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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ReUseData_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.1.0’
* 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 R 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 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
dataUpdate    16.626  1.162  17.791
getCloudData  10.832  0.522  14.403
dataHub-class  8.696  0.508   9.212
getData        4.946  0.283   5.223
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ReUseData_data.Rmd’ using ‘UTF-8’... OK
  ‘ReUseData_quickStart.Rmd’ using ‘UTF-8’... OK
  ‘ReUseData_recipe.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/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) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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...
1aef7c2a1a76a2_GRCh38.primary_assembly.genome.fa.1.bt2 added
1aef7c1d4cec4c_GRCh38.primary_assembly.genome.fa.2.bt2 added
1aef7c54845ac8_GRCh38.primary_assembly.genome.fa.3.bt2 added
1aef7c70fb44f4_GRCh38.primary_assembly.genome.fa.4.bt2 added
1aef7c80ff51b_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1aef7c78e8eabf_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1aef7c7a27b753_outfile.txt added
1aef7c313d6ef0_GRCh37_to_GRCh38.chain added
1aef7c6493db94_GRCh37_to_NCBI34.chain added
1aef7c7888527a_GRCh37_to_NCBI35.chain added
1aef7c541f7acf_GRCh37_to_NCBI36.chain added
1aef7c23e21767_GRCh38_to_GRCh37.chain added
1aef7c6b176306_GRCh38_to_NCBI34.chain added
1aef7c3d3d19a9_GRCh38_to_NCBI35.chain added
1aef7c62cae750_GRCh38_to_NCBI36.chain added
1aef7c2b9e1baa_NCBI34_to_GRCh37.chain added
1aef7c6c8a734_NCBI34_to_GRCh38.chain added
1aef7c4a4e7fd5_NCBI35_to_GRCh37.chain added
1aef7c75f72769_NCBI35_to_GRCh38.chain added
1aef7c5bfdce9c_NCBI36_to_GRCh37.chain added
1aef7c45a387e8_NCBI36_to_GRCh38.chain added
1aef7c2f3f0cd0_GRCm38_to_NCBIM36.chain added
1aef7cd8a386_GRCm38_to_NCBIM37.chain added
1aef7c3f65d220_NCBIM36_to_GRCm38.chain added
1aef7c5f1633c6_NCBIM37_to_GRCm38.chain added
1aef7c1d042d02_1000G_omni2.5.b37.vcf.gz added
1aef7c2a8ad741_1000G_omni2.5.b37.vcf.gz.tbi added
1aef7c605c6097_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1aef7c7308ddd1_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1aef7c388fbb76_1000G_omni2.5.hg38.vcf.gz added
1aef7c5b735be5_1000G_omni2.5.hg38.vcf.gz.tbi added
1aef7c1d235473_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1aef7c55dca7c2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1aef7c2ff7b6ae_af-only-gnomad.raw.sites.vcf added
1aef7ce1e9967_af-only-gnomad.raw.sites.vcf.idx added
1aef7c5dec9cdd_Mutect2-exome-panel.vcf.idx added
1aef7c28e0a16d_Mutect2-WGS-panel-b37.vcf added
1aef7c84650ba_Mutect2-WGS-panel-b37.vcf.idx added
1aef7cf2a0bce_small_exac_common_3.vcf added
1aef7cd747d01_small_exac_common_3.vcf.idx added
1aef7ccea335_1000g_pon.hg38.vcf.gz added
1aef7c6349869d_1000g_pon.hg38.vcf.gz.tbi added
1aef7c31569468_af-only-gnomad.hg38.vcf.gz added
1aef7c6be6063b_af-only-gnomad.hg38.vcf.gz.tbi added
1aef7c2086a046_small_exac_common_3.hg38.vcf.gz added
1aef7c14217bb8_small_exac_common_3.hg38.vcf.gz.tbi added
1aef7c178421e5_gencode.v41.annotation.gtf added
1aef7c274f477b_gencode.v42.annotation.gtf added
1aef7c5e6ffb8d_gencode.vM30.annotation.gtf added
1aef7cd7b494e_gencode.vM31.annotation.gtf added
1aef7c34d1617_gencode.v41.transcripts.fa added
1aef7c24138375_gencode.v41.transcripts.fa.fai added
1aef7c3cba561f_gencode.v42.transcripts.fa added
