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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_1.7.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* 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 ‘1.7.0’
* 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 8.912  0.494   9.446
getCloudData  3.657  0.124   8.101
* 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.

##############################################################################
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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-devel_2024-11-24/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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 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...
37ad2e71812660_GRCh38.primary_assembly.genome.fa.1.bt2 added
37ad2e4b6164a3_GRCh38.primary_assembly.genome.fa.2.bt2 added
37ad2e7f435c74_GRCh38.primary_assembly.genome.fa.3.bt2 added
37ad2e4cf3062_GRCh38.primary_assembly.genome.fa.4.bt2 added
37ad2e563e5a21_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
37ad2e1a795443_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
37ad2e77716d05_outfile.txt added
37ad2e2ea92432_GRCh37_to_GRCh38.chain added
37ad2e5b7c292f_GRCh37_to_NCBI34.chain added
37ad2e7021ace8_GRCh37_to_NCBI35.chain added
37ad2e18fde59f_GRCh37_to_NCBI36.chain added
37ad2ed49f3da_GRCh38_to_GRCh37.chain added
37ad2e12f400e9_GRCh38_to_NCBI34.chain added
37ad2e664caf7b_GRCh38_to_NCBI35.chain added
37ad2e24b703a_GRCh38_to_NCBI36.chain added
37ad2ef6d0203_NCBI34_to_GRCh37.chain added
37ad2e50ddd4c1_NCBI34_to_GRCh38.chain added
37ad2e4f74f35a_NCBI35_to_GRCh37.chain added
37ad2e20ecf11c_NCBI35_to_GRCh38.chain added
37ad2e12478fbe_NCBI36_to_GRCh37.chain added
37ad2e43c8e9e5_NCBI36_to_GRCh38.chain added
37ad2e46709644_GRCm38_to_NCBIM36.chain added
37ad2e2731b98e_GRCm38_to_NCBIM37.chain added
37ad2e6c4fb21_NCBIM36_to_GRCm38.chain added
37ad2e5277d2ab_NCBIM37_to_GRCm38.chain added
37ad2e4faca187_1000G_omni2.5.b37.vcf.gz added
37ad2e2ba57d23_1000G_omni2.5.b37.vcf.gz.tbi added
37ad2e5062bc8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
37ad2e5af89ad6_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
37ad2e7cda391c_1000G_omni2.5.hg38.vcf.gz added
37ad2e451e4198_1000G_omni2.5.hg38.vcf.gz.tbi added
37ad2e4c79c136_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
37ad2e483b9dbf_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
37ad2e44619e0d_af-only-gnomad.raw.sites.vcf added
37ad2e5148f198_af-only-gnomad.raw.sites.vcf.idx added
37ad2e1e79f7e1_Mutect2-exome-panel.vcf.idx added
37ad2e5edaf250_Mutect2-WGS-panel-b37.vcf added
37ad2e48ba5e9e_Mutect2-WGS-panel-b37.vcf.idx added
37ad2e4d231c13_small_exac_common_3.vcf added
37ad2e3a571b7f_small_exac_common_3.vcf.idx added
37ad2e38dc0b86_1000g_pon.hg38.vcf.gz added
37ad2e662101b2_1000g_pon.hg38.vcf.gz.tbi added
37ad2e47a10f5a_af-only-gnomad.hg38.vcf.gz added
37ad2e4bd00c6f_af-only-gnomad.hg38.vcf.gz.tbi added
37ad2e4c6db12d_small_exac_common_3.hg38.vcf.gz added
37ad2e49ec7f94_small_exac_common_3.hg38.vcf.gz.tbi added
37ad2e5b3d0e72_gencode.v41.annotation.gtf added
37ad2e1d4b85ef_gencode.v42.annotation.gtf added
37ad2e196172ef_gencode.vM30.annotation.gtf added
37ad2e7c29ff8e_gencode.vM31.annotation.gtf added
37ad2e2f9315ad_gencode.v41.transcripts.fa added
37ad2e5d2a5cd4_gencode.v41.transcripts.fa.fai added
37ad2e429a95d2_gencode.v42.transcripts.fa added
