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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.9.0’
* 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 6.091  0.373   6.468
* 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-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ReUseData
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.9.0’
** 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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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...
1b7aa57afc60e_GRCh38.primary_assembly.genome.fa.1.bt2 added
1b7aa26de399e_GRCh38.primary_assembly.genome.fa.2.bt2 added
1b7aa31a126c7_GRCh38.primary_assembly.genome.fa.3.bt2 added
1b7aa2909aaf8_GRCh38.primary_assembly.genome.fa.4.bt2 added
1b7aa3b3d663e_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1b7aa22484de4_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1b7aa785a7635_outfile.txt added
1b7aa7c69c95e_GRCh37_to_GRCh38.chain added
1b7aa1a8bed42_GRCh37_to_NCBI34.chain added
1b7aa3a3ebb75_GRCh37_to_NCBI35.chain added
1b7aa20f39446_GRCh37_to_NCBI36.chain added
1b7aa74688c98_GRCh38_to_GRCh37.chain added
1b7aa6f0fa633_GRCh38_to_NCBI34.chain added
1b7aa53505025_GRCh38_to_NCBI35.chain added
1b7aa5f35372d_GRCh38_to_NCBI36.chain added
1b7aa6be63247_NCBI34_to_GRCh37.chain added
1b7aa521a7281_NCBI34_to_GRCh38.chain added
1b7aa23a7e0b9_NCBI35_to_GRCh37.chain added
1b7aa69df47e8_NCBI35_to_GRCh38.chain added
1b7aa3c4690d0_NCBI36_to_GRCh37.chain added
1b7aaabfb0e3_NCBI36_to_GRCh38.chain added
1b7aa7a8617cd_GRCm38_to_NCBIM36.chain added
1b7aa4ca8cc8_GRCm38_to_NCBIM37.chain added
1b7aa72e3de58_NCBIM36_to_GRCm38.chain added
1b7aa44063ce4_NCBIM37_to_GRCm38.chain added
1b7aa274dedcc_1000G_omni2.5.b37.vcf.gz added
1b7aa60001ad1_1000G_omni2.5.b37.vcf.gz.tbi added
1b7aa94f04ec_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1b7aa4e1df01f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1b7aa61416843_1000G_omni2.5.hg38.vcf.gz added
1b7aa684104bf_1000G_omni2.5.hg38.vcf.gz.tbi added
1b7aa25cdb62e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1b7aa81fa1e1_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1b7aa19e22b86_af-only-gnomad.raw.sites.vcf added
1b7aa4ed76126_af-only-gnomad.raw.sites.vcf.idx added
1b7aa435d081f_Mutect2-exome-panel.vcf.idx added
1b7aa3c2a796b_Mutect2-WGS-panel-b37.vcf added
1b7aa4731d75b_Mutect2-WGS-panel-b37.vcf.idx added
1b7aa3fc6d17d_small_exac_common_3.vcf added
1b7aa56b666ad_small_exac_common_3.vcf.idx added
1b7aa17092d0_1000g_pon.hg38.vcf.gz added
1b7aa60ba65c4_1000g_pon.hg38.vcf.gz.tbi added
1b7aa4b1ef345_af-only-gnomad.hg38.vcf.gz added
1b7aa70803903_af-only-gnomad.hg38.vcf.gz.tbi added
1b7aa340ab5e9_small_exac_common_3.hg38.vcf.gz added
1b7aa2a542a73_small_exac_common_3.hg38.vcf.gz.tbi added
1b7aa5c666b4b_gencode.v41.annotation.gtf added
1b7aa625286a_gencode.v42.annotation.gtf added
1b7aa4dfc0b2c_gencode.vM30.annotation.gtf added
1b7aa4645b333_gencode.vM31.annotation.gtf added
1b7aa426bb93b_gencode.v41.transcripts.fa added
1b7aa58bbbc0f_gencode.v41.transcripts.fa.fai added
1b7aa40cbcb00_gencode.v42.transcripts.fa added
1b7aa47364603_gencode.v42.transcripts.fa.fai added
1b7aa4b9f9a68_gencode.vM30.pc_transcripts.fa added
1b7aa4d207e4_gencode.vM30.pc_transcripts.fa.fai added
