##############################################################################
##############################################################################
###
### 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_1.9.0.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 ‘1.9.0’
* 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 8.506  0.501   9.067
getCloudData  3.325  0.721   8.794
* 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.

##############################################################################
##############################################################################
###
### 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 ‘1.9.0’
** 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...
3436894fda045a_GRCh38.primary_assembly.genome.fa.1.bt2 added
3436893d4b083c_GRCh38.primary_assembly.genome.fa.2.bt2 added
34368947665684_GRCh38.primary_assembly.genome.fa.3.bt2 added
3436895709fc45_GRCh38.primary_assembly.genome.fa.4.bt2 added
34368919c19f42_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
343689413589e3_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3436891b58bc7c_outfile.txt added
3436894e5a2535_GRCh37_to_GRCh38.chain added
3436893a5680a9_GRCh37_to_NCBI34.chain added
34368977994104_GRCh37_to_NCBI35.chain added
343689530d91f9_GRCh37_to_NCBI36.chain added
34368959b8e6b1_GRCh38_to_GRCh37.chain added
3436894d1e560b_GRCh38_to_NCBI34.chain added
34368977fc0384_GRCh38_to_NCBI35.chain added
34368973005aa4_GRCh38_to_NCBI36.chain added
343689618710b9_NCBI34_to_GRCh37.chain added
3436897137f6e5_NCBI34_to_GRCh38.chain added
34368979588368_NCBI35_to_GRCh37.chain added
34368914507283_NCBI35_to_GRCh38.chain added
3436891b0ccd7f_NCBI36_to_GRCh37.chain added
3436891158a8d8_NCBI36_to_GRCh38.chain added
3436893c2af6ca_GRCm38_to_NCBIM36.chain added
3436891ecc8dbc_GRCm38_to_NCBIM37.chain added
3436895e18242d_NCBIM36_to_GRCm38.chain added
34368965914e4e_NCBIM37_to_GRCm38.chain added
3436893fabeb3e_1000G_omni2.5.b37.vcf.gz added
343689305bbf2a_1000G_omni2.5.b37.vcf.gz.tbi added
3436894f57d800_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3436891a2e0b30_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
34368948989e9_1000G_omni2.5.hg38.vcf.gz added
3436897b4fdd44_1000G_omni2.5.hg38.vcf.gz.tbi added
3436896a080f8a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
34368941d49226_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
34368942b633c8_af-only-gnomad.raw.sites.vcf added
34368941120bcf_af-only-gnomad.raw.sites.vcf.idx added
3436895b963168_Mutect2-exome-panel.vcf.idx added
3436893ebbdac_Mutect2-WGS-panel-b37.vcf added
3436895c6ac84b_Mutect2-WGS-panel-b37.vcf.idx added
34368929f0569d_small_exac_common_3.vcf added
3436893e423e55_small_exac_common_3.vcf.idx added
3436895404094f_1000g_pon.hg38.vcf.gz added
3436897cfde896_1000g_pon.hg38.vcf.gz.tbi added
34368917fb2506_af-only-gnomad.hg38.vcf.gz added
34368921225f5b_af-only-gnomad.hg38.vcf.gz.tbi added
34368974f9ec1a_small_exac_common_3.hg38.vcf.gz added
343689afb7fab_small_exac_common_3.hg38.vcf.gz.tbi added
3436892a97014_gencode.v41.annotation.gtf added
3436896631e2ff_gencode.v42.annotation.gtf added
3436894540313_gencode.vM30.annotation.gtf added
34368916f9e298_gencode.vM31.annotation.gtf added
34368913eb07f_gencode.v41.transcripts.fa added
34368915acabeb_gencode.v41.transcripts.fa.fai added
3436895324d962_gencode.v42.transcripts.fa added
343689200b3e3b_gencode.v42.transcripts.fa.fai added
