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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ReUseData_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 7.487  0.455   7.945
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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-pc-linux-gnu

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...
3c25b718267d20_GRCh38.primary_assembly.genome.fa.1.bt2 added
3c25b744f8a22c_GRCh38.primary_assembly.genome.fa.2.bt2 added
3c25b766cae999_GRCh38.primary_assembly.genome.fa.3.bt2 added
3c25b713844774_GRCh38.primary_assembly.genome.fa.4.bt2 added
3c25b7763bd3bd_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3c25b772d41733_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3c25b721fff352_outfile.txt added
3c25b735473ee9_GRCh37_to_GRCh38.chain added
3c25b751713a94_GRCh37_to_NCBI34.chain added
3c25b74c93abb8_GRCh37_to_NCBI35.chain added
3c25b768214865_GRCh37_to_NCBI36.chain added
3c25b7222da71b_GRCh38_to_GRCh37.chain added
3c25b71948a778_GRCh38_to_NCBI34.chain added
3c25b75d4c79f_GRCh38_to_NCBI35.chain added
3c25b756ef6e8f_GRCh38_to_NCBI36.chain added
3c25b71cacd6b1_NCBI34_to_GRCh37.chain added
3c25b71e67f2d3_NCBI34_to_GRCh38.chain added
3c25b74d633e6b_NCBI35_to_GRCh37.chain added
3c25b740084c13_NCBI35_to_GRCh38.chain added
3c25b74f999efd_NCBI36_to_GRCh37.chain added
3c25b7437e2f10_NCBI36_to_GRCh38.chain added
3c25b73538713d_GRCm38_to_NCBIM36.chain added
3c25b774a608f4_GRCm38_to_NCBIM37.chain added
3c25b72fdf5495_NCBIM36_to_GRCm38.chain added
3c25b7484f6096_NCBIM37_to_GRCm38.chain added
3c25b751b9cf5d_1000G_omni2.5.b37.vcf.gz added
3c25b75805f1d6_1000G_omni2.5.b37.vcf.gz.tbi added
3c25b717875c25_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3c25b7c0b6183_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3c25b7437cb6df_1000G_omni2.5.hg38.vcf.gz added
3c25b7214cc1c1_1000G_omni2.5.hg38.vcf.gz.tbi added
3c25b72431dea3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3c25b7875590b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3c25b7817ab5a_af-only-gnomad.raw.sites.vcf added
3c25b737b62617_af-only-gnomad.raw.sites.vcf.idx added
3c25b77eb12cc8_Mutect2-exome-panel.vcf.idx added
3c25b77aebc28d_Mutect2-WGS-panel-b37.vcf added
3c25b759b61969_Mutect2-WGS-panel-b37.vcf.idx added
3c25b733f86bb1_small_exac_common_3.vcf added
3c25b74c5cfd21_small_exac_common_3.vcf.idx added
3c25b72649c522_1000g_pon.hg38.vcf.gz added
3c25b71c19b417_1000g_pon.hg38.vcf.gz.tbi added
3c25b76e8aa43c_af-only-gnomad.hg38.vcf.gz added
3c25b73f926c9a_af-only-gnomad.hg38.vcf.gz.tbi added
3c25b721ee7bb6_small_exac_common_3.hg38.vcf.gz added
3c25b7457a12cc_small_exac_common_3.hg38.vcf.gz.tbi added
3c25b75c3f434b_gencode.v41.annotation.gtf added
3c25b740566e8a_gencode.v42.annotation.gtf added
3c25b712dd5137_gencode.vM30.annotation.gtf added
3c25b71c478f5e_gencode.vM31.annotation.gtf added
3c25b7ff00d87_gencode.v41.transcripts.fa added
3c25b7565b8047_gencode.v41.transcripts.fa.fai added
3c25b75180009b_gencode.v42.transcripts.fa added
3c25b7496167b_gencode.v42.transcripts.fa.fai added
3c25b763ad4dc_gencode.vM30.pc_transcripts.fa added
3c25b719cf6132_gencode.vM30.pc_transcripts.fa.fai added
3c25b7564fe5d8_gencode.vM31.pc_transcripts.fa added
