##############################################################################
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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 version 4.6.0 alpha (2026-04-05 r89794)
* 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: 2026-04-13 08:16:55 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 6.105  0.396   6.504
* 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 version 4.6.0 alpha (2026-04-05 r89794)
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...
132f066e3eadbc_GRCh38.primary_assembly.genome.fa.1.bt2 added
132f063f11c900_GRCh38.primary_assembly.genome.fa.2.bt2 added
132f0673d2372b_GRCh38.primary_assembly.genome.fa.3.bt2 added
132f0668b48b30_GRCh38.primary_assembly.genome.fa.4.bt2 added
132f0640f4960b_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
132f064a567175_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
132f064c41bd7a_outfile.txt added
132f06672d0756_GRCh37_to_GRCh38.chain added
132f065417fc52_GRCh37_to_NCBI34.chain added
132f061bcceda8_GRCh37_to_NCBI35.chain added
132f0668bcb7dc_GRCh37_to_NCBI36.chain added
132f06732ea6da_GRCh38_to_GRCh37.chain added
132f06417d54d_GRCh38_to_NCBI34.chain added
132f062ca7152e_GRCh38_to_NCBI35.chain added
132f0640f16353_GRCh38_to_NCBI36.chain added
132f061d8d65e7_NCBI34_to_GRCh37.chain added
132f063872769e_NCBI34_to_GRCh38.chain added
132f065e68ce09_NCBI35_to_GRCh37.chain added
132f062d4e4d60_NCBI35_to_GRCh38.chain added
132f066c3267f_NCBI36_to_GRCh37.chain added
132f0654dbb416_NCBI36_to_GRCh38.chain added
132f067e87fa98_GRCm38_to_NCBIM36.chain added
132f064b8233e0_GRCm38_to_NCBIM37.chain added
132f06268e553_NCBIM36_to_GRCm38.chain added
132f0676b32a89_NCBIM37_to_GRCm38.chain added
132f067e782e5f_1000G_omni2.5.b37.vcf.gz added
132f065cbe989e_1000G_omni2.5.b37.vcf.gz.tbi added
132f064a576a4d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
132f06cb81147_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
132f065f9a74e4_1000G_omni2.5.hg38.vcf.gz added
132f0670a748ed_1000G_omni2.5.hg38.vcf.gz.tbi added
132f067af6bf04_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
132f061eac3de4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
132f0664798019_af-only-gnomad.raw.sites.vcf added
132f0663ab4a34_af-only-gnomad.raw.sites.vcf.idx added
132f065fa0d3ef_Mutect2-exome-panel.vcf.idx added
132f062ecff18e_Mutect2-WGS-panel-b37.vcf added
132f062fed07ae_Mutect2-WGS-panel-b37.vcf.idx added
132f0646cddb45_small_exac_common_3.vcf added
132f062e7ede0_small_exac_common_3.vcf.idx added
132f064bb9f556_1000g_pon.hg38.vcf.gz added
132f062f8a9321_1000g_pon.hg38.vcf.gz.tbi added
132f06761694ba_af-only-gnomad.hg38.vcf.gz added
132f064fd1caa3_af-only-gnomad.hg38.vcf.gz.tbi added
132f065c31a850_small_exac_common_3.hg38.vcf.gz added
132f063707f80d_small_exac_common_3.hg38.vcf.gz.tbi added
132f066d5f308a_gencode.v41.annotation.gtf added
132f0614a41eee_gencode.v42.annotation.gtf added
132f061570c617_gencode.vM30.annotation.gtf added
132f061aad7dea_gencode.vM31.annotation.gtf added
132f061b67456e_gencode.v41.transcripts.fa added
132f066a4c7a2d_gencode.v41.transcripts.fa.fai added
132f0619357882_gencode.v42.transcripts.fa added
132f0666e9794e_gencode.v42.transcripts.fa.fai added
132f066cb55f81_gencode.vM30.pc_transcripts.fa added
132f06fe8a30c_gencode.vM30.pc_transcripts.fa.fai added
