##############################################################################
##############################################################################
###
### 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 6.163  0.437   6.601
* 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.

##############################################################################
##############################################################################
###
### 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...
1f87405d1ef8a4_GRCh38.primary_assembly.genome.fa.1.bt2 added
1f874066a41f3f_GRCh38.primary_assembly.genome.fa.2.bt2 added
1f87401a0dce12_GRCh38.primary_assembly.genome.fa.3.bt2 added
1f874022411cfe_GRCh38.primary_assembly.genome.fa.4.bt2 added
1f87407ddad877_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1f874016701546_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1f8740505d3d84_outfile.txt added
1f87404cc76099_GRCh37_to_GRCh38.chain added
1f87401b6ddb0b_GRCh37_to_NCBI34.chain added
1f87405da7ac3c_GRCh37_to_NCBI35.chain added
1f874043696a68_GRCh37_to_NCBI36.chain added
1f87401e1178b0_GRCh38_to_GRCh37.chain added
1f874064f53cb9_GRCh38_to_NCBI34.chain added
1f87404ff63b9b_GRCh38_to_NCBI35.chain added
1f87401f6046f7_GRCh38_to_NCBI36.chain added
1f87401976967e_NCBI34_to_GRCh37.chain added
1f87404d76b9e4_NCBI34_to_GRCh38.chain added
1f87405b1f0e9d_NCBI35_to_GRCh37.chain added
1f87406b15b3d5_NCBI35_to_GRCh38.chain added
1f874068edb8cb_NCBI36_to_GRCh37.chain added
1f8740496948fd_NCBI36_to_GRCh38.chain added
1f874034fff10d_GRCm38_to_NCBIM36.chain added
1f87402c3bb08d_GRCm38_to_NCBIM37.chain added
1f87401f7c8fe7_NCBIM36_to_GRCm38.chain added
1f8740228f22fd_NCBIM37_to_GRCm38.chain added
1f874068838a06_1000G_omni2.5.b37.vcf.gz added
1f87405b2c8437_1000G_omni2.5.b37.vcf.gz.tbi added
1f874034ab20d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1f8740124a8254_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1f87402147fb0f_1000G_omni2.5.hg38.vcf.gz added
1f874016db1aa9_1000G_omni2.5.hg38.vcf.gz.tbi added
1f87406f697af8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1f87407ec1a4e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1f874030e8e8bb_af-only-gnomad.raw.sites.vcf added
1f874011aa97f7_af-only-gnomad.raw.sites.vcf.idx added
1f87405c6f2c5_Mutect2-exome-panel.vcf.idx added
1f87404758fe01_Mutect2-WGS-panel-b37.vcf added
1f87406207d57b_Mutect2-WGS-panel-b37.vcf.idx added
1f8740528e535e_small_exac_common_3.vcf added
1f874062c6d90c_small_exac_common_3.vcf.idx added
1f87403faf81b7_1000g_pon.hg38.vcf.gz added
1f874015f7bdc7_1000g_pon.hg38.vcf.gz.tbi added
1f8740d851bd_af-only-gnomad.hg38.vcf.gz added
1f874024a4be71_af-only-gnomad.hg38.vcf.gz.tbi added
1f874065edf962_small_exac_common_3.hg38.vcf.gz added
1f8740203898b4_small_exac_common_3.hg38.vcf.gz.tbi added
1f87403e1b54ef_gencode.v41.annotation.gtf added
1f87403364b346_gencode.v42.annotation.gtf added
1f87407b57a751_gencode.vM30.annotation.gtf added
1f8740293108c4_gencode.vM31.annotation.gtf added
1f87401c526c12_gencode.v41.transcripts.fa added
1f874044c0f04e_gencode.v41.transcripts.fa.fai added
1f87405e30f9d1_gencode.v42.transcripts.fa added
1f8740488e1c9f_gencode.v42.transcripts.fa.fai added
1f8740643d8036_gencode.vM30.pc_transcripts.fa added
1f8740c01ccf_gencode.vM30.pc_transcripts.fa.fai added
