##############################################################################
##############################################################################
###
### 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 8.618  0.566   9.229
getCloudData  3.326  0.637  10.905
* 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...
54b15775c43c6_GRCh38.primary_assembly.genome.fa.1.bt2 added
54b15e405f82_GRCh38.primary_assembly.genome.fa.2.bt2 added
54b152fb35437_GRCh38.primary_assembly.genome.fa.3.bt2 added
54b15a9115c9_GRCh38.primary_assembly.genome.fa.4.bt2 added
54b1578a5cf69_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
54b151c642ce_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
54b153fc544_outfile.txt added
54b15353bec0b_GRCh37_to_GRCh38.chain added
54b157e85d81e_GRCh37_to_NCBI34.chain added
54b1550c0e995_GRCh37_to_NCBI35.chain added
54b155bc29efc_GRCh37_to_NCBI36.chain added
54b1557dcc7a4_GRCh38_to_GRCh37.chain added
54b1591330fb_GRCh38_to_NCBI34.chain added
54b155dcfb84a_GRCh38_to_NCBI35.chain added
54b155bdcdf30_GRCh38_to_NCBI36.chain added
54b151393109e_NCBI34_to_GRCh37.chain added
54b151e4fc702_NCBI34_to_GRCh38.chain added
54b155d1aaa19_NCBI35_to_GRCh37.chain added
54b155ee95799_NCBI35_to_GRCh38.chain added
54b15355c6f64_NCBI36_to_GRCh37.chain added
54b1576242330_NCBI36_to_GRCh38.chain added
54b153dba5633_GRCm38_to_NCBIM36.chain added
54b15764ebc61_GRCm38_to_NCBIM37.chain added
54b152e056c7e_NCBIM36_to_GRCm38.chain added
54b157253386_NCBIM37_to_GRCm38.chain added
54b155315b632_1000G_omni2.5.b37.vcf.gz added
54b1529ac186a_1000G_omni2.5.b37.vcf.gz.tbi added
54b152ed3bb2f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
54b15e58978a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
54b1583dbe32_1000G_omni2.5.hg38.vcf.gz added
54b151d862636_1000G_omni2.5.hg38.vcf.gz.tbi added
54b155b4db50_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
54b15167e1db5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
54b154d397a6d_af-only-gnomad.raw.sites.vcf added
54b151045f119_af-only-gnomad.raw.sites.vcf.idx added
54b15f23ed1e_Mutect2-exome-panel.vcf.idx added
54b154effbd3b_Mutect2-WGS-panel-b37.vcf added
54b151085b65e_Mutect2-WGS-panel-b37.vcf.idx added
54b15445fd92a_small_exac_common_3.vcf added
54b154d859559_small_exac_common_3.vcf.idx added
54b1561469ff3_1000g_pon.hg38.vcf.gz added
54b1520227826_1000g_pon.hg38.vcf.gz.tbi added
54b1525625cfd_af-only-gnomad.hg38.vcf.gz added
54b156a59d0ee_af-only-gnomad.hg38.vcf.gz.tbi added
54b157df23070_small_exac_common_3.hg38.vcf.gz added
54b1513f3c2e_small_exac_common_3.hg38.vcf.gz.tbi added
54b157dece18d_gencode.v41.annotation.gtf added
54b151c41f772_gencode.v42.annotation.gtf added
54b155e59e647_gencode.vM30.annotation.gtf added
54b155cd63926_gencode.vM31.annotation.gtf added
54b15519e66d7_gencode.v41.transcripts.fa added
54b15547e0977_gencode.v41.transcripts.fa.fai added
54b151a908f5a_gencode.v42.transcripts.fa added
54b1547ed2338_gencode.v42.transcripts.fa.fai added
54b1528375f5_gencode.vM30.pc_transcripts.fa added
54b1521b5c2e0_gencode.vM30.pc_transcripts.fa.fai added
54b151b02d96a_gencode.vM31.pc_transcripts.fa added
