##############################################################################
##############################################################################
###
### 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.11.0’
* 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 8.869  0.327   9.231
getCloudData  3.481  0.158   6.694
* 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-3.23-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-devel_2025-02-19/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.11.0’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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...
233e5644a171cc_GRCh38.primary_assembly.genome.fa.1.bt2 added
233e5646355f0c_GRCh38.primary_assembly.genome.fa.2.bt2 added
233e5628270a5b_GRCh38.primary_assembly.genome.fa.3.bt2 added
233e563ce2052f_GRCh38.primary_assembly.genome.fa.4.bt2 added
233e561c0034e3_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
233e5665077a75_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
233e566a10c3a5_outfile.txt added
233e5629cdf40d_GRCh37_to_GRCh38.chain added
233e566206b0ff_GRCh37_to_NCBI34.chain added
233e5662f3babe_GRCh37_to_NCBI35.chain added
233e564461089_GRCh37_to_NCBI36.chain added
233e566fdbe007_GRCh38_to_GRCh37.chain added
233e5646014be2_GRCh38_to_NCBI34.chain added
233e5648d6580a_GRCh38_to_NCBI35.chain added
233e565e98a18b_GRCh38_to_NCBI36.chain added
233e56265f3476_NCBI34_to_GRCh37.chain added
233e56258fe8a3_NCBI34_to_GRCh38.chain added
233e561c45f741_NCBI35_to_GRCh37.chain added
233e56340e0d08_NCBI35_to_GRCh38.chain added
233e5637a7f29c_NCBI36_to_GRCh37.chain added
233e56ad9b7e8_NCBI36_to_GRCh38.chain added
233e566aee1e8c_GRCm38_to_NCBIM36.chain added
233e562e1b6934_GRCm38_to_NCBIM37.chain added
233e561d5920cb_NCBIM36_to_GRCm38.chain added
233e56508c064e_NCBIM37_to_GRCm38.chain added
233e56638d4cc4_1000G_omni2.5.b37.vcf.gz added
233e5642931dce_1000G_omni2.5.b37.vcf.gz.tbi added
233e567892e09c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
233e5637bce2d3_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
233e567e6ef561_1000G_omni2.5.hg38.vcf.gz added
233e5636064c21_1000G_omni2.5.hg38.vcf.gz.tbi added
233e567c5e54a0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
233e5644a4546e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
233e565e2d567c_af-only-gnomad.raw.sites.vcf added
233e56394059cf_af-only-gnomad.raw.sites.vcf.idx added
233e5660a48951_Mutect2-exome-panel.vcf.idx added
233e564334d0f2_Mutect2-WGS-panel-b37.vcf added
233e5623511d74_Mutect2-WGS-panel-b37.vcf.idx added
233e56a727d5e_small_exac_common_3.vcf added
233e56253b81f1_small_exac_common_3.vcf.idx added
233e56644d833_1000g_pon.hg38.vcf.gz added
233e56eb88de7_1000g_pon.hg38.vcf.gz.tbi added
233e56151761f8_af-only-gnomad.hg38.vcf.gz added
233e564c462415_af-only-gnomad.hg38.vcf.gz.tbi added
233e56578ee5f1_small_exac_common_3.hg38.vcf.gz added
233e5673b00384_small_exac_common_3.hg38.vcf.gz.tbi added
233e5672a5588b_gencode.v41.annotation.gtf added
233e567d1ece95_gencode.v42.annotation.gtf added
233e56ff5fac5_gencode.vM30.annotation.gtf added
233e5626b36593_gencode.vM31.annotation.gtf added
233e5634c6c131_gencode.v41.transcripts.fa added
233e561acfb2ad_gencode.v41.transcripts.fa.fai added
233e5611a18420_gencode.v42.transcripts.fa added
233e5662e22a66_gencode.v42.transcripts.fa.fai added
233e563828d378_gencode.vM30.pc_transcripts.fa added
