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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReUseData_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.10.0’
* 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 8.718  0.363   9.118
getCloudData  3.213  0.232   8.027
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* 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/R/R/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.10.0’
** 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: aarch64-unknown-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...
1e774b65e9ca7b_GRCh38.primary_assembly.genome.fa.1.bt2 added
1e774b7ef3b715_GRCh38.primary_assembly.genome.fa.2.bt2 added
1e774b4aaf4d5a_GRCh38.primary_assembly.genome.fa.3.bt2 added
1e774b4712bf91_GRCh38.primary_assembly.genome.fa.4.bt2 added
1e774b6c93ea25_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1e774b2bfbd699_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1e774b114b03b0_outfile.txt added
1e774b21040747_GRCh37_to_GRCh38.chain added
1e774b4d9f1373_GRCh37_to_NCBI34.chain added
1e774b1cd42f94_GRCh37_to_NCBI35.chain added
1e774b46ffe7f_GRCh37_to_NCBI36.chain added
1e774b202af6b7_GRCh38_to_GRCh37.chain added
1e774b15a7390c_GRCh38_to_NCBI34.chain added
1e774b613e5712_GRCh38_to_NCBI35.chain added
1e774b3f693bab_GRCh38_to_NCBI36.chain added
1e774b6a4734bd_NCBI34_to_GRCh37.chain added
1e774b5c2548_NCBI34_to_GRCh38.chain added
1e774b7082a818_NCBI35_to_GRCh37.chain added
1e774b16eed104_NCBI35_to_GRCh38.chain added
1e774b552a31ca_NCBI36_to_GRCh37.chain added
1e774b4820b01e_NCBI36_to_GRCh38.chain added
1e774b65740f62_GRCm38_to_NCBIM36.chain added
1e774b3f8c1f21_GRCm38_to_NCBIM37.chain added
1e774b20ef7535_NCBIM36_to_GRCm38.chain added
1e774b6d90b042_NCBIM37_to_GRCm38.chain added
1e774b6fd93144_1000G_omni2.5.b37.vcf.gz added
1e774b10f3d415_1000G_omni2.5.b37.vcf.gz.tbi added
1e774b5d62a787_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1e774b33105bfa_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1e774b353c6a16_1000G_omni2.5.hg38.vcf.gz added
1e774b725e7ce5_1000G_omni2.5.hg38.vcf.gz.tbi added
1e774b18fa2675_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1e774b3430212b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1e774b3d0dca3f_af-only-gnomad.raw.sites.vcf added
1e774b600ce607_af-only-gnomad.raw.sites.vcf.idx added
1e774b20c40b51_Mutect2-exome-panel.vcf.idx added
1e774b6909a0d8_Mutect2-WGS-panel-b37.vcf added
1e774b7157e9b7_Mutect2-WGS-panel-b37.vcf.idx added
1e774b41c81298_small_exac_common_3.vcf added
1e774b36a8b44b_small_exac_common_3.vcf.idx added
1e774be2c194b_1000g_pon.hg38.vcf.gz added
1e774b46381117_1000g_pon.hg38.vcf.gz.tbi added
1e774b56d3ab03_af-only-gnomad.hg38.vcf.gz added
1e774b23d35258_af-only-gnomad.hg38.vcf.gz.tbi added
1e774b27766829_small_exac_common_3.hg38.vcf.gz added
1e774b163ce6ae_small_exac_common_3.hg38.vcf.gz.tbi added
1e774be1a8715_gencode.v41.annotation.gtf added
1e774b27d28d71_gencode.v42.annotation.gtf added
1e774b6bf8ec6_gencode.vM30.annotation.gtf added
1e774b25095819_gencode.vM31.annotation.gtf added
1e774b7cfcbf3b_gencode.v41.transcripts.fa added
1e774b4ee03ee4_gencode.v41.transcripts.fa.fai added
1e774ba7d677b_gencode.v42.transcripts.fa added
1e774b3c88de5d_gencode.v42.transcripts.fa.fai added
1e774b6fcfb419_gencode.vM30.pc_transcripts.fa added
