##############################################################################
##############################################################################
###
### 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 8.652  0.334   9.535
getCloudData  3.351  0.058   7.497
* 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...
228b0d6a8546b8_GRCh38.primary_assembly.genome.fa.1.bt2 added
228b0d59aa6fb2_GRCh38.primary_assembly.genome.fa.2.bt2 added
228b0d341ed14f_GRCh38.primary_assembly.genome.fa.3.bt2 added
228b0d1f30602c_GRCh38.primary_assembly.genome.fa.4.bt2 added
228b0d452ebf09_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
228b0d439c6d2b_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
228b0d4a3edaa5_outfile.txt added
228b0d631261e7_GRCh37_to_GRCh38.chain added
228b0d59e941f_GRCh37_to_NCBI34.chain added
228b0d332dcf06_GRCh37_to_NCBI35.chain added
228b0d23e67062_GRCh37_to_NCBI36.chain added
228b0d2a41922a_GRCh38_to_GRCh37.chain added
228b0d76a89c7_GRCh38_to_NCBI34.chain added
228b0d688b367_GRCh38_to_NCBI35.chain added
228b0d2e2c0ef5_GRCh38_to_NCBI36.chain added
228b0d47f094d0_NCBI34_to_GRCh37.chain added
228b0d52872e96_NCBI34_to_GRCh38.chain added
228b0d6b3ca74d_NCBI35_to_GRCh37.chain added
228b0d46dce76f_NCBI35_to_GRCh38.chain added
228b0d5a9173cc_NCBI36_to_GRCh37.chain added
228b0d2f6d80eb_NCBI36_to_GRCh38.chain added
228b0d2fc8b52d_GRCm38_to_NCBIM36.chain added
228b0d137dbf23_GRCm38_to_NCBIM37.chain added
228b0d2d8bbc05_NCBIM36_to_GRCm38.chain added
228b0d2f721108_NCBIM37_to_GRCm38.chain added
228b0d31ce0de0_1000G_omni2.5.b37.vcf.gz added
228b0d5057c618_1000G_omni2.5.b37.vcf.gz.tbi added
228b0d2f09eeb9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
228b0d205694f3_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
228b0dd3eee55_1000G_omni2.5.hg38.vcf.gz added
228b0d494fee0a_1000G_omni2.5.hg38.vcf.gz.tbi added
228b0dadbdbab_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
228b0d66e95e07_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
228b0d7d6ebf59_af-only-gnomad.raw.sites.vcf added
228b0d2a0c3bd7_af-only-gnomad.raw.sites.vcf.idx added
228b0d2c181d10_Mutect2-exome-panel.vcf.idx added
228b0d410b2c84_Mutect2-WGS-panel-b37.vcf added
228b0d744b167c_Mutect2-WGS-panel-b37.vcf.idx added
228b0df2a7ef7_small_exac_common_3.vcf added
228b0d46a9c0a4_small_exac_common_3.vcf.idx added
228b0d2778e582_1000g_pon.hg38.vcf.gz added
228b0d3310ef5a_1000g_pon.hg38.vcf.gz.tbi added
228b0d70eb52ce_af-only-gnomad.hg38.vcf.gz added
228b0d2ee36f4a_af-only-gnomad.hg38.vcf.gz.tbi added
228b0d3999a2c1_small_exac_common_3.hg38.vcf.gz added
228b0d1f1761c3_small_exac_common_3.hg38.vcf.gz.tbi added
228b0d76d4041a_gencode.v41.annotation.gtf added
228b0dc20d157_gencode.v42.annotation.gtf added
228b0da540910_gencode.vM30.annotation.gtf added
228b0d3db0eb8a_gencode.vM31.annotation.gtf added
228b0d66b24523_gencode.v41.transcripts.fa added
228b0d39c189fb_gencode.v41.transcripts.fa.fai added
228b0d6d79a0b7_gencode.v42.transcripts.fa added
228b0d7a300446_gencode.v42.transcripts.fa.fai added
228b0d674d4601_gencode.vM30.pc_transcripts.fa added
228b0d1cebb1c0_gencode.vM30.pc_transcripts.fa.fai added
228b0d2bfe1227_gencode.vM31.pc_transcripts.fa added