132f066561a7ad_gencode.vM31.pc_transcripts.fa added
132f064973f81f_gencode.vM31.pc_transcripts.fa.fai added
132f065a400d59_GRCh38.primary_assembly.genome.fa.1.ht2 added
132f067219b8f5_GRCh38.primary_assembly.genome.fa.2.ht2 added
132f06290e6d03_GRCh38.primary_assembly.genome.fa.3.ht2 added
132f064ae75646_GRCh38.primary_assembly.genome.fa.4.ht2 added
132f066d1077f9_GRCh38.primary_assembly.genome.fa.5.ht2 added
132f0647baaae7_GRCh38.primary_assembly.genome.fa.6.ht2 added
132f062f60d65f_GRCh38.primary_assembly.genome.fa.7.ht2 added
132f0650bbc22d_GRCh38.primary_assembly.genome.fa.8.ht2 added
132f06275b7ed7_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
132f065e30c7ee_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
132f06a8c9db_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
132f066e295a1c_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
132f066118b5ce_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
132f064c62bf31_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
132f061db3ed3e_GRCh38_full_analysis_set_plus_decoy_hla.fa added
132f06572f4a89_GRCh38.primary_assembly.genome.fa.fai added
132f061c3489d4_GRCh38.primary_assembly.genome.fa.amb added
132f0679e5958e_GRCh38.primary_assembly.genome.fa.ann added
132f06e374296_GRCh38.primary_assembly.genome.fa.bwt added
132f06993ba5e_GRCh38.primary_assembly.genome.fa.pac added
132f06e89b47c_GRCh38.primary_assembly.genome.fa.sa added
132f0623a808ad_GRCh38.primary_assembly.genome.fa added
132f0624413849_hs37d5.fa.fai added
132f0629f0f9ea_hs37d5.fa.amb added
132f06df482db_hs37d5.fa.ann added
132f063d76b0cb_hs37d5.fa.bwt added
132f0610da7339_hs37d5.fa.pac added
132f067aa9e25c_hs37d5.fa.sa added
132f064d5f53d7_hs37d5.fa added
132f06763c1ae6_complete_ref_lens.bin added
132f06441dda7b_ctable.bin added
132f06279f6130_ctg_offsets.bin added
132f066855d3db_duplicate_clusters.tsv added
132f066d2c477f_info.json added
132f067286b777_mphf.bin added
132f0655664bd4_pos.bin added
132f0634e6f266_pre_indexing.log added
132f0621e78dd6_rank.bin added
132f0626220e01_ref_indexing.log added
132f065c42713d_refAccumLengths.bin added
132f061855c4_reflengths.bin added
132f0626cad7dc_refseq.bin added
132f064a6bcb5a_seq.bin added
132f0661310b93_versionInfo.json added
132f06732d970d_salmon_index added
132f06681fb898_chrLength.txt added
132f063860561c_chrName.txt added
132f06f6220e1_chrNameLength.txt added
132f0662054e26_chrStart.txt added
132f06469798b2_exonGeTrInfo.tab added
132f0618f5db40_exonInfo.tab added
132f06708f02a2_geneInfo.tab added
132f066a3fa160_Genome added
132f063d371389_genomeParameters.txt added
132f061a7ffc8d_Log.out added
132f067834243b_SA added
132f067aadc454_SAindex added
132f062b5a6fc6_sjdbInfo.txt added
132f0672de0697_sjdbList.fromGTF.out.tab added
132f06480d182c_sjdbList.out.tab added
132f0621968aac_transcriptInfo.tab added
132f0636fbe112_GRCh38.GENCODE.v42_100 added
132f066fac795c_knownGene_hg38.sql added
132f069ec5e88_knownGene_hg38.txt added
132f0624282891_refGene_hg38.sql added
132f06623330d3_refGene_hg38.txt added
132f065f52aa5c_knownGene_mm39.sql added
132f06590f1af8_knownGene_mm39.txt added
132f0641abeaa_refGene_mm39.sql added
132f06574b85e_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/RtmpOUUTKE/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 
 18.301   1.179  19.802