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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_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 ‘1.3.2’
* 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 R 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 12.477  1.284   16.86
getCloudData   4.689  0.214    6.50
* 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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
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...
cf2c6c050b31_GRCh38.primary_assembly.genome.fa.1.bt2 added
cf2c3f21f55e_GRCh38.primary_assembly.genome.fa.2.bt2 added
cf2c4e740eb3_GRCh38.primary_assembly.genome.fa.3.bt2 added
cf2c25713202_GRCh38.primary_assembly.genome.fa.4.bt2 added
cf2c2a8a3482_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
cf2c577d589f_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
cf2c66455b98_outfile.txt added
cf2c53808c9c_GRCh37_to_GRCh38.chain added
cf2c1c8f8098_GRCh37_to_NCBI34.chain added
cf2c114389ce_GRCh37_to_NCBI35.chain added
cf2c690c3c3c_GRCh37_to_NCBI36.chain added
cf2c2246bd05_GRCh38_to_GRCh37.chain added
cf2c5223a4d7_GRCh38_to_NCBI34.chain added
cf2c221b4962_GRCh38_to_NCBI35.chain added
cf2c2d6ed26c_GRCh38_to_NCBI36.chain added
cf2c46b8c7c1_NCBI34_to_GRCh37.chain added
cf2cd42742d_NCBI34_to_GRCh38.chain added
cf2c5d93d28_NCBI35_to_GRCh37.chain added
cf2c793e1017_NCBI35_to_GRCh38.chain added
cf2c59929430_NCBI36_to_GRCh37.chain added
cf2c263f0941_NCBI36_to_GRCh38.chain added
cf2c74789e04_GRCm38_to_NCBIM36.chain added
cf2c1ace5459_GRCm38_to_NCBIM37.chain added
cf2c6003acce_NCBIM36_to_GRCm38.chain added
cf2c114639a1_NCBIM37_to_GRCm38.chain added
cf2c197181e3_1000G_omni2.5.b37.vcf.gz added
cf2c6b066b21_1000G_omni2.5.b37.vcf.gz.tbi added
cf2c72637a6b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
cf2c60fa4178_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
cf2c4de05f05_1000G_omni2.5.hg38.vcf.gz added
cf2c457e6934_1000G_omni2.5.hg38.vcf.gz.tbi added
cf2c6e2cf890_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
cf2c4a72ee72_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
cf2c3f84a48d_af-only-gnomad.raw.sites.vcf added
cf2c1d4f458f_af-only-gnomad.raw.sites.vcf.idx added
cf2c3f5fbe51_Mutect2-exome-panel.vcf.idx added
cf2c26c7d858_Mutect2-WGS-panel-b37.vcf added
cf2ca4c8d4c_Mutect2-WGS-panel-b37.vcf.idx added
cf2c27d07ddc_small_exac_common_3.vcf added
cf2c68f70aef_small_exac_common_3.vcf.idx added
cf2c32ef06bf_1000g_pon.hg38.vcf.gz added
cf2c6aa3ffb8_1000g_pon.hg38.vcf.gz.tbi added
cf2c34e9bfba_af-only-gnomad.hg38.vcf.gz added
cf2c5e2a6779_af-only-gnomad.hg38.vcf.gz.tbi added
cf2c31ef693b_small_exac_common_3.hg38.vcf.gz added
cf2c5ce5ba19_small_exac_common_3.hg38.vcf.gz.tbi added
cf2c6e1ceef4_gencode.v41.annotation.gtf added
cf2c2d8c0da6_gencode.v42.annotation.gtf added
cf2c45d424a6_gencode.vM30.annotation.gtf added
cf2c6ab2321a_gencode.vM31.annotation.gtf added
cf2c58f77faf_gencode.v41.transcripts.fa added
cf2c60dfe7ca_gencode.v41.transcripts.fa.fai added
cf2cbeab076_gencode.v42.transcripts.fa added
cf2c5ce71916_gencode.v42.transcripts.fa.fai added
cf2c48202300_gencode.vM30.pc_transcripts.fa added
cf2c35d9f9fe_gencode.vM30.pc_transcripts.fa.fai added
