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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.4.0’
* 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 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 8.504  1.051   9.785
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReUseData
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘ReUseData’ ...
** 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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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...
dc204c7bf4ed_GRCh38.primary_assembly.genome.fa.1.bt2 added
dc205e0d1ad5_GRCh38.primary_assembly.genome.fa.2.bt2 added
dc202e5cc630_GRCh38.primary_assembly.genome.fa.3.bt2 added
dc204cd79117_GRCh38.primary_assembly.genome.fa.4.bt2 added
dc205c76a46a_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
dc2071245a92_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
dc209b66146_outfile.txt added
dc2024ac3fa5_GRCh37_to_GRCh38.chain added
dc2028867c72_GRCh37_to_NCBI34.chain added
dc2015543527_GRCh37_to_NCBI35.chain added
dc204b6d9e61_GRCh37_to_NCBI36.chain added
dc209b918f7_GRCh38_to_GRCh37.chain added
dc205716051d_GRCh38_to_NCBI34.chain added
dc2066a9df95_GRCh38_to_NCBI35.chain added
dc201a95e3db_GRCh38_to_NCBI36.chain added
dc2066a24c7f_NCBI34_to_GRCh37.chain added
dc20294c5a7d_NCBI34_to_GRCh38.chain added
dc2053c8d9b9_NCBI35_to_GRCh37.chain added
dc20274e2ba8_NCBI35_to_GRCh38.chain added
dc207d1436c0_NCBI36_to_GRCh37.chain added
dc203a16b767_NCBI36_to_GRCh38.chain added
dc202962e8fc_GRCm38_to_NCBIM36.chain added
dc201cae0d9e_GRCm38_to_NCBIM37.chain added
dc2067000ec7_NCBIM36_to_GRCm38.chain added
dc2034ca5fa5_NCBIM37_to_GRCm38.chain added
dc20524d64b6_1000G_omni2.5.b37.vcf.gz added
dc20570f12f0_1000G_omni2.5.b37.vcf.gz.tbi added
dc201ea47737_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
dc203f8ecb98_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
dc2037d888c1_1000G_omni2.5.hg38.vcf.gz added
dc2068fa538b_1000G_omni2.5.hg38.vcf.gz.tbi added
dc20a830085_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
dc201e972127_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
dc2054019721_af-only-gnomad.raw.sites.vcf added
dc203469229d_af-only-gnomad.raw.sites.vcf.idx added
dc20625f8c4c_Mutect2-exome-panel.vcf.idx added
dc206ef40408_Mutect2-WGS-panel-b37.vcf added
dc205634e220_Mutect2-WGS-panel-b37.vcf.idx added
dc2029e9cf17_small_exac_common_3.vcf added
dc20351b0480_small_exac_common_3.vcf.idx added
dc20c48abd_1000g_pon.hg38.vcf.gz added
dc2067707eaf_1000g_pon.hg38.vcf.gz.tbi added
dc20a8d4837_af-only-gnomad.hg38.vcf.gz added
dc204180184a_af-only-gnomad.hg38.vcf.gz.tbi added
dc2040bac3de_small_exac_common_3.hg38.vcf.gz added
dc2025914505_small_exac_common_3.hg38.vcf.gz.tbi added
dc20644a5e87_gencode.v41.annotation.gtf added
dc204e842481_gencode.v42.annotation.gtf added
dc204578b96c_gencode.vM30.annotation.gtf added
dc2078d58515_gencode.vM31.annotation.gtf added
dc20a1463ad_gencode.v41.transcripts.fa added
dc20409bf806_gencode.v41.transcripts.fa.fai added
dc203fb8730d_gencode.v42.transcripts.fa added
dc2066897b29_gencode.v42.transcripts.fa.fai added
dc204bf4f556_gencode.vM30.pc_transcripts.fa added