1e774b780e17bd_gencode.vM30.pc_transcripts.fa.fai added
1e774b2c620fa1_gencode.vM31.pc_transcripts.fa added
1e774bc3882e_gencode.vM31.pc_transcripts.fa.fai added
1e774b5570bf44_GRCh38.primary_assembly.genome.fa.1.ht2 added
1e774b5f726b9b_GRCh38.primary_assembly.genome.fa.2.ht2 added
1e774b35fff245_GRCh38.primary_assembly.genome.fa.3.ht2 added
1e774b47cf3c29_GRCh38.primary_assembly.genome.fa.4.ht2 added
1e774b786c9211_GRCh38.primary_assembly.genome.fa.5.ht2 added
1e774b6a301370_GRCh38.primary_assembly.genome.fa.6.ht2 added
1e774b4dd0669_GRCh38.primary_assembly.genome.fa.7.ht2 added
1e774b58797818_GRCh38.primary_assembly.genome.fa.8.ht2 added
1e774baf41ec1_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1e774b6de6a741_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1e774b49d161cf_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1e774b4cbc3159_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1e774b248f5b8d_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1e774b57fd7b1b_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1e774b12f44271_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1e774b7b630690_GRCh38.primary_assembly.genome.fa.fai added
1e774b7bd0cd73_GRCh38.primary_assembly.genome.fa.amb added
1e774b3a6aaa9a_GRCh38.primary_assembly.genome.fa.ann added
1e774b119fed3e_GRCh38.primary_assembly.genome.fa.bwt added
1e774b9eb5488_GRCh38.primary_assembly.genome.fa.pac added
1e774b623d380c_GRCh38.primary_assembly.genome.fa.sa added
1e774b185f7c05_GRCh38.primary_assembly.genome.fa added
1e774b2ef4aca2_hs37d5.fa.fai added
1e774b5f39f747_hs37d5.fa.amb added
1e774b673fbae9_hs37d5.fa.ann added
1e774b3972141d_hs37d5.fa.bwt added
1e774b1bc2d5a4_hs37d5.fa.pac added
1e774b570f6f03_hs37d5.fa.sa added
1e774b31802bdb_hs37d5.fa added
1e774b4824e546_complete_ref_lens.bin added
1e774b57d2f731_ctable.bin added
1e774b6f0eb1f_ctg_offsets.bin added
1e774b279750e1_duplicate_clusters.tsv added
1e774bdd2e976_info.json added
1e774b4ec02749_mphf.bin added
1e774b2003e2f2_pos.bin added
1e774b7802fce7_pre_indexing.log added
1e774b539d2db2_rank.bin added
1e774b787d5b0a_ref_indexing.log added
1e774b2f71ba8_refAccumLengths.bin added
1e774b4183d4f3_reflengths.bin added
1e774b424ebcda_refseq.bin added
1e774b4fb34d02_seq.bin added
1e774b66133080_versionInfo.json added
1e774b1a4c37f5_salmon_index added
1e774b62a78f73_chrLength.txt added
1e774b61763710_chrName.txt added
1e774b161d0568_chrNameLength.txt added
1e774b1d123a0d_chrStart.txt added
1e774b7316244f_exonGeTrInfo.tab added
1e774b200859f0_exonInfo.tab added
1e774b7f4f7219_geneInfo.tab added
1e774bb75a054_Genome added
1e774b4efd0692_genomeParameters.txt added
1e774b5e896961_Log.out added
1e774b72b55b3d_SA added
1e774b86f1ab0_SAindex added
1e774b7a4c3f05_sjdbInfo.txt added
1e774b49c4ca40_sjdbList.fromGTF.out.tab added
1e774b39ef468b_sjdbList.out.tab added
1e774b4271244b_transcriptInfo.tab added
1e774b2197c172_GRCh38.GENCODE.v42_100 added
1e774b40e031aa_knownGene_hg38.sql added
1e774b6a08752d_knownGene_hg38.txt added
1e774b2f6aaae8_refGene_hg38.sql added
1e774bfa058f3_refGene_hg38.txt added
1e774ba0c581f_knownGene_mm39.sql added
1e774b276da7cf_knownGene_mm39.txt added
1e774b633d86a5_refGene_mm39.sql added
1e774b289b32a_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: 
/home/biocbuild/tmp/RtmpGbXq42/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 
 24.501   1.320  28.237