37ad2e56c4cf3b_gencode.v42.transcripts.fa.fai added
37ad2e63ef57f5_gencode.vM30.pc_transcripts.fa added
37ad2e1512687e_gencode.vM30.pc_transcripts.fa.fai added
37ad2e267170c3_gencode.vM31.pc_transcripts.fa added
37ad2ef94d518_gencode.vM31.pc_transcripts.fa.fai added
37ad2e1a189446_GRCh38.primary_assembly.genome.fa.1.ht2 added
37ad2e16a0b99_GRCh38.primary_assembly.genome.fa.2.ht2 added
37ad2ec6f0e34_GRCh38.primary_assembly.genome.fa.3.ht2 added
37ad2e5f36d5df_GRCh38.primary_assembly.genome.fa.4.ht2 added
37ad2e4de3cccf_GRCh38.primary_assembly.genome.fa.5.ht2 added
37ad2e54aaabf3_GRCh38.primary_assembly.genome.fa.6.ht2 added
37ad2e239873ec_GRCh38.primary_assembly.genome.fa.7.ht2 added
37ad2e1f2cbe68_GRCh38.primary_assembly.genome.fa.8.ht2 added
37ad2e7324a3d4_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
37ad2e273663c_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
37ad2e67e71d06_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
37ad2e4047bfe8_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
37ad2e3cca81bc_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
37ad2e20c3288c_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
37ad2e2668c19a_GRCh38_full_analysis_set_plus_decoy_hla.fa added
37ad2e46b9116_GRCh38.primary_assembly.genome.fa.fai added
37ad2e6c9334fb_GRCh38.primary_assembly.genome.fa.amb added
37ad2e72d672c8_GRCh38.primary_assembly.genome.fa.ann added
37ad2e4e5810aa_GRCh38.primary_assembly.genome.fa.bwt added
37ad2e47d0436e_GRCh38.primary_assembly.genome.fa.pac added
37ad2e1021f8b7_GRCh38.primary_assembly.genome.fa.sa added
37ad2e67b98399_GRCh38.primary_assembly.genome.fa added
37ad2e43fa42fc_hs37d5.fa.fai added
37ad2e3fb50e64_hs37d5.fa.amb added
37ad2e44e3e06d_hs37d5.fa.ann added
37ad2e694d8cf_hs37d5.fa.bwt added
37ad2e1679dd9f_hs37d5.fa.pac added
37ad2e28d33862_hs37d5.fa.sa added
37ad2e1ba7414d_hs37d5.fa added
37ad2e3ceb4e62_complete_ref_lens.bin added
37ad2e38680d7a_ctable.bin added
37ad2e35bfd593_ctg_offsets.bin added
37ad2e3e5559fb_duplicate_clusters.tsv added
37ad2e44d71bae_info.json added
37ad2e14f6ab72_mphf.bin added
37ad2ec3926cb_pos.bin added
37ad2e1981c7a2_pre_indexing.log added
37ad2e388f1f5e_rank.bin added
37ad2e2b65e533_ref_indexing.log added
37ad2eca66b76_refAccumLengths.bin added
37ad2e3b02859b_reflengths.bin added
37ad2e134d0239_refseq.bin added
37ad2e4cee2b5e_seq.bin added
37ad2e77cd0757_versionInfo.json added
37ad2e34102ac5_salmon_index added
37ad2e7356ecf9_chrLength.txt added
37ad2e7c38986d_chrName.txt added
37ad2e20a35fc0_chrNameLength.txt added
37ad2e662d5fc1_chrStart.txt added
37ad2e4a90a917_exonGeTrInfo.tab added
37ad2e6873a32e_exonInfo.tab added
37ad2e764f5878_geneInfo.tab added
37ad2e324a2cb1_Genome added
37ad2e2c6de62b_genomeParameters.txt added
37ad2e360466dc_Log.out added
37ad2e772e0d1e_SA added
37ad2e3302befa_SAindex added
37ad2e4c7e447b_sjdbInfo.txt added
37ad2e20014581_sjdbList.fromGTF.out.tab added
37ad2e4eaa0047_sjdbList.out.tab added
37ad2e96992de_transcriptInfo.tab added
37ad2e586952fb_GRCh38.GENCODE.v42_100 added
37ad2e469d5da_knownGene_hg38.sql added
37ad2e47beecd9_knownGene_hg38.txt added
37ad2e1d406eaa_refGene_hg38.sql added
37ad2e1960814d_refGene_hg38.txt added
37ad2e53f813a4_knownGene_mm39.sql added
37ad2e36c2364c_knownGene_mm39.txt added
37ad2e51efa0ab_refGene_mm39.sql added
37ad2e7f5df8d7_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/Rtmpfg4kaf/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 
 29.192   1.879  34.393