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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_0.99.38.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 ‘0.99.38’
* 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    16.210  1.658  18.447
getCloudData  10.340  1.024  14.939
dataHub-class  8.649  0.392   9.045
* 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
###
##############################################################################
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* 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...
2b3de34afb8eba_GRCh38.primary_assembly.genome.fa.1.bt2 added
2b3de3b3a487d_GRCh38.primary_assembly.genome.fa.2.bt2 added
2b3de37973139c_GRCh38.primary_assembly.genome.fa.3.bt2 added
2b3de31c829a2_GRCh38.primary_assembly.genome.fa.4.bt2 added
2b3de37c60930_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2b3de330a9939e_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2b3de33b3c39c7_outfile.txt added
2b3de3715619a8_GRCh37_to_GRCh38.chain added
2b3de3731efa89_GRCh37_to_NCBI34.chain added
2b3de33a7be4a1_GRCh37_to_NCBI35.chain added
2b3de32dc6cda1_GRCh37_to_NCBI36.chain added
2b3de35cbc17f2_GRCh38_to_GRCh37.chain added
2b3de36488a156_GRCh38_to_NCBI34.chain added
2b3de348e1b70c_GRCh38_to_NCBI35.chain added
2b3de32d0c9c60_GRCh38_to_NCBI36.chain added
2b3de34faec925_NCBI34_to_GRCh37.chain added
2b3de3681f08b_NCBI34_to_GRCh38.chain added
2b3de3121131e3_NCBI35_to_GRCh37.chain added
2b3de358ba77b1_NCBI35_to_GRCh38.chain added
2b3de37c299077_NCBI36_to_GRCh37.chain added
2b3de34c62ff91_NCBI36_to_GRCh38.chain added
2b3de31a47231a_GRCm38_to_NCBIM36.chain added
2b3de347a220cd_GRCm38_to_NCBIM37.chain added
2b3de31b75fbf_NCBIM36_to_GRCm38.chain added
2b3de33b199736_NCBIM37_to_GRCm38.chain added
2b3de315a1e978_1000G_omni2.5.b37.vcf.gz added
2b3de372a00c5c_1000G_omni2.5.b37.vcf.gz.tbi added
2b3de3285ea42e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2b3de36f9dedac_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2b3de3552c7b1d_1000G_omni2.5.hg38.vcf.gz added
2b3de36dfe9fd5_1000G_omni2.5.hg38.vcf.gz.tbi added
2b3de33a997c66_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2b3de36066c39a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2b3de36771b371_af-only-gnomad.raw.sites.vcf added
2b3de33c61a608_af-only-gnomad.raw.sites.vcf.idx added
2b3de3682cccca_Mutect2-exome-panel.vcf.idx added
2b3de3181b470f_Mutect2-WGS-panel-b37.vcf added
2b3de3779ddfcf_Mutect2-WGS-panel-b37.vcf.idx added
2b3de35982e672_small_exac_common_3.vcf added
2b3de3b3a4198_small_exac_common_3.vcf.idx added
2b3de33219c470_1000g_pon.hg38.vcf.gz added
2b3de3749b414_1000g_pon.hg38.vcf.gz.tbi added
2b3de367f6598a_af-only-gnomad.hg38.vcf.gz added
2b3de316a265c6_af-only-gnomad.hg38.vcf.gz.tbi added
2b3de3502b6b20_small_exac_common_3.hg38.vcf.gz added
2b3de31502f5ea_small_exac_common_3.hg38.vcf.gz.tbi added
2b3de366512eec_gencode.v41.annotation.gtf added
2b3de356ad5bab_gencode.v42.annotation.gtf added
2b3de3271427cd_gencode.vM30.annotation.gtf added
2b3de33f0ba69d_gencode.vM31.annotation.gtf added
2b3de352d6ec23_gencode.v41.transcripts.fa added
2b3de37377275f_gencode.v41.transcripts.fa.fai added
2b3de35952c9b8_gencode.v42.transcripts.fa added
2b3de31a790cf0_gencode.v42.transcripts.fa.fai added
2b3de3752e871e_gencode.vM30.pc_transcripts.fa added
