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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_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.9.0’
* 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
* 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-3.22-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/4.5-arm64/Resources/library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.9.0’
** 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 (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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...
c73144fddb51_GRCh38.primary_assembly.genome.fa.1.bt2 added
c7317649c639_GRCh38.primary_assembly.genome.fa.2.bt2 added
c731657504da_GRCh38.primary_assembly.genome.fa.3.bt2 added
c7316591b83f_GRCh38.primary_assembly.genome.fa.4.bt2 added
c73141d76431_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
c73123f2eebc_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
c73122178b14_outfile.txt added
c73137abdf88_GRCh37_to_GRCh38.chain added
c73174e07645_GRCh37_to_NCBI34.chain added
c7313c74e7f5_GRCh37_to_NCBI35.chain added
c7311f28a4d5_GRCh37_to_NCBI36.chain added
c731255dabee_GRCh38_to_GRCh37.chain added
c73128c2a96c_GRCh38_to_NCBI34.chain added
c731401065c_GRCh38_to_NCBI35.chain added
c7315f488411_GRCh38_to_NCBI36.chain added
c73111d6a8f6_NCBI34_to_GRCh37.chain added
c73123eeb7a0_NCBI34_to_GRCh38.chain added
c731d597bce_NCBI35_to_GRCh37.chain added
c7316dcf183a_NCBI35_to_GRCh38.chain added
c731373fc028_NCBI36_to_GRCh37.chain added
c7313a609e6e_NCBI36_to_GRCh38.chain added
c7311d4165b3_GRCm38_to_NCBIM36.chain added
c731307bd9c6_GRCm38_to_NCBIM37.chain added
c73113166f08_NCBIM36_to_GRCm38.chain added
c73125d38002_NCBIM37_to_GRCm38.chain added
c731607916b4_1000G_omni2.5.b37.vcf.gz added
c7312dc1b4e7_1000G_omni2.5.b37.vcf.gz.tbi added
c73184bc129_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
c73125766f00_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
c7312717c37_1000G_omni2.5.hg38.vcf.gz added
c73168920021_1000G_omni2.5.hg38.vcf.gz.tbi added
c7314946ac29_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
c7313ed0dd54_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
c731272d604_af-only-gnomad.raw.sites.vcf added
c7314140a1dd_af-only-gnomad.raw.sites.vcf.idx added
c7317a42d5a2_Mutect2-exome-panel.vcf.idx added
c73139d7bd63_Mutect2-WGS-panel-b37.vcf added
c7312d2cc40_Mutect2-WGS-panel-b37.vcf.idx added
c7315d5f7f32_small_exac_common_3.vcf added
c7312897db82_small_exac_common_3.vcf.idx added
c7319cc48a0_1000g_pon.hg38.vcf.gz added
c73142b40566_1000g_pon.hg38.vcf.gz.tbi added
c73138ce8dc0_af-only-gnomad.hg38.vcf.gz added
c731bc5563_af-only-gnomad.hg38.vcf.gz.tbi added
c7314c89d6f5_small_exac_common_3.hg38.vcf.gz added
c7316d7f9614_small_exac_common_3.hg38.vcf.gz.tbi added
c73153563335_gencode.v41.annotation.gtf added
c731403c0751_gencode.v42.annotation.gtf added
c731250477c9_gencode.vM30.annotation.gtf added
c7314854401b_gencode.vM31.annotation.gtf added
c731133cd1b6_gencode.v41.transcripts.fa added
c7317dec0d97_gencode.v41.transcripts.fa.fai added
c73114707517_gencode.v42.transcripts.fa added
c7316317437c_gencode.v42.transcripts.fa.fai added
c731c4fb4b7_gencode.vM30.pc_transcripts.fa added