cf2c79abae50_gencode.vM31.pc_transcripts.fa added
cf2c76414497_gencode.vM31.pc_transcripts.fa.fai added
cf2c36fe5228_GRCh38.primary_assembly.genome.fa.1.ht2 added
cf2c72c3dc4c_GRCh38.primary_assembly.genome.fa.2.ht2 added
cf2c18b43c71_GRCh38.primary_assembly.genome.fa.3.ht2 added
cf2c60ec2b62_GRCh38.primary_assembly.genome.fa.4.ht2 added
cf2c311460a4_GRCh38.primary_assembly.genome.fa.5.ht2 added
cf2c30d4c828_GRCh38.primary_assembly.genome.fa.6.ht2 added
cf2c61a0d323_GRCh38.primary_assembly.genome.fa.7.ht2 added
cf2c585d0e8_GRCh38.primary_assembly.genome.fa.8.ht2 added
cf2c1456322d_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
cf2c26f832c9_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
cf2c70ce3e1b_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
cf2c744f9878_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
cf2c15a329f0_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
cf2cb1656a9_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
cf2c679376ee_GRCh38_full_analysis_set_plus_decoy_hla.fa added
cf2c2653862_GRCh38.primary_assembly.genome.fa.fai added
cf2c4358ab28_GRCh38.primary_assembly.genome.fa.amb added
cf2c724cf1a2_GRCh38.primary_assembly.genome.fa.ann added
cf2c198bfd4e_GRCh38.primary_assembly.genome.fa.bwt added
cf2c35a318fc_GRCh38.primary_assembly.genome.fa.pac added
cf2c66bd63e6_GRCh38.primary_assembly.genome.fa.sa added
cf2c1be9c5bc_GRCh38.primary_assembly.genome.fa added
cf2c10b4c7f5_hs37d5.fa.fai added
cf2c4cb3ae64_hs37d5.fa.amb added
cf2c287e4e93_hs37d5.fa.ann added
cf2c7c58a9a9_hs37d5.fa.bwt added
cf2c20ead606_hs37d5.fa.pac added
cf2c198934cc_hs37d5.fa.sa added
cf2c7ee94a2c_hs37d5.fa added
cf2c604cfcc_complete_ref_lens.bin added
cf2c25e65d2a_ctable.bin added
cf2c36ee83d6_ctg_offsets.bin added
cf2c651172c6_duplicate_clusters.tsv added
cf2c5c865900_info.json added
cf2c783d3e74_mphf.bin added
cf2c7ccf6f57_pos.bin added
cf2c1696f8c5_pre_indexing.log added
cf2c11a65919_rank.bin added
cf2c4023815c_ref_indexing.log added
cf2c5b01dfe9_refAccumLengths.bin added
cf2c581368ac_reflengths.bin added
cf2c623d2160_refseq.bin added
cf2c1b5a5803_seq.bin added
cf2c48483afc_versionInfo.json added
cf2c7e189b76_salmon_index added
cf2c186a0a7_chrLength.txt added
cf2c2d9d34b9_chrName.txt added
cf2c2bf07514_chrNameLength.txt added
cf2c37968a95_chrStart.txt added
cf2c7c6458b5_exonGeTrInfo.tab added
cf2c1ffc12e0_exonInfo.tab added
cf2c5e3b4087_geneInfo.tab added
cf2c4098f66_Genome added
cf2cfa5739c_genomeParameters.txt added
cf2c37490eca_Log.out added
cf2c1d6a0c21_SA added
cf2c1d42599d_SAindex added
cf2c6f09616c_sjdbInfo.txt added
cf2c50db3267_sjdbList.fromGTF.out.tab added
cf2c66ca31a9_sjdbList.out.tab added
cf2c648282f7_transcriptInfo.tab added
cf2c346459ae_GRCh38.GENCODE.v42_100 added
cf2c283bc961_knownGene_hg38.sql added
cf2c6d2213e9_knownGene_hg38.txt added
cf2c58495df8_refGene_hg38.sql added
cf2c38b87210_refGene_hg38.txt added
cf2c55489587_knownGene_mm39.sql added
cf2c1050fdcf_knownGene_mm39.txt added
cf2c35472967_refGene_mm39.sql added
cf2c52ef4484_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/RtmpY5mzM1/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 
 43.141   5.072  53.675