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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 Under development (unstable) (2025-12-22 r89219)
* 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 ‘1.11.0’
* 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 6.128  0.361   6.492
* 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 Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences"
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...
afe0e33b9ad0_GRCh38.primary_assembly.genome.fa.1.bt2 added
afe0e50e79189_GRCh38.primary_assembly.genome.fa.2.bt2 added
afe0e61b26df4_GRCh38.primary_assembly.genome.fa.3.bt2 added
afe0e4be7727_GRCh38.primary_assembly.genome.fa.4.bt2 added
afe0e6d89b691_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
afe0ea822497_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
afe0e10ef10cf_outfile.txt added
afe0e52e0dbeb_GRCh37_to_GRCh38.chain added
afe0e27c7c6d2_GRCh37_to_NCBI34.chain added
afe0e5bbe8443_GRCh37_to_NCBI35.chain added
afe0e19dea90c_GRCh37_to_NCBI36.chain added
afe0e9c4ebbf_GRCh38_to_GRCh37.chain added
afe0e1fbbcc96_GRCh38_to_NCBI34.chain added
afe0e15dc8c75_GRCh38_to_NCBI35.chain added
afe0e3a758a36_GRCh38_to_NCBI36.chain added
afe0e57b7303_NCBI34_to_GRCh37.chain added
afe0e26e8ba1_NCBI34_to_GRCh38.chain added
afe0e5f23b4c8_NCBI35_to_GRCh37.chain added
afe0e6711cf58_NCBI35_to_GRCh38.chain added
afe0e7a3f4126_NCBI36_to_GRCh37.chain added
afe0e2124ed1a_NCBI36_to_GRCh38.chain added
afe0e553e4423_GRCm38_to_NCBIM36.chain added
afe0e372561d1_GRCm38_to_NCBIM37.chain added
afe0e37652ad3_NCBIM36_to_GRCm38.chain added
afe0e3a63b710_NCBIM37_to_GRCm38.chain added
afe0e6515c85_1000G_omni2.5.b37.vcf.gz added
afe0e33ebdf29_1000G_omni2.5.b37.vcf.gz.tbi added
afe0e67499d2c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
afe0e59b8c30f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
afe0e4144efd0_1000G_omni2.5.hg38.vcf.gz added
afe0e792a5c93_1000G_omni2.5.hg38.vcf.gz.tbi added
afe0e5cf45ddf_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
afe0e122c8159_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
afe0e5adcca87_af-only-gnomad.raw.sites.vcf added
afe0e61b2d507_af-only-gnomad.raw.sites.vcf.idx added
afe0e7fb637ea_Mutect2-exome-panel.vcf.idx added
afe0e655eef1f_Mutect2-WGS-panel-b37.vcf added
afe0e72a1e5d6_Mutect2-WGS-panel-b37.vcf.idx added
afe0e529713d5_small_exac_common_3.vcf added
afe0ed26b5f1_small_exac_common_3.vcf.idx added
afe0e4e606a1a_1000g_pon.hg38.vcf.gz added
afe0e6c75bce1_1000g_pon.hg38.vcf.gz.tbi added
afe0e16eba1b0_af-only-gnomad.hg38.vcf.gz added
afe0e6e1c36b0_af-only-gnomad.hg38.vcf.gz.tbi added
afe0e2524956_small_exac_common_3.hg38.vcf.gz added
afe0e51612be7_small_exac_common_3.hg38.vcf.gz.tbi added
afe0e7397a9b4_gencode.v41.annotation.gtf added
afe0e4c0d4f7_gencode.v42.annotation.gtf added
afe0e3084e0af_gencode.vM30.annotation.gtf added
afe0e5aa9790c_gencode.vM31.annotation.gtf added
afe0e7f00161e_gencode.v41.transcripts.fa added
afe0e51a9cdc9_gencode.v41.transcripts.fa.fai added
afe0e2fe7bd2f_gencode.v42.transcripts.fa added
afe0e362577ef_gencode.v42.transcripts.fa.fai added
afe0e90ef89d_gencode.vM30.pc_transcripts.fa added
afe0e6a4b743f_gencode.vM30.pc_transcripts.fa.fai added
