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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 4.5.1 Patched (2025-08-23 r88802)
* 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 5.859  0.223   6.084
* 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
###
##############################################################################
##############################################################################


* 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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...
2e9b7698e0dce_GRCh38.primary_assembly.genome.fa.1.bt2 added
2e9b761082b3b_GRCh38.primary_assembly.genome.fa.2.bt2 added
2e9b764a8f07d_GRCh38.primary_assembly.genome.fa.3.bt2 added
2e9b73c827ec5_GRCh38.primary_assembly.genome.fa.4.bt2 added
2e9b715dc9780_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2e9b73709601d_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2e9b736d0915a_outfile.txt added
2e9b752ec2a96_GRCh37_to_GRCh38.chain added
2e9b7f0d8c28_GRCh37_to_NCBI34.chain added
2e9b74eaa8e5c_GRCh37_to_NCBI35.chain added
2e9b71d61c3c5_GRCh37_to_NCBI36.chain added
2e9b7265ae972_GRCh38_to_GRCh37.chain added
2e9b77bf48aa2_GRCh38_to_NCBI34.chain added
2e9b71f0643c8_GRCh38_to_NCBI35.chain added
2e9b73ee25e4f_GRCh38_to_NCBI36.chain added
2e9b74aff3922_NCBI34_to_GRCh37.chain added
2e9b75544e7dc_NCBI34_to_GRCh38.chain added
2e9b72fd14437_NCBI35_to_GRCh37.chain added
2e9b76873299c_NCBI35_to_GRCh38.chain added
2e9b7693cc1d2_NCBI36_to_GRCh37.chain added
2e9b722312526_NCBI36_to_GRCh38.chain added
2e9b74fc373b9_GRCm38_to_NCBIM36.chain added
2e9b76013e2a2_GRCm38_to_NCBIM37.chain added
2e9b716c69247_NCBIM36_to_GRCm38.chain added
2e9b759688326_NCBIM37_to_GRCm38.chain added
2e9b776553cd4_1000G_omni2.5.b37.vcf.gz added
2e9b771a7fd27_1000G_omni2.5.b37.vcf.gz.tbi added
2e9b77f2ade3f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2e9b733b2b376_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2e9b72edba9f8_1000G_omni2.5.hg38.vcf.gz added
2e9b721e284d5_1000G_omni2.5.hg38.vcf.gz.tbi added
2e9b71d40c145_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2e9b7fe3d533_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2e9b768b7553_af-only-gnomad.raw.sites.vcf added
2e9b759c3400a_af-only-gnomad.raw.sites.vcf.idx added
2e9b725c06cb3_Mutect2-exome-panel.vcf.idx added
2e9b73d94d570_Mutect2-WGS-panel-b37.vcf added
2e9b71093d164_Mutect2-WGS-panel-b37.vcf.idx added
2e9b778ac9749_small_exac_common_3.vcf added
2e9b74ca26198_small_exac_common_3.vcf.idx added
2e9b75f3e5fc0_1000g_pon.hg38.vcf.gz added
2e9b7160e5b0f_1000g_pon.hg38.vcf.gz.tbi added
2e9b772fd4b0a_af-only-gnomad.hg38.vcf.gz added
2e9b75b32ea63_af-only-gnomad.hg38.vcf.gz.tbi added
2e9b735149ed7_small_exac_common_3.hg38.vcf.gz added
2e9b731dfa95a_small_exac_common_3.hg38.vcf.gz.tbi added
2e9b726322385_gencode.v41.annotation.gtf added
2e9b7a5986b3_gencode.v42.annotation.gtf added
2e9b761b0ed91_gencode.vM30.annotation.gtf added
2e9b7ea54d21_gencode.vM31.annotation.gtf added
2e9b773964886_gencode.v41.transcripts.fa added
2e9b73e212b7_gencode.v41.transcripts.fa.fai added
2e9b75e68c0da_gencode.v42.transcripts.fa added
2e9b753aa2b28_gencode.v42.transcripts.fa.fai added
2e9b71aa8a4ff_gencode.vM30.pc_transcripts.fa added
