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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 4.4.0 (2024-04-24)
* 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 ‘1.4.0’
* 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 6.017   0.54   6.559
* 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 4.4.0 (2024-04-24) -- "Puppy Cup"
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...
644277398f203_GRCh38.primary_assembly.genome.fa.1.bt2 added
644277550450_GRCh38.primary_assembly.genome.fa.2.bt2 added
64427303bd9a_GRCh38.primary_assembly.genome.fa.3.bt2 added
644277a493bd5_GRCh38.primary_assembly.genome.fa.4.bt2 added
64427416c7a8a_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
644275ef54056_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
644271e07446b_outfile.txt added
644272a8fc6f7_GRCh37_to_GRCh38.chain added
644276e83b379_GRCh37_to_NCBI34.chain added
644276756df39_GRCh37_to_NCBI35.chain added
644272903f7c_GRCh37_to_NCBI36.chain added
6442748577745_GRCh38_to_GRCh37.chain added
6442763033d16_GRCh38_to_NCBI34.chain added
644273388c73d_GRCh38_to_NCBI35.chain added
644276cce846d_GRCh38_to_NCBI36.chain added
644271063a515_NCBI34_to_GRCh37.chain added
6442730f58300_NCBI34_to_GRCh38.chain added
644272daf911f_NCBI35_to_GRCh37.chain added
64427114733ef_NCBI35_to_GRCh38.chain added
64427e7f0f98_NCBI36_to_GRCh37.chain added
6442753f12b3a_NCBI36_to_GRCh38.chain added
64427452893e7_GRCm38_to_NCBIM36.chain added
644272e2aff1b_GRCm38_to_NCBIM37.chain added
644271be1d489_NCBIM36_to_GRCm38.chain added
6442773c8d23d_NCBIM37_to_GRCm38.chain added
6442712a6da89_1000G_omni2.5.b37.vcf.gz added
64427795a4742_1000G_omni2.5.b37.vcf.gz.tbi added
644273f47f59e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
6442725f6d32a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
644274bcb3d18_1000G_omni2.5.hg38.vcf.gz added
644273edad1a0_1000G_omni2.5.hg38.vcf.gz.tbi added
64427198fc52d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
6442753204169_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
6442741de8f3b_af-only-gnomad.raw.sites.vcf added
6442713d90102_af-only-gnomad.raw.sites.vcf.idx added
64427148cbbf3_Mutect2-exome-panel.vcf.idx added
6442720d3cf91_Mutect2-WGS-panel-b37.vcf added
6442731e0456d_Mutect2-WGS-panel-b37.vcf.idx added
644273f1c82eb_small_exac_common_3.vcf added
64427f57830b_small_exac_common_3.vcf.idx added
64427193724a6_1000g_pon.hg38.vcf.gz added
6442741acc267_1000g_pon.hg38.vcf.gz.tbi added
6442757aefa50_af-only-gnomad.hg38.vcf.gz added
644277c3a61bc_af-only-gnomad.hg38.vcf.gz.tbi added
64427753589a4_small_exac_common_3.hg38.vcf.gz added
64427447d7ebd_small_exac_common_3.hg38.vcf.gz.tbi added
64427c9e06d2_gencode.v41.annotation.gtf added
64427262b0ca4_gencode.v42.annotation.gtf added
64427722d0fdd_gencode.vM30.annotation.gtf added
644271de53ac1_gencode.vM31.annotation.gtf added
6442734aa1c3d_gencode.v41.transcripts.fa added
64427461e3b17_gencode.v41.transcripts.fa.fai added
64427630dcea8_gencode.v42.transcripts.fa added
6442762d51b58_gencode.v42.transcripts.fa.fai added
6442762000fa1_gencode.vM30.pc_transcripts.fa added
6442756d6a0e5_gencode.vM30.pc_transcripts.fa.fai added
64427757bf5e1_gencode.vM31.pc_transcripts.fa added
