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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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 6.009  0.736   6.844
* 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-3.20-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

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


* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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...
14b336c09389c_GRCh38.primary_assembly.genome.fa.1.bt2 added
14b335163c12d_GRCh38.primary_assembly.genome.fa.2.bt2 added
14b336c1f9b19_GRCh38.primary_assembly.genome.fa.3.bt2 added
14b33effbdc4_GRCh38.primary_assembly.genome.fa.4.bt2 added
14b333803968d_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
14b3373911fb5_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
14b333cb8df59_outfile.txt added
14b33d4f6b34_GRCh37_to_GRCh38.chain added
14b33590729bf_GRCh37_to_NCBI34.chain added
14b336545e842_GRCh37_to_NCBI35.chain added
14b33509378ff_GRCh37_to_NCBI36.chain added
14b331ecd6ad_GRCh38_to_GRCh37.chain added
14b336401f8d7_GRCh38_to_NCBI34.chain added
14b333d781e8c_GRCh38_to_NCBI35.chain added
14b33191d98db_GRCh38_to_NCBI36.chain added
14b33661e5ebe_NCBI34_to_GRCh37.chain added
14b3353de4052_NCBI34_to_GRCh38.chain added
14b332450f282_NCBI35_to_GRCh37.chain added
14b333e61476e_NCBI35_to_GRCh38.chain added
14b336498a6c0_NCBI36_to_GRCh37.chain added
14b3361ebbad8_NCBI36_to_GRCh38.chain added
14b333b37ed21_GRCm38_to_NCBIM36.chain added
14b3354b12fe6_GRCm38_to_NCBIM37.chain added
14b333cbfd07a_NCBIM36_to_GRCm38.chain added
14b33551018be_NCBIM37_to_GRCm38.chain added
14b3313c88d93_1000G_omni2.5.b37.vcf.gz added
14b3353c6b80a_1000G_omni2.5.b37.vcf.gz.tbi added
14b331b5cc37e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
14b336726933a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
14b33158bf9be_1000G_omni2.5.hg38.vcf.gz added
14b3318b933ff_1000G_omni2.5.hg38.vcf.gz.tbi added
14b332704b707_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
14b33268c4094_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
14b3341e3c851_af-only-gnomad.raw.sites.vcf added
14b3351745fa2_af-only-gnomad.raw.sites.vcf.idx added
14b332f32ae75_Mutect2-exome-panel.vcf.idx added
14b33285b9b88_Mutect2-WGS-panel-b37.vcf added
14b331640126b_Mutect2-WGS-panel-b37.vcf.idx added
14b3348793a36_small_exac_common_3.vcf added
14b33edcd466_small_exac_common_3.vcf.idx added
14b3343fc7c29_1000g_pon.hg38.vcf.gz added
14b33753b8a9d_1000g_pon.hg38.vcf.gz.tbi added
14b331809858c_af-only-gnomad.hg38.vcf.gz added
14b33191eb6a8_af-only-gnomad.hg38.vcf.gz.tbi added
14b332f69dc7a_small_exac_common_3.hg38.vcf.gz added
14b334f09e5e7_small_exac_common_3.hg38.vcf.gz.tbi added
14b3312d4c93b_gencode.v41.annotation.gtf added
14b334fe74a25_gencode.v42.annotation.gtf added
14b3359b4ec1e_gencode.vM30.annotation.gtf added
14b3374f9d394_gencode.vM31.annotation.gtf added
14b333db1d58b_gencode.v41.transcripts.fa added
14b33663ab851_gencode.v41.transcripts.fa.fai added
14b33191b0246_gencode.v42.transcripts.fa added
14b333c324e8a_gencode.v42.transcripts.fa.fai added
14b33ac264e6_gencode.vM30.pc_transcripts.fa added
14b33606e3d8e_gencode.vM30.pc_transcripts.fa.fai added
