##############################################################################
##############################################################################
###
### 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.10.0’
* 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 5.804  0.224   6.031
getCloudData  2.779  0.194   5.526
* 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.10.0’
** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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...
8996d5fbc2930_GRCh38.primary_assembly.genome.fa.1.bt2 added
8996d5944a680_GRCh38.primary_assembly.genome.fa.2.bt2 added
8996dcf08e16_GRCh38.primary_assembly.genome.fa.3.bt2 added
8996d7924a0c_GRCh38.primary_assembly.genome.fa.4.bt2 added
8996d2330d1cd_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
8996d4d288a63_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
8996d503f5b66_outfile.txt added
8996d43a9b372_GRCh37_to_GRCh38.chain added
8996d1188e7b0_GRCh37_to_NCBI34.chain added
8996d59fbac5d_GRCh37_to_NCBI35.chain added
8996d19472658_GRCh37_to_NCBI36.chain added
8996d3e645136_GRCh38_to_GRCh37.chain added
8996d398da637_GRCh38_to_NCBI34.chain added
8996d3831bc05_GRCh38_to_NCBI35.chain added
8996ddf34ad6_GRCh38_to_NCBI36.chain added
8996d5a9b6888_NCBI34_to_GRCh37.chain added
8996d37665992_NCBI34_to_GRCh38.chain added
8996d10fde898_NCBI35_to_GRCh37.chain added
8996d5e6cbe2_NCBI35_to_GRCh38.chain added
8996d4dc5e8a4_NCBI36_to_GRCh37.chain added
8996d4dbebdea_NCBI36_to_GRCh38.chain added
8996d30f1376c_GRCm38_to_NCBIM36.chain added
8996d5a2dad48_GRCm38_to_NCBIM37.chain added
8996d7d530d28_NCBIM36_to_GRCm38.chain added
8996d46d89075_NCBIM37_to_GRCm38.chain added
8996d6900a686_1000G_omni2.5.b37.vcf.gz added
8996d54b3325c_1000G_omni2.5.b37.vcf.gz.tbi added
8996d5076049d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
8996d1090c60c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
8996d4c9527da_1000G_omni2.5.hg38.vcf.gz added
8996d5c0c86aa_1000G_omni2.5.hg38.vcf.gz.tbi added
8996d704cef3c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
8996d25d9ce5a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
8996d68fd14c0_af-only-gnomad.raw.sites.vcf added
8996d77df3948_af-only-gnomad.raw.sites.vcf.idx added
8996d490aa027_Mutect2-exome-panel.vcf.idx added
8996d36259f23_Mutect2-WGS-panel-b37.vcf added
8996d481e94ae_Mutect2-WGS-panel-b37.vcf.idx added
8996dcb4539a_small_exac_common_3.vcf added
8996d47ae86d3_small_exac_common_3.vcf.idx added
8996d221a410b_1000g_pon.hg38.vcf.gz added
8996d25fb79f2_1000g_pon.hg38.vcf.gz.tbi added
8996d612d809_af-only-gnomad.hg38.vcf.gz added
8996d5ba7e742_af-only-gnomad.hg38.vcf.gz.tbi added
8996d5e2d35f7_small_exac_common_3.hg38.vcf.gz added
8996d140622e0_small_exac_common_3.hg38.vcf.gz.tbi added
8996d36434fcb_gencode.v41.annotation.gtf added
8996d15938f89_gencode.v42.annotation.gtf added
8996d25040b78_gencode.vM30.annotation.gtf added
8996d3c2a1bad_gencode.vM31.annotation.gtf added
8996d6359782d_gencode.v41.transcripts.fa added
8996d72c2c963_gencode.v41.transcripts.fa.fai added
8996d6d1b5319_gencode.v42.transcripts.fa added
8996d3d872575_gencode.v42.transcripts.fa.fai added
8996d7015d68b_gencode.vM30.pc_transcripts.fa added
8996d33f3e38e_gencode.vM30.pc_transcripts.fa.fai added