afe0e3c76d475_gencode.vM31.pc_transcripts.fa added
afe0e3cfad7c6_gencode.vM31.pc_transcripts.fa.fai added
afe0e5195116b_GRCh38.primary_assembly.genome.fa.1.ht2 added
afe0e162f9784_GRCh38.primary_assembly.genome.fa.2.ht2 added
afe0e7e3fc796_GRCh38.primary_assembly.genome.fa.3.ht2 added
afe0e4abf6dff_GRCh38.primary_assembly.genome.fa.4.ht2 added
afe0e7323f563_GRCh38.primary_assembly.genome.fa.5.ht2 added
afe0e106c48ef_GRCh38.primary_assembly.genome.fa.6.ht2 added
afe0e259c3886_GRCh38.primary_assembly.genome.fa.7.ht2 added
afe0e54d6ca6a_GRCh38.primary_assembly.genome.fa.8.ht2 added
afe0e102280d9_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
afe0eafb27a5_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
afe0e4778b041_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
afe0e62b994ae_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
afe0e1821dd97_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
afe0e15d91a5b_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
afe0e4f2f5190_GRCh38_full_analysis_set_plus_decoy_hla.fa added
afe0e2f0d7f47_GRCh38.primary_assembly.genome.fa.fai added
afe0e3f5510b_GRCh38.primary_assembly.genome.fa.amb added
afe0e51819ae6_GRCh38.primary_assembly.genome.fa.ann added
afe0e6eab2e_GRCh38.primary_assembly.genome.fa.bwt added
afe0e778cfabf_GRCh38.primary_assembly.genome.fa.pac added
afe0e56426fde_GRCh38.primary_assembly.genome.fa.sa added
afe0e30f38bdd_GRCh38.primary_assembly.genome.fa added
afe0e523673cb_hs37d5.fa.fai added
afe0e554285fc_hs37d5.fa.amb added
afe0e29d59a7_hs37d5.fa.ann added
afe0e21e30fa_hs37d5.fa.bwt added
afe0eb67fdeb_hs37d5.fa.pac added
afe0ebac5244_hs37d5.fa.sa added
afe0e6c69a53a_hs37d5.fa added
afe0e47ded260_complete_ref_lens.bin added
afe0e48a72a0a_ctable.bin added
afe0e3dfeb6a5_ctg_offsets.bin added
afe0e5e0e69e4_duplicate_clusters.tsv added
afe0e46e6f1a1_info.json added
afe0e8be24a4_mphf.bin added
afe0e51325f48_pos.bin added
afe0e57533a90_pre_indexing.log added
afe0e2e5a5d2b_rank.bin added
afe0e260929b2_ref_indexing.log added
afe0e6775bb6a_refAccumLengths.bin added
afe0e395584d0_reflengths.bin added
afe0e6d81d9f3_refseq.bin added
afe0e4a2f5018_seq.bin added
afe0e51776267_versionInfo.json added
afe0e35af44e_salmon_index added
afe0e195ea1a8_chrLength.txt added
afe0e84e1af_chrName.txt added
afe0e750455a_chrNameLength.txt added
afe0e6ae03c8f_chrStart.txt added
afe0ef38cdd_exonGeTrInfo.tab added
afe0e7edd4019_exonInfo.tab added
afe0e4122ac6d_geneInfo.tab added
afe0e31e718bb_Genome added
afe0e5113b3e5_genomeParameters.txt added
afe0e16653269_Log.out added
afe0e34847262_SA added
afe0e5331e4df_SAindex added
afe0e21cd3054_sjdbInfo.txt added
afe0e4030c4a6_sjdbList.fromGTF.out.tab added
afe0e3f9b8a19_sjdbList.out.tab added
afe0e69ac02b5_transcriptInfo.tab added
afe0e8d7eeb0_GRCh38.GENCODE.v42_100 added
afe0e7d9a40bf_knownGene_hg38.sql added
afe0e47ba6c99_knownGene_hg38.txt added
afe0e4fbee051_refGene_hg38.sql added
afe0e6586563_refGene_hg38.txt added
afe0e18eccbe1_knownGene_mm39.sql added
afe0e27121ae2_knownGene_mm39.txt added
afe0e34b2c28e_refGene_mm39.sql added
afe0e3ef5f594_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/RtmpHasasF/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 
 18.506   1.352  20.398