##############################################################################
##############################################################################
###
### 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.7.0’
* 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 7.087  0.858   8.048
* 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-3.21-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.7.0’
** 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) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 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...
83a31a449ab6_GRCh38.primary_assembly.genome.fa.1.bt2 added
83a3e093033_GRCh38.primary_assembly.genome.fa.2.bt2 added
83a37d3b6b77_GRCh38.primary_assembly.genome.fa.3.bt2 added
83a3480c91dc_GRCh38.primary_assembly.genome.fa.4.bt2 added
83a3313c2778_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
83a364435088_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
83a37f5c4424_outfile.txt added
83a327dd8cf_GRCh37_to_GRCh38.chain added
83a31424ff50_GRCh37_to_NCBI34.chain added
83a38f5e785_GRCh37_to_NCBI35.chain added
83a34832d15b_GRCh37_to_NCBI36.chain added
83a34ed265_GRCh38_to_GRCh37.chain added
83a336d6e50b_GRCh38_to_NCBI34.chain added
83a35657514d_GRCh38_to_NCBI35.chain added
83a37e9ac283_GRCh38_to_NCBI36.chain added
83a362586764_NCBI34_to_GRCh37.chain added
83a319ec08ad_NCBI34_to_GRCh38.chain added
83a3572da326_NCBI35_to_GRCh37.chain added
83a375324080_NCBI35_to_GRCh38.chain added
83a33628cf9c_NCBI36_to_GRCh37.chain added
83a33156268b_NCBI36_to_GRCh38.chain added
83a3efc88fb_GRCm38_to_NCBIM36.chain added
83a365851e6c_GRCm38_to_NCBIM37.chain added
83a36907886_NCBIM36_to_GRCm38.chain added
83a376d8a8c7_NCBIM37_to_GRCm38.chain added
83a3a30ddc6_1000G_omni2.5.b37.vcf.gz added
83a3e2ff764_1000G_omni2.5.b37.vcf.gz.tbi added
83a36f1acd82_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
83a348aa4aca_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
83a32414390b_1000G_omni2.5.hg38.vcf.gz added
83a32bad13ae_1000G_omni2.5.hg38.vcf.gz.tbi added
83a36fe71ae8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
83a32d97aebd_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
83a3415111ad_af-only-gnomad.raw.sites.vcf added
83a3315f965b_af-only-gnomad.raw.sites.vcf.idx added
83a37a8849af_Mutect2-exome-panel.vcf.idx added
83a399dbf02_Mutect2-WGS-panel-b37.vcf added
83a35367213c_Mutect2-WGS-panel-b37.vcf.idx added
83a317b714eb_small_exac_common_3.vcf added
83a374be5c76_small_exac_common_3.vcf.idx added
83a37da882da_1000g_pon.hg38.vcf.gz added
83a34226f6a9_1000g_pon.hg38.vcf.gz.tbi added
83a3c0bf32d_af-only-gnomad.hg38.vcf.gz added
83a3648a1588_af-only-gnomad.hg38.vcf.gz.tbi added
83a3258bc749_small_exac_common_3.hg38.vcf.gz added
83a37bc89ce0_small_exac_common_3.hg38.vcf.gz.tbi added
83a32fb3759d_gencode.v41.annotation.gtf added
83a32eeeaee2_gencode.v42.annotation.gtf added
83a3381b8f80_gencode.vM30.annotation.gtf added
83a3196a3947_gencode.vM31.annotation.gtf added
83a3cd6715a_gencode.v41.transcripts.fa added
83a352abd24b_gencode.v41.transcripts.fa.fai added
83a3e7b6454_gencode.v42.transcripts.fa added
83a346f7ce39_gencode.v42.transcripts.fa.fai added
83a337042495_gencode.vM30.pc_transcripts.fa added