14b33658b6717_gencode.vM31.pc_transcripts.fa added
14b33231d4b16_gencode.vM31.pc_transcripts.fa.fai added
14b33582ca35c_GRCh38.primary_assembly.genome.fa.1.ht2 added
14b335a991a3d_GRCh38.primary_assembly.genome.fa.2.ht2 added
14b337989c942_GRCh38.primary_assembly.genome.fa.3.ht2 added
14b3344fc4a64_GRCh38.primary_assembly.genome.fa.4.ht2 added
14b33f780e9e_GRCh38.primary_assembly.genome.fa.5.ht2 added
14b331307af01_GRCh38.primary_assembly.genome.fa.6.ht2 added
14b335d727469_GRCh38.primary_assembly.genome.fa.7.ht2 added
14b33538c96d_GRCh38.primary_assembly.genome.fa.8.ht2 added
14b33533015c8_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
14b3379e62822_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
14b3375550eb3_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
14b33233845f3_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
14b3343786695_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
14b331596e2ce_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
14b3365044d74_GRCh38_full_analysis_set_plus_decoy_hla.fa added
14b337d792e7b_GRCh38.primary_assembly.genome.fa.fai added
14b331edacd98_GRCh38.primary_assembly.genome.fa.amb added
14b332eefc5fb_GRCh38.primary_assembly.genome.fa.ann added
14b337faef9cf_GRCh38.primary_assembly.genome.fa.bwt added
14b333892c686_GRCh38.primary_assembly.genome.fa.pac added
14b332c27a46e_GRCh38.primary_assembly.genome.fa.sa added
14b335e9c4867_GRCh38.primary_assembly.genome.fa added
14b33665592b7_hs37d5.fa.fai added
14b337c1360dd_hs37d5.fa.amb added
14b335c3c8cce_hs37d5.fa.ann added
14b33b4057b1_hs37d5.fa.bwt added
14b332d3d2b3c_hs37d5.fa.pac added
14b33ae18758_hs37d5.fa.sa added
14b335c7ca7fc_hs37d5.fa added
14b337bf8c0d3_complete_ref_lens.bin added
14b3383b9c3b_ctable.bin added
14b3318de9b6_ctg_offsets.bin added
14b33beaac86_duplicate_clusters.tsv added
14b335be49786_info.json added
14b337c980d8b_mphf.bin added
14b3362a16094_pos.bin added
14b3350cbc722_pre_indexing.log added
14b33727eb29e_rank.bin added
14b335c00ddcb_ref_indexing.log added
14b333ce1699d_refAccumLengths.bin added
14b3372dce1a4_reflengths.bin added
14b3336210e6_refseq.bin added
14b331b436dc6_seq.bin added
14b3367dbf025_versionInfo.json added
14b3318734268_salmon_index added
14b33370cc662_chrLength.txt added
14b3327b4682a_chrName.txt added
14b333522b1c3_chrNameLength.txt added
14b3378c49475_chrStart.txt added
14b3331eecb44_exonGeTrInfo.tab added
14b333462f6f8_exonInfo.tab added
14b334d442ea6_geneInfo.tab added
14b333752bbeb_Genome added
14b3318af5dad_genomeParameters.txt added
14b33212f1584_Log.out added
14b331a2d9e21_SA added
14b3328e895f4_SAindex added
14b333dccdb27_sjdbInfo.txt added
14b335447fd23_sjdbList.fromGTF.out.tab added
14b33423c300f_sjdbList.out.tab added
14b337d774ac1_transcriptInfo.tab added
14b3322cd0541_GRCh38.GENCODE.v42_100 added
14b3342140040_knownGene_hg38.sql added
14b332f1c8ba4_knownGene_hg38.txt added
14b337b13d425_refGene_hg38.sql added
14b3352cd0843_refGene_hg38.txt added
14b3312d9912d_knownGene_mm39.sql added
14b339ca2b06_knownGene_mm39.txt added
14b3337ce9bef_refGene_mm39.sql added
14b335d5f8488_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/RtmpuCkr4a/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 
 18.710   2.499  22.297