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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) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-17 07:00:29 UTC
* 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 5.971  0.382   6.353
* 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
###
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* 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) (2026-03-05 r89546) -- "Unsuffered Consequences"
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...
d7fe36aa834fd_GRCh38.primary_assembly.genome.fa.1.bt2 added
d7fe3511c6254_GRCh38.primary_assembly.genome.fa.2.bt2 added
d7fe35313bc4_GRCh38.primary_assembly.genome.fa.3.bt2 added
d7fe3789b7770_GRCh38.primary_assembly.genome.fa.4.bt2 added
d7fe330fcdfeb_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
d7fe3a597023_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
d7fe3fd2247_outfile.txt added
d7fe360e15f24_GRCh37_to_GRCh38.chain added
d7fe37d903d7c_GRCh37_to_NCBI34.chain added
d7fe37f33a4fd_GRCh37_to_NCBI35.chain added
d7fe37a0f4d16_GRCh37_to_NCBI36.chain added
d7fe37ca458ec_GRCh38_to_GRCh37.chain added
d7fe3371dbcf_GRCh38_to_NCBI34.chain added
d7fe3da1f2fe_GRCh38_to_NCBI35.chain added
d7fe3721cfff9_GRCh38_to_NCBI36.chain added
d7fe34e9b0c05_NCBI34_to_GRCh37.chain added
d7fe3be0f5db_NCBI34_to_GRCh38.chain added
d7fe3693f3de4_NCBI35_to_GRCh37.chain added
d7fe36c3b4e8e_NCBI35_to_GRCh38.chain added
d7fe34129a1b5_NCBI36_to_GRCh37.chain added
d7fe315b6776e_NCBI36_to_GRCh38.chain added
d7fe377aa3733_GRCm38_to_NCBIM36.chain added
d7fe3189265c4_GRCm38_to_NCBIM37.chain added
d7fe37dbde319_NCBIM36_to_GRCm38.chain added
d7fe32c6fa30c_NCBIM37_to_GRCm38.chain added
d7fe3540ad07_1000G_omni2.5.b37.vcf.gz added
d7fe33f00526a_1000G_omni2.5.b37.vcf.gz.tbi added
d7fe338d7ed5f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
d7fe3584163d5_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
d7fe3f9d5239_1000G_omni2.5.hg38.vcf.gz added
d7fe363ee0212_1000G_omni2.5.hg38.vcf.gz.tbi added
d7fe342e998d3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
d7fe360b9b48e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
d7fe3691f3dd6_af-only-gnomad.raw.sites.vcf added
d7fe33b851043_af-only-gnomad.raw.sites.vcf.idx added
d7fe311b69479_Mutect2-exome-panel.vcf.idx added
d7fe37378adf9_Mutect2-WGS-panel-b37.vcf added
d7fe33c82328a_Mutect2-WGS-panel-b37.vcf.idx added
d7fe37297f39d_small_exac_common_3.vcf added
d7fe37108eb75_small_exac_common_3.vcf.idx added
d7fe33bb5d787_1000g_pon.hg38.vcf.gz added
d7fe36ca740b3_1000g_pon.hg38.vcf.gz.tbi added
d7fe36dad4462_af-only-gnomad.hg38.vcf.gz added
d7fe33f27b357_af-only-gnomad.hg38.vcf.gz.tbi added
d7fe37a4933b1_small_exac_common_3.hg38.vcf.gz added
d7fe35fca445b_small_exac_common_3.hg38.vcf.gz.tbi added
d7fe3dc2bf5c_gencode.v41.annotation.gtf added
d7fe362a298d_gencode.v42.annotation.gtf added
d7fe34909823f_gencode.vM30.annotation.gtf added
d7fe379fe0dea_gencode.vM31.annotation.gtf added
d7fe34753cb42_gencode.v41.transcripts.fa added
d7fe35ebff9ae_gencode.v41.transcripts.fa.fai added
d7fe371a8451d_gencode.v42.transcripts.fa added
d7fe35fe63106_gencode.v42.transcripts.fa.fai added
d7fe35c7ddcc7_gencode.vM30.pc_transcripts.fa added
d7fe31e17e829_gencode.vM30.pc_transcripts.fa.fai added
