##############################################################################
##############################################################################
###
### 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_1.9.0.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 ‘1.9.0’
* 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 8.986  0.287   9.307
getCloudData  3.593  0.399   8.732
* 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.

##############################################################################
##############################################################################
###
### 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 ‘1.9.0’
** 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: 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...
2a521c1ff0a4cd_GRCh38.primary_assembly.genome.fa.1.bt2 added
2a521c67f75963_GRCh38.primary_assembly.genome.fa.2.bt2 added
2a521c5c24c9e_GRCh38.primary_assembly.genome.fa.3.bt2 added
2a521c50a524ed_GRCh38.primary_assembly.genome.fa.4.bt2 added
2a521c2cc2273_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2a521c40164527_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2a521c1ccd4675_outfile.txt added
2a521c2c7259b2_GRCh37_to_GRCh38.chain added
2a521c3cd0ed5b_GRCh37_to_NCBI34.chain added
2a521c2855ca17_GRCh37_to_NCBI35.chain added
2a521c45c78f49_GRCh37_to_NCBI36.chain added
2a521c3d635135_GRCh38_to_GRCh37.chain added
2a521c56f617d6_GRCh38_to_NCBI34.chain added
2a521c2c350ccd_GRCh38_to_NCBI35.chain added
2a521c326e066e_GRCh38_to_NCBI36.chain added
2a521c1e1139e2_NCBI34_to_GRCh37.chain added
2a521c493bede8_NCBI34_to_GRCh38.chain added
2a521c69931ad7_NCBI35_to_GRCh37.chain added
2a521c34beb078_NCBI35_to_GRCh38.chain added
2a521c69c67449_NCBI36_to_GRCh37.chain added
2a521c60a6317c_NCBI36_to_GRCh38.chain added
2a521c2add13cb_GRCm38_to_NCBIM36.chain added
2a521c1be7c7cd_GRCm38_to_NCBIM37.chain added
2a521c6bd674a6_NCBIM36_to_GRCm38.chain added
2a521c4f2f0a4b_NCBIM37_to_GRCm38.chain added
2a521c6baf6ede_1000G_omni2.5.b37.vcf.gz added
2a521c7d8bc02e_1000G_omni2.5.b37.vcf.gz.tbi added
2a521c62d26952_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2a521c3e138ee8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2a521c2c4458a4_1000G_omni2.5.hg38.vcf.gz added
2a521c24f0262c_1000G_omni2.5.hg38.vcf.gz.tbi added
2a521c5e0433b5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2a521c143bb207_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2a521c2ab272ca_af-only-gnomad.raw.sites.vcf added
2a521c2ea958a2_af-only-gnomad.raw.sites.vcf.idx added
2a521c1707d47a_Mutect2-exome-panel.vcf.idx added
2a521c6ac8b7f1_Mutect2-WGS-panel-b37.vcf added
2a521c4b769f17_Mutect2-WGS-panel-b37.vcf.idx added
2a521c437a2e2d_small_exac_common_3.vcf added
2a521c2799a54c_small_exac_common_3.vcf.idx added
2a521c73cc692e_1000g_pon.hg38.vcf.gz added
2a521c941bd76_1000g_pon.hg38.vcf.gz.tbi added
2a521c64fcf682_af-only-gnomad.hg38.vcf.gz added
2a521c4ac28104_af-only-gnomad.hg38.vcf.gz.tbi added
2a521c3576ca43_small_exac_common_3.hg38.vcf.gz added
2a521c176afcf0_small_exac_common_3.hg38.vcf.gz.tbi added
2a521c68d3bae6_gencode.v41.annotation.gtf added
2a521c7eb2b82b_gencode.v42.annotation.gtf added
2a521cfe17c7_gencode.vM30.annotation.gtf added
2a521c1d926b5e_gencode.vM31.annotation.gtf added
2a521c68792c74_gencode.v41.transcripts.fa added
2a521c61a44943_gencode.v41.transcripts.fa.fai added
2a521c486f7f29_gencode.v42.transcripts.fa added
