##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ReUseData_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-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 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.5.0’
* 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 6.229  0.293   6.526
* 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-3.20-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-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...
f168774b9051_GRCh38.primary_assembly.genome.fa.1.bt2 added
f168448962bd_GRCh38.primary_assembly.genome.fa.2.bt2 added
f168483478a7_GRCh38.primary_assembly.genome.fa.3.bt2 added
f1682cf33d91_GRCh38.primary_assembly.genome.fa.4.bt2 added
f1686185a0b4_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
f16817920f09_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
f1681cedd48_outfile.txt added
f1685e36268f_GRCh37_to_GRCh38.chain added
f168704a4169_GRCh37_to_NCBI34.chain added
f16888626bf_GRCh37_to_NCBI35.chain added
f1686b66d87b_GRCh37_to_NCBI36.chain added
f168e4815a4_GRCh38_to_GRCh37.chain added
f1681ca18152_GRCh38_to_NCBI34.chain added
f1687d6d2f19_GRCh38_to_NCBI35.chain added
f168609a3fb_GRCh38_to_NCBI36.chain added
f1685b436f0f_NCBI34_to_GRCh37.chain added
f1684f401056_NCBI34_to_GRCh38.chain added
f16852b664d7_NCBI35_to_GRCh37.chain added
f1686a32eba3_NCBI35_to_GRCh38.chain added
f16851b5de73_NCBI36_to_GRCh37.chain added
f168767b6d8e_NCBI36_to_GRCh38.chain added
f16856f329f3_GRCm38_to_NCBIM36.chain added
f16877534cd5_GRCm38_to_NCBIM37.chain added
f16819774838_NCBIM36_to_GRCm38.chain added
f1686668130_NCBIM37_to_GRCm38.chain added
f1688861171_1000G_omni2.5.b37.vcf.gz added
f168287a60be_1000G_omni2.5.b37.vcf.gz.tbi added
f1684a65f0ce_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
f1683e22cb47_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
f1685dbe4187_1000G_omni2.5.hg38.vcf.gz added
f16848b30f2b_1000G_omni2.5.hg38.vcf.gz.tbi added
f168356e5b98_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
f1682247a444_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
f16810e787d2_af-only-gnomad.raw.sites.vcf added
f1686261992a_af-only-gnomad.raw.sites.vcf.idx added
f1683cd44f8_Mutect2-exome-panel.vcf.idx added
f168287996dc_Mutect2-WGS-panel-b37.vcf added
f16864307672_Mutect2-WGS-panel-b37.vcf.idx added
f16862036b87_small_exac_common_3.vcf added
f16818c3d845_small_exac_common_3.vcf.idx added
f1686cb69d31_1000g_pon.hg38.vcf.gz added
f1684d6a4402_1000g_pon.hg38.vcf.gz.tbi added
f168270bede9_af-only-gnomad.hg38.vcf.gz added
f1689581e83_af-only-gnomad.hg38.vcf.gz.tbi added
f1684ad7731c_small_exac_common_3.hg38.vcf.gz added
f1682d1591e5_small_exac_common_3.hg38.vcf.gz.tbi added
f168649b8d92_gencode.v41.annotation.gtf added
f1681a178372_gencode.v42.annotation.gtf added
f1687fcbf6bc_gencode.vM30.annotation.gtf added
f1684ece7935_gencode.vM31.annotation.gtf added
f1686bcd61e5_gencode.v41.transcripts.fa added
f1687647644a_gencode.v41.transcripts.fa.fai added
f16825c1a328_gencode.v42.transcripts.fa added
f1686320aeba_gencode.v42.transcripts.fa.fai added
f168fbeac82_gencode.vM30.pc_transcripts.fa added
f1682c282459_gencode.vM30.pc_transcripts.fa.fai added
