##############################################################################
##############################################################################
###
### 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-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 ‘1.8.0’
* 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 8.635  0.331   9.002
getCloudData  3.395  0.159   7.123
* 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-3.21-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 ‘1.8.0’
** 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...
364933504e49e7_GRCh38.primary_assembly.genome.fa.1.bt2 added
3649333bff5c32_GRCh38.primary_assembly.genome.fa.2.bt2 added
364933677c2832_GRCh38.primary_assembly.genome.fa.3.bt2 added
36493367fb88cc_GRCh38.primary_assembly.genome.fa.4.bt2 added
36493311c91b87_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
36493337e57cd5_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3649332ede8945_outfile.txt added
36493363e3a3c4_GRCh37_to_GRCh38.chain added
3649337ff78424_GRCh37_to_NCBI34.chain added
36493358155dbc_GRCh37_to_NCBI35.chain added
364933b90fd12_GRCh37_to_NCBI36.chain added
3649333c0cd8ca_GRCh38_to_GRCh37.chain added
3649331f8210c7_GRCh38_to_NCBI34.chain added
3649331356af3f_GRCh38_to_NCBI35.chain added
36493339f01c95_GRCh38_to_NCBI36.chain added
36493323336017_NCBI34_to_GRCh37.chain added
3649333c968fc3_NCBI34_to_GRCh38.chain added
3649331946d362_NCBI35_to_GRCh37.chain added
364933163078a2_NCBI35_to_GRCh38.chain added
3649331d6a6608_NCBI36_to_GRCh37.chain added
36493325a146cf_NCBI36_to_GRCh38.chain added
3649336e96cbf0_GRCm38_to_NCBIM36.chain added
3649336d3095eb_GRCm38_to_NCBIM37.chain added
3649339a1fe8e_NCBIM36_to_GRCm38.chain added
36493353b68dc7_NCBIM37_to_GRCm38.chain added
3649337903de19_1000G_omni2.5.b37.vcf.gz added
36493377aab05_1000G_omni2.5.b37.vcf.gz.tbi added
364933437c9657_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3649335ff40c11_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3649333b0771aa_1000G_omni2.5.hg38.vcf.gz added
3649337b035d0a_1000G_omni2.5.hg38.vcf.gz.tbi added
364933304255f8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3649337706cddc_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
364933627f853c_af-only-gnomad.raw.sites.vcf added
364933183ddec4_af-only-gnomad.raw.sites.vcf.idx added
3649338cfe963_Mutect2-exome-panel.vcf.idx added
3649331a650211_Mutect2-WGS-panel-b37.vcf added
364933471c6809_Mutect2-WGS-panel-b37.vcf.idx added
3649336cb38d28_small_exac_common_3.vcf added
3649331a5c8636_small_exac_common_3.vcf.idx added
3649331f31c5c5_1000g_pon.hg38.vcf.gz added
36493378448a3a_1000g_pon.hg38.vcf.gz.tbi added
36493356695f00_af-only-gnomad.hg38.vcf.gz added
3649333eb3d68c_af-only-gnomad.hg38.vcf.gz.tbi added
364933b9b3979_small_exac_common_3.hg38.vcf.gz added
36493310597b96_small_exac_common_3.hg38.vcf.gz.tbi added
36493361e736a3_gencode.v41.annotation.gtf added
3649334831c93c_gencode.v42.annotation.gtf added
36493329a04ef8_gencode.vM30.annotation.gtf added
3649337817af46_gencode.vM31.annotation.gtf added
364933659c2f44_gencode.v41.transcripts.fa added
3649334f4195c7_gencode.v41.transcripts.fa.fai added
36493366ae7b36_gencode.v42.transcripts.fa added
36493352ccc52f_gencode.v42.transcripts.fa.fai added
36493358e39455_gencode.vM30.pc_transcripts.fa added