8996d2687cbfb_gencode.vM31.pc_transcripts.fa added
8996d44c908e7_gencode.vM31.pc_transcripts.fa.fai added
8996d469e82b_GRCh38.primary_assembly.genome.fa.1.ht2 added
8996d37189207_GRCh38.primary_assembly.genome.fa.2.ht2 added
8996d115e30c1_GRCh38.primary_assembly.genome.fa.3.ht2 added
8996d60766ed5_GRCh38.primary_assembly.genome.fa.4.ht2 added
8996d27658144_GRCh38.primary_assembly.genome.fa.5.ht2 added
8996d3737ff1c_GRCh38.primary_assembly.genome.fa.6.ht2 added
8996d49738396_GRCh38.primary_assembly.genome.fa.7.ht2 added
8996d1f44ba8c_GRCh38.primary_assembly.genome.fa.8.ht2 added
8996d429f43_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
8996d7f9922b9_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
8996d67634f3b_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
8996dcf6f2dd_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
8996d4747a98d_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
8996d97d9046_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
8996d32f26ccf_GRCh38_full_analysis_set_plus_decoy_hla.fa added
8996d4d5a8196_GRCh38.primary_assembly.genome.fa.fai added
8996d65257789_GRCh38.primary_assembly.genome.fa.amb added
8996d111fa2c6_GRCh38.primary_assembly.genome.fa.ann added
8996d6160a476_GRCh38.primary_assembly.genome.fa.bwt added
8996d1b68c754_GRCh38.primary_assembly.genome.fa.pac added
8996d26b3324f_GRCh38.primary_assembly.genome.fa.sa added
8996d664afef_GRCh38.primary_assembly.genome.fa added
8996d5792e301_hs37d5.fa.fai added
8996da0caa7c_hs37d5.fa.amb added
8996d79277952_hs37d5.fa.ann added
8996d44ae361a_hs37d5.fa.bwt added
8996d4793cff1_hs37d5.fa.pac added
8996d693d4fdd_hs37d5.fa.sa added
8996d78a219a8_hs37d5.fa added
8996d6e1b9bed_complete_ref_lens.bin added
8996d2e0658c5_ctable.bin added
8996d7d0c01d4_ctg_offsets.bin added
8996d25342df4_duplicate_clusters.tsv added
8996d3f648986_info.json added
8996d5d8270a9_mphf.bin added
8996d4c99af38_pos.bin added
8996d769c88a2_pre_indexing.log added
8996d26f5f43f_rank.bin added
8996d6bde69c5_ref_indexing.log added
8996d76df27e6_refAccumLengths.bin added
8996d268f16f9_reflengths.bin added
8996d5341b900_refseq.bin added
8996d3d61ac3_seq.bin added
8996d6dd6c086_versionInfo.json added
8996d5cbf4946_salmon_index added
8996d36c88793_chrLength.txt added
8996d3b31421c_chrName.txt added
8996d41e4c0cf_chrNameLength.txt added
8996d47e82a59_chrStart.txt added
8996d1c91e693_exonGeTrInfo.tab added
8996d5d4d8823_exonInfo.tab added
8996d6e9b5ca9_geneInfo.tab added
8996d22f69682_Genome added
8996d34e06b24_genomeParameters.txt added
8996d78a80725_Log.out added
8996d1c1e0fd4_SA added
8996d798ea13e_SAindex added
8996d403bd717_sjdbInfo.txt added
8996d55b5fb1_sjdbList.fromGTF.out.tab added
8996d7230bae7_sjdbList.out.tab added
8996d2e577304_transcriptInfo.tab added
8996d3361b876_GRCh38.GENCODE.v42_100 added
8996d6f3cbcbb_knownGene_hg38.sql added
8996d538ba0f8_knownGene_hg38.txt added
8996d72c641fd_refGene_hg38.sql added
8996d4cbf2d64_refGene_hg38.txt added
8996d20255031_knownGene_mm39.sql added
8996d6962ca9f_knownGene_mm39.txt added
8996d73b521a4_refGene_mm39.sql added
8996dc03b9f6_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/RtmpaeZazC/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 
 18.314   1.142  20.134