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


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 6.015  0.225   6.244
* 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
###
##############################################################################
##############################################################################


* 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 4.5.1 Patched (2025-08-23 r88802) -- "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...
30ce5e3839f049_GRCh38.primary_assembly.genome.fa.1.bt2 added
30ce5ef1da115_GRCh38.primary_assembly.genome.fa.2.bt2 added
30ce5e676339d7_GRCh38.primary_assembly.genome.fa.3.bt2 added
30ce5e7fbe009a_GRCh38.primary_assembly.genome.fa.4.bt2 added
30ce5e6f938c3f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
30ce5e7dacba19_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
30ce5e26513177_outfile.txt added
30ce5e561f6b70_GRCh37_to_GRCh38.chain added
30ce5e153e7c51_GRCh37_to_NCBI34.chain added
30ce5e44d43357_GRCh37_to_NCBI35.chain added
30ce5e103bed8b_GRCh37_to_NCBI36.chain added
30ce5e1e3c74dd_GRCh38_to_GRCh37.chain added
30ce5e2ae0bbb5_GRCh38_to_NCBI34.chain added
30ce5e3ee42a15_GRCh38_to_NCBI35.chain added
30ce5e5254e9aa_GRCh38_to_NCBI36.chain added
30ce5e7ab664c3_NCBI34_to_GRCh37.chain added
30ce5e71ffa7ee_NCBI34_to_GRCh38.chain added
30ce5e6d76f6c0_NCBI35_to_GRCh37.chain added
30ce5e5ff80392_NCBI35_to_GRCh38.chain added
30ce5e68dc01fc_NCBI36_to_GRCh37.chain added
30ce5e15a50983_NCBI36_to_GRCh38.chain added
30ce5e7b1faba6_GRCm38_to_NCBIM36.chain added
30ce5ede5618e_GRCm38_to_NCBIM37.chain added
30ce5e3a023cb3_NCBIM36_to_GRCm38.chain added
30ce5eaf134d8_NCBIM37_to_GRCm38.chain added
30ce5e1f01c8d3_1000G_omni2.5.b37.vcf.gz added
30ce5e26c11093_1000G_omni2.5.b37.vcf.gz.tbi added
30ce5e4f786ad6_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
30ce5edd4ef43_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
30ce5e7f4b871c_1000G_omni2.5.hg38.vcf.gz added
30ce5e7f1bee57_1000G_omni2.5.hg38.vcf.gz.tbi added
30ce5e460edf8c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
30ce5ee692831_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
30ce5e667f282f_af-only-gnomad.raw.sites.vcf added
30ce5e45cce027_af-only-gnomad.raw.sites.vcf.idx added
30ce5e7dfcb470_Mutect2-exome-panel.vcf.idx added
30ce5e642be248_Mutect2-WGS-panel-b37.vcf added
30ce5e6c1e119e_Mutect2-WGS-panel-b37.vcf.idx added
30ce5e541c1fe1_small_exac_common_3.vcf added
30ce5e796a5e99_small_exac_common_3.vcf.idx added
30ce5e30f244f5_1000g_pon.hg38.vcf.gz added
30ce5e64580d6c_1000g_pon.hg38.vcf.gz.tbi added
30ce5e17a6d377_af-only-gnomad.hg38.vcf.gz added
30ce5e5bd300ab_af-only-gnomad.hg38.vcf.gz.tbi added
30ce5e233c3782_small_exac_common_3.hg38.vcf.gz added
30ce5e69fbbd21_small_exac_common_3.hg38.vcf.gz.tbi added
30ce5e5689656e_gencode.v41.annotation.gtf added
30ce5e153bdf70_gencode.v42.annotation.gtf added
30ce5e5772b3e1_gencode.vM30.annotation.gtf added
30ce5e36816900_gencode.vM31.annotation.gtf added
30ce5e7e17e16c_gencode.v41.transcripts.fa added
30ce5e6d17bd64_gencode.v41.transcripts.fa.fai added
30ce5e31a114a6_gencode.v42.transcripts.fa added
30ce5ebfd42fb_gencode.v42.transcripts.fa.fai added
30ce5e2719fa18_gencode.vM30.pc_transcripts.fa added
30ce5e3c92497e_gencode.vM30.pc_transcripts.fa.fai added