644275b5a56e3_gencode.vM31.pc_transcripts.fa.fai added
64427161e9684_GRCh38.primary_assembly.genome.fa.1.ht2 added
644271b72c90b_GRCh38.primary_assembly.genome.fa.2.ht2 added
64427272593fc_GRCh38.primary_assembly.genome.fa.3.ht2 added
6442754f96824_GRCh38.primary_assembly.genome.fa.4.ht2 added
6442735028e38_GRCh38.primary_assembly.genome.fa.5.ht2 added
644277a45d565_GRCh38.primary_assembly.genome.fa.6.ht2 added
6442716d7f75f_GRCh38.primary_assembly.genome.fa.7.ht2 added
6442748db8f3a_GRCh38.primary_assembly.genome.fa.8.ht2 added
64427ed29158_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
6442737abc6f1_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
644277abbd4a7_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
644274def1443_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
64427470349fc_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
6442713f2f94d_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
64427f9bd6ab_GRCh38_full_analysis_set_plus_decoy_hla.fa added
644271eb2444c_GRCh38.primary_assembly.genome.fa.fai added
64427102d5b0a_GRCh38.primary_assembly.genome.fa.amb added
644274d1604f_GRCh38.primary_assembly.genome.fa.ann added
64427632fc30a_GRCh38.primary_assembly.genome.fa.bwt added
644271ccb61dc_GRCh38.primary_assembly.genome.fa.pac added
644272afc6cf4_GRCh38.primary_assembly.genome.fa.sa added
64427555cd2e7_GRCh38.primary_assembly.genome.fa added
644273ab09c9d_hs37d5.fa.fai added
644275fa68931_hs37d5.fa.amb added
644271b7b0dfe_hs37d5.fa.ann added
644271dbe6b45_hs37d5.fa.bwt added
64427427ba489_hs37d5.fa.pac added
644277d7b1d9f_hs37d5.fa.sa added
6442774950c2b_hs37d5.fa added
6442737f79a6a_complete_ref_lens.bin added
6442758d57483_ctable.bin added
64427ab3a2af_ctg_offsets.bin added
64427536a6375_duplicate_clusters.tsv added
644277ffb087f_info.json added
644275fad0ad3_mphf.bin added
6442786cf1ad_pos.bin added
644277a40dde4_pre_indexing.log added
6442776850233_rank.bin added
64427514880e7_ref_indexing.log added
644279136f3c_refAccumLengths.bin added
644272e30c924_reflengths.bin added
644274c04558e_refseq.bin added
6442757028380_seq.bin added
6442775341320_versionInfo.json added
644275ff74edb_salmon_index added
64427669e5a2b_chrLength.txt added
6442713e6576c_chrName.txt added
644277024a9e5_chrNameLength.txt added
644276b6fba7a_chrStart.txt added
6442777161a76_exonGeTrInfo.tab added
64427cf00bc1_exonInfo.tab added
64427166c276e_geneInfo.tab added
644274c72ed5d_Genome added
6442747a0a85e_genomeParameters.txt added
644277612b09f_Log.out added
6442767edfb5c_SA added
64427655f13a4_SAindex added
64427388e5528_sjdbInfo.txt added
64427656918fb_sjdbList.fromGTF.out.tab added
6442759f41fcf_sjdbList.out.tab added
644277085ef92_transcriptInfo.tab added
644273e3e8d7e_GRCh38.GENCODE.v42_100 added
6442764a7c27e_knownGene_hg38.sql added
6442743f05307_knownGene_hg38.txt added
644273e3995fd_refGene_hg38.sql added
644274454cd51_refGene_hg38.txt added
644274c5d44b4_knownGene_mm39.sql added
64427387a73e1_knownGene_mm39.txt added
644273ad9cf84_refGene_mm39.sql added
644271da5c59b_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/RtmpTJ08cC/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 
 19.844   1.285  21.592