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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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 ‘1.6.0’
* 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 8.453  0.407   8.897
getCloudData  3.031  0.120   5.663
* 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-3.20-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-4.4.3/site-library’
* installing *source* package ‘ReUseData’ ...
** 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 4.4.3 (2025-02-28) -- "Trophy Case"
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...
3b82004c435dd5_GRCh38.primary_assembly.genome.fa.1.bt2 added
3b82007b067e87_GRCh38.primary_assembly.genome.fa.2.bt2 added
3b820015d7975b_GRCh38.primary_assembly.genome.fa.3.bt2 added
3b8200614de6b8_GRCh38.primary_assembly.genome.fa.4.bt2 added
3b82005159d1a2_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3b8200e25d935_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3b82002e634880_outfile.txt added
3b820036f5614f_GRCh37_to_GRCh38.chain added
3b82006deffe77_GRCh37_to_NCBI34.chain added
3b820071e69d7c_GRCh37_to_NCBI35.chain added
3b820024dc25fb_GRCh37_to_NCBI36.chain added
3b82001cbd2050_GRCh38_to_GRCh37.chain added
3b82004319364e_GRCh38_to_NCBI34.chain added
3b82002f825f7d_GRCh38_to_NCBI35.chain added
3b82002a1ad2fe_GRCh38_to_NCBI36.chain added
3b8200421ce7e8_NCBI34_to_GRCh37.chain added
3b820014e6b24c_NCBI34_to_GRCh38.chain added
3b82001167f5d_NCBI35_to_GRCh37.chain added
3b82005113bf57_NCBI35_to_GRCh38.chain added
3b82004f11af8e_NCBI36_to_GRCh37.chain added
3b82002560d776_NCBI36_to_GRCh38.chain added
3b820048d7decc_GRCm38_to_NCBIM36.chain added
3b82003898983e_GRCm38_to_NCBIM37.chain added
3b82004b5a1998_NCBIM36_to_GRCm38.chain added
3b82003b450b09_NCBIM37_to_GRCm38.chain added
3b820031c93138_1000G_omni2.5.b37.vcf.gz added
3b82004954b869_1000G_omni2.5.b37.vcf.gz.tbi added
3b82006e49c010_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3b820018333436_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3b82003c273558_1000G_omni2.5.hg38.vcf.gz added
3b82001428392d_1000G_omni2.5.hg38.vcf.gz.tbi added
3b82006476920b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3b8200372db3df_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3b820029ffd088_af-only-gnomad.raw.sites.vcf added
3b820045c478c3_af-only-gnomad.raw.sites.vcf.idx added
3b82008878581_Mutect2-exome-panel.vcf.idx added
3b82003825a9bd_Mutect2-WGS-panel-b37.vcf added
3b82007427c143_Mutect2-WGS-panel-b37.vcf.idx added
3b82003f7ce6d0_small_exac_common_3.vcf added
3b82002615a834_small_exac_common_3.vcf.idx added
3b8200660e5ec0_1000g_pon.hg38.vcf.gz added
3b820064590ccc_1000g_pon.hg38.vcf.gz.tbi added
3b820042d2c884_af-only-gnomad.hg38.vcf.gz added
3b82002927950e_af-only-gnomad.hg38.vcf.gz.tbi added
3b820013db6c49_small_exac_common_3.hg38.vcf.gz added
3b82006ced9b82_small_exac_common_3.hg38.vcf.gz.tbi added
3b82006b447cf6_gencode.v41.annotation.gtf added
3b820028c21e95_gencode.v42.annotation.gtf added
3b82006e041ae0_gencode.vM30.annotation.gtf added
3b82003c583c4d_gencode.vM31.annotation.gtf added
3b820077d3ce24_gencode.v41.transcripts.fa added
3b82001364f256_gencode.v41.transcripts.fa.fai added
3b82005301b19_gencode.v42.transcripts.fa added
3b8200306c6662_gencode.v42.transcripts.fa.fai added
3b82005ebf0bee_gencode.vM30.pc_transcripts.fa added