83a370fdce6a_gencode.vM30.pc_transcripts.fa.fai added
83a326facb1a_gencode.vM31.pc_transcripts.fa added
83a31b2c2bf4_gencode.vM31.pc_transcripts.fa.fai added
83a370f9ae1b_GRCh38.primary_assembly.genome.fa.1.ht2 added
83a31815a88f_GRCh38.primary_assembly.genome.fa.2.ht2 added
83a335ed50a3_GRCh38.primary_assembly.genome.fa.3.ht2 added
83a36f4918fd_GRCh38.primary_assembly.genome.fa.4.ht2 added
83a32807c31f_GRCh38.primary_assembly.genome.fa.5.ht2 added
83a3159b3cc1_GRCh38.primary_assembly.genome.fa.6.ht2 added
83a32b1adfc_GRCh38.primary_assembly.genome.fa.7.ht2 added
83a35f157cc5_GRCh38.primary_assembly.genome.fa.8.ht2 added
83a37bb29a47_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
83a3aaeeac3_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
83a361b6adaf_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
83a32044ee47_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
83a3d7787de_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
83a3227906ba_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
83a337a8af04_GRCh38_full_analysis_set_plus_decoy_hla.fa added
83a3237a4c28_GRCh38.primary_assembly.genome.fa.fai added
83a3321de84a_GRCh38.primary_assembly.genome.fa.amb added
83a3497d6bfa_GRCh38.primary_assembly.genome.fa.ann added
83a3493c0fc7_GRCh38.primary_assembly.genome.fa.bwt added
83a362ff761_GRCh38.primary_assembly.genome.fa.pac added
83a3371a0473_GRCh38.primary_assembly.genome.fa.sa added
83a3d1a3648_GRCh38.primary_assembly.genome.fa added
83a333e1b7b0_hs37d5.fa.fai added
83a327e29e6c_hs37d5.fa.amb added
83a3f0ed8e9_hs37d5.fa.ann added
83a317c2b0b8_hs37d5.fa.bwt added
83a36ee00c37_hs37d5.fa.pac added
83a3374227bf_hs37d5.fa.sa added
83a3583f88f0_hs37d5.fa added
83a3333771d3_complete_ref_lens.bin added
83a37d11ede9_ctable.bin added
83a3241a9c25_ctg_offsets.bin added
83a34f0153a7_duplicate_clusters.tsv added
83a3601b2176_info.json added
83a31531fb45_mphf.bin added
83a346779e2_pos.bin added
83a32572e6b0_pre_indexing.log added
83a31a874005_rank.bin added
83a3257c15de_ref_indexing.log added
83a3757fb50b_refAccumLengths.bin added
83a313472171_reflengths.bin added
83a322e48b9a_refseq.bin added
83a34a893d5b_seq.bin added
83a3781b4797_versionInfo.json added
83a346f9481b_salmon_index added
83a317ed0904_chrLength.txt added
83a34aeaf1e1_chrName.txt added
83a36ae1134_chrNameLength.txt added
83a3deb7059_chrStart.txt added
83a35c1cea32_exonGeTrInfo.tab added
83a36e53a7dc_exonInfo.tab added
83a33631951a_geneInfo.tab added
83a37133f9c1_Genome added
83a3b5227f7_genomeParameters.txt added
83a33ebdceef_Log.out added
83a31f5ccd17_SA added
83a359cb117_SAindex added
83a3722e5fe1_sjdbInfo.txt added
83a34298e757_sjdbList.fromGTF.out.tab added
83a3447c22e9_sjdbList.out.tab added
83a331d8121f_transcriptInfo.tab added
83a3608dcac9_GRCh38.GENCODE.v42_100 added
83a37cfc83a4_knownGene_hg38.sql added
83a32626c417_knownGene_hg38.txt added
83a33b13d592_refGene_hg38.sql added
83a3132a828b_refGene_hg38.txt added
83a34be07d81_knownGene_mm39.sql added
83a37f4fc711_knownGene_mm39.txt added
83a34e966e63_refGene_mm39.sql added
83a376294de3_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/Rtmp12zVSj/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 
 24.869   3.692  29.600