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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_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-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: 2026-05-02 08:07:34 UTC
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.12.0’
* 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 6.437  0.396   6.834
* 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 ‘1.12.0’
** 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...
3acef157669e2d_GRCh38.primary_assembly.genome.fa.1.bt2 added
3acef164af641a_GRCh38.primary_assembly.genome.fa.2.bt2 added
3acef1562b1292_GRCh38.primary_assembly.genome.fa.3.bt2 added
3acef174bc06aa_GRCh38.primary_assembly.genome.fa.4.bt2 added
3acef158d3c716_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3acef149a5698_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3acef168caffd4_outfile.txt added
3acef17e17379_GRCh37_to_GRCh38.chain added
3acef14797d03e_GRCh37_to_NCBI34.chain added
3acef1677f7af1_GRCh37_to_NCBI35.chain added
3acef1653bada1_GRCh37_to_NCBI36.chain added
3acef16060c4be_GRCh38_to_GRCh37.chain added
3acef1e4cbd13_GRCh38_to_NCBI34.chain added
3acef12d86a911_GRCh38_to_NCBI35.chain added
3acef17fcc342b_GRCh38_to_NCBI36.chain added
3acef1a02dad9_NCBI34_to_GRCh37.chain added
3acef177b947b0_NCBI34_to_GRCh38.chain added
3acef164bf35ab_NCBI35_to_GRCh37.chain added
3acef159d313d0_NCBI35_to_GRCh38.chain added
3acef14f7bdc6d_NCBI36_to_GRCh37.chain added
3acef1a37061a_NCBI36_to_GRCh38.chain added
3acef16828d7c5_GRCm38_to_NCBIM36.chain added
3acef1509c0a46_GRCm38_to_NCBIM37.chain added
3acef121ef4cb1_NCBIM36_to_GRCm38.chain added
3acef17f263139_NCBIM37_to_GRCm38.chain added
3acef15d904f16_1000G_omni2.5.b37.vcf.gz added
3acef13ad70fb9_1000G_omni2.5.b37.vcf.gz.tbi added
3acef15c6d4ffd_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3acef1654f627f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3acef16965abd1_1000G_omni2.5.hg38.vcf.gz added
3acef1bf9e537_1000G_omni2.5.hg38.vcf.gz.tbi added
3acef13cb600ac_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3acef14e150feb_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3acef16224f7c9_af-only-gnomad.raw.sites.vcf added
3acef131720756_af-only-gnomad.raw.sites.vcf.idx added
3acef126e8d702_Mutect2-exome-panel.vcf.idx added
3acef166bf4e61_Mutect2-WGS-panel-b37.vcf added
3acef11a3d072b_Mutect2-WGS-panel-b37.vcf.idx added
3acef12eca4a7b_small_exac_common_3.vcf added
3acef12e571e9f_small_exac_common_3.vcf.idx added
3acef11bc821c_1000g_pon.hg38.vcf.gz added
3acef11405f81d_1000g_pon.hg38.vcf.gz.tbi added
3acef1eb7e35e_af-only-gnomad.hg38.vcf.gz added
3acef110093f2f_af-only-gnomad.hg38.vcf.gz.tbi added
3acef1418ca12e_small_exac_common_3.hg38.vcf.gz added
3acef1e841789_small_exac_common_3.hg38.vcf.gz.tbi added
3acef11a0c1a08_gencode.v41.annotation.gtf added
3acef13945e8de_gencode.v42.annotation.gtf added
3acef173434d34_gencode.vM30.annotation.gtf added
3acef173df2dd8_gencode.vM31.annotation.gtf added
3acef18c1c54b_gencode.v41.transcripts.fa added
3acef17d7a534e_gencode.v41.transcripts.fa.fai added
3acef15c08059d_gencode.v42.transcripts.fa added
3acef1595dcf91_gencode.v42.transcripts.fa.fai added
3acef11f699fff_gencode.vM30.pc_transcripts.fa added
3acef15b2e36d6_gencode.vM30.pc_transcripts.fa.fai added