1f87403111a6a5_gencode.vM31.pc_transcripts.fa added
1f87403f6a046d_gencode.vM31.pc_transcripts.fa.fai added
1f874040acedc_GRCh38.primary_assembly.genome.fa.1.ht2 added
1f8740435c28fa_GRCh38.primary_assembly.genome.fa.2.ht2 added
1f874060b1ff7c_GRCh38.primary_assembly.genome.fa.3.ht2 added
1f87401ae5e985_GRCh38.primary_assembly.genome.fa.4.ht2 added
1f874032c5a3f2_GRCh38.primary_assembly.genome.fa.5.ht2 added
1f8740689e19ca_GRCh38.primary_assembly.genome.fa.6.ht2 added
1f87404bced240_GRCh38.primary_assembly.genome.fa.7.ht2 added
1f874044703be9_GRCh38.primary_assembly.genome.fa.8.ht2 added
1f87406e650c90_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1f87401327d042_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1f874026781165_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1f874040f35fee_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1f874075eea94e_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1f87406627931c_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1f874056eb1db5_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1f874076c6fb0b_GRCh38.primary_assembly.genome.fa.fai added
1f8740acc518d_GRCh38.primary_assembly.genome.fa.amb added
1f87403cd91718_GRCh38.primary_assembly.genome.fa.ann added
1f874016ff93bf_GRCh38.primary_assembly.genome.fa.bwt added
1f874048e7a67d_GRCh38.primary_assembly.genome.fa.pac added
1f8740703dca5e_GRCh38.primary_assembly.genome.fa.sa added
1f874012573b10_GRCh38.primary_assembly.genome.fa added
1f87407218af41_hs37d5.fa.fai added
1f8740c903670_hs37d5.fa.amb added
1f874057182b5f_hs37d5.fa.ann added
1f87405049a913_hs37d5.fa.bwt added
1f8740551e5310_hs37d5.fa.pac added
1f87403b55ab95_hs37d5.fa.sa added
1f87405109c5e2_hs37d5.fa added
1f874062ff9b5_complete_ref_lens.bin added
1f87407abfb002_ctable.bin added
1f8740551494be_ctg_offsets.bin added
1f8740498c22af_duplicate_clusters.tsv added
1f87405b71af7e_info.json added
1f87406ffa7e43_mphf.bin added
1f87407c51c6a2_pos.bin added
1f8740440fc948_pre_indexing.log added
1f87403bc95083_rank.bin added
1f874040c2028b_ref_indexing.log added
1f87403274d5d8_refAccumLengths.bin added
1f87404ef120c5_reflengths.bin added
1f8740673a13f0_refseq.bin added
1f8740736835c7_seq.bin added
1f874044dfca14_versionInfo.json added
1f87404d61a70d_salmon_index added
1f87404a53537c_chrLength.txt added
1f87403ba6c51f_chrName.txt added
1f8740582df89a_chrNameLength.txt added
1f874072c6a94_chrStart.txt added
1f874052a658df_exonGeTrInfo.tab added
1f874021159f17_exonInfo.tab added
1f8740776a34f3_geneInfo.tab added
1f874064fd93ef_Genome added
1f8740132e4e59_genomeParameters.txt added
1f87403fa6b63_Log.out added
1f87403c15bf4e_SA added
1f87406377f76c_SAindex added
1f87405918be73_sjdbInfo.txt added
1f8740776b6ae3_sjdbList.fromGTF.out.tab added
1f87403481bd4e_sjdbList.out.tab added
1f87405f48b829_transcriptInfo.tab added
1f8740722b1ae5_GRCh38.GENCODE.v42_100 added
1f8740996520c_knownGene_hg38.sql added
1f874028d4dad8_knownGene_hg38.txt added
1f87404d9cca63_refGene_hg38.sql added
1f87407990d04f_refGene_hg38.txt added
1f87402526a17a_knownGene_mm39.sql added
1f874011ac93ac_knownGene_mm39.txt added
1f8740355a20d2_refGene_mm39.sql added
1f874065e8a406_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/RtmpncSkX8/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 
 19.953   1.475  21.906