##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings ReUseData_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-26 07:38:47 UTC
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.13.0’
* 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 5.729  0.258   5.993
* 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-3.24-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.13.0’
** 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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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...
73e57250e61a2_GRCh38.primary_assembly.genome.fa.1.bt2 added
73e5747a6293c_GRCh38.primary_assembly.genome.fa.2.bt2 added
73e575a2d3daa_GRCh38.primary_assembly.genome.fa.3.bt2 added
73e574d4afcec_GRCh38.primary_assembly.genome.fa.4.bt2 added
73e572ee3d324_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
73e578466173_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
73e571a023940_outfile.txt added
73e57260bce15_GRCh37_to_GRCh38.chain added
73e57413daac0_GRCh37_to_NCBI34.chain added
73e572e9e7fc4_GRCh37_to_NCBI35.chain added
73e575fcbefdb_GRCh37_to_NCBI36.chain added
73e577a4c5aab_GRCh38_to_GRCh37.chain added
73e57117cfc01_GRCh38_to_NCBI34.chain added
73e5743761f2d_GRCh38_to_NCBI35.chain added
73e5743674238_GRCh38_to_NCBI36.chain added
73e57743e9cc0_NCBI34_to_GRCh37.chain added
73e576b73c19c_NCBI34_to_GRCh38.chain added
73e571e7cb858_NCBI35_to_GRCh37.chain added
73e577c6217a7_NCBI35_to_GRCh38.chain added
73e577696ca6d_NCBI36_to_GRCh37.chain added
73e57ec4f05a_NCBI36_to_GRCh38.chain added
73e572c967bdf_GRCm38_to_NCBIM36.chain added
73e57345038b5_GRCm38_to_NCBIM37.chain added
73e577c88f969_NCBIM36_to_GRCm38.chain added
73e573f622a8d_NCBIM37_to_GRCm38.chain added
73e57172d857d_1000G_omni2.5.b37.vcf.gz added
73e5718fe7e56_1000G_omni2.5.b37.vcf.gz.tbi added
73e57559c0e68_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
73e5760f682aa_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
73e5710ce9c32_1000G_omni2.5.hg38.vcf.gz added
73e572fd8080c_1000G_omni2.5.hg38.vcf.gz.tbi added
73e57604e44d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
73e575874c56e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
73e57a0545b6_af-only-gnomad.raw.sites.vcf added
73e57534fe139_af-only-gnomad.raw.sites.vcf.idx added
73e577589892_Mutect2-exome-panel.vcf.idx added
73e57124ba729_Mutect2-WGS-panel-b37.vcf added
73e576d521a79_Mutect2-WGS-panel-b37.vcf.idx added
73e572d6466a7_small_exac_common_3.vcf added
73e57538951ea_small_exac_common_3.vcf.idx added
73e571bf09a3d_1000g_pon.hg38.vcf.gz added
73e57d305682_1000g_pon.hg38.vcf.gz.tbi added
73e574dd5ac95_af-only-gnomad.hg38.vcf.gz added
73e572d6d963f_af-only-gnomad.hg38.vcf.gz.tbi added
73e5750a675b0_small_exac_common_3.hg38.vcf.gz added
73e57113ceecd_small_exac_common_3.hg38.vcf.gz.tbi added
73e5721ac32ff_gencode.v41.annotation.gtf added
73e573c1a374c_gencode.v42.annotation.gtf added
73e572fb9a726_gencode.vM30.annotation.gtf added
73e571e0e4aa6_gencode.vM31.annotation.gtf added
73e5732b101b9_gencode.v41.transcripts.fa added
73e573e7e9780_gencode.v41.transcripts.fa.fai added
73e574aa4c686_gencode.v42.transcripts.fa added
73e5767013a6f_gencode.v42.transcripts.fa.fai added
73e573b0790e9_gencode.vM30.pc_transcripts.fa added
73e57a06f113_gencode.vM30.pc_transcripts.fa.fai added
