##############################################################################
##############################################################################
###
### 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_1.7.0.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 ‘1.7.0’
* 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 8.750  0.407   9.426
getCloudData  3.453  0.196   7.403
* 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 ‘1.7.0’
** 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...
f67467072c6d5_GRCh38.primary_assembly.genome.fa.1.bt2 added
f67465274a1a8_GRCh38.primary_assembly.genome.fa.2.bt2 added
f6746976d33_GRCh38.primary_assembly.genome.fa.3.bt2 added
f674673f1979b_GRCh38.primary_assembly.genome.fa.4.bt2 added
f67462d3777e0_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
f674656182bbc_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
f674624c560b6_outfile.txt added
f674661d48dca_GRCh37_to_GRCh38.chain added
f67461ab6eafe_GRCh37_to_NCBI34.chain added
f67466b8dc294_GRCh37_to_NCBI35.chain added
f674666314da0_GRCh37_to_NCBI36.chain added
f6746bc58520_GRCh38_to_GRCh37.chain added
f674632560d81_GRCh38_to_NCBI34.chain added
f67461e79ecd1_GRCh38_to_NCBI35.chain added
f67464542a060_GRCh38_to_NCBI36.chain added
f67463e33d914_NCBI34_to_GRCh37.chain added
f67461460c5ca_NCBI34_to_GRCh38.chain added
f6746344a723_NCBI35_to_GRCh37.chain added
f67467c12a2c9_NCBI35_to_GRCh38.chain added
f6746738edbda_NCBI36_to_GRCh37.chain added
f6746467c358d_NCBI36_to_GRCh38.chain added
f67462f448bd3_GRCm38_to_NCBIM36.chain added
f674622b05639_GRCm38_to_NCBIM37.chain added
f67465201716e_NCBIM36_to_GRCm38.chain added
f674640d442a2_NCBIM37_to_GRCm38.chain added
f6746390c6334_1000G_omni2.5.b37.vcf.gz added
f67462e49322b_1000G_omni2.5.b37.vcf.gz.tbi added
f674613bd62d8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
f6746142511ce_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
f67466a935547_1000G_omni2.5.hg38.vcf.gz added
f67467642acca_1000G_omni2.5.hg38.vcf.gz.tbi added
f6746497d8a3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
f67463d07f6ef_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
f674676da19fe_af-only-gnomad.raw.sites.vcf added
f67467889703f_af-only-gnomad.raw.sites.vcf.idx added
f67466a3f6ed0_Mutect2-exome-panel.vcf.idx added
f67464cf245ba_Mutect2-WGS-panel-b37.vcf added
f67461d4ed0f5_Mutect2-WGS-panel-b37.vcf.idx added
f67464c13fc9a_small_exac_common_3.vcf added
f674667a930b8_small_exac_common_3.vcf.idx added
f67468dc9389_1000g_pon.hg38.vcf.gz added
f674632454a3b_1000g_pon.hg38.vcf.gz.tbi added
f6746736eb5d8_af-only-gnomad.hg38.vcf.gz added
f67463b32a10a_af-only-gnomad.hg38.vcf.gz.tbi added
f674650bf370c_small_exac_common_3.hg38.vcf.gz added
f674638b15639_small_exac_common_3.hg38.vcf.gz.tbi added
f674679667a1f_gencode.v41.annotation.gtf added
f6746651ffcd7_gencode.v42.annotation.gtf added
f67463bf5fd5c_gencode.vM30.annotation.gtf added
f674675791ce8_gencode.vM31.annotation.gtf added
f674658aed8b1_gencode.v41.transcripts.fa added
f674627232ea_gencode.v41.transcripts.fa.fai added
f674624bda8bb_gencode.v42.transcripts.fa added
f67467b5f2eea_gencode.v42.transcripts.fa.fai added
f67465473a458_gencode.vM30.pc_transcripts.fa added
f67466591eb5d_gencode.vM30.pc_transcripts.fa.fai added
