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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 4.5.0 (2025-04-11)
* 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 ‘1.9.0’
* 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 5.899  0.241   6.143
* 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
###
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* 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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...
37f58339510417_GRCh38.primary_assembly.genome.fa.1.bt2 added
37f5831e8af82b_GRCh38.primary_assembly.genome.fa.2.bt2 added
37f58372981146_GRCh38.primary_assembly.genome.fa.3.bt2 added
37f58319b6a2be_GRCh38.primary_assembly.genome.fa.4.bt2 added
37f5831c2c9381_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
37f5837b4f6676_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
37f58349765688_outfile.txt added
37f58353f4bd16_GRCh37_to_GRCh38.chain added
37f5835373fa2d_GRCh37_to_NCBI34.chain added
37f5835b946662_GRCh37_to_NCBI35.chain added
37f583303bdf1c_GRCh37_to_NCBI36.chain added
37f58338fac8bc_GRCh38_to_GRCh37.chain added
37f58335577352_GRCh38_to_NCBI34.chain added
37f58343a71149_GRCh38_to_NCBI35.chain added
37f5833e47880a_GRCh38_to_NCBI36.chain added
37f58328209d27_NCBI34_to_GRCh37.chain added
37f5835bcec723_NCBI34_to_GRCh38.chain added
37f58345f6cccd_NCBI35_to_GRCh37.chain added
37f5831e8c0bb2_NCBI35_to_GRCh38.chain added
37f58336c9c261_NCBI36_to_GRCh37.chain added
37f58354c3463c_NCBI36_to_GRCh38.chain added
37f58315263490_GRCm38_to_NCBIM36.chain added
37f5832150dac1_GRCm38_to_NCBIM37.chain added
37f5832e8fdefb_NCBIM36_to_GRCm38.chain added
37f583275a8754_NCBIM37_to_GRCm38.chain added
37f5836a0352d2_1000G_omni2.5.b37.vcf.gz added
37f58310aeaf0b_1000G_omni2.5.b37.vcf.gz.tbi added
37f5831b34d02d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
37f58342b301be_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
37f58332aeef22_1000G_omni2.5.hg38.vcf.gz added
37f5837b57c6d5_1000G_omni2.5.hg38.vcf.gz.tbi added
37f5837c0405d6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
37f5835139e74e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
37f5836defd81b_af-only-gnomad.raw.sites.vcf added
37f58315baa894_af-only-gnomad.raw.sites.vcf.idx added
37f5836d667acf_Mutect2-exome-panel.vcf.idx added
37f583693f3e91_Mutect2-WGS-panel-b37.vcf added
37f5835f30ff1c_Mutect2-WGS-panel-b37.vcf.idx added
37f583415b37e5_small_exac_common_3.vcf added
37f5833cb338bf_small_exac_common_3.vcf.idx added
37f5833ac5657f_1000g_pon.hg38.vcf.gz added
37f58371971701_1000g_pon.hg38.vcf.gz.tbi added
37f58375ae017b_af-only-gnomad.hg38.vcf.gz added
37f583701cd8d1_af-only-gnomad.hg38.vcf.gz.tbi added
37f583353e284b_small_exac_common_3.hg38.vcf.gz added
37f58333f58985_small_exac_common_3.hg38.vcf.gz.tbi added
37f583183d75f8_gencode.v41.annotation.gtf added
37f583110cef6e_gencode.v42.annotation.gtf added
37f58379ec5652_gencode.vM30.annotation.gtf added
37f58336c981ab_gencode.vM31.annotation.gtf added
37f58347d6b1cf_gencode.v41.transcripts.fa added
37f5834eaf9c8e_gencode.v41.transcripts.fa.fai added
37f5834befb63b_gencode.v42.transcripts.fa added
37f58369278c91_gencode.v42.transcripts.fa.fai added
37f5837d3f7b89_gencode.vM30.pc_transcripts.fa added
37f583734a3d8f_gencode.vM30.pc_transcripts.fa.fai added