73e577e2ebfec_gencode.vM31.pc_transcripts.fa added
73e5754060f3f_gencode.vM31.pc_transcripts.fa.fai added
73e575fa2ff7b_GRCh38.primary_assembly.genome.fa.1.ht2 added
73e575f254296_GRCh38.primary_assembly.genome.fa.2.ht2 added
73e5764d4ab71_GRCh38.primary_assembly.genome.fa.3.ht2 added
73e57f7b0788_GRCh38.primary_assembly.genome.fa.4.ht2 added
73e57652a26e3_GRCh38.primary_assembly.genome.fa.5.ht2 added
73e573d4970df_GRCh38.primary_assembly.genome.fa.6.ht2 added
73e5719804d3e_GRCh38.primary_assembly.genome.fa.7.ht2 added
73e57387a081d_GRCh38.primary_assembly.genome.fa.8.ht2 added
73e5744a20971_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
73e572bcbf468_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
73e5725cc2296_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
73e5772067019_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
73e577f554652_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
73e5741bcbcd4_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
73e577f36c69b_GRCh38_full_analysis_set_plus_decoy_hla.fa added
73e574d2af2e7_GRCh38.primary_assembly.genome.fa.fai added
73e576f2a5313_GRCh38.primary_assembly.genome.fa.amb added
73e574fdd3c4b_GRCh38.primary_assembly.genome.fa.ann added
73e575e67e1b4_GRCh38.primary_assembly.genome.fa.bwt added
73e5710d68612_GRCh38.primary_assembly.genome.fa.pac added
73e57bf77397_GRCh38.primary_assembly.genome.fa.sa added
73e57e2188da_GRCh38.primary_assembly.genome.fa added
73e572ee4d0b8_hs37d5.fa.fai added
73e573ea87551_hs37d5.fa.amb added
73e574ca0205b_hs37d5.fa.ann added
73e577989973e_hs37d5.fa.bwt added
73e5725a9afc0_hs37d5.fa.pac added
73e577a7b144_hs37d5.fa.sa added
73e573908851_hs37d5.fa added
73e5723d86fac_complete_ref_lens.bin added
73e575badc084_ctable.bin added
73e57633387cd_ctg_offsets.bin added
73e572fdb242_duplicate_clusters.tsv added
73e5740826bf5_info.json added
73e5772ae8f55_mphf.bin added
73e576827d926_pos.bin added
73e577dcbdcd5_pre_indexing.log added
73e57c2edc93_rank.bin added
73e5720a1e143_ref_indexing.log added
73e57426de646_refAccumLengths.bin added
73e5737fad0fb_reflengths.bin added
73e57466e03d9_refseq.bin added
73e573474565f_seq.bin added
73e573750174d_versionInfo.json added
73e5782ac0ad_salmon_index added
73e5733ab1cfb_chrLength.txt added
73e5747b0a34_chrName.txt added
73e57775513c0_chrNameLength.txt added
73e573885946_chrStart.txt added
73e5762e2ebe9_exonGeTrInfo.tab added
73e5782b99d2_exonInfo.tab added
73e57f7fccde_geneInfo.tab added
73e57710474c3_Genome added
73e5737106a8b_genomeParameters.txt added
73e574e28422f_Log.out added
73e573da4951e_SA added
73e57309a01c9_SAindex added
73e5773d1f1ef_sjdbInfo.txt added
73e57454c4663_sjdbList.fromGTF.out.tab added
73e57342a8a1b_sjdbList.out.tab added
73e5717aa619b_transcriptInfo.tab added
73e5720fa06e7_GRCh38.GENCODE.v42_100 added
73e57175e11e8_knownGene_hg38.sql added
73e571aa813dd_knownGene_hg38.txt added
73e57617c72dc_refGene_hg38.sql added
73e57a0ca13d_refGene_hg38.txt added
73e572cfed03_knownGene_mm39.sql added
73e575f484fb1_knownGene_mm39.txt added
73e57163b7dd0_refGene_mm39.sql added
73e572371ce46_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/Rtmp8g0Ky8/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 1 | SKIP 0 | PASS 44 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
> 
> 
> 
> proc.time()
   user  system elapsed 
 18.276   1.069  20.030