54b152c2f8e60_gencode.vM31.pc_transcripts.fa.fai added
54b1550897e0f_GRCh38.primary_assembly.genome.fa.1.ht2 added
54b15295b70f5_GRCh38.primary_assembly.genome.fa.2.ht2 added
54b15346d4c92_GRCh38.primary_assembly.genome.fa.3.ht2 added
54b156e0fa445_GRCh38.primary_assembly.genome.fa.4.ht2 added
54b152f104c45_GRCh38.primary_assembly.genome.fa.5.ht2 added
54b154aeb6a47_GRCh38.primary_assembly.genome.fa.6.ht2 added
54b153b491eb2_GRCh38.primary_assembly.genome.fa.7.ht2 added
54b153f563d5f_GRCh38.primary_assembly.genome.fa.8.ht2 added
54b155a0f5766_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
54b15a48dbed_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
54b154fdbf3bd_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
54b151e6f3090_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
54b1557ce7146_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
54b15312293b0_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
54b153e91a8b6_GRCh38_full_analysis_set_plus_decoy_hla.fa added
54b157d30ce44_GRCh38.primary_assembly.genome.fa.fai added
54b151b7c649f_GRCh38.primary_assembly.genome.fa.amb added
54b153c83d927_GRCh38.primary_assembly.genome.fa.ann added
54b157e700a72_GRCh38.primary_assembly.genome.fa.bwt added
54b151969462c_GRCh38.primary_assembly.genome.fa.pac added
54b1558c5d099_GRCh38.primary_assembly.genome.fa.sa added
54b155cc9f0b9_GRCh38.primary_assembly.genome.fa added
54b15763f7f52_hs37d5.fa.fai added
54b152a643770_hs37d5.fa.amb added
54b153147fa31_hs37d5.fa.ann added
54b1510d00eac_hs37d5.fa.bwt added
54b1572515aa8_hs37d5.fa.pac added
54b1533cb7026_hs37d5.fa.sa added
54b153285d18c_hs37d5.fa added
54b15d543413_complete_ref_lens.bin added
54b155ffafe86_ctable.bin added
54b1530f4f9c_ctg_offsets.bin added
54b1536afa508_duplicate_clusters.tsv added
54b1514684b19_info.json added
54b15711ef3e1_mphf.bin added
54b1565bff14d_pos.bin added
54b155f53b560_pre_indexing.log added
54b152c681294_rank.bin added
54b1525162eac_ref_indexing.log added
54b1539630cc6_refAccumLengths.bin added
54b1536b0ee81_reflengths.bin added
54b1574f22269_refseq.bin added
54b1557d23d56_seq.bin added
54b15e7f5fc8_versionInfo.json added
54b152614b61a_salmon_index added
54b151663e60d_chrLength.txt added
54b15bb02e0c_chrName.txt added
54b1541911ab9_chrNameLength.txt added
54b1552e7bf34_chrStart.txt added
54b15a20387e_exonGeTrInfo.tab added
54b155afa60e5_exonInfo.tab added
54b152bad8fcd_geneInfo.tab added
54b1566ea2937_Genome added
54b155139e037_genomeParameters.txt added
54b155611c73e_Log.out added
54b1518322368_SA added
54b156209eee4_SAindex added
54b15486321e6_sjdbInfo.txt added
54b154bfd938f_sjdbList.fromGTF.out.tab added
54b15148fc070_sjdbList.out.tab added
54b1555b755f9_transcriptInfo.tab added
54b152bf89215_GRCh38.GENCODE.v42_100 added
54b15179f100c_knownGene_hg38.sql added
54b15c66fb01_knownGene_hg38.txt added
54b154060dd2e_refGene_hg38.sql added
54b158be03ee_refGene_hg38.txt added
54b157226ec4f_knownGene_mm39.sql added
54b151fb4928f_knownGene_mm39.txt added
54b1535261682_refGene_mm39.sql added
54b15173d1afb_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/RtmpTlIQZr/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 
 24.104   1.723  27.907