37f583532adf63_gencode.vM31.pc_transcripts.fa added
37f583dee2a94_gencode.vM31.pc_transcripts.fa.fai added
37f583e7f0dbc_GRCh38.primary_assembly.genome.fa.1.ht2 added
37f58315dde122_GRCh38.primary_assembly.genome.fa.2.ht2 added
37f583409d19b7_GRCh38.primary_assembly.genome.fa.3.ht2 added
37f5839d6d491_GRCh38.primary_assembly.genome.fa.4.ht2 added
37f58311e1e6f8_GRCh38.primary_assembly.genome.fa.5.ht2 added
37f58311d70105_GRCh38.primary_assembly.genome.fa.6.ht2 added
37f58377c6acac_GRCh38.primary_assembly.genome.fa.7.ht2 added
37f583279c8f8c_GRCh38.primary_assembly.genome.fa.8.ht2 added
37f5837f3d7bd4_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
37f5836105eb3d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
37f5836cd8ea9_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
37f5834098b3ba_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
37f5831db923fc_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
37f5834192f428_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
37f583322fcabb_GRCh38_full_analysis_set_plus_decoy_hla.fa added
37f58313672577_GRCh38.primary_assembly.genome.fa.fai added
37f58331afccf9_GRCh38.primary_assembly.genome.fa.amb added
37f583676df306_GRCh38.primary_assembly.genome.fa.ann added
37f583475caefd_GRCh38.primary_assembly.genome.fa.bwt added
37f58349ed42f1_GRCh38.primary_assembly.genome.fa.pac added
37f583787ae274_GRCh38.primary_assembly.genome.fa.sa added
37f5834149054f_GRCh38.primary_assembly.genome.fa added
37f583b6c49c_hs37d5.fa.fai added
37f58340519444_hs37d5.fa.amb added
37f583ff8a1de_hs37d5.fa.ann added
37f5834ca67ad7_hs37d5.fa.bwt added
37f583297920d5_hs37d5.fa.pac added
37f583d381d67_hs37d5.fa.sa added
37f5833ff0b866_hs37d5.fa added
37f5837ca40038_complete_ref_lens.bin added
37f5831b2647fc_ctable.bin added
37f5834e6fc622_ctg_offsets.bin added
37f5831281e15a_duplicate_clusters.tsv added
37f5835bc361b3_info.json added
37f58358469ab3_mphf.bin added
37f5832463c852_pos.bin added
37f5836d9a62b8_pre_indexing.log added
37f583500d475f_rank.bin added
37f5834c0057df_ref_indexing.log added
37f5836cd7de8c_refAccumLengths.bin added
37f5833113329d_reflengths.bin added
37f58352cde688_refseq.bin added
37f5832d709246_seq.bin added
37f5834ecc5699_versionInfo.json added
37f5831460dab0_salmon_index added
37f5835fa05d02_chrLength.txt added
37f58362337c11_chrName.txt added
37f5834610a7a9_chrNameLength.txt added
37f583470e5008_chrStart.txt added
37f58329902b0e_exonGeTrInfo.tab added
37f583ffdea9a_exonInfo.tab added
37f5833f89327d_geneInfo.tab added
37f5836ad9305d_Genome added
37f58310b4af37_genomeParameters.txt added
37f5837fdac6c1_Log.out added
37f5837ad1d23b_SA added
37f5835d5b2a0e_SAindex added
37f5832953e796_sjdbInfo.txt added
37f583809efa3_sjdbList.fromGTF.out.tab added
37f5831d4be275_sjdbList.out.tab added
37f58325f7e7ce_transcriptInfo.tab added
37f5832330379f_GRCh38.GENCODE.v42_100 added
37f5836bbba897_knownGene_hg38.sql added
37f5833879c929_knownGene_hg38.txt added
37f5837ef39952_refGene_hg38.sql added
37f5834402434b_refGene_hg38.txt added
37f5835cdd917b_knownGene_mm39.sql added
37f5836c8dfc0a_knownGene_mm39.txt added
37f583140f8aaa_refGene_mm39.sql added
37f58328dde95a_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/Rtmp7tHhCD/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 
 18.275   0.956  19.285