##############################################################################
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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 9.256  0.319  11.126
getCloudData  3.482  0.147   7.938
* 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...
3fae212b7270d4_GRCh38.primary_assembly.genome.fa.1.bt2 added
3fae211c842982_GRCh38.primary_assembly.genome.fa.2.bt2 added
3fae21588d964a_GRCh38.primary_assembly.genome.fa.3.bt2 added
3fae21565f1bd8_GRCh38.primary_assembly.genome.fa.4.bt2 added
3fae214521f554_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3fae21420c0b84_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3fae21d84d228_outfile.txt added
3fae2159a0dd48_GRCh37_to_GRCh38.chain added
3fae212a12101a_GRCh37_to_NCBI34.chain added
3fae218fea5be_GRCh37_to_NCBI35.chain added
3fae21634e2edb_GRCh37_to_NCBI36.chain added
3fae216e2ee4d1_GRCh38_to_GRCh37.chain added
3fae2130f43584_GRCh38_to_NCBI34.chain added
3fae2123d292b6_GRCh38_to_NCBI35.chain added
3fae21634a65af_GRCh38_to_NCBI36.chain added
3fae214d0e61e_NCBI34_to_GRCh37.chain added
3fae2126404ca6_NCBI34_to_GRCh38.chain added
3fae214e4342bf_NCBI35_to_GRCh37.chain added
3fae212f7198bf_NCBI35_to_GRCh38.chain added
3fae216b0b1ec0_NCBI36_to_GRCh37.chain added
3fae215feff850_NCBI36_to_GRCh38.chain added
3fae214b86a0ac_GRCm38_to_NCBIM36.chain added
3fae2139fe0479_GRCm38_to_NCBIM37.chain added
3fae211f50ed15_NCBIM36_to_GRCm38.chain added
3fae2188c6d32_NCBIM37_to_GRCm38.chain added
3fae213af4fd99_1000G_omni2.5.b37.vcf.gz added
3fae212bc0f411_1000G_omni2.5.b37.vcf.gz.tbi added
3fae216f9eb2b0_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3fae21127e1e47_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3fae2167514cd6_1000G_omni2.5.hg38.vcf.gz added
3fae2113b45641_1000G_omni2.5.hg38.vcf.gz.tbi added
3fae213df08f1b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3fae213d57658_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3fae216c41ec8b_af-only-gnomad.raw.sites.vcf added
3fae21144faaf4_af-only-gnomad.raw.sites.vcf.idx added
3fae2148f76bad_Mutect2-exome-panel.vcf.idx added
3fae212e4df80f_Mutect2-WGS-panel-b37.vcf added
3fae2121d47d1c_Mutect2-WGS-panel-b37.vcf.idx added
3fae21229848f5_small_exac_common_3.vcf added
3fae215860082a_small_exac_common_3.vcf.idx added
3fae212ad322db_1000g_pon.hg38.vcf.gz added
3fae215e677d1_1000g_pon.hg38.vcf.gz.tbi added
3fae21468eecfb_af-only-gnomad.hg38.vcf.gz added
3fae215bc7585f_af-only-gnomad.hg38.vcf.gz.tbi added
3fae2129b90a87_small_exac_common_3.hg38.vcf.gz added
3fae2129d952aa_small_exac_common_3.hg38.vcf.gz.tbi added
3fae2160983e7d_gencode.v41.annotation.gtf added
3fae214ff9572e_gencode.v42.annotation.gtf added
3fae21781c956a_gencode.vM30.annotation.gtf added
3fae211009d73d_gencode.vM31.annotation.gtf added
3fae213b0475ee_gencode.v41.transcripts.fa added
3fae21580c8dba_gencode.v41.transcripts.fa.fai added
3fae215b9077e9_gencode.v42.transcripts.fa added
3fae2175027a68_gencode.v42.transcripts.fa.fai added
3fae21775d7acf_gencode.vM30.pc_transcripts.fa added
3fae21641ce51b_gencode.vM30.pc_transcripts.fa.fai added
3fae212ff77801_gencode.vM31.pc_transcripts.fa added
3fae21231e6ee0_gencode.vM31.pc_transcripts.fa.fai added