30ce5e2aff0bce_gencode.vM31.pc_transcripts.fa added
30ce5e4ddb0aab_gencode.vM31.pc_transcripts.fa.fai added
30ce5ec0ab455_GRCh38.primary_assembly.genome.fa.1.ht2 added
30ce5e38d3fb11_GRCh38.primary_assembly.genome.fa.2.ht2 added
30ce5e4d2691c7_GRCh38.primary_assembly.genome.fa.3.ht2 added
30ce5eb26a2ac_GRCh38.primary_assembly.genome.fa.4.ht2 added
30ce5e7ee2da9e_GRCh38.primary_assembly.genome.fa.5.ht2 added
30ce5e5b8fb9f8_GRCh38.primary_assembly.genome.fa.6.ht2 added
30ce5e71a5cadb_GRCh38.primary_assembly.genome.fa.7.ht2 added
30ce5e44afbac5_GRCh38.primary_assembly.genome.fa.8.ht2 added
30ce5e598c6e69_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
30ce5e55d1ad23_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
30ce5e30cdcc63_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
30ce5e2da88e4a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
30ce5e4f3c0bbd_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
30ce5e61c01158_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
30ce5e12009bb6_GRCh38_full_analysis_set_plus_decoy_hla.fa added
30ce5e66e2df34_GRCh38.primary_assembly.genome.fa.fai added
30ce5e3d931203_GRCh38.primary_assembly.genome.fa.amb added
30ce5e353cd338_GRCh38.primary_assembly.genome.fa.ann added
30ce5e50de9c55_GRCh38.primary_assembly.genome.fa.bwt added
30ce5e141c7771_GRCh38.primary_assembly.genome.fa.pac added
30ce5e4a78b2a9_GRCh38.primary_assembly.genome.fa.sa added
30ce5e28515037_GRCh38.primary_assembly.genome.fa added
30ce5e4a9de071_hs37d5.fa.fai added
30ce5e48909415_hs37d5.fa.amb added
30ce5e15690d9b_hs37d5.fa.ann added
30ce5e7c3ef517_hs37d5.fa.bwt added
30ce5e548dd710_hs37d5.fa.pac added
30ce5e3c8307b3_hs37d5.fa.sa added
30ce5e38d13e96_hs37d5.fa added
30ce5e7f8ce2de_complete_ref_lens.bin added
30ce5ea5e125f_ctable.bin added
30ce5e44dbf2eb_ctg_offsets.bin added
30ce5e3860ddf0_duplicate_clusters.tsv added
30ce5e5784a426_info.json added
30ce5e50029597_mphf.bin added
30ce5e3743b88e_pos.bin added
30ce5e33145e1f_pre_indexing.log added
30ce5e41a86073_rank.bin added
30ce5e7bf37353_ref_indexing.log added
30ce5eca0cc88_refAccumLengths.bin added
30ce5e177a0d96_reflengths.bin added
30ce5e2cc13fb6_refseq.bin added
30ce5e3a495ad2_seq.bin added
30ce5e66b61953_versionInfo.json added
30ce5ee81510e_salmon_index added
30ce5e4c49f688_chrLength.txt added
30ce5e4d98f887_chrName.txt added
30ce5e4c146312_chrNameLength.txt added
30ce5e186c9c1_chrStart.txt added
30ce5e1e7794dd_exonGeTrInfo.tab added
30ce5e6030da83_exonInfo.tab added
30ce5e4bff7c6a_geneInfo.tab added
30ce5e46c8e514_Genome added
30ce5e2acebaf5_genomeParameters.txt added
30ce5e1490107f_Log.out added
30ce5e5c31f2af_SA added
30ce5e270db00c_SAindex added
30ce5e691de790_sjdbInfo.txt added
30ce5e18b4fa63_sjdbList.fromGTF.out.tab added
30ce5e5fdeeea2_sjdbList.out.tab added
30ce5e68aaca6e_transcriptInfo.tab added
30ce5e23130cc2_GRCh38.GENCODE.v42_100 added
30ce5e24bae18d_knownGene_hg38.sql added
30ce5e210ba85e_knownGene_hg38.txt added
30ce5e7a97b0e8_refGene_hg38.sql added
30ce5e74bd7725_refGene_hg38.txt added
30ce5e584f60ec_knownGene_mm39.sql added
30ce5e2dac0f07_knownGene_mm39.txt added
30ce5e3665d798_refGene_mm39.sql added
30ce5e5442d43f_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/RtmpQh32We/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 
 18.085   1.096  19.702