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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ReUseData_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.4.0’
* 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 6.037  0.632   6.671
getCloudData  2.725  0.207   5.382
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ReUseData
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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...
2ff9ecb66f4af_GRCh38.primary_assembly.genome.fa.1.bt2 added
2ff9ec3d518d8_GRCh38.primary_assembly.genome.fa.2.bt2 added
2ff9ec1fc2a61f_GRCh38.primary_assembly.genome.fa.3.bt2 added
2ff9ec6e5c1ef4_GRCh38.primary_assembly.genome.fa.4.bt2 added
2ff9ec2c3907c2_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2ff9ec19667103_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2ff9ec2daecea5_outfile.txt added
2ff9ec798b80f8_GRCh37_to_GRCh38.chain added
2ff9ec3173c5ca_GRCh37_to_NCBI34.chain added
2ff9ec52793bba_GRCh37_to_NCBI35.chain added
2ff9ec10c38731_GRCh37_to_NCBI36.chain added
2ff9ec42029bdb_GRCh38_to_GRCh37.chain added
2ff9ec54946822_GRCh38_to_NCBI34.chain added
2ff9ec1d8399c6_GRCh38_to_NCBI35.chain added
2ff9ec247504e0_GRCh38_to_NCBI36.chain added
2ff9ec3731c149_NCBI34_to_GRCh37.chain added
2ff9ec273c22d5_NCBI34_to_GRCh38.chain added
2ff9ec1b67a0ec_NCBI35_to_GRCh37.chain added
2ff9ec91b9313_NCBI35_to_GRCh38.chain added
2ff9ec7e1a0501_NCBI36_to_GRCh37.chain added
2ff9ecb626690_NCBI36_to_GRCh38.chain added
2ff9ec253fc8b4_GRCm38_to_NCBIM36.chain added
2ff9ec28889d5f_GRCm38_to_NCBIM37.chain added
2ff9ec1eabd9a9_NCBIM36_to_GRCm38.chain added
2ff9ec5420c5bc_NCBIM37_to_GRCm38.chain added
2ff9ec2268bc46_1000G_omni2.5.b37.vcf.gz added
2ff9ec4fa7f1db_1000G_omni2.5.b37.vcf.gz.tbi added
2ff9ec5cb42293_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2ff9ec119bd820_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2ff9ec10ce8574_1000G_omni2.5.hg38.vcf.gz added
2ff9ec7f2d1a3d_1000G_omni2.5.hg38.vcf.gz.tbi added
2ff9ec1d02cccf_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2ff9ec14a39e4d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2ff9ec1eefc05d_af-only-gnomad.raw.sites.vcf added
2ff9ecb5eebc4_af-only-gnomad.raw.sites.vcf.idx added
2ff9ec40dca60f_Mutect2-exome-panel.vcf.idx added
2ff9ec38563160_Mutect2-WGS-panel-b37.vcf added
2ff9ec390dba69_Mutect2-WGS-panel-b37.vcf.idx added
2ff9ec3a682707_small_exac_common_3.vcf added
2ff9ec69c9f72b_small_exac_common_3.vcf.idx added
2ff9ecb86f623_1000g_pon.hg38.vcf.gz added
2ff9ec4b2bae39_1000g_pon.hg38.vcf.gz.tbi added
2ff9ec2bcc9306_af-only-gnomad.hg38.vcf.gz added
2ff9ec601b5e45_af-only-gnomad.hg38.vcf.gz.tbi added
2ff9ec68af47ff_small_exac_common_3.hg38.vcf.gz added
2ff9ec504197e6_small_exac_common_3.hg38.vcf.gz.tbi added
2ff9ec174d1f8e_gencode.v41.annotation.gtf added
2ff9ecfeb6ad4_gencode.v42.annotation.gtf added
2ff9ec6ba938d3_gencode.vM30.annotation.gtf added
2ff9ec2068b2a1_gencode.vM31.annotation.gtf added
2ff9ece056fd5_gencode.v41.transcripts.fa added
2ff9ec770b9f63_gencode.v41.transcripts.fa.fai added
2ff9ec45a87b55_gencode.v42.transcripts.fa added
2ff9ec368e0d34_gencode.v42.transcripts.fa.fai added
2ff9ec15b7790c_gencode.vM30.pc_transcripts.fa added
2ff9ec19c94111_gencode.vM30.pc_transcripts.fa.fai added
