##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReUseData_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.7.0’
* 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 5.93   0.41   6.343
* 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-3.21-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.7.0’
** 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 Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"
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...
36c96445871eac_GRCh38.primary_assembly.genome.fa.1.bt2 added
36c9642cf8615a_GRCh38.primary_assembly.genome.fa.2.bt2 added
36c96421d6ef0d_GRCh38.primary_assembly.genome.fa.3.bt2 added
36c9646ec3c8be_GRCh38.primary_assembly.genome.fa.4.bt2 added
36c9646a864a8e_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
36c964370fdc92_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
36c9642e756d7_outfile.txt added
36c96467b571be_GRCh37_to_GRCh38.chain added
36c9645f03546d_GRCh37_to_NCBI34.chain added
36c964758cfcc9_GRCh37_to_NCBI35.chain added
36c964155850e2_GRCh37_to_NCBI36.chain added
36c964539b2ce6_GRCh38_to_GRCh37.chain added
36c964486330b5_GRCh38_to_NCBI34.chain added
36c96423b4c6f8_GRCh38_to_NCBI35.chain added
36c9649168a36_GRCh38_to_NCBI36.chain added
36c96466acda8d_NCBI34_to_GRCh37.chain added
36c9646f29c526_NCBI34_to_GRCh38.chain added
36c9645e8a6357_NCBI35_to_GRCh37.chain added
36c96436d727e8_NCBI35_to_GRCh38.chain added
36c9646bf32886_NCBI36_to_GRCh37.chain added
36c9642314593d_NCBI36_to_GRCh38.chain added
36c9643d39830c_GRCm38_to_NCBIM36.chain added
36c96445c19334_GRCm38_to_NCBIM37.chain added
36c9645e6bb6ac_NCBIM36_to_GRCm38.chain added
36c96459f24b89_NCBIM37_to_GRCm38.chain added
36c9643bf06874_1000G_omni2.5.b37.vcf.gz added
36c96447065f69_1000G_omni2.5.b37.vcf.gz.tbi added
36c964101f539f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
36c9645e72a135_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
36c964702d1af3_1000G_omni2.5.hg38.vcf.gz added
36c964ad5b22f_1000G_omni2.5.hg38.vcf.gz.tbi added
36c96423f9bfe2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
36c9641d257c4d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
36c9642caca13c_af-only-gnomad.raw.sites.vcf added
36c96412bd88a0_af-only-gnomad.raw.sites.vcf.idx added
36c9647abc6db_Mutect2-exome-panel.vcf.idx added
36c96463bc7dce_Mutect2-WGS-panel-b37.vcf added
36c96415a4df77_Mutect2-WGS-panel-b37.vcf.idx added
36c9646f613899_small_exac_common_3.vcf added
36c96442bfd23b_small_exac_common_3.vcf.idx added
36c964b31dc41_1000g_pon.hg38.vcf.gz added
36c9644b9897c_1000g_pon.hg38.vcf.gz.tbi added
36c964165aff22_af-only-gnomad.hg38.vcf.gz added
36c96453950cf6_af-only-gnomad.hg38.vcf.gz.tbi added
36c964286e5074_small_exac_common_3.hg38.vcf.gz added
36c9641f718958_small_exac_common_3.hg38.vcf.gz.tbi added
36c9643a41e783_gencode.v41.annotation.gtf added
36c9641798159a_gencode.v42.annotation.gtf added
36c9647dfbecaf_gencode.vM30.annotation.gtf added
36c96471190f6c_gencode.vM31.annotation.gtf added
36c96438b3e20_gencode.v41.transcripts.fa added
36c964211045ec_gencode.v41.transcripts.fa.fai added
36c9642e529278_gencode.v42.transcripts.fa added
36c964494cd154_gencode.v42.transcripts.fa.fai added
36c9647f7bfc98_gencode.vM30.pc_transcripts.fa added
36c964844de01_gencode.vM30.pc_transcripts.fa.fai added