1b7aa6e8433d0_gencode.vM31.pc_transcripts.fa added
1b7aa2b9fb539_gencode.vM31.pc_transcripts.fa.fai added
1b7aae210cd1_GRCh38.primary_assembly.genome.fa.1.ht2 added
1b7aa3ca223ef_GRCh38.primary_assembly.genome.fa.2.ht2 added
1b7aace11d7c_GRCh38.primary_assembly.genome.fa.3.ht2 added
1b7aa76621190_GRCh38.primary_assembly.genome.fa.4.ht2 added
1b7aa626fda1d_GRCh38.primary_assembly.genome.fa.5.ht2 added
1b7aa1500bf5e_GRCh38.primary_assembly.genome.fa.6.ht2 added
1b7aa10443d16_GRCh38.primary_assembly.genome.fa.7.ht2 added
1b7aa31473b43_GRCh38.primary_assembly.genome.fa.8.ht2 added
1b7aa585dc77d_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1b7aa4c6eb681_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1b7aa7879129f_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1b7aa182498fb_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1b7aa23251d2e_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1b7aa79e9a56f_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1b7aa78defebf_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1b7aa6e441074_GRCh38.primary_assembly.genome.fa.fai added
1b7aa6a69de73_GRCh38.primary_assembly.genome.fa.amb added
1b7aa2ce9b4a8_GRCh38.primary_assembly.genome.fa.ann added
1b7aa18983ae7_GRCh38.primary_assembly.genome.fa.bwt added
1b7aa46d049be_GRCh38.primary_assembly.genome.fa.pac added
1b7aa330edd13_GRCh38.primary_assembly.genome.fa.sa added
1b7aa66944613_GRCh38.primary_assembly.genome.fa added
1b7aad15fcf1_hs37d5.fa.fai added
1b7aa757a964e_hs37d5.fa.amb added
1b7aa3f500222_hs37d5.fa.ann added
1b7aa4de1c7f2_hs37d5.fa.bwt added
1b7aa3cb0dc51_hs37d5.fa.pac added
1b7aaaef9c8a_hs37d5.fa.sa added
1b7aa52b3cfd6_hs37d5.fa added
1b7aa2b351021_complete_ref_lens.bin added
1b7aa368f51c3_ctable.bin added
1b7aa60d4dca7_ctg_offsets.bin added
1b7aa67d73411_duplicate_clusters.tsv added
1b7aa43706f40_info.json added
1b7aa5736ee37_mphf.bin added
1b7aa4a470e2e_pos.bin added
1b7aa58712e9e_pre_indexing.log added
1b7aa677b2b4e_rank.bin added
1b7aa7b8e4972_ref_indexing.log added
1b7aa30cef61b_refAccumLengths.bin added
1b7aa33e9e1cf_reflengths.bin added
1b7aa74075c11_refseq.bin added
1b7aa48f38f16_seq.bin added
1b7aa570efefe_versionInfo.json added
1b7aa6df10180_salmon_index added
1b7aa41d28dd5_chrLength.txt added
1b7aa45530f72_chrName.txt added
1b7aa585adff3_chrNameLength.txt added
1b7aa6ebc427e_chrStart.txt added
1b7aa5deb4a59_exonGeTrInfo.tab added
1b7aa1f2b29b1_exonInfo.tab added
1b7aa21cb1f91_geneInfo.tab added
1b7aa447f906c_Genome added
1b7aa2c4126a3_genomeParameters.txt added
1b7aa1745b5df_Log.out added
1b7aa3cf928e_SA added
1b7aa7a22ee95_SAindex added
1b7aa53f69230_sjdbInfo.txt added
1b7aaebf2f19_sjdbList.fromGTF.out.tab added
1b7aa4cd6be6b_sjdbList.out.tab added
1b7aa7f2ba252_transcriptInfo.tab added
1b7aa454e80dc_GRCh38.GENCODE.v42_100 added
1b7aa2dab9b13_knownGene_hg38.sql added
1b7aa6702d663_knownGene_hg38.txt added
1b7aa8bef01c_refGene_hg38.sql added
1b7aa4e2894a_refGene_hg38.txt added
1b7aa3149e491_knownGene_mm39.sql added
1b7aa61301eba_knownGene_mm39.txt added
1b7aa6c5db498_refGene_mm39.sql added
1b7aa2cd82e03_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/RtmpJZpdnj/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 0 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
> 
> 
> 
> proc.time()
   user  system elapsed 
 18.725   1.603  20.694