##############################################################################
##############################################################################
###
### 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 8.512  0.323  10.173
getCloudData  3.476  0.183   6.999
* 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...
35ce236add83ca_GRCh38.primary_assembly.genome.fa.1.bt2 added
35ce23212bbb08_GRCh38.primary_assembly.genome.fa.2.bt2 added
35ce23740ec47c_GRCh38.primary_assembly.genome.fa.3.bt2 added
35ce232992d1f0_GRCh38.primary_assembly.genome.fa.4.bt2 added
35ce2337026303_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
35ce23305ea0a8_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
35ce23161e7d36_outfile.txt added
35ce23381cef68_GRCh37_to_GRCh38.chain added
35ce232d00d690_GRCh37_to_NCBI34.chain added
35ce237a7ad0df_GRCh37_to_NCBI35.chain added
35ce232d5cb057_GRCh37_to_NCBI36.chain added
35ce23182ffc3b_GRCh38_to_GRCh37.chain added
35ce2325ed7737_GRCh38_to_NCBI34.chain added
35ce236d822c7d_GRCh38_to_NCBI35.chain added
35ce234a53627b_GRCh38_to_NCBI36.chain added
35ce23152f2632_NCBI34_to_GRCh37.chain added
35ce2373a6aae0_NCBI34_to_GRCh38.chain added
35ce231cc08ab4_NCBI35_to_GRCh37.chain added
35ce231e3f776c_NCBI35_to_GRCh38.chain added
35ce2332748abe_NCBI36_to_GRCh37.chain added
35ce2316f463a5_NCBI36_to_GRCh38.chain added
35ce236ddb2b95_GRCm38_to_NCBIM36.chain added
35ce23acb2abc_GRCm38_to_NCBIM37.chain added
35ce2328009533_NCBIM36_to_GRCm38.chain added
35ce2322b7f204_NCBIM37_to_GRCm38.chain added
35ce23e3f01a1_1000G_omni2.5.b37.vcf.gz added
35ce234aea9c1d_1000G_omni2.5.b37.vcf.gz.tbi added
35ce233ffa10c8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
35ce234d5a95be_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
35ce235bcaf427_1000G_omni2.5.hg38.vcf.gz added
35ce232e773f02_1000G_omni2.5.hg38.vcf.gz.tbi added
35ce2338381989_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
35ce237cf6af2f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
35ce232286037e_af-only-gnomad.raw.sites.vcf added
35ce2361caeb79_af-only-gnomad.raw.sites.vcf.idx added
35ce2333f91232_Mutect2-exome-panel.vcf.idx added
35ce2352e4a427_Mutect2-WGS-panel-b37.vcf added
35ce2377e968af_Mutect2-WGS-panel-b37.vcf.idx added
35ce236c16019b_small_exac_common_3.vcf added
35ce237fe57ab7_small_exac_common_3.vcf.idx added
35ce237264398e_1000g_pon.hg38.vcf.gz added
35ce231972b1f2_1000g_pon.hg38.vcf.gz.tbi added
35ce23181576f2_af-only-gnomad.hg38.vcf.gz added
35ce231851b0c6_af-only-gnomad.hg38.vcf.gz.tbi added
35ce236f4de6f_small_exac_common_3.hg38.vcf.gz added
35ce236268d96d_small_exac_common_3.hg38.vcf.gz.tbi added
35ce232d80d6f8_gencode.v41.annotation.gtf added
35ce237a9b894f_gencode.v42.annotation.gtf added
35ce237f296421_gencode.vM30.annotation.gtf added
35ce234bc04e64_gencode.vM31.annotation.gtf added
35ce232d10140d_gencode.v41.transcripts.fa added
35ce23161dc7c6_gencode.v41.transcripts.fa.fai added
35ce23399b79f9_gencode.v42.transcripts.fa added
35ce2337db3ec9_gencode.v42.transcripts.fa.fai added
35ce233e1e5cfa_gencode.vM30.pc_transcripts.fa added
35ce235c536bfe_gencode.vM30.pc_transcripts.fa.fai added
35ce23461a406a_gencode.vM31.pc_transcripts.fa added