2ff9ec58f6c97a_gencode.vM31.pc_transcripts.fa added
2ff9ec655f6ae7_gencode.vM31.pc_transcripts.fa.fai added
2ff9ec767d63a5_GRCh38.primary_assembly.genome.fa.1.ht2 added
2ff9ec6a92a19a_GRCh38.primary_assembly.genome.fa.2.ht2 added
2ff9ec762df05c_GRCh38.primary_assembly.genome.fa.3.ht2 added
2ff9ec75aa7de2_GRCh38.primary_assembly.genome.fa.4.ht2 added
2ff9ec7956e6a_GRCh38.primary_assembly.genome.fa.5.ht2 added
2ff9ecad18ea9_GRCh38.primary_assembly.genome.fa.6.ht2 added
2ff9ec149a3e3f_GRCh38.primary_assembly.genome.fa.7.ht2 added
2ff9ec12f45a2e_GRCh38.primary_assembly.genome.fa.8.ht2 added
2ff9ec4bae34b8_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2ff9ec4cf06fa0_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2ff9ec4c021497_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2ff9ec6165bbf_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2ff9ec36ba66cb_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2ff9ec57890aba_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2ff9ec514209f8_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2ff9ec6286f9d1_GRCh38.primary_assembly.genome.fa.fai added
2ff9ec37a46900_GRCh38.primary_assembly.genome.fa.amb added
2ff9ec39f151f8_GRCh38.primary_assembly.genome.fa.ann added
2ff9ec32c891b8_GRCh38.primary_assembly.genome.fa.bwt added
2ff9ec4ef1888e_GRCh38.primary_assembly.genome.fa.pac added
2ff9ec49dcbccc_GRCh38.primary_assembly.genome.fa.sa added
2ff9ec1e71ca8b_GRCh38.primary_assembly.genome.fa added
2ff9ec6f5a3b30_hs37d5.fa.fai added
2ff9ec57e22ca2_hs37d5.fa.amb added
2ff9ec157d69ee_hs37d5.fa.ann added
2ff9ec3502b685_hs37d5.fa.bwt added
2ff9ece7039d6_hs37d5.fa.pac added
2ff9ec2b34e2fb_hs37d5.fa.sa added
2ff9ec4ecbf797_hs37d5.fa added
2ff9ec67670351_complete_ref_lens.bin added
2ff9ec10944de2_ctable.bin added
2ff9ec45495b3c_ctg_offsets.bin added
2ff9ec51f9a4eb_duplicate_clusters.tsv added
2ff9ec6c23e3e_info.json added
2ff9ec3af3d91e_mphf.bin added
2ff9ec598f1355_pos.bin added
2ff9ec1193cce7_pre_indexing.log added
2ff9ec4f8e175e_rank.bin added
2ff9ec6c836d83_ref_indexing.log added
2ff9ec5d42019f_refAccumLengths.bin added
2ff9ec1c7e86fe_reflengths.bin added
2ff9ec3885821a_refseq.bin added
2ff9ec63585d5f_seq.bin added
2ff9ec5338edc9_versionInfo.json added
2ff9ec100e8cd5_salmon_index added
2ff9ec349a6757_chrLength.txt added
2ff9ec35bfe79a_chrName.txt added
2ff9ec47b2f5d5_chrNameLength.txt added
2ff9ec6e8bb94f_chrStart.txt added
2ff9ec68887952_exonGeTrInfo.tab added
2ff9ec16a47e63_exonInfo.tab added
2ff9ec3868761c_geneInfo.tab added
2ff9ec6fa43dd_Genome added
2ff9ec5feb993_genomeParameters.txt added
2ff9ec104aa2be_Log.out added
2ff9ec1c77adcc_SA added
2ff9ec3b017019_SAindex added
2ff9ec1ebadc94_sjdbInfo.txt added
2ff9ec47ac90c7_sjdbList.fromGTF.out.tab added
2ff9ec9cd67b0_sjdbList.out.tab added
2ff9ec621dfe5_transcriptInfo.tab added
2ff9ec5840dea9_GRCh38.GENCODE.v42_100 added
2ff9ec4f16c2ec_knownGene_hg38.sql added
2ff9ec581b84d1_knownGene_hg38.txt added
2ff9ec5f031ce8_refGene_hg38.sql added
2ff9eca0a9c0a_refGene_hg38.txt added
2ff9ec31aa9826_knownGene_mm39.sql added
2ff9ec7096e9cf_knownGene_mm39.txt added
2ff9ec5998b368_refGene_mm39.sql added
2ff9ec1e2e05aa_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/Rtmp7I8EXq/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 
 19.808   1.797  22.475