##############################################################################
##############################################################################
###
### 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 5.904  0.242   6.151
* 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...
3851ee5b8a166b_GRCh38.primary_assembly.genome.fa.1.bt2 added
3851ee57548ec1_GRCh38.primary_assembly.genome.fa.2.bt2 added
3851ee19764fee_GRCh38.primary_assembly.genome.fa.3.bt2 added
3851ee3fc6b803_GRCh38.primary_assembly.genome.fa.4.bt2 added
3851ee2590dda1_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3851ee546c2950_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3851ee49e7d30f_outfile.txt added
3851ee4fc2cb8c_GRCh37_to_GRCh38.chain added
3851ee64339215_GRCh37_to_NCBI34.chain added
3851ee15946451_GRCh37_to_NCBI35.chain added
3851ee4d638998_GRCh37_to_NCBI36.chain added
3851ee6fdd0ac7_GRCh38_to_GRCh37.chain added
3851ee54814a3_GRCh38_to_NCBI34.chain added
3851ee45eb5dc7_GRCh38_to_NCBI35.chain added
3851ee6a1e8089_GRCh38_to_NCBI36.chain added
3851ee4355d5e8_NCBI34_to_GRCh37.chain added
3851ee2f0578ab_NCBI34_to_GRCh38.chain added
3851ee47995465_NCBI35_to_GRCh37.chain added
3851ee6e854ead_NCBI35_to_GRCh38.chain added
3851ee32f0704d_NCBI36_to_GRCh37.chain added
3851ee4dd3b1a6_NCBI36_to_GRCh38.chain added
3851ee6a1d889a_GRCm38_to_NCBIM36.chain added
3851ee2e1d8246_GRCm38_to_NCBIM37.chain added
3851ee1aaca642_NCBIM36_to_GRCm38.chain added
3851ee18005e0e_NCBIM37_to_GRCm38.chain added
3851ee1d21eab8_1000G_omni2.5.b37.vcf.gz added
3851ee88a80fe_1000G_omni2.5.b37.vcf.gz.tbi added
3851ee30c7d3ae_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3851ee4e828fc4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3851ee282050a3_1000G_omni2.5.hg38.vcf.gz added
3851ee38ba3702_1000G_omni2.5.hg38.vcf.gz.tbi added
3851ee2a0ca62f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3851ee7f74df65_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3851ee523086f1_af-only-gnomad.raw.sites.vcf added
3851ee69d35e32_af-only-gnomad.raw.sites.vcf.idx added
3851ee2505bd06_Mutect2-exome-panel.vcf.idx added
3851ee269cb041_Mutect2-WGS-panel-b37.vcf added
3851ee33bb3141_Mutect2-WGS-panel-b37.vcf.idx added
3851ee74c88892_small_exac_common_3.vcf added
3851eead04256_small_exac_common_3.vcf.idx added
3851ee494f9592_1000g_pon.hg38.vcf.gz added
3851ee422c122b_1000g_pon.hg38.vcf.gz.tbi added
3851ee7aad4d1e_af-only-gnomad.hg38.vcf.gz added
3851ee4e97aa35_af-only-gnomad.hg38.vcf.gz.tbi added
3851ee8176ff2_small_exac_common_3.hg38.vcf.gz added
3851ee64cbcda7_small_exac_common_3.hg38.vcf.gz.tbi added
3851ee11ed801d_gencode.v41.annotation.gtf added
3851ee371ce89d_gencode.v42.annotation.gtf added
3851ee2c65220c_gencode.vM30.annotation.gtf added
3851ee72cecb_gencode.vM31.annotation.gtf added
3851ee6a0d58eb_gencode.v41.transcripts.fa added
3851ee7a38d3b2_gencode.v41.transcripts.fa.fai added
3851ee6a905765_gencode.v42.transcripts.fa added
3851ee182adb31_gencode.v42.transcripts.fa.fai added
3851ee14e579f4_gencode.vM30.pc_transcripts.fa added
3851ee290b573_gencode.vM30.pc_transcripts.fa.fai added
3851ee354cc5e9_gencode.vM31.pc_transcripts.fa added
3851ee1d6ffaf2_gencode.vM31.pc_transcripts.fa.fai added