34368973c4d019_gencode.vM30.pc_transcripts.fa added
34368938b627b0_gencode.vM30.pc_transcripts.fa.fai added
3436895fb72979_gencode.vM31.pc_transcripts.fa added
34368924208f43_gencode.vM31.pc_transcripts.fa.fai added
34368980dffb0_GRCh38.primary_assembly.genome.fa.1.ht2 added
34368979e534a9_GRCh38.primary_assembly.genome.fa.2.ht2 added
34368928aa192d_GRCh38.primary_assembly.genome.fa.3.ht2 added
34368935ddcf5_GRCh38.primary_assembly.genome.fa.4.ht2 added
34368963ed4433_GRCh38.primary_assembly.genome.fa.5.ht2 added
3436896a7eab53_GRCh38.primary_assembly.genome.fa.6.ht2 added
343689461410bd_GRCh38.primary_assembly.genome.fa.7.ht2 added
34368924ff5002_GRCh38.primary_assembly.genome.fa.8.ht2 added
3436894614dcbb_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
34368949ffce69_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
34368916a184d_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
34368970053358_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3436898420cbf_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
343689556e219d_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3436896d031bee_GRCh38_full_analysis_set_plus_decoy_hla.fa added
343689203d31c5_GRCh38.primary_assembly.genome.fa.fai added
343689769080f8_GRCh38.primary_assembly.genome.fa.amb added
34368961fd0808_GRCh38.primary_assembly.genome.fa.ann added
3436892b38b170_GRCh38.primary_assembly.genome.fa.bwt added
3436897939f10c_GRCh38.primary_assembly.genome.fa.pac added
343689482eeb08_GRCh38.primary_assembly.genome.fa.sa added
3436892f8cb483_GRCh38.primary_assembly.genome.fa added
3436891033d3a4_hs37d5.fa.fai added
343689496d9b87_hs37d5.fa.amb added
3436894539606f_hs37d5.fa.ann added
3436896358ad06_hs37d5.fa.bwt added
3436896978d9c2_hs37d5.fa.pac added
34368938fe3088_hs37d5.fa.sa added
3436891c0ed4b6_hs37d5.fa added
3436894930033b_complete_ref_lens.bin added
3436895d1ebfcb_ctable.bin added
343689241cd467_ctg_offsets.bin added
343689431537e4_duplicate_clusters.tsv added
3436895c8d8f8_info.json added
343689277ab15c_mphf.bin added
34368927027c17_pos.bin added
3436897047844b_pre_indexing.log added
3436896d8ec219_rank.bin added
3436894c01cc19_ref_indexing.log added
343689365c6106_refAccumLengths.bin added
343689378e9083_reflengths.bin added
3436894d6be466_refseq.bin added
3436892661945e_seq.bin added
3436893fd09d42_versionInfo.json added
34368922da0603_salmon_index added
3436891364b04c_chrLength.txt added
343689600dcf07_chrName.txt added
343689196a86fb_chrNameLength.txt added
3436897561b855_chrStart.txt added
343689b468078_exonGeTrInfo.tab added
34368912a47808_exonInfo.tab added
3436893d90a35d_geneInfo.tab added
3436893ad334fb_Genome added
34368922d84bac_genomeParameters.txt added
3436896fe3ee4_Log.out added
343689c956a_SA added
343689630f8b3_SAindex added
343689707718a6_sjdbInfo.txt added
343689390ac5f2_sjdbList.fromGTF.out.tab added
343689223fcd69_sjdbList.out.tab added
34368939a71be1_transcriptInfo.tab added
343689162985be_GRCh38.GENCODE.v42_100 added
343689465ca1d0_knownGene_hg38.sql added
3436897cbc53c5_knownGene_hg38.txt added
3436891bf25eb6_refGene_hg38.sql added
3436896dd7532c_refGene_hg38.txt added
34368923becfdc_knownGene_mm39.sql added
343689c39e302_knownGene_mm39.txt added
3436895b661546_refGene_mm39.sql added
3436896fc09bf5_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/RtmpDKD3Je/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 
 24.525   1.924  30.256