36c96453d39c8_gencode.vM31.pc_transcripts.fa added
36c96446825c02_gencode.vM31.pc_transcripts.fa.fai added
36c964186431a0_GRCh38.primary_assembly.genome.fa.1.ht2 added
36c96463afdafe_GRCh38.primary_assembly.genome.fa.2.ht2 added
36c96436af76f5_GRCh38.primary_assembly.genome.fa.3.ht2 added
36c9642339e3cf_GRCh38.primary_assembly.genome.fa.4.ht2 added
36c9647a99ae0_GRCh38.primary_assembly.genome.fa.5.ht2 added
36c96453d4f342_GRCh38.primary_assembly.genome.fa.6.ht2 added
36c9644fe6850b_GRCh38.primary_assembly.genome.fa.7.ht2 added
36c9641a672380_GRCh38.primary_assembly.genome.fa.8.ht2 added
36c9645b80ba1d_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
36c96433a302da_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
36c964300c02f8_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
36c9644ae1f2b7_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
36c9647662d515_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
36c9643b3ddf39_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
36c9644f9b7c33_GRCh38_full_analysis_set_plus_decoy_hla.fa added
36c964cbdd437_GRCh38.primary_assembly.genome.fa.fai added
36c964ed2ec2f_GRCh38.primary_assembly.genome.fa.amb added
36c9647809cca7_GRCh38.primary_assembly.genome.fa.ann added
36c9642c2f5d90_GRCh38.primary_assembly.genome.fa.bwt added
36c9644914d3b3_GRCh38.primary_assembly.genome.fa.pac added
36c964fa1e241_GRCh38.primary_assembly.genome.fa.sa added
36c9642a2b4a3f_GRCh38.primary_assembly.genome.fa added
36c9643a2de31f_hs37d5.fa.fai added
36c964132d2061_hs37d5.fa.amb added
36c9644b3b902c_hs37d5.fa.ann added
36c96468807597_hs37d5.fa.bwt added
36c9645c79f1b6_hs37d5.fa.pac added
36c9644ab78cc4_hs37d5.fa.sa added
36c96470c55398_hs37d5.fa added
36c96461b72b7e_complete_ref_lens.bin added
36c9641139e8c6_ctable.bin added
36c9649298539_ctg_offsets.bin added
36c9644567067c_duplicate_clusters.tsv added
36c96447e95fbb_info.json added
36c9642c636908_mphf.bin added
36c9644d10a15c_pos.bin added
36c9641bbe52fd_pre_indexing.log added
36c9647c49ee14_rank.bin added
36c9646777c4dd_ref_indexing.log added
36c964773f0d1b_refAccumLengths.bin added
36c9642fecf0ee_reflengths.bin added
36c9641783c7d5_refseq.bin added
36c9644220ffd2_seq.bin added
36c964264fc603_versionInfo.json added
36c96452c1a70e_salmon_index added
36c96411bc7c05_chrLength.txt added
36c964330d9a3b_chrName.txt added
36c9646194933d_chrNameLength.txt added
36c9649c648ac_chrStart.txt added
36c9645f3cf7cb_exonGeTrInfo.tab added
36c9642aa966f0_exonInfo.tab added
36c96419682aed_geneInfo.tab added
36c964968420a_Genome added
36c96464d74a0f_genomeParameters.txt added
36c9642c954b4e_Log.out added
36c96454a3d236_SA added
36c9644d57bfa6_SAindex added
36c96490f3d04_sjdbInfo.txt added
36c9641f5b5efb_sjdbList.fromGTF.out.tab added
36c9643e1d133f_sjdbList.out.tab added
36c9646ac66883_transcriptInfo.tab added
36c964309547c1_GRCh38.GENCODE.v42_100 added
36c96447469878_knownGene_hg38.sql added
36c964302d6eff_knownGene_hg38.txt added
36c964787ea77d_refGene_hg38.sql added
36c96473aa0180_refGene_hg38.txt added
36c9647d3e105c_knownGene_mm39.sql added
36c964143cfa7a_knownGene_mm39.txt added
36c9646ff3ef94_refGene_mm39.sql added
36c96464b5d539_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/RtmpkdizAH/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 
 20.107   1.761  22.088