233e56622d8a6e_gencode.vM30.pc_transcripts.fa.fai added
233e56466f772a_gencode.vM31.pc_transcripts.fa added
233e567abbf147_gencode.vM31.pc_transcripts.fa.fai added
233e565ac06b0a_GRCh38.primary_assembly.genome.fa.1.ht2 added
233e567e2c59fd_GRCh38.primary_assembly.genome.fa.2.ht2 added
233e56792ae6a8_GRCh38.primary_assembly.genome.fa.3.ht2 added
233e5610c6b72b_GRCh38.primary_assembly.genome.fa.4.ht2 added
233e567a8aae9d_GRCh38.primary_assembly.genome.fa.5.ht2 added
233e563dcf3b16_GRCh38.primary_assembly.genome.fa.6.ht2 added
233e566ef40da7_GRCh38.primary_assembly.genome.fa.7.ht2 added
233e5633cb086d_GRCh38.primary_assembly.genome.fa.8.ht2 added
233e561e73c467_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
233e563228de99_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
233e56571c25e1_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
233e5628e641c5_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
233e565764608b_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
233e565d60fe14_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
233e56379ecfad_GRCh38_full_analysis_set_plus_decoy_hla.fa added
233e566c7bc283_GRCh38.primary_assembly.genome.fa.fai added
233e5629a72229_GRCh38.primary_assembly.genome.fa.amb added
233e56f2db59e_GRCh38.primary_assembly.genome.fa.ann added
233e56602bc607_GRCh38.primary_assembly.genome.fa.bwt added
233e561c4c7ab4_GRCh38.primary_assembly.genome.fa.pac added
233e56c4c8433_GRCh38.primary_assembly.genome.fa.sa added
233e567021c0cd_GRCh38.primary_assembly.genome.fa added
233e5642ffe048_hs37d5.fa.fai added
233e5641134565_hs37d5.fa.amb added
233e56af1737a_hs37d5.fa.ann added
233e5654a16468_hs37d5.fa.bwt added
233e5623f56fcb_hs37d5.fa.pac added
233e56431a46f3_hs37d5.fa.sa added
233e5636ceeed6_hs37d5.fa added
233e566a64e6f5_complete_ref_lens.bin added
233e563dd6383a_ctable.bin added
233e56118f59e0_ctg_offsets.bin added
233e56689140f2_duplicate_clusters.tsv added
233e5637011ee2_info.json added
233e562256110b_mphf.bin added
233e56631bef90_pos.bin added
233e5674d059f9_pre_indexing.log added
233e56114a1eb2_rank.bin added
233e5616e6f7fd_ref_indexing.log added
233e5613441e60_refAccumLengths.bin added
233e564372fd4c_reflengths.bin added
233e566e031dde_refseq.bin added
233e563c2a6026_seq.bin added
233e561ad75dd7_versionInfo.json added
233e564b641bf3_salmon_index added
233e5673c92fd3_chrLength.txt added
233e56753205a_chrName.txt added
233e56750b3e1c_chrNameLength.txt added
233e562f6e571_chrStart.txt added
233e56677ee662_exonGeTrInfo.tab added
233e561157b8d1_exonInfo.tab added
233e56f4369a5_geneInfo.tab added
233e5657a0a72f_Genome added
233e5654579919_genomeParameters.txt added
233e565056af0a_Log.out added
233e5662921aa9_SA added
233e5628f8fd81_SAindex added
233e56744c1ed5_sjdbInfo.txt added
233e5625ac619c_sjdbList.fromGTF.out.tab added
233e565fc7ec57_sjdbList.out.tab added
233e565eb105ca_transcriptInfo.tab added
233e56638299d6_GRCh38.GENCODE.v42_100 added
233e5671574637_knownGene_hg38.sql added
233e56474246bc_knownGene_hg38.txt added
233e561a83b8b9_refGene_hg38.sql added
233e5613ad5742_refGene_hg38.txt added
233e562a5e364c_knownGene_mm39.sql added
233e56f5412b2_knownGene_mm39.txt added
233e5624f775f4_refGene_mm39.sql added
233e5641452e49_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/RtmpS5luAQ/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 
 24.879   1.380  27.936