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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: 2026-05-22 09:06:32 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 6.006  0.264   6.276
* 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...
e23092f5ecc7a_GRCh38.primary_assembly.genome.fa.1.bt2 added
e230925f4104b_GRCh38.primary_assembly.genome.fa.2.bt2 added
e23094b2126b9_GRCh38.primary_assembly.genome.fa.3.bt2 added
e23097f3aef50_GRCh38.primary_assembly.genome.fa.4.bt2 added
e23092ad3c271_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
e2309278f5986_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
e2309685795b6_outfile.txt added
e23094849a1c7_GRCh37_to_GRCh38.chain added
e23091f4fed30_GRCh37_to_NCBI34.chain added
e230944094a0a_GRCh37_to_NCBI35.chain added
e230919bdbeba_GRCh37_to_NCBI36.chain added
e23091f490fc4_GRCh38_to_GRCh37.chain added
e230944433673_GRCh38_to_NCBI34.chain added
e2309ad29943_GRCh38_to_NCBI35.chain added
e23092ca575b1_GRCh38_to_NCBI36.chain added
e230946377d6a_NCBI34_to_GRCh37.chain added
e230964089a7e_NCBI34_to_GRCh38.chain added
e2309487fb545_NCBI35_to_GRCh37.chain added
e230943477166_NCBI35_to_GRCh38.chain added
e2309fe16267_NCBI36_to_GRCh37.chain added
e230918c5d368_NCBI36_to_GRCh38.chain added
e23097c84dcea_GRCm38_to_NCBIM36.chain added
e23096310e4c4_GRCm38_to_NCBIM37.chain added
e23097bc448d8_NCBIM36_to_GRCm38.chain added
e2309548b893f_NCBIM37_to_GRCm38.chain added
e230924f29397_1000G_omni2.5.b37.vcf.gz added
e230958196c50_1000G_omni2.5.b37.vcf.gz.tbi added
e230930250a8c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
e23097d8d28cc_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
e2309300f010b_1000G_omni2.5.hg38.vcf.gz added
e2309761445fd_1000G_omni2.5.hg38.vcf.gz.tbi added
e23092cebf547_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
e230956031156_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
e230941356cb7_af-only-gnomad.raw.sites.vcf added
e23092c26e497_af-only-gnomad.raw.sites.vcf.idx added
e2309d6d3c7_Mutect2-exome-panel.vcf.idx added
e230968c4c63d_Mutect2-WGS-panel-b37.vcf added
e2309147e7a4d_Mutect2-WGS-panel-b37.vcf.idx added
e23094920758f_small_exac_common_3.vcf added
e2309814b36d_small_exac_common_3.vcf.idx added
e23095887c457_1000g_pon.hg38.vcf.gz added
e230962de3449_1000g_pon.hg38.vcf.gz.tbi added
e2309275dc331_af-only-gnomad.hg38.vcf.gz added
e23091ccafacb_af-only-gnomad.hg38.vcf.gz.tbi added
e23096db0cd8c_small_exac_common_3.hg38.vcf.gz added
e2309540338e3_small_exac_common_3.hg38.vcf.gz.tbi added
e230963027835_gencode.v41.annotation.gtf added
e230951b9680b_gencode.v42.annotation.gtf added
e23091c82ee28_gencode.vM30.annotation.gtf added
e23092649e99c_gencode.vM31.annotation.gtf added
e2309619aca72_gencode.v41.transcripts.fa added
e23093548c190_gencode.v41.transcripts.fa.fai added
e230922cec686_gencode.v42.transcripts.fa added
e230944abaf37_gencode.v42.transcripts.fa.fai added
e2309310d0a69_gencode.vM30.pc_transcripts.fa added
e2309775a4fc5_gencode.vM30.pc_transcripts.fa.fai added
e2309699e42ce_gencode.vM31.pc_transcripts.fa added
e230992676b9_gencode.vM31.pc_transcripts.fa.fai added