2a521c460f441_gencode.v42.transcripts.fa.fai added
2a521c4d7abde9_gencode.vM30.pc_transcripts.fa added
2a521c179e8975_gencode.vM30.pc_transcripts.fa.fai added
2a521c70106320_gencode.vM31.pc_transcripts.fa added
2a521c4b067e18_gencode.vM31.pc_transcripts.fa.fai added
2a521c7a70f2c7_GRCh38.primary_assembly.genome.fa.1.ht2 added
2a521c2e23f208_GRCh38.primary_assembly.genome.fa.2.ht2 added
2a521c774ad6bc_GRCh38.primary_assembly.genome.fa.3.ht2 added
2a521c1f6118f3_GRCh38.primary_assembly.genome.fa.4.ht2 added
2a521cc2825bd_GRCh38.primary_assembly.genome.fa.5.ht2 added
2a521cb8688c3_GRCh38.primary_assembly.genome.fa.6.ht2 added
2a521c4a138bbe_GRCh38.primary_assembly.genome.fa.7.ht2 added
2a521c3ad17e5f_GRCh38.primary_assembly.genome.fa.8.ht2 added
2a521c228e5d3e_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2a521c34dc43af_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2a521c6481d76_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2a521c66088b6b_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2a521c5c75e8fc_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2a521c7a1486a4_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2a521c6f4a48e1_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2a521c4172df7e_GRCh38.primary_assembly.genome.fa.fai added
2a521c44d707a9_GRCh38.primary_assembly.genome.fa.amb added
2a521c24c11324_GRCh38.primary_assembly.genome.fa.ann added
2a521c58dddc6e_GRCh38.primary_assembly.genome.fa.bwt added
2a521c2daac28f_GRCh38.primary_assembly.genome.fa.pac added
2a521c2373cb4f_GRCh38.primary_assembly.genome.fa.sa added
2a521c59dbf435_GRCh38.primary_assembly.genome.fa added
2a521c4b3d2dee_hs37d5.fa.fai added
2a521cbecf7c3_hs37d5.fa.amb added
2a521c3b803d78_hs37d5.fa.ann added
2a521c13acad17_hs37d5.fa.bwt added
2a521c104dec05_hs37d5.fa.pac added
2a521c8fafb62_hs37d5.fa.sa added
2a521c2b4b368c_hs37d5.fa added
2a521c5e4f25_complete_ref_lens.bin added
2a521c5401797a_ctable.bin added
2a521c25bc2953_ctg_offsets.bin added
2a521c2e82412d_duplicate_clusters.tsv added
2a521c4b4c5036_info.json added
2a521c451d4247_mphf.bin added
2a521c3aaa66ea_pos.bin added
2a521c56d2d8f9_pre_indexing.log added
2a521cf30ce05_rank.bin added
2a521c757be549_ref_indexing.log added
2a521c79613637_refAccumLengths.bin added
2a521c440d11b4_reflengths.bin added
2a521c7bc402bf_refseq.bin added
2a521c5f69c1a2_seq.bin added
2a521c2082fab0_versionInfo.json added
2a521c75d88963_salmon_index added
2a521c4eb40a83_chrLength.txt added
2a521c61f5da2e_chrName.txt added
2a521c3aaf910c_chrNameLength.txt added
2a521c73751da7_chrStart.txt added
2a521c3ad3b69c_exonGeTrInfo.tab added
2a521c685a539c_exonInfo.tab added
2a521c16e8e8f6_geneInfo.tab added
2a521c14afaad1_Genome added
2a521c3397818a_genomeParameters.txt added
2a521c22d5e0ba_Log.out added
2a521c502fe84a_SA added
2a521c47442ea1_SAindex added
2a521c3323ccbf_sjdbInfo.txt added
2a521c592ae3ac_sjdbList.fromGTF.out.tab added
2a521c728f652e_sjdbList.out.tab added
2a521c33821be4_transcriptInfo.tab added
2a521c2d2c5d26_GRCh38.GENCODE.v42_100 added
2a521c184b8e81_knownGene_hg38.sql added
2a521c62045d11_knownGene_hg38.txt added
2a521c7878ad5c_refGene_hg38.sql added
2a521c5d68d0c8_refGene_hg38.txt added
2a521c1caec3fb_knownGene_mm39.sql added
2a521c4f4b8655_knownGene_mm39.txt added
2a521c6c999ecd_refGene_mm39.sql added
2a521c122aa944_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/RtmpnrmSee/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 
 25.436   2.093  30.637