f1686ba6c02c_gencode.vM31.pc_transcripts.fa added
f16838390d40_gencode.vM31.pc_transcripts.fa.fai added
f168768e1527_GRCh38.primary_assembly.genome.fa.1.ht2 added
f16829c98b73_GRCh38.primary_assembly.genome.fa.2.ht2 added
f16815f74ec7_GRCh38.primary_assembly.genome.fa.3.ht2 added
f1683f412452_GRCh38.primary_assembly.genome.fa.4.ht2 added
f1685f37e70c_GRCh38.primary_assembly.genome.fa.5.ht2 added
f168383ef30b_GRCh38.primary_assembly.genome.fa.6.ht2 added
f1685028ac25_GRCh38.primary_assembly.genome.fa.7.ht2 added
f16841998036_GRCh38.primary_assembly.genome.fa.8.ht2 added
f1683c0c3804_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
f16878a24301_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
f16825c9f6a8_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
f1681e0fa38b_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
f16811661b46_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
f168128093d9_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
f1686b79e78e_GRCh38_full_analysis_set_plus_decoy_hla.fa added
f1683872092f_GRCh38.primary_assembly.genome.fa.fai added
f1681bd8b25c_GRCh38.primary_assembly.genome.fa.amb added
f16836515aaa_GRCh38.primary_assembly.genome.fa.ann added
f16865879b14_GRCh38.primary_assembly.genome.fa.bwt added
f168743fef_GRCh38.primary_assembly.genome.fa.pac added
f1685068de1c_GRCh38.primary_assembly.genome.fa.sa added
f168655391d0_GRCh38.primary_assembly.genome.fa added
f1684f42b924_hs37d5.fa.fai added
f1683c364002_hs37d5.fa.amb added
f1685b9af61a_hs37d5.fa.ann added
f16875045c4d_hs37d5.fa.bwt added
f1681f56eebc_hs37d5.fa.pac added
f1686b59a29c_hs37d5.fa.sa added
f168212c80a6_hs37d5.fa added
f168afdaee8_complete_ref_lens.bin added
f1682392afdd_ctable.bin added
f16817ba95cd_ctg_offsets.bin added
f16834c73a5c_duplicate_clusters.tsv added
f1683989fea4_info.json added
f16856fbba20_mphf.bin added
f16813ff2168_pos.bin added
f16871c8f1b0_pre_indexing.log added
f16827246645_rank.bin added
f1685598a19e_ref_indexing.log added
f1682dd529b4_refAccumLengths.bin added
f1681fc6a946_reflengths.bin added
f1687b629846_refseq.bin added
f1684be4cd3f_seq.bin added
f168312cc48c_versionInfo.json added
f168de32c1f_salmon_index added
f168375eb4cd_chrLength.txt added
f168699ecdbb_chrName.txt added
f16829bbde7b_chrNameLength.txt added
f1686db00f77_chrStart.txt added
f1684f2668d0_exonGeTrInfo.tab added
f1682a301e6a_exonInfo.tab added
f1683e18ed94_geneInfo.tab added
f1683479faa0_Genome added
f1687972d78f_genomeParameters.txt added
f1687a4f2d96_Log.out added
f1681014f0bb_SA added
f1686e7733dc_SAindex added
f16819a61c52_sjdbInfo.txt added
f1687b6e9357_sjdbList.fromGTF.out.tab added
f168fa3b482_sjdbList.out.tab added
f16824a3cb3b_transcriptInfo.tab added
f1681f014334_GRCh38.GENCODE.v42_100 added
f168275e4a4f_knownGene_hg38.sql added
f168596b0597_knownGene_hg38.txt added
f168588b41d9_refGene_hg38.sql added
f1687e5a046f_refGene_hg38.txt added
f1686d6a26ff_knownGene_mm39.sql added
f1684a543389_knownGene_mm39.txt added
f168257e6ab4_refGene_mm39.sql added
f1684302c89d_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/RtmpjLF7gg/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 
 20.371   1.506  22.201