35ce23908f917_gencode.vM31.pc_transcripts.fa.fai added
35ce231c4d7cc6_GRCh38.primary_assembly.genome.fa.1.ht2 added
35ce231374d629_GRCh38.primary_assembly.genome.fa.2.ht2 added
35ce2364d3ed3f_GRCh38.primary_assembly.genome.fa.3.ht2 added
35ce234ac4bbc9_GRCh38.primary_assembly.genome.fa.4.ht2 added
35ce234bacefb2_GRCh38.primary_assembly.genome.fa.5.ht2 added
35ce2361ca9c6e_GRCh38.primary_assembly.genome.fa.6.ht2 added
35ce236d4abf47_GRCh38.primary_assembly.genome.fa.7.ht2 added
35ce232d77db2b_GRCh38.primary_assembly.genome.fa.8.ht2 added
35ce2315c3aea1_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
35ce23402f636e_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
35ce23256143da_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
35ce231d9b03c_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
35ce234014de25_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
35ce2317c57d68_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
35ce231b4c622e_GRCh38_full_analysis_set_plus_decoy_hla.fa added
35ce23582a5517_GRCh38.primary_assembly.genome.fa.fai added
35ce2330172e2e_GRCh38.primary_assembly.genome.fa.amb added
35ce232241409e_GRCh38.primary_assembly.genome.fa.ann added
35ce233a932e85_GRCh38.primary_assembly.genome.fa.bwt added
35ce235d980526_GRCh38.primary_assembly.genome.fa.pac added
35ce231cdcc9ed_GRCh38.primary_assembly.genome.fa.sa added
35ce2339bc92a6_GRCh38.primary_assembly.genome.fa added
35ce232958538a_hs37d5.fa.fai added
35ce2349ecddfb_hs37d5.fa.amb added
35ce234fda5a6d_hs37d5.fa.ann added
35ce2362f3cd84_hs37d5.fa.bwt added
35ce231c81cc4_hs37d5.fa.pac added
35ce23df8b767_hs37d5.fa.sa added
35ce233f473982_hs37d5.fa added
35ce2347e25d2f_complete_ref_lens.bin added
35ce231701b07e_ctable.bin added
35ce235b94b648_ctg_offsets.bin added
35ce235b573358_duplicate_clusters.tsv added
35ce237bd59dbd_info.json added
35ce2326597211_mphf.bin added
35ce232704230a_pos.bin added
35ce235da03a2c_pre_indexing.log added
35ce2313a43159_rank.bin added
35ce23547bfe35_ref_indexing.log added
35ce237363e8cd_refAccumLengths.bin added
35ce2353d394c7_reflengths.bin added
35ce2379dd420f_refseq.bin added
35ce23753d9909_seq.bin added
35ce2313e872ed_versionInfo.json added
35ce2311a2bf77_salmon_index added
35ce231089fb37_chrLength.txt added
35ce236c12c804_chrName.txt added
35ce2341b9eda6_chrNameLength.txt added
35ce2332cb3bd5_chrStart.txt added
35ce2326a5f689_exonGeTrInfo.tab added
35ce231f51f2cc_exonInfo.tab added
35ce234fa805c3_geneInfo.tab added
35ce2360628930_Genome added
35ce2348aa4657_genomeParameters.txt added
35ce231994e3be_Log.out added
35ce23303ce39d_SA added
35ce232b9e13db_SAindex added
35ce231b5d0082_sjdbInfo.txt added
35ce233e359b04_sjdbList.fromGTF.out.tab added
35ce236ae54d5d_sjdbList.out.tab added
35ce23633f5db1_transcriptInfo.tab added
35ce2355374b82_GRCh38.GENCODE.v42_100 added
35ce23467a03a5_knownGene_hg38.sql added
35ce233e969109_knownGene_hg38.txt added
35ce23510ce940_refGene_hg38.sql added
35ce236cd375b7_refGene_hg38.txt added
35ce23659ab413_knownGene_mm39.sql added
35ce232ead236c_knownGene_mm39.txt added
35ce2377a710_refGene_mm39.sql added
35ce233a16b248_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/RtmpQEnbxh/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 
 25.048   1.202  33.450