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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.9.0.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.9.0’
* 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 5.986   0.25   6.239
* 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-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.9.0’
** 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 version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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...
a54ef130bd0de_GRCh38.primary_assembly.genome.fa.1.bt2 added
a54ef635c062c_GRCh38.primary_assembly.genome.fa.2.bt2 added
a54ef697b543c_GRCh38.primary_assembly.genome.fa.3.bt2 added
a54ef5bad288d_GRCh38.primary_assembly.genome.fa.4.bt2 added
a54ef2af5666d_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
a54ef712fe8d2_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
a54ef6ce4592a_outfile.txt added
a54ef7f94be8b_GRCh37_to_GRCh38.chain added
a54ef13271075_GRCh37_to_NCBI34.chain added
a54ef6efd7588_GRCh37_to_NCBI35.chain added
a54ef5623f276_GRCh37_to_NCBI36.chain added
a54ef7354d719_GRCh38_to_GRCh37.chain added
a54ef3c007c_GRCh38_to_NCBI34.chain added
a54ef2ab8410f_GRCh38_to_NCBI35.chain added
a54ef3bc2830b_GRCh38_to_NCBI36.chain added
a54ef3382a91e_NCBI34_to_GRCh37.chain added
a54ef54937bd5_NCBI34_to_GRCh38.chain added
a54ef53ff2275_NCBI35_to_GRCh37.chain added
a54ef4a2edfdf_NCBI35_to_GRCh38.chain added
a54ef75ed2c1a_NCBI36_to_GRCh37.chain added
a54ef24957060_NCBI36_to_GRCh38.chain added
a54ef183182e7_GRCm38_to_NCBIM36.chain added
a54ef147de6cc_GRCm38_to_NCBIM37.chain added
a54ef476f0f6b_NCBIM36_to_GRCm38.chain added
a54ef3af060cd_NCBIM37_to_GRCm38.chain added
a54ef5b450e0c_1000G_omni2.5.b37.vcf.gz added
a54ef1bf9ba52_1000G_omni2.5.b37.vcf.gz.tbi added
a54efb89ace9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
a54ef6726f8d6_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
a54ef6b8e6314_1000G_omni2.5.hg38.vcf.gz added
a54ef582acc43_1000G_omni2.5.hg38.vcf.gz.tbi added
a54ef7a32c9b5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
a54ef4eea6940_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
a54ef41a6207f_af-only-gnomad.raw.sites.vcf added
a54ef55dff242_af-only-gnomad.raw.sites.vcf.idx added
a54ef79dfcfad_Mutect2-exome-panel.vcf.idx added
a54ef32d60951_Mutect2-WGS-panel-b37.vcf added
a54ef42c44b6c_Mutect2-WGS-panel-b37.vcf.idx added
a54ef79748e38_small_exac_common_3.vcf added
a54ef45fd19c6_small_exac_common_3.vcf.idx added
a54ef31c1c0f4_1000g_pon.hg38.vcf.gz added
a54ef4f9880ae_1000g_pon.hg38.vcf.gz.tbi added
a54ef3951f0df_af-only-gnomad.hg38.vcf.gz added
a54ef31fdc170_af-only-gnomad.hg38.vcf.gz.tbi added
a54ef7a50c1bd_small_exac_common_3.hg38.vcf.gz added
a54ef751473ea_small_exac_common_3.hg38.vcf.gz.tbi added
a54ef65806a8e_gencode.v41.annotation.gtf added
a54ef4ee43d93_gencode.v42.annotation.gtf added
a54ef49139660_gencode.vM30.annotation.gtf added
a54ef2faf4a6e_gencode.vM31.annotation.gtf added
a54ef44d169ad_gencode.v41.transcripts.fa added
a54ef6da906c0_gencode.v41.transcripts.fa.fai added
a54ef47e0cd55_gencode.v42.transcripts.fa added
a54ef594f5079_gencode.v42.transcripts.fa.fai added
a54ef3518162b_gencode.vM30.pc_transcripts.fa added