228b0d37a50c19_gencode.vM31.pc_transcripts.fa.fai added
228b0d4bf5a079_GRCh38.primary_assembly.genome.fa.1.ht2 added
228b0d4c54a71a_GRCh38.primary_assembly.genome.fa.2.ht2 added
228b0d44e3fa6e_GRCh38.primary_assembly.genome.fa.3.ht2 added
228b0d15458e83_GRCh38.primary_assembly.genome.fa.4.ht2 added
228b0d573082c5_GRCh38.primary_assembly.genome.fa.5.ht2 added
228b0d2bcd5875_GRCh38.primary_assembly.genome.fa.6.ht2 added
228b0d12b44ddc_GRCh38.primary_assembly.genome.fa.7.ht2 added
228b0d13cbe9c_GRCh38.primary_assembly.genome.fa.8.ht2 added
228b0d57e57585_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
228b0d53bf7a60_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
228b0d7587d518_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
228b0d670ff47c_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
228b0d1a693b04_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
228b0d1d00ba9b_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
228b0d1a20e3d6_GRCh38_full_analysis_set_plus_decoy_hla.fa added
228b0db548dd2_GRCh38.primary_assembly.genome.fa.fai added
228b0d4be429e5_GRCh38.primary_assembly.genome.fa.amb added
228b0d53ba8697_GRCh38.primary_assembly.genome.fa.ann added
228b0d2a6bef95_GRCh38.primary_assembly.genome.fa.bwt added
228b0d42b82dff_GRCh38.primary_assembly.genome.fa.pac added
228b0d5fdb57ee_GRCh38.primary_assembly.genome.fa.sa added
228b0d34bff8a5_GRCh38.primary_assembly.genome.fa added
228b0d691989_hs37d5.fa.fai added
228b0d468d9d11_hs37d5.fa.amb added
228b0d6e8182a1_hs37d5.fa.ann added
228b0d6de2ba41_hs37d5.fa.bwt added
228b0d40bda158_hs37d5.fa.pac added
228b0d55cec8a2_hs37d5.fa.sa added
228b0dace6c01_hs37d5.fa added
228b0d6cbbb37f_complete_ref_lens.bin added
228b0dd73d4bb_ctable.bin added
228b0d56c40c7a_ctg_offsets.bin added
228b0d39105a99_duplicate_clusters.tsv added
228b0d5257cf29_info.json added
228b0d6c099afd_mphf.bin added
228b0d1040dd5e_pos.bin added
228b0d7e25279e_pre_indexing.log added
228b0d7ebde8d9_rank.bin added
228b0d117d9bfa_ref_indexing.log added
228b0d560a9d23_refAccumLengths.bin added
228b0d527d6339_reflengths.bin added
228b0d7057112_refseq.bin added
228b0d3d1a919f_seq.bin added
228b0d6ce69e3e_versionInfo.json added
228b0d24062bad_salmon_index added
228b0d573b7576_chrLength.txt added
228b0d783b2c10_chrName.txt added
228b0d6fea5592_chrNameLength.txt added
228b0d2af5fc0d_chrStart.txt added
228b0d22a71ba6_exonGeTrInfo.tab added
228b0d32a28392_exonInfo.tab added
228b0dad153fc_geneInfo.tab added
228b0d5767144b_Genome added
228b0d330b9d1b_genomeParameters.txt added
228b0d515ef10d_Log.out added
228b0d45e896ec_SA added
228b0d20ee575c_SAindex added
228b0d121c9265_sjdbInfo.txt added
228b0d1bb75f8e_sjdbList.fromGTF.out.tab added
228b0d2bbcc35d_sjdbList.out.tab added
228b0d7ed845e4_transcriptInfo.tab added
228b0d292b3449_GRCh38.GENCODE.v42_100 added
228b0d280cfd7_knownGene_hg38.sql added
228b0d37e8a07d_knownGene_hg38.txt added
228b0d7b830372_refGene_hg38.sql added
228b0d6e8a6ad4_refGene_hg38.txt added
228b0d48297ddb_knownGene_mm39.sql added
228b0d79a82b10_knownGene_mm39.txt added
228b0d6d4853ad_refGene_mm39.sql added
228b0d59a719d5_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/RtmpY3Udnd/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 
 24.646   1.248  32.605