3649333a6508fd_gencode.vM30.pc_transcripts.fa.fai added
3649334bd0a348_gencode.vM31.pc_transcripts.fa added
364933605e3f5b_gencode.vM31.pc_transcripts.fa.fai added
3649337de19f55_GRCh38.primary_assembly.genome.fa.1.ht2 added
3649332bc4af59_GRCh38.primary_assembly.genome.fa.2.ht2 added
3649331b65b105_GRCh38.primary_assembly.genome.fa.3.ht2 added
36493378e4fc5f_GRCh38.primary_assembly.genome.fa.4.ht2 added
3649335c070551_GRCh38.primary_assembly.genome.fa.5.ht2 added
364933126c7ee2_GRCh38.primary_assembly.genome.fa.6.ht2 added
3649335b64819b_GRCh38.primary_assembly.genome.fa.7.ht2 added
3649337444e416_GRCh38.primary_assembly.genome.fa.8.ht2 added
3649331b3c6845_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
36493375c983ad_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3649333b614c1f_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3649337eff56d_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
364933102609e3_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3649335a9311e5_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
364933347fa7_GRCh38_full_analysis_set_plus_decoy_hla.fa added
364933668f68e3_GRCh38.primary_assembly.genome.fa.fai added
3649331946e871_GRCh38.primary_assembly.genome.fa.amb added
364933bcfb920_GRCh38.primary_assembly.genome.fa.ann added
36493376e8e479_GRCh38.primary_assembly.genome.fa.bwt added
3649337b2e1f15_GRCh38.primary_assembly.genome.fa.pac added
3649335401825c_GRCh38.primary_assembly.genome.fa.sa added
36493320893371_GRCh38.primary_assembly.genome.fa added
3649337345ce5b_hs37d5.fa.fai added
364933399db1a1_hs37d5.fa.amb added
3649336fcac938_hs37d5.fa.ann added
36493359f44991_hs37d5.fa.bwt added
364933c6a76d0_hs37d5.fa.pac added
36493348ae5d8e_hs37d5.fa.sa added
3649331459528f_hs37d5.fa added
364933583b1a19_complete_ref_lens.bin added
364933290c9ce9_ctable.bin added
364933123af1e4_ctg_offsets.bin added
3649333ffc972_duplicate_clusters.tsv added
36493344724dee_info.json added
364933b1fee43_mphf.bin added
3649336006cec4_pos.bin added
36493356deccd0_pre_indexing.log added
36493366846fde_rank.bin added
364933544bb2da_ref_indexing.log added
364933721b3516_refAccumLengths.bin added
3649335c4df38b_reflengths.bin added
364933facfef9_refseq.bin added
3649337a0b2a83_seq.bin added
3649336c73fd6e_versionInfo.json added
3649336a4010de_salmon_index added
3649337a3faa2b_chrLength.txt added
36493353036652_chrName.txt added
364933386f950_chrNameLength.txt added
36493360f634b_chrStart.txt added
36493349ec4acb_exonGeTrInfo.tab added
3649337eb51865_exonInfo.tab added
3649335a10e5a8_geneInfo.tab added
3649336a757e3d_Genome added
36493371fae6c0_genomeParameters.txt added
36493313ae9749_Log.out added
3649335a404775_SA added
3649334bef3051_SAindex added
36493320190e19_sjdbInfo.txt added
36493322eea503_sjdbList.fromGTF.out.tab added
364933604882e0_sjdbList.out.tab added
36493378542832_transcriptInfo.tab added
3649334bfb41ec_GRCh38.GENCODE.v42_100 added
364933728374c4_knownGene_hg38.sql added
3649337c53f1a5_knownGene_hg38.txt added
364933106d8fdb_refGene_hg38.sql added
3649337da36307_refGene_hg38.txt added
3649335c5ac069_knownGene_mm39.sql added
364933674c5cab_knownGene_mm39.txt added
3649336427d2e6_refGene_mm39.sql added
36493330a67343_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/RtmpqI7FRh/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 
 30.698   2.211  36.005