a54ef2d12e22_gencode.vM30.pc_transcripts.fa.fai added
a54ef34945e85_gencode.vM31.pc_transcripts.fa added
a54ef5111d07d_gencode.vM31.pc_transcripts.fa.fai added
a54efe5adb0b_GRCh38.primary_assembly.genome.fa.1.ht2 added
a54ef1bbb575b_GRCh38.primary_assembly.genome.fa.2.ht2 added
a54ef3ca03391_GRCh38.primary_assembly.genome.fa.3.ht2 added
a54ef6685a74e_GRCh38.primary_assembly.genome.fa.4.ht2 added
a54ef15ee2110_GRCh38.primary_assembly.genome.fa.5.ht2 added
a54efb8a9cd1_GRCh38.primary_assembly.genome.fa.6.ht2 added
a54ef282bc7cd_GRCh38.primary_assembly.genome.fa.7.ht2 added
a54ef6bce1353_GRCh38.primary_assembly.genome.fa.8.ht2 added
a54ef56a6c7e_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
a54ef5b01d11e_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
a54ef2e925ebf_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
a54ef7edefab6_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
a54ef20feeae4_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
a54ef60541fb4_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
a54ef4e777b65_GRCh38_full_analysis_set_plus_decoy_hla.fa added
a54ef5a50dbc3_GRCh38.primary_assembly.genome.fa.fai added
a54ef1251e124_GRCh38.primary_assembly.genome.fa.amb added
a54ef48c83d22_GRCh38.primary_assembly.genome.fa.ann added
a54ef4f654fae_GRCh38.primary_assembly.genome.fa.bwt added
a54ef77d24bb3_GRCh38.primary_assembly.genome.fa.pac added
a54ef17ac7ab5_GRCh38.primary_assembly.genome.fa.sa added
a54ef1878e60e_GRCh38.primary_assembly.genome.fa added
a54ef27819621_hs37d5.fa.fai added
a54ef5c7de462_hs37d5.fa.amb added
a54ef621ecce_hs37d5.fa.ann added
a54ef6f626376_hs37d5.fa.bwt added
a54ef35cd34db_hs37d5.fa.pac added
a54ef3b3a02f9_hs37d5.fa.sa added
a54ef72339199_hs37d5.fa added
a54ef6a619360_complete_ref_lens.bin added
a54efc4bd376_ctable.bin added
a54ef8e6ca4_ctg_offsets.bin added
a54ef61ceabc_duplicate_clusters.tsv added
a54ef48ec0707_info.json added
a54ef671413f3_mphf.bin added
a54ef1c0b0bcc_pos.bin added
a54ef5476a3d8_pre_indexing.log added
a54eff3fdbc0_rank.bin added
a54ef7d91f1f_ref_indexing.log added
a54ef59e11056_refAccumLengths.bin added
a54ef6a41acdf_reflengths.bin added
a54ef366b7ddf_refseq.bin added
a54ef58c00b0c_seq.bin added
a54efb4097c3_versionInfo.json added
a54ef16bf9d93_salmon_index added
a54ef27378671_chrLength.txt added
a54ef65917387_chrName.txt added
a54ef29117eb7_chrNameLength.txt added
a54ef6fffc394_chrStart.txt added
a54ef34f6c335_exonGeTrInfo.tab added
a54ef20e3ca6a_exonInfo.tab added
a54ef7ac3e49_geneInfo.tab added
a54ef4d6fa943_Genome added
a54ef4865608b_genomeParameters.txt added
a54ef642a22ac_Log.out added
a54ef53919611_SA added
a54ef37c7c402_SAindex added
a54ef19f75787_sjdbInfo.txt added
a54efecb990a_sjdbList.fromGTF.out.tab added
a54ef29fb559b_sjdbList.out.tab added
a54ef458eae8_transcriptInfo.tab added
a54ef1b176c80_GRCh38.GENCODE.v42_100 added
a54ef2a89c23f_knownGene_hg38.sql added
a54efa75d5a4_knownGene_hg38.txt added
a54ef64037387_refGene_hg38.sql added
a54ef119dd632_refGene_hg38.txt added
a54ef2680e170_knownGene_mm39.sql added
a54ef387a175f_knownGene_mm39.txt added
a54ef20ddb1f3_refGene_mm39.sql added
a54ef2e5a0090_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/RtmpSFWvGm/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 
 17.976   1.053  19.381