2b3de3146c60ee_gencode.vM30.pc_transcripts.fa.fai added
2b3de3301af668_gencode.vM31.pc_transcripts.fa added
2b3de367ce937a_gencode.vM31.pc_transcripts.fa.fai added
2b3de33ccb051c_GRCh38.primary_assembly.genome.fa.1.ht2 added
2b3de31fb8e415_GRCh38.primary_assembly.genome.fa.2.ht2 added
2b3de33cfb0e97_GRCh38.primary_assembly.genome.fa.3.ht2 added
2b3de32ac9a4f1_GRCh38.primary_assembly.genome.fa.4.ht2 added
2b3de35a52607b_GRCh38.primary_assembly.genome.fa.5.ht2 added
2b3de31d61d232_GRCh38.primary_assembly.genome.fa.6.ht2 added
2b3de3123b5862_GRCh38.primary_assembly.genome.fa.7.ht2 added
2b3de316b40684_GRCh38.primary_assembly.genome.fa.8.ht2 added
2b3de358e9efc_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2b3de32a569f71_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2b3de3e51e653_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2b3de35f11856f_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2b3de33590e109_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2b3de3406baac4_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2b3de3665b3983_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2b3de31d873a94_GRCh38.primary_assembly.genome.fa.fai added
2b3de3570e108a_GRCh38.primary_assembly.genome.fa.amb added
2b3de33686a4a3_GRCh38.primary_assembly.genome.fa.ann added
2b3de3328a307e_GRCh38.primary_assembly.genome.fa.bwt added
2b3de33d5f3f76_GRCh38.primary_assembly.genome.fa.pac added
2b3de3d34004f_GRCh38.primary_assembly.genome.fa.sa added
2b3de3599e584c_GRCh38.primary_assembly.genome.fa added
2b3de37c6ae614_hs37d5.fa.fai added
2b3de3600aec72_hs37d5.fa.amb added
2b3de34d157fab_hs37d5.fa.ann added
2b3de355bdafcc_hs37d5.fa.bwt added
2b3de37a83f962_hs37d5.fa.pac added
2b3de3424406c9_hs37d5.fa.sa added
2b3de36a2a10ba_hs37d5.fa added
2b3de32a9eefca_complete_ref_lens.bin added
2b3de32a129a44_ctable.bin added
2b3de326f515d6_ctg_offsets.bin added
2b3de34a57d3df_duplicate_clusters.tsv added
2b3de3670da8db_info.json added
2b3de351bebac7_mphf.bin added
2b3de324aa345b_pos.bin added
2b3de346f7b0d_pre_indexing.log added
2b3de363fa1329_rank.bin added
2b3de33b5e3adf_ref_indexing.log added
2b3de39fe1a0a_refAccumLengths.bin added
2b3de3e50b29a_reflengths.bin added
2b3de349b02132_refseq.bin added
2b3de3690f9f79_seq.bin added
2b3de343e193a3_versionInfo.json added
2b3de3a1bcbf6_salmon_index added
2b3de34f6ad8fc_chrLength.txt added
2b3de36168ce37_chrName.txt added
2b3de36129dc81_chrNameLength.txt added
2b3de35f17d9f_chrStart.txt added
2b3de313f2feb6_exonGeTrInfo.tab added
2b3de31e891bf7_exonInfo.tab added
2b3de313257dee_geneInfo.tab added
2b3de36d915702_Genome added
2b3de31af4020b_genomeParameters.txt added
2b3de373306a60_Log.out added
2b3de33aa6d6ad_SA added
2b3de370b1b1d7_SAindex added
2b3de36db463c2_sjdbInfo.txt added
2b3de37ceadd76_sjdbList.fromGTF.out.tab added
2b3de35adbc291_sjdbList.out.tab added
2b3de31853538d_transcriptInfo.tab added
2b3de326fd77ba_GRCh38.GENCODE.v42_100 added
2b3de31d0d867_knownGene_hg38.sql added
2b3de362ab276c_knownGene_hg38.txt added
2b3de3e0b2096_refGene_hg38.sql added
2b3de3538f932e_refGene_hg38.txt added
2b3de37555bc7_knownGene_mm39.sql added
2b3de3127a9ba3_knownGene_mm39.txt added
2b3de33789a657_refGene_mm39.sql added
2b3de342b396a6_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/Rtmp9J1Hli/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 
 31.129   1.968  34.633