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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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.24-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 ‘1.13.0’
* 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 8.955  0.320   9.362
getCloudData  3.345  0.138   6.712
* 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-3.24-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 ‘1.13.0’
** 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...
fcbe671530e42_GRCh38.primary_assembly.genome.fa.1.bt2 added
fcbe667e461eb_GRCh38.primary_assembly.genome.fa.2.bt2 added
fcbe6105fc81e_GRCh38.primary_assembly.genome.fa.3.bt2 added
fcbe64d30b84a_GRCh38.primary_assembly.genome.fa.4.bt2 added
fcbe67216452f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
fcbe62424f8bc_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
fcbe648dfa8d0_outfile.txt added
fcbe640799ed3_GRCh37_to_GRCh38.chain added
fcbe6431e0aba_GRCh37_to_NCBI34.chain added
fcbe637f33dee_GRCh37_to_NCBI35.chain added
fcbe65125379b_GRCh37_to_NCBI36.chain added
fcbe6628ba5bc_GRCh38_to_GRCh37.chain added
fcbe65503d368_GRCh38_to_NCBI34.chain added
fcbe6590af76d_GRCh38_to_NCBI35.chain added
fcbe643f14b60_GRCh38_to_NCBI36.chain added
fcbe648c58e63_NCBI34_to_GRCh37.chain added
fcbe6444db09b_NCBI34_to_GRCh38.chain added
fcbe6387c28d4_NCBI35_to_GRCh37.chain added
fcbe663e637a_NCBI35_to_GRCh38.chain added
fcbe67705dd58_NCBI36_to_GRCh37.chain added
fcbe6a96cb30_NCBI36_to_GRCh38.chain added
fcbe6279df7a8_GRCm38_to_NCBIM36.chain added
fcbe6184090e_GRCm38_to_NCBIM37.chain added
fcbe64ce97e9a_NCBIM36_to_GRCm38.chain added
fcbe620af16c6_NCBIM37_to_GRCm38.chain added
fcbe68acf4f1_1000G_omni2.5.b37.vcf.gz added
fcbe65c4bf67_1000G_omni2.5.b37.vcf.gz.tbi added
fcbe610b2d803_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
fcbe65449184e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
fcbe615fc7af0_1000G_omni2.5.hg38.vcf.gz added
fcbe61e0e663f_1000G_omni2.5.hg38.vcf.gz.tbi added
fcbe6459c2691_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
fcbe67de0dcdb_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
fcbe62e6e2e5d_af-only-gnomad.raw.sites.vcf added
fcbe612ccdedb_af-only-gnomad.raw.sites.vcf.idx added
fcbe66ff7220a_Mutect2-exome-panel.vcf.idx added
fcbe652932719_Mutect2-WGS-panel-b37.vcf added
fcbe65bac87ab_Mutect2-WGS-panel-b37.vcf.idx added
fcbe63070c0dd_small_exac_common_3.vcf added
fcbe615b131d4_small_exac_common_3.vcf.idx added
fcbe6139fc59a_1000g_pon.hg38.vcf.gz added
fcbe6195f879_1000g_pon.hg38.vcf.gz.tbi added
fcbe6783cd790_af-only-gnomad.hg38.vcf.gz added
fcbe668a39902_af-only-gnomad.hg38.vcf.gz.tbi added
fcbe65aa0efe6_small_exac_common_3.hg38.vcf.gz added
fcbe63c2e22f0_small_exac_common_3.hg38.vcf.gz.tbi added
fcbe631692766_gencode.v41.annotation.gtf added
fcbe61eeea082_gencode.v42.annotation.gtf added
fcbe674aa4bc4_gencode.vM30.annotation.gtf added
fcbe637a78ae0_gencode.vM31.annotation.gtf added
fcbe615f47dda_gencode.v41.transcripts.fa added
fcbe67f4116f5_gencode.v41.transcripts.fa.fai added
fcbe65f458288_gencode.v42.transcripts.fa added
fcbe6177886e9_gencode.v42.transcripts.fa.fai added
fcbe64c2a958f_gencode.vM30.pc_transcripts.fa added
fcbe67ff4994e_gencode.vM30.pc_transcripts.fa.fai added