d7fe36526de0d_gencode.vM31.pc_transcripts.fa added
d7fe31b7e2f32_gencode.vM31.pc_transcripts.fa.fai added
d7fe356efd588_GRCh38.primary_assembly.genome.fa.1.ht2 added
d7fe33d6841e3_GRCh38.primary_assembly.genome.fa.2.ht2 added
d7fe32b1b816b_GRCh38.primary_assembly.genome.fa.3.ht2 added
d7fe33addd79a_GRCh38.primary_assembly.genome.fa.4.ht2 added
d7fe351dab6_GRCh38.primary_assembly.genome.fa.5.ht2 added
d7fe3bd535f9_GRCh38.primary_assembly.genome.fa.6.ht2 added
d7fe323fd1571_GRCh38.primary_assembly.genome.fa.7.ht2 added
d7fe33bd6eaf9_GRCh38.primary_assembly.genome.fa.8.ht2 added
d7fe31d8bca73_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
d7fe31775c36a_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
d7fe378591d84_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
d7fe31023be10_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
d7fe387eaee0_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
d7fe3340ef50b_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
d7fe37ccafec4_GRCh38_full_analysis_set_plus_decoy_hla.fa added
d7fe3762bf342_GRCh38.primary_assembly.genome.fa.fai added
d7fe37336a862_GRCh38.primary_assembly.genome.fa.amb added
d7fe377143275_GRCh38.primary_assembly.genome.fa.ann added
d7fe355f6379d_GRCh38.primary_assembly.genome.fa.bwt added
d7fe3f967be_GRCh38.primary_assembly.genome.fa.pac added
d7fe37d3e5c02_GRCh38.primary_assembly.genome.fa.sa added
d7fe31effb9dd_GRCh38.primary_assembly.genome.fa added
d7fe37af775a8_hs37d5.fa.fai added
d7fe344922744_hs37d5.fa.amb added
d7fe37dbfb38b_hs37d5.fa.ann added
d7fe36c9fbac5_hs37d5.fa.bwt added
d7fe32478584a_hs37d5.fa.pac added
d7fe35a3d9052_hs37d5.fa.sa added
d7fe3ab7a2ee_hs37d5.fa added
d7fe399f3658_complete_ref_lens.bin added
d7fe375bbbf84_ctable.bin added
d7fe361a77877_ctg_offsets.bin added
d7fe34707783b_duplicate_clusters.tsv added
d7fe320d740f0_info.json added
d7fe31c855011_mphf.bin added
d7fe3475952f1_pos.bin added
d7fe32cac76e9_pre_indexing.log added
d7fe340826582_rank.bin added
d7fe33303dea_ref_indexing.log added
d7fe34a38415c_refAccumLengths.bin added
d7fe357f828ed_reflengths.bin added
d7fe37b895b6e_refseq.bin added
d7fe35a5bff6d_seq.bin added
d7fe36076d7cd_versionInfo.json added
d7fe32f98507a_salmon_index added
d7fe35726fe31_chrLength.txt added
d7fe356a2cb0f_chrName.txt added
d7fe322cef8dc_chrNameLength.txt added
d7fe34e3b30a6_chrStart.txt added
d7fe32c9902ac_exonGeTrInfo.tab added
d7fe323c8609b_exonInfo.tab added
d7fe34b798ca9_geneInfo.tab added
d7fe34b98bc89_Genome added
d7fe31ebfd643_genomeParameters.txt added
d7fe3100bb3ed_Log.out added
d7fe349587014_SA added
d7fe3b5f9109_SAindex added
d7fe334840c38_sjdbInfo.txt added
d7fe323960067_sjdbList.fromGTF.out.tab added
d7fe3161733f7_sjdbList.out.tab added
d7fe33e234290_transcriptInfo.tab added
d7fe31951bfeb_GRCh38.GENCODE.v42_100 added
d7fe377beac6e_knownGene_hg38.sql added
d7fe352abacb_knownGene_hg38.txt added
d7fe33a2900db_refGene_hg38.sql added
d7fe31443fc80_refGene_hg38.txt added
d7fe34c840dbc_knownGene_mm39.sql added
d7fe366d577c5_knownGene_mm39.txt added
d7fe354c66202_refGene_mm39.sql added
d7fe34fb44ba6_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/RtmpwyFkPq/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 
 17.488   1.117  18.852