3acef136ee1ea8_gencode.vM31.pc_transcripts.fa added
3acef15a40afb9_gencode.vM31.pc_transcripts.fa.fai added
3acef1379b86d3_GRCh38.primary_assembly.genome.fa.1.ht2 added
3acef11c3d8127_GRCh38.primary_assembly.genome.fa.2.ht2 added
3acef143a65b8a_GRCh38.primary_assembly.genome.fa.3.ht2 added
3acef143956c0a_GRCh38.primary_assembly.genome.fa.4.ht2 added
3acef158f381d4_GRCh38.primary_assembly.genome.fa.5.ht2 added
3acef111bb6b76_GRCh38.primary_assembly.genome.fa.6.ht2 added
3acef125ba63d3_GRCh38.primary_assembly.genome.fa.7.ht2 added
3acef1a65892a_GRCh38.primary_assembly.genome.fa.8.ht2 added
3acef138a44278_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3acef1c79b234_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3acef124a29055_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3acef1676e8cf3_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3acef13ad0d0d4_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3acef1265f1271_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3acef17b748510_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3acef14988b432_GRCh38.primary_assembly.genome.fa.fai added
3acef1366851a0_GRCh38.primary_assembly.genome.fa.amb added
3acef13d01263e_GRCh38.primary_assembly.genome.fa.ann added
3acef1580ccbbb_GRCh38.primary_assembly.genome.fa.bwt added
3acef150746ba8_GRCh38.primary_assembly.genome.fa.pac added
3acef176470f1d_GRCh38.primary_assembly.genome.fa.sa added
3acef14b5018ef_GRCh38.primary_assembly.genome.fa added
3acef144539980_hs37d5.fa.fai added
3acef17f08d468_hs37d5.fa.amb added
3acef148ca6c3e_hs37d5.fa.ann added
3acef1205b9f1d_hs37d5.fa.bwt added
3acef15866a3fa_hs37d5.fa.pac added
3acef168340c3d_hs37d5.fa.sa added
3acef17b89d5f4_hs37d5.fa added
3acef1f54c2a2_complete_ref_lens.bin added
3acef14274bbf6_ctable.bin added
3acef133255cc7_ctg_offsets.bin added
3acef12b9243c9_duplicate_clusters.tsv added
3acef161b1781_info.json added
3acef176bac8d2_mphf.bin added
3acef1485c59d_pos.bin added
3acef117d682f7_pre_indexing.log added
3acef11c752ca5_rank.bin added
3acef1eeb4ec8_ref_indexing.log added
3acef1507ac56f_refAccumLengths.bin added
3acef128eededa_reflengths.bin added
3acef1338ddf1d_refseq.bin added
3acef137e95262_seq.bin added
3acef163bfafae_versionInfo.json added
3acef159ecf18f_salmon_index added
3acef1335dd773_chrLength.txt added
3acef12d4863e0_chrName.txt added
3acef11055432f_chrNameLength.txt added
3acef1705efdb1_chrStart.txt added
3acef15552f9b_exonGeTrInfo.tab added
3acef160c9aed8_exonInfo.tab added
3acef166a60cce_geneInfo.tab added
3acef150a5488a_Genome added
3acef1251d4858_genomeParameters.txt added
3acef165aee137_Log.out added
3acef1196fb4c8_SA added
3acef14578e776_SAindex added
3acef13e158531_sjdbInfo.txt added
3acef11a3c106_sjdbList.fromGTF.out.tab added
3acef14102bd6a_sjdbList.out.tab added
3acef14d6a47d3_transcriptInfo.tab added
3acef144187cfc_GRCh38.GENCODE.v42_100 added
3acef174281a31_knownGene_hg38.sql added
3acef178fc8b9c_knownGene_hg38.txt added
3acef14a33947d_refGene_hg38.sql added
3acef16ae2e303_refGene_hg38.txt added
3acef17d82513a_knownGene_mm39.sql added
3acef1620a1774_knownGene_mm39.txt added
3acef17580fa9_refGene_mm39.sql added
3acef1c6da002_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/RtmpVBKjPJ/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 
 18.840   1.215  20.404