fcbe620257bda_gencode.vM31.pc_transcripts.fa added
fcbe651ef54f6_gencode.vM31.pc_transcripts.fa.fai added
fcbe610a77151_GRCh38.primary_assembly.genome.fa.1.ht2 added
fcbe6746e9429_GRCh38.primary_assembly.genome.fa.2.ht2 added
fcbe667ebcfe6_GRCh38.primary_assembly.genome.fa.3.ht2 added
fcbe62eb5d790_GRCh38.primary_assembly.genome.fa.4.ht2 added
fcbe63a0ababa_GRCh38.primary_assembly.genome.fa.5.ht2 added
fcbe665ccacc1_GRCh38.primary_assembly.genome.fa.6.ht2 added
fcbe65d2405ed_GRCh38.primary_assembly.genome.fa.7.ht2 added
fcbe64cd79995_GRCh38.primary_assembly.genome.fa.8.ht2 added
fcbe655c3cecc_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
fcbe62fb72d07_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
fcbe628842141_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
fcbe66348fa9_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
fcbe645685edb_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
fcbe63c23e6db_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
fcbe67ca8822_GRCh38_full_analysis_set_plus_decoy_hla.fa added
fcbe63da5366b_GRCh38.primary_assembly.genome.fa.fai added
fcbe624c77fdd_GRCh38.primary_assembly.genome.fa.amb added
fcbe6626b7809_GRCh38.primary_assembly.genome.fa.ann added
fcbe679d3595b_GRCh38.primary_assembly.genome.fa.bwt added
fcbe65630a743_GRCh38.primary_assembly.genome.fa.pac added
fcbe615a188b_GRCh38.primary_assembly.genome.fa.sa added
fcbe66e7da520_GRCh38.primary_assembly.genome.fa added
fcbe6dd83224_hs37d5.fa.fai added
fcbe6174e9665_hs37d5.fa.amb added
fcbe66dbebc15_hs37d5.fa.ann added
fcbe66d1db4ac_hs37d5.fa.bwt added
fcbe62ec71d4e_hs37d5.fa.pac added
fcbe639e951a4_hs37d5.fa.sa added
fcbe66d124dfb_hs37d5.fa added
fcbe64eec9929_complete_ref_lens.bin added
fcbe6bd8a69b_ctable.bin added
fcbe67db9bf4c_ctg_offsets.bin added
fcbe6435b2d52_duplicate_clusters.tsv added
fcbe673c47681_info.json added
fcbe62c6f96dd_mphf.bin added
fcbe67d65e80c_pos.bin added
fcbe659912343_pre_indexing.log added
fcbe69939cca_rank.bin added
fcbe64a3d81a1_ref_indexing.log added
fcbe62f54f20f_refAccumLengths.bin added
fcbe6394ac9d1_reflengths.bin added
fcbe672c1a2e2_refseq.bin added
fcbe6358981b8_seq.bin added
fcbe67eb328ac_versionInfo.json added
fcbe62ee589bd_salmon_index added
fcbe63d5409db_chrLength.txt added
fcbe63c585f17_chrName.txt added
fcbe653ad099b_chrNameLength.txt added
fcbe61fbf81e4_chrStart.txt added
fcbe6362bb873_exonGeTrInfo.tab added
fcbe629ddb0de_exonInfo.tab added
fcbe621199a6f_geneInfo.tab added
fcbe624a95d93_Genome added
fcbe637b5e302_genomeParameters.txt added
fcbe6386830d4_Log.out added
fcbe6126819a8_SA added
fcbe624d397af_SAindex added
fcbe6672f4e23_sjdbInfo.txt added
fcbe64c516b4c_sjdbList.fromGTF.out.tab added
fcbe611e5e5aa_sjdbList.out.tab added
fcbe6361be74c_transcriptInfo.tab added
fcbe6582a11e7_GRCh38.GENCODE.v42_100 added
fcbe6f9fa4f6_knownGene_hg38.sql added
fcbe67977149e_knownGene_hg38.txt added
fcbe64bee8869_refGene_hg38.sql added
fcbe63c0f3bd3_refGene_hg38.txt added
fcbe676dcfcaa_knownGene_mm39.sql added
fcbe6257fabac_knownGene_mm39.txt added
fcbe645a2d89e_refGene_mm39.sql added
fcbe6411a7e4b_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/RtmpA3Gov2/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 
 25.496   1.632  30.593