3b820040752623_gencode.vM30.pc_transcripts.fa.fai added
3b82006235979a_gencode.vM31.pc_transcripts.fa added
3b82002813c458_gencode.vM31.pc_transcripts.fa.fai added
3b82002ebee633_GRCh38.primary_assembly.genome.fa.1.ht2 added
3b82007a68cbd0_GRCh38.primary_assembly.genome.fa.2.ht2 added
3b8200643af9b0_GRCh38.primary_assembly.genome.fa.3.ht2 added
3b820042e71f60_GRCh38.primary_assembly.genome.fa.4.ht2 added
3b82005edf5ddb_GRCh38.primary_assembly.genome.fa.5.ht2 added
3b82001b68ad8f_GRCh38.primary_assembly.genome.fa.6.ht2 added
3b82006ce6efe8_GRCh38.primary_assembly.genome.fa.7.ht2 added
3b820024a3d69e_GRCh38.primary_assembly.genome.fa.8.ht2 added
3b820023f03310_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3b8200250c99a5_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3b820018cb97e2_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3b8200636d19e0_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3b82004b2241d9_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3b82007ed9f6a2_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3b820047c626ac_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3b8200df50a5d_GRCh38.primary_assembly.genome.fa.fai added
3b820028018bb0_GRCh38.primary_assembly.genome.fa.amb added
3b82005ba192f6_GRCh38.primary_assembly.genome.fa.ann added
3b82007ae2a5e0_GRCh38.primary_assembly.genome.fa.bwt added
3b8200134608a6_GRCh38.primary_assembly.genome.fa.pac added
3b8200463b18b_GRCh38.primary_assembly.genome.fa.sa added
3b820068e6c0c0_GRCh38.primary_assembly.genome.fa added
3b82004f9e44f3_hs37d5.fa.fai added
3b82007c377faf_hs37d5.fa.amb added
3b82007c4bb316_hs37d5.fa.ann added
3b820054ce600c_hs37d5.fa.bwt added
3b82002ca3e611_hs37d5.fa.pac added
3b82005b0abf04_hs37d5.fa.sa added
3b82001543862f_hs37d5.fa added
3b8200ed97dac_complete_ref_lens.bin added
3b820031e835c_ctable.bin added
3b820044026c62_ctg_offsets.bin added
3b8200942497c_duplicate_clusters.tsv added
3b820067597d0c_info.json added
3b82006e98bc2_mphf.bin added
3b82006821a758_pos.bin added
3b82002c22a9b_pre_indexing.log added
3b820073d07baa_rank.bin added
3b8200cc57df6_ref_indexing.log added
3b820026b25dab_refAccumLengths.bin added
3b820018dd154f_reflengths.bin added
3b8200259115d8_refseq.bin added
3b8200a1f778c_seq.bin added
3b820063ff5728_versionInfo.json added
3b8200246b0c7a_salmon_index added
3b820051e59e38_chrLength.txt added
3b820071f46186_chrName.txt added
3b82004c6c982a_chrNameLength.txt added
3b82002d87312e_chrStart.txt added
3b82006cd70766_exonGeTrInfo.tab added
3b82005fb2a0d0_exonInfo.tab added
3b820031eae2ba_geneInfo.tab added
3b820055bdc826_Genome added
3b82002f50e5c3_genomeParameters.txt added
3b82002e226269_Log.out added
3b820052097b3c_SA added
3b820041f45d0_SAindex added
3b82005ac6487b_sjdbInfo.txt added
3b82002d143a40_sjdbList.fromGTF.out.tab added
3b82001962cbff_sjdbList.out.tab added
3b8200699fc627_transcriptInfo.tab added
3b82003032bd9d_GRCh38.GENCODE.v42_100 added
3b82005d653862_knownGene_hg38.sql added
3b820072e20fa3_knownGene_hg38.txt added
3b8200178c3aa9_refGene_hg38.sql added
3b8200644ec424_refGene_hg38.txt added
3b82005b03b6fb_knownGene_mm39.sql added
3b82001a4e6545_knownGene_mm39.txt added
3b8200581f3fcf_refGene_mm39.sql added
3b820067c934f2_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/Rtmpd0eVip/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 
 26.363   2.581  30.444