dc203f17080f_gencode.vM30.pc_transcripts.fa.fai added
dc201123125_gencode.vM31.pc_transcripts.fa added
dc20515874af_gencode.vM31.pc_transcripts.fa.fai added
dc20654b6e2_GRCh38.primary_assembly.genome.fa.1.ht2 added
dc2023b2b2ad_GRCh38.primary_assembly.genome.fa.2.ht2 added
dc2028f08e2a_GRCh38.primary_assembly.genome.fa.3.ht2 added
dc2049057c65_GRCh38.primary_assembly.genome.fa.4.ht2 added
dc20729f057_GRCh38.primary_assembly.genome.fa.5.ht2 added
dc205261e36d_GRCh38.primary_assembly.genome.fa.6.ht2 added
dc20189a335c_GRCh38.primary_assembly.genome.fa.7.ht2 added
dc2033a1e9a2_GRCh38.primary_assembly.genome.fa.8.ht2 added
dc204af1a529_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
dc203e924d2f_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
dc20770968c0_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
dc20abc524e_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
dc2051bf8463_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
dc20748ca982_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
dc203eccd195_GRCh38_full_analysis_set_plus_decoy_hla.fa added
dc2078d3ad68_GRCh38.primary_assembly.genome.fa.fai added
dc20111dc4d1_GRCh38.primary_assembly.genome.fa.amb added
dc2039647e1e_GRCh38.primary_assembly.genome.fa.ann added
dc2074940101_GRCh38.primary_assembly.genome.fa.bwt added
dc2020ce2472_GRCh38.primary_assembly.genome.fa.pac added
dc203dbac931_GRCh38.primary_assembly.genome.fa.sa added
dc2031eecfa0_GRCh38.primary_assembly.genome.fa added
dc2035812afc_hs37d5.fa.fai added
dc20332d21d5_hs37d5.fa.amb added
dc2058084132_hs37d5.fa.ann added
dc205f066c5_hs37d5.fa.bwt added
dc2069eb128e_hs37d5.fa.pac added
dc20480f5ef5_hs37d5.fa.sa added
dc2069234bc8_hs37d5.fa added
dc20c446d65_complete_ref_lens.bin added
dc20606a082d_ctable.bin added
dc20513ef3ce_ctg_offsets.bin added
dc207bf8830d_duplicate_clusters.tsv added
dc2078640a10_info.json added
dc206fd0de2f_mphf.bin added
dc2079ab1902_pos.bin added
dc204ff710b5_pre_indexing.log added
dc20656a0416_rank.bin added
dc201332745e_ref_indexing.log added
dc205575d12a_refAccumLengths.bin added
dc2029f7483b_reflengths.bin added
dc2029a72f03_refseq.bin added
dc201eff8352_seq.bin added
dc2019068c64_versionInfo.json added
dc207ceb0611_salmon_index added
dc2029db8629_chrLength.txt added
dc20b450337_chrName.txt added
dc205fd615a8_chrNameLength.txt added
dc206027f9bf_chrStart.txt added
dc20607d9bea_exonGeTrInfo.tab added
dc2056875123_exonInfo.tab added
dc204ddffd36_geneInfo.tab added
dc202c690c2b_Genome added
dc20249df1d4_genomeParameters.txt added
dc207d6fa813_Log.out added
dc202d83b7bb_SA added
dc2022936d55_SAindex added
dc207ceef92e_sjdbInfo.txt added
dc202d297b16_sjdbList.fromGTF.out.tab added
dc207e4ff883_sjdbList.out.tab added
dc203444a13e_transcriptInfo.tab added
dc205b60841_GRCh38.GENCODE.v42_100 added
dc2071d7e654_knownGene_hg38.sql added
dc201552cf30_knownGene_hg38.txt added
dc206fa0633f_refGene_hg38.sql added
dc20ad3f65a_refGene_hg38.txt added
dc2061d29443_knownGene_mm39.sql added
dc204803ece1_knownGene_mm39.txt added
dc2079b4ccb6_refGene_mm39.sql added
dc204cebff26_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/RtmpYivN20/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 
 26.987   3.723  31.860