e2309277f5a51_GRCh38.primary_assembly.genome.fa.1.ht2 added
e2309672b6b9b_GRCh38.primary_assembly.genome.fa.2.ht2 added
e2309393577c4_GRCh38.primary_assembly.genome.fa.3.ht2 added
e23091d93a04e_GRCh38.primary_assembly.genome.fa.4.ht2 added
e2309141760e2_GRCh38.primary_assembly.genome.fa.5.ht2 added
e2309f38891b_GRCh38.primary_assembly.genome.fa.6.ht2 added
e23095ec90d05_GRCh38.primary_assembly.genome.fa.7.ht2 added
e2309403e4579_GRCh38.primary_assembly.genome.fa.8.ht2 added
e2309100f5ce2_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
e2309478dd343_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
e230954bcbfc6_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
e2309592fd271_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
e23094fa286b0_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
e23092d44841e_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
e23093c0e06ba_GRCh38_full_analysis_set_plus_decoy_hla.fa added
e2309770049e2_GRCh38.primary_assembly.genome.fa.fai added
e23094a0f7ee9_GRCh38.primary_assembly.genome.fa.amb added
e230929bed447_GRCh38.primary_assembly.genome.fa.ann added
e23094b0382c5_GRCh38.primary_assembly.genome.fa.bwt added
e23092d11f71e_GRCh38.primary_assembly.genome.fa.pac added
e23097b783c52_GRCh38.primary_assembly.genome.fa.sa added
e2309678670ed_GRCh38.primary_assembly.genome.fa added
e2309535be0ba_hs37d5.fa.fai added
e23095d1306c4_hs37d5.fa.amb added
e23091ccf327d_hs37d5.fa.ann added
e2309762aa740_hs37d5.fa.bwt added
e230921beb5fb_hs37d5.fa.pac added
e23094ddc3ce6_hs37d5.fa.sa added
e23096d84f705_hs37d5.fa added
e2309b5cf8ca_complete_ref_lens.bin added
e23095702b39f_ctable.bin added
e230915045156_ctg_offsets.bin added
e230972886465_duplicate_clusters.tsv added
e230910382b64_info.json added
e23093297f1a5_mphf.bin added
e230969fc547_pos.bin added
e23091f70b47f_pre_indexing.log added
e23091160feaa_rank.bin added
e230946de0ac0_ref_indexing.log added
e23092f801161_refAccumLengths.bin added
e230958eed1ed_reflengths.bin added
e23091b9aca86_refseq.bin added
e23098afe3d3_seq.bin added
e23092891589e_versionInfo.json added
e230948df4ea4_salmon_index added
e230944bdea8d_chrLength.txt added
e23091f91a280_chrName.txt added
e230912eecd8d_chrNameLength.txt added
e23096e7cbed4_chrStart.txt added
e23096a952545_exonGeTrInfo.tab added
e23094000c4ac_exonInfo.tab added
e230969f4fb26_geneInfo.tab added
e2309521b9632_Genome added
e2309135ca566_genomeParameters.txt added
e2309470801eb_Log.out added
e23096eeac8af_SA added
e23099874ca7_SAindex added
e230968c6b7e6_sjdbInfo.txt added
e23093cc70596_sjdbList.fromGTF.out.tab added
e2309770c43ac_sjdbList.out.tab added
e23097423b0b0_transcriptInfo.tab added
e230913c9b935_GRCh38.GENCODE.v42_100 added
e2309c109503_knownGene_hg38.sql added
e230966ac1515_knownGene_hg38.txt added
e23092401e499_refGene_hg38.sql added
e23093ea886a8_refGene_hg38.txt added
e23096d4bda5c_knownGene_mm39.sql added
e230943729918_knownGene_mm39.txt added
e230950098552_refGene_mm39.sql added
e23093429e51c_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/Rtmpha3XZ3/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 
 18.622   1.043  20.100