb14212131ee_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
14bb141b27d028_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
14bb14215e5c37_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
14bb1423f332d1_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
14bb147f82290d_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
14bb142ac6de1d_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
14bb142ae6fed1_GRCh38_full_analysis_set_plus_decoy_hla.fa added
14bb141f448e6d_GRCh38.primary_assembly.genome.fa.fai added
14bb14d35514d_GRCh38.primary_assembly.genome.fa.amb added
14bb146bba11e4_GRCh38.primary_assembly.genome.fa.ann added
14bb14e276244_GRCh38.primary_assembly.genome.fa.bwt added
14bb1429e07459_GRCh38.primary_assembly.genome.fa.pac added
14bb14eab01b0_GRCh38.primary_assembly.genome.fa.sa added
14bb14568dccf9_GRCh38.primary_assembly.genome.fa added
14bb1470608738_hs37d5.fa.fai added
14bb147ebcbae5_hs37d5.fa.amb added
14bb1428cec59_hs37d5.fa.ann added
14bb141437053e_hs37d5.fa.bwt added
14bb1427fa4b58_hs37d5.fa.pac added
14bb1468779c01_hs37d5.fa.sa added
14bb141ffea7b5_hs37d5.fa added
14bb1452afdd86_complete_ref_lens.bin added
14bb142ea50197_ctable.bin added
14bb143e1e59f9_ctg_offsets.bin added
14bb14565983ff_duplicate_clusters.tsv added
14bb144079e7a4_info.json added
14bb1463a4f34e_mphf.bin added
14bb144758ce51_pos.bin added
14bb142120a98_pre_indexing.log added
14bb146510dac2_rank.bin added
14bb1454345b3e_ref_indexing.log added
14bb1423333c86_refAccumLengths.bin added
14bb1438aaeb_reflengths.bin added
14bb147592b776_refseq.bin added
14bb1447266f57_seq.bin added
14bb147fbad3f8_versionInfo.json added
14bb1420599593_salmon_index added
14bb14720d6e28_chrLength.txt added
14bb141eff6265_chrName.txt added
14bb142d8ee6e0_chrNameLength.txt added
14bb145dc7800d_chrStart.txt added
14bb142d26c4a9_exonGeTrInfo.tab added
14bb14576f5b39_exonInfo.tab added
14bb146c7281bd_geneInfo.tab added
14bb143b491a2_Genome added
14bb1447cfe271_genomeParameters.txt added
14bb146b2f3ca3_Log.out added
14bb146417dfc_SA added
14bb145c06e7b0_SAindex added
14bb14132987fb_sjdbInfo.txt added
14bb146eb919fd_sjdbList.fromGTF.out.tab added
14bb147c058f65_sjdbList.out.tab added
14bb1465d96582_transcriptInfo.tab added
14bb141d5e1b95_GRCh38.GENCODE.v42_100 added
14bb143a23e95e_knownGene_hg38.sql added
14bb143c32e981_knownGene_hg38.txt added
14bb145dd80339_refGene_hg38.sql added
14bb141dc8dcac_refGene_hg38.txt added
14bb1438bb7d2_knownGene_mm39.sql added
14bb145fea0dd1_knownGene_mm39.txt added
14bb142d9b76f_refGene_mm39.sql added
14bb1457c01311_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/RtmpBiNX4K/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 
 18.022   1.105  19.727