1aef7c425b99d_gencode.v42.transcripts.fa.fai added
1aef7c63795595_gencode.vM30.pc_transcripts.fa added
1aef7c1bd089e5_gencode.vM30.pc_transcripts.fa.fai added
1aef7c2129e6a0_gencode.vM31.pc_transcripts.fa added
1aef7ce042cd6_gencode.vM31.pc_transcripts.fa.fai added
1aef7c7c2cea7d_GRCh38.primary_assembly.genome.fa.1.ht2 added
1aef7c1432c471_GRCh38.primary_assembly.genome.fa.2.ht2 added
1aef7c4693e84c_GRCh38.primary_assembly.genome.fa.3.ht2 added
1aef7c57a04662_GRCh38.primary_assembly.genome.fa.4.ht2 added
1aef7c315618e4_GRCh38.primary_assembly.genome.fa.5.ht2 added
1aef7c1c70900e_GRCh38.primary_assembly.genome.fa.6.ht2 added
1aef7c797fd10_GRCh38.primary_assembly.genome.fa.7.ht2 added
1aef7c3f74b24b_GRCh38.primary_assembly.genome.fa.8.ht2 added
1aef7c7a5d2cec_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1aef7c30789e7d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1aef7c47bb0306_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1aef7c98738ba_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1aef7c3ded1b7e_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1aef7c4889a63b_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1aef7c6cd0bf57_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1aef7c6f43afe6_GRCh38.primary_assembly.genome.fa.fai added
1aef7c346fac76_GRCh38.primary_assembly.genome.fa.amb added
1aef7cd575f9e_GRCh38.primary_assembly.genome.fa.ann added
1aef7c3652b9e_GRCh38.primary_assembly.genome.fa.bwt added
1aef7c4bf3ce5b_GRCh38.primary_assembly.genome.fa.pac added
1aef7c34a6a719_GRCh38.primary_assembly.genome.fa.sa added
1aef7c61d5272b_GRCh38.primary_assembly.genome.fa added
1aef7c596f17a9_hs37d5.fa.fai added
1aef7c37f3bd30_hs37d5.fa.amb added
1aef7c5e8aaa1_hs37d5.fa.ann added
1aef7c16296dc8_hs37d5.fa.bwt added
1aef7c3c1976cd_hs37d5.fa.pac added
1aef7c69620036_hs37d5.fa.sa added
1aef7c31f9f7ae_hs37d5.fa added
1aef7c5d435d6d_complete_ref_lens.bin added
1aef7c77662d0d_ctable.bin added
1aef7c2e26e22b_ctg_offsets.bin added
1aef7c717621de_duplicate_clusters.tsv added
1aef7c3dfa1559_info.json added
1aef7c5c7288d_mphf.bin added
1aef7c22cc3ac2_pos.bin added
1aef7c5a6aa568_pre_indexing.log added
1aef7cd5f259e_rank.bin added
1aef7c6240ed0e_ref_indexing.log added
1aef7c54c7d254_refAccumLengths.bin added
1aef7c3dd7c41b_reflengths.bin added
1aef7c29fbf014_refseq.bin added
1aef7c5e4f0b0e_seq.bin added
1aef7c7bc4df9a_versionInfo.json added
1aef7c7285964f_salmon_index added
1aef7c4b1fca65_chrLength.txt added
1aef7c6b088f80_chrName.txt added
1aef7c26f542c5_chrNameLength.txt added
1aef7c58772a03_chrStart.txt added
1aef7c6e6dbb1f_exonGeTrInfo.tab added
1aef7c72e91120_exonInfo.tab added
1aef7cd1dd11c_geneInfo.tab added
1aef7c5042e24a_Genome added
1aef7c4c5828c9_genomeParameters.txt added
1aef7c45118e4c_Log.out added
1aef7c562b8ceb_SA added
1aef7c62819692_SAindex added
1aef7c12b051a_sjdbInfo.txt added
1aef7c3f8d8d22_sjdbList.fromGTF.out.tab added
1aef7c147b8e40_sjdbList.out.tab added
1aef7c5e6e6287_transcriptInfo.tab added
1aef7c36f3ba2f_GRCh38.GENCODE.v42_100 added
1aef7c42a2706b_knownGene_hg38.sql added
1aef7c4fe48466_knownGene_hg38.txt added
1aef7c74edcf88_refGene_hg38.sql added
1aef7c486998f8_refGene_hg38.txt added
1aef7c72b0bf28_knownGene_mm39.sql added
1aef7c4f5874f0_knownGene_mm39.txt added
1aef7c55c8be96_refGene_mm39.sql added
1aef7c54f1ac36_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: 
/tmp/RtmpHHEGkj/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 ]
> 
> proc.time()
   user  system elapsed 
 31.459   2.414  37.854