2e9b737d14401_gencode.vM30.pc_transcripts.fa.fai added
2e9b749ff67fc_gencode.vM31.pc_transcripts.fa added
2e9b7c50a226_gencode.vM31.pc_transcripts.fa.fai added
2e9b736fc2240_GRCh38.primary_assembly.genome.fa.1.ht2 added
2e9b77db21b73_GRCh38.primary_assembly.genome.fa.2.ht2 added
2e9b73b2c4c1e_GRCh38.primary_assembly.genome.fa.3.ht2 added
2e9b758dea715_GRCh38.primary_assembly.genome.fa.4.ht2 added
2e9b71af2dcb8_GRCh38.primary_assembly.genome.fa.5.ht2 added
2e9b74b102151_GRCh38.primary_assembly.genome.fa.6.ht2 added
2e9b75f6a1c68_GRCh38.primary_assembly.genome.fa.7.ht2 added
2e9b774b61cc2_GRCh38.primary_assembly.genome.fa.8.ht2 added
2e9b770d08e05_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2e9b71cfef1d9_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2e9b7549ee27_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2e9b7697d254e_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2e9b769a15371_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2e9b764884de7_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2e9b77f8b805d_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2e9b75c9e9e7c_GRCh38.primary_assembly.genome.fa.fai added
2e9b73fbb384a_GRCh38.primary_assembly.genome.fa.amb added
2e9b734a01f34_GRCh38.primary_assembly.genome.fa.ann added
2e9b7e7e47d6_GRCh38.primary_assembly.genome.fa.bwt added
2e9b765ed5bd0_GRCh38.primary_assembly.genome.fa.pac added
2e9b73ef9a5e8_GRCh38.primary_assembly.genome.fa.sa added
2e9b7702f3567_GRCh38.primary_assembly.genome.fa added
2e9b77492a8f1_hs37d5.fa.fai added
2e9b7328fee6e_hs37d5.fa.amb added
2e9b77411481f_hs37d5.fa.ann added
2e9b752fb69cc_hs37d5.fa.bwt added
2e9b763a1996_hs37d5.fa.pac added
2e9b7eb9ed1e_hs37d5.fa.sa added
2e9b7accadcd_hs37d5.fa added
2e9b750398192_complete_ref_lens.bin added
2e9b71b0a8f44_ctable.bin added
2e9b741c8d00d_ctg_offsets.bin added
2e9b74deb9d05_duplicate_clusters.tsv added
2e9b75636db63_info.json added
2e9b71aa77722_mphf.bin added
2e9b768de79bd_pos.bin added
2e9b72146fcb4_pre_indexing.log added
2e9b77a11938b_rank.bin added
2e9b75d949680_ref_indexing.log added
2e9b712178ab9_refAccumLengths.bin added
2e9b717108564_reflengths.bin added
2e9b762de84a7_refseq.bin added
2e9b77b94b008_seq.bin added
2e9b7b1d8d5_versionInfo.json added
2e9b74766d28e_salmon_index added
2e9b77b203065_chrLength.txt added
2e9b75d507751_chrName.txt added
2e9b77220ad9_chrNameLength.txt added
2e9b72fc04f9a_chrStart.txt added
2e9b76bcebf27_exonGeTrInfo.tab added
2e9b76d0f66a9_exonInfo.tab added
2e9b76eb9f582_geneInfo.tab added
2e9b75bfdf48f_Genome added
2e9b761a20f9a_genomeParameters.txt added
2e9b72149e3f0_Log.out added
2e9b7500f3cae_SA added
2e9b7349d7966_SAindex added
2e9b72783fd86_sjdbInfo.txt added
2e9b75ec929cc_sjdbList.fromGTF.out.tab added
2e9b73f6a2733_sjdbList.out.tab added
2e9b777bd7f18_transcriptInfo.tab added
2e9b779d3b910_GRCh38.GENCODE.v42_100 added
2e9b7132f740_knownGene_hg38.sql added
2e9b745a91c1e_knownGene_hg38.txt added
2e9b7500a9473_refGene_hg38.sql added
2e9b71bda6e63_refGene_hg38.txt added
2e9b72e8795db_knownGene_mm39.sql added
2e9b771519128_knownGene_mm39.txt added
2e9b715ec01ee_refGene_mm39.sql added
2e9b7c1c2c5b_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/RtmpgEgYfs/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 
 17.940   0.908  19.725