c73144e160b1_gencode.vM30.pc_transcripts.fa.fai added
c731289327cb_gencode.vM31.pc_transcripts.fa added
c7315519953c_gencode.vM31.pc_transcripts.fa.fai added
c731294c1ca_GRCh38.primary_assembly.genome.fa.1.ht2 added
c731743eb618_GRCh38.primary_assembly.genome.fa.2.ht2 added
c73141251d47_GRCh38.primary_assembly.genome.fa.3.ht2 added
c7316ba541ba_GRCh38.primary_assembly.genome.fa.4.ht2 added
c7312e7e518c_GRCh38.primary_assembly.genome.fa.5.ht2 added
c731671bd62c_GRCh38.primary_assembly.genome.fa.6.ht2 added
c731548a1796_GRCh38.primary_assembly.genome.fa.7.ht2 added
c7313612a436_GRCh38.primary_assembly.genome.fa.8.ht2 added
c7311daf0f6_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
c7314d01a76d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
c73127970c9a_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
c7312dbc66c4_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
c7312bfee551_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
c7316b813f67_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
c7317269ba54_GRCh38_full_analysis_set_plus_decoy_hla.fa added
c7317b481b7a_GRCh38.primary_assembly.genome.fa.fai added
c7313b0425d1_GRCh38.primary_assembly.genome.fa.amb added
c731d4eda9c_GRCh38.primary_assembly.genome.fa.ann added
c73133f23e97_GRCh38.primary_assembly.genome.fa.bwt added
c73164eb4625_GRCh38.primary_assembly.genome.fa.pac added
c731124a5ae6_GRCh38.primary_assembly.genome.fa.sa added
c7314f95bb6b_GRCh38.primary_assembly.genome.fa added
c7316f43969e_hs37d5.fa.fai added
c7313e559823_hs37d5.fa.amb added
c731657741cd_hs37d5.fa.ann added
c73178812dc5_hs37d5.fa.bwt added
c73168e41e51_hs37d5.fa.pac added
c73158828da3_hs37d5.fa.sa added
c7316320f5ba_hs37d5.fa added
c7318e4b92e_complete_ref_lens.bin added
c73160397f91_ctable.bin added
c7315ee639f1_ctg_offsets.bin added
c7315ce62de3_duplicate_clusters.tsv added
c731bcec1bb_info.json added
c7313310e20b_mphf.bin added
c73119685a5e_pos.bin added
c7311204de5a_pre_indexing.log added
c7317da1eff3_rank.bin added
c73112907af5_ref_indexing.log added
c7314b787458_refAccumLengths.bin added
c731511e641d_reflengths.bin added
c731223ed586_refseq.bin added
c7314b3461fa_seq.bin added
c7315c0c8aa8_versionInfo.json added
c7313b634ace_salmon_index added
c73173c438d7_chrLength.txt added
c731576fe6a1_chrName.txt added
c731738e80df_chrNameLength.txt added
c73110aeebbe_chrStart.txt added
c7314bf70f80_exonGeTrInfo.tab added
c731491ac376_exonInfo.tab added
c7317c169d78_geneInfo.tab added
c73130bc70ed_Genome added
c7312399f09a_genomeParameters.txt added
c7314f8320b8_Log.out added
c73129d938d0_SA added
c7317420f526_SAindex added
c7311fbecd5a_sjdbInfo.txt added
c731279bdffe_sjdbList.fromGTF.out.tab added
c7316a8eb102_sjdbList.out.tab added
c7313e0730f5_transcriptInfo.tab added
c7314a1f44a3_GRCh38.GENCODE.v42_100 added
c7314ad34f59_knownGene_hg38.sql added
c73176fe826f_knownGene_hg38.txt added
c7313f258271_refGene_hg38.sql added
c7313796e91a_refGene_hg38.txt added
c73114a1c679_knownGene_mm39.sql added
c7318ed3c84_knownGene_mm39.txt added
c731f2002b0_refGene_mm39.sql added
c7317e907891_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: 
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp6JouOx/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 
  6.185   0.674   7.586