3c25b75e40c6b2_gencode.vM31.pc_transcripts.fa.fai added
3c25b73156bd57_GRCh38.primary_assembly.genome.fa.1.ht2 added
3c25b7625b475b_GRCh38.primary_assembly.genome.fa.2.ht2 added
3c25b721bd7d91_GRCh38.primary_assembly.genome.fa.3.ht2 added
3c25b752a37f18_GRCh38.primary_assembly.genome.fa.4.ht2 added
3c25b768d25fe_GRCh38.primary_assembly.genome.fa.5.ht2 added
3c25b72a32d69c_GRCh38.primary_assembly.genome.fa.6.ht2 added
3c25b75abb2a73_GRCh38.primary_assembly.genome.fa.7.ht2 added
3c25b73e434c16_GRCh38.primary_assembly.genome.fa.8.ht2 added
3c25b728e40365_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3c25b755a6ed00_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3c25b717f9657f_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3c25b75cdc6f16_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3c25b72203ea22_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3c25b73e432aa1_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3c25b778f6232d_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3c25b7108e8e5e_GRCh38.primary_assembly.genome.fa.fai added
3c25b77dd5973c_GRCh38.primary_assembly.genome.fa.amb added
3c25b71ae49ee4_GRCh38.primary_assembly.genome.fa.ann added
3c25b75608a12a_GRCh38.primary_assembly.genome.fa.bwt added
3c25b75a14da87_GRCh38.primary_assembly.genome.fa.pac added
3c25b75b3b0d6e_GRCh38.primary_assembly.genome.fa.sa added
3c25b768e5f261_GRCh38.primary_assembly.genome.fa added
3c25b7765c69e6_hs37d5.fa.fai added
3c25b76b2b1af5_hs37d5.fa.amb added
3c25b73f4172a8_hs37d5.fa.ann added
3c25b747dc6a81_hs37d5.fa.bwt added
3c25b76fc13171_hs37d5.fa.pac added
3c25b7457c4784_hs37d5.fa.sa added
3c25b761abcbb3_hs37d5.fa added
3c25b746111749_complete_ref_lens.bin added
3c25b723bd0e36_ctable.bin added
3c25b71302890a_ctg_offsets.bin added
3c25b7286c5ea5_duplicate_clusters.tsv added
3c25b7457a8bc7_info.json added
3c25b765a60823_mphf.bin added
3c25b72ef984a3_pos.bin added
3c25b76fad6264_pre_indexing.log added
3c25b740613296_rank.bin added
3c25b76d3cd0b9_ref_indexing.log added
3c25b7189165c9_refAccumLengths.bin added
3c25b716081f96_reflengths.bin added
3c25b75363639_refseq.bin added
3c25b7756dd4df_seq.bin added
3c25b7380c09b8_versionInfo.json added
3c25b7437960da_salmon_index added
3c25b76e63f80d_chrLength.txt added
3c25b7489a9817_chrName.txt added
3c25b7414ef816_chrNameLength.txt added
3c25b794896f1_chrStart.txt added
3c25b71ea33941_exonGeTrInfo.tab added
3c25b71b63d29e_exonInfo.tab added
3c25b76483a45f_geneInfo.tab added
3c25b77892ba3_Genome added
3c25b711c03c84_genomeParameters.txt added
3c25b74faebf54_Log.out added
3c25b746ca9e4b_SA added
3c25b7599ca705_SAindex added
3c25b73f6ff0c5_sjdbInfo.txt added
3c25b7c46e5d0_sjdbList.fromGTF.out.tab added
3c25b73b4872b9_sjdbList.out.tab added
3c25b7581080f_transcriptInfo.tab added
3c25b73003f406_GRCh38.GENCODE.v42_100 added
3c25b74e4afbc3_knownGene_hg38.sql added
3c25b72ded66b4_knownGene_hg38.txt added
3c25b7757e7fce_refGene_hg38.sql added
3c25b733f103e6_refGene_hg38.txt added
3c25b75ce6eb57_knownGene_mm39.sql added
3c25b7652be232_knownGene_mm39.txt added
3c25b77452367c_refGene_mm39.sql added
3c25b74a23bc11_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/RtmppGtZCJ/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 
 22.557   1.940  24.934