f6746346b921f_gencode.vM31.pc_transcripts.fa added
f67462bcd683_gencode.vM31.pc_transcripts.fa.fai added
f6746794f4e35_GRCh38.primary_assembly.genome.fa.1.ht2 added
f67464890a3ed_GRCh38.primary_assembly.genome.fa.2.ht2 added
f67466d502bca_GRCh38.primary_assembly.genome.fa.3.ht2 added
f67466f91faff_GRCh38.primary_assembly.genome.fa.4.ht2 added
f67464d287c91_GRCh38.primary_assembly.genome.fa.5.ht2 added
f67462a5822ba_GRCh38.primary_assembly.genome.fa.6.ht2 added
f6746666c14fd_GRCh38.primary_assembly.genome.fa.7.ht2 added
f674645b1ecd0_GRCh38.primary_assembly.genome.fa.8.ht2 added
f67461497918a_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
f6746335e5ab7_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
f67466300bdc5_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
f674660ab8e24_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
f67461b078b6f_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
f67466bdd514e_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
f674612f0d85f_GRCh38_full_analysis_set_plus_decoy_hla.fa added
f6746e764148_GRCh38.primary_assembly.genome.fa.fai added
f6746270ff259_GRCh38.primary_assembly.genome.fa.amb added
f674663b00f6c_GRCh38.primary_assembly.genome.fa.ann added
f674647279781_GRCh38.primary_assembly.genome.fa.bwt added
f674620766c78_GRCh38.primary_assembly.genome.fa.pac added
f674648d00c43_GRCh38.primary_assembly.genome.fa.sa added
f674631d94dd_GRCh38.primary_assembly.genome.fa added
f674615ef8960_hs37d5.fa.fai added
f6746217ee4f4_hs37d5.fa.amb added
f674658fc7c7_hs37d5.fa.ann added
f67463aad321b_hs37d5.fa.bwt added
f67461cde13de_hs37d5.fa.pac added
f67465a036c1f_hs37d5.fa.sa added
f6746203f1d78_hs37d5.fa added
f67465149a5fd_complete_ref_lens.bin added
f67465cc042a3_ctable.bin added
f6746198e6bad_ctg_offsets.bin added
f674619da49eb_duplicate_clusters.tsv added
f67464a106e6d_info.json added
f674692066ac_mphf.bin added
f67466702c67c_pos.bin added
f674674689127_pre_indexing.log added
f67466f8c7baa_rank.bin added
f67462cb4b34c_ref_indexing.log added
f674690022b1_refAccumLengths.bin added
f674622ead661_reflengths.bin added
f6746fb57111_refseq.bin added
f674669abb0d6_seq.bin added
f67463df261d1_versionInfo.json added
f67467b92c25f_salmon_index added
f67467c9c8935_chrLength.txt added
f67464c68a319_chrName.txt added
f674622a2b4b8_chrNameLength.txt added
f6746604c98a1_chrStart.txt added
f674613903a9a_exonGeTrInfo.tab added
f674643192130_exonInfo.tab added
f6746291ca4e4_geneInfo.tab added
f674616adcf77_Genome added
f67465908aa90_genomeParameters.txt added
f67464a9b89d8_Log.out added
f67461c3d973f_SA added
f674613b5dcab_SAindex added
f674667799db7_sjdbInfo.txt added
f67467641035e_sjdbList.fromGTF.out.tab added
f674633f4fa23_sjdbList.out.tab added
f674638c343b4_transcriptInfo.tab added
f674653014601_GRCh38.GENCODE.v42_100 added
f67464d8365d0_knownGene_hg38.sql added
f6746529d8d9f_knownGene_hg38.txt added
f67461d11b46f_refGene_hg38.sql added
f674656a3cc7d_refGene_hg38.txt added
f674639a0541b_knownGene_mm39.sql added
f6746117a4596_knownGene_mm39.txt added
f674646304827_refGene_mm39.sql added
f674666550767_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/RtmpGQ7ZbC/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 
 30.498   1.680  37.189