3851ee33588921_GRCh38.primary_assembly.genome.fa.1.ht2 added
3851ee3cf55ad_GRCh38.primary_assembly.genome.fa.2.ht2 added
3851ee45904b96_GRCh38.primary_assembly.genome.fa.3.ht2 added
3851ee6c12c024_GRCh38.primary_assembly.genome.fa.4.ht2 added
3851ee2ddbfbdc_GRCh38.primary_assembly.genome.fa.5.ht2 added
3851ee45052afb_GRCh38.primary_assembly.genome.fa.6.ht2 added
3851ee3e434715_GRCh38.primary_assembly.genome.fa.7.ht2 added
3851ee17af5a0e_GRCh38.primary_assembly.genome.fa.8.ht2 added
3851ee6a0ae801_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3851ee64dff756_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3851ee4b6a8b4f_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3851ee5ed37094_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3851ee6fb039ac_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3851ee14ba20e1_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3851ee20ff82bf_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3851ee6a5d86ca_GRCh38.primary_assembly.genome.fa.fai added
3851ee6351cb17_GRCh38.primary_assembly.genome.fa.amb added
3851ee2916f2b1_GRCh38.primary_assembly.genome.fa.ann added
3851ee4f295471_GRCh38.primary_assembly.genome.fa.bwt added
3851ee753f4b34_GRCh38.primary_assembly.genome.fa.pac added
3851ee6033db4f_GRCh38.primary_assembly.genome.fa.sa added
3851ee7b8e767e_GRCh38.primary_assembly.genome.fa added
3851ee75b219ff_hs37d5.fa.fai added
3851ee4a41343a_hs37d5.fa.amb added
3851ee75c74a30_hs37d5.fa.ann added
3851ee60427164_hs37d5.fa.bwt added
3851ee626c0f6b_hs37d5.fa.pac added
3851eeaacc425_hs37d5.fa.sa added
3851ee62d326d7_hs37d5.fa added
3851ee17b8d554_complete_ref_lens.bin added
3851ee281cbf17_ctable.bin added
3851ee162baff9_ctg_offsets.bin added
3851ee1b882b01_duplicate_clusters.tsv added
3851ee6dad0aad_info.json added
3851ee23e701d_mphf.bin added
3851ee496426dd_pos.bin added
3851ee32b235a8_pre_indexing.log added
3851ee4081b732_rank.bin added
3851ee611380eb_ref_indexing.log added
3851ee1cbd1daa_refAccumLengths.bin added
3851ee2561ae88_reflengths.bin added
3851ee2c7e0c3a_refseq.bin added
3851ee7b908e3e_seq.bin added
3851ee1511e834_versionInfo.json added
3851ee41382d1b_salmon_index added
3851ee1c9010fd_chrLength.txt added
3851ee7f6f6eff_chrName.txt added
3851ee2489f832_chrNameLength.txt added
3851ee45a703ae_chrStart.txt added
3851ee4e98c370_exonGeTrInfo.tab added
3851ee19c94367_exonInfo.tab added
3851ee25dadefd_geneInfo.tab added
3851ee4a2739ee_Genome added
3851eef7b5d66_genomeParameters.txt added
3851ee701c1337_Log.out added
3851ee3fee841f_SA added
3851ee6fbdcecb_SAindex added
3851ee528822a2_sjdbInfo.txt added
3851ee4a9b4844_sjdbList.fromGTF.out.tab added
3851ee5290f5a2_sjdbList.out.tab added
3851ee6a40f7f6_transcriptInfo.tab added
3851ee72b8075b_GRCh38.GENCODE.v42_100 added
3851ee68bca59b_knownGene_hg38.sql added
3851ee5c922f7_knownGene_hg38.txt added
3851ee60651209_refGene_hg38.sql added
3851ee6afb15b8_refGene_hg38.txt added
3851ee4f2d49d4_knownGene_mm39.sql added
3851ee131747b1_knownGene_mm39.txt added
3851ee2b7cccea_refGene_mm39.sql added
3851ee3040cabf_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/RtmpQJJVHA/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 
 18.320   1.259  20.197