3fae2153bb97cb_GRCh38.primary_assembly.genome.fa.1.ht2 added
3fae2142759648_GRCh38.primary_assembly.genome.fa.2.ht2 added
3fae21a6fbbb7_GRCh38.primary_assembly.genome.fa.3.ht2 added
3fae21676fee0d_GRCh38.primary_assembly.genome.fa.4.ht2 added
3fae21662563_GRCh38.primary_assembly.genome.fa.5.ht2 added
3fae21e45320f_GRCh38.primary_assembly.genome.fa.6.ht2 added
3fae2153b1da98_GRCh38.primary_assembly.genome.fa.7.ht2 added
3fae2114b5d057_GRCh38.primary_assembly.genome.fa.8.ht2 added
3fae21573c9dbc_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3fae211ffd2a8_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3fae21368a4d74_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3fae2179d4e6b2_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3fae215a5fdad2_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3fae21615d704f_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3fae217fbb5e83_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3fae2120eec7cd_GRCh38.primary_assembly.genome.fa.fai added
3fae213d24c8ae_GRCh38.primary_assembly.genome.fa.amb added
3fae212974690a_GRCh38.primary_assembly.genome.fa.ann added
3fae214ac81a78_GRCh38.primary_assembly.genome.fa.bwt added
3fae211dbd072b_GRCh38.primary_assembly.genome.fa.pac added
3fae21796dc038_GRCh38.primary_assembly.genome.fa.sa added
3fae2142e4afe2_GRCh38.primary_assembly.genome.fa added
3fae212dc6de68_hs37d5.fa.fai added
3fae2134723627_hs37d5.fa.amb added
3fae211af13d9c_hs37d5.fa.ann added
3fae219575651_hs37d5.fa.bwt added
3fae212974b08f_hs37d5.fa.pac added
3fae21124eb86b_hs37d5.fa.sa added
3fae216d743b6c_hs37d5.fa added
3fae21596c2890_complete_ref_lens.bin added
3fae21356d274b_ctable.bin added
3fae21412fd338_ctg_offsets.bin added
3fae211be1bed8_duplicate_clusters.tsv added
3fae213fdce302_info.json added
3fae21289fc145_mphf.bin added
3fae211c47e43b_pos.bin added
3fae214e221512_pre_indexing.log added
3fae217c519bdd_rank.bin added
3fae2130fdb493_ref_indexing.log added
3fae21255eb2ce_refAccumLengths.bin added
3fae217e516e85_reflengths.bin added
3fae2167880207_refseq.bin added
3fae211f339980_seq.bin added
3fae2158b14957_versionInfo.json added
3fae2148e57256_salmon_index added
3fae211eeef803_chrLength.txt added
3fae2179a01125_chrName.txt added
3fae2160a3b04_chrNameLength.txt added
3fae214863610e_chrStart.txt added
3fae2144682b9d_exonGeTrInfo.tab added
3fae2123c7422f_exonInfo.tab added
3fae2141d12146_geneInfo.tab added
3fae2174cdb7f_Genome added
3fae21518e2098_genomeParameters.txt added
3fae217643576d_Log.out added
3fae21223e191b_SA added
3fae215ae576e9_SAindex added
3fae211fb807fc_sjdbInfo.txt added
3fae21348cd186_sjdbList.fromGTF.out.tab added
3fae214859b256_sjdbList.out.tab added
3fae217924308c_transcriptInfo.tab added
3fae2169f9f8d1_GRCh38.GENCODE.v42_100 added
3fae21989858e_knownGene_hg38.sql added
3fae211505ef64_knownGene_hg38.txt added
3fae2129d6dbd4_refGene_hg38.sql added
3fae21322946d3_refGene_hg38.txt added
3fae21314dd3a0_knownGene_mm39.sql added
3fae2177f8f0e6_knownGene_mm39.txt added
3fae212e7ae2b0_refGene_mm39.sql added
3fae21624b8833_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/Rtmpr88X14/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 
 24.057   1.339  31.849