##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReUseData_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.7.0’
* 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 6.001  0.322   6.324
* 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-3.21-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.7.0’
** 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) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 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...
1324bf579d4bee_GRCh38.primary_assembly.genome.fa.1.bt2 added
1324bf44803e73_GRCh38.primary_assembly.genome.fa.2.bt2 added
1324bf3c56d594_GRCh38.primary_assembly.genome.fa.3.bt2 added
1324bf53237976_GRCh38.primary_assembly.genome.fa.4.bt2 added
1324bf2f62685f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1324bf23d5f603_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1324bf26e0cf62_outfile.txt added
1324bf201d5c80_GRCh37_to_GRCh38.chain added
1324bf573cb1ff_GRCh37_to_NCBI34.chain added
1324bf471242ae_GRCh37_to_NCBI35.chain added
1324bf5ac08b59_GRCh37_to_NCBI36.chain added
1324bf2e94545f_GRCh38_to_GRCh37.chain added
1324bf7ffd9960_GRCh38_to_NCBI34.chain added
1324bf1a9b1b_GRCh38_to_NCBI35.chain added
1324bf692475ef_GRCh38_to_NCBI36.chain added
1324bf35199bbc_NCBI34_to_GRCh37.chain added
1324bf360fb684_NCBI34_to_GRCh38.chain added
1324bf5fb31ece_NCBI35_to_GRCh37.chain added
1324bf3c99de00_NCBI35_to_GRCh38.chain added
1324bf330e81eb_NCBI36_to_GRCh37.chain added
1324bf4d666874_NCBI36_to_GRCh38.chain added
1324bf59be0204_GRCm38_to_NCBIM36.chain added
1324bf69180968_GRCm38_to_NCBIM37.chain added
1324bf3e532f58_NCBIM36_to_GRCm38.chain added
1324bf67a418ab_NCBIM37_to_GRCm38.chain added
1324bf5f5a66aa_1000G_omni2.5.b37.vcf.gz added
1324bf7b8dbf66_1000G_omni2.5.b37.vcf.gz.tbi added
1324bf13558b0b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1324bf7ddc5a48_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1324bf423e5b58_1000G_omni2.5.hg38.vcf.gz added
1324bf4588b3b1_1000G_omni2.5.hg38.vcf.gz.tbi added
1324bf5579a637_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1324bf6be99cb_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1324bf1df8945_af-only-gnomad.raw.sites.vcf added
1324bf289d1fad_af-only-gnomad.raw.sites.vcf.idx added
1324bf3621022a_Mutect2-exome-panel.vcf.idx added
1324bf25b57f49_Mutect2-WGS-panel-b37.vcf added
1324bf4f7def0f_Mutect2-WGS-panel-b37.vcf.idx added
1324bf563e5eaa_small_exac_common_3.vcf added
1324bf7cf23148_small_exac_common_3.vcf.idx added
1324bf169031bd_1000g_pon.hg38.vcf.gz added
1324bf30feea03_1000g_pon.hg38.vcf.gz.tbi added
1324bf2b8685a7_af-only-gnomad.hg38.vcf.gz added
1324bf168dcb1d_af-only-gnomad.hg38.vcf.gz.tbi added
1324bf3119851e_small_exac_common_3.hg38.vcf.gz added
1324bf14aafb96_small_exac_common_3.hg38.vcf.gz.tbi added
1324bf4ba766da_gencode.v41.annotation.gtf added
1324bf67293ba2_gencode.v42.annotation.gtf added
1324bf745e1a64_gencode.vM30.annotation.gtf added
1324bf84144da_gencode.vM31.annotation.gtf added
1324bf1a37bd8d_gencode.v41.transcripts.fa added
1324bf41c482d8_gencode.v41.transcripts.fa.fai added
1324bf61ff46de_gencode.v42.transcripts.fa added
1324bf34fc6f6_gencode.v42.transcripts.fa.fai added
1324bf17b231_gencode.vM30.pc_transcripts.fa added
1324bf49a35f8a_gencode.vM30.pc_transcripts.fa.fai added
1324bf62aa2da0_gencode.vM31.pc_transcripts.fa added
1324bf7ba57197_gencode.vM31.pc_transcripts.fa.fai added
1324bf5cf8ea95_GRCh38.primary_assembly.genome.fa.1.ht2 added
1324bf608687e9_GRCh38.primary_assembly.genome.fa.2.ht2 added
1324bf3de3ccef_GRCh38.primary_assembly.genome.fa.3.ht2 added
1324bf22819e46_GRCh38.primary_assembly.genome.fa.4.ht2 added
1324bf36002e20_GRCh38.primary_assembly.genome.fa.5.ht2 added
1324bf44a266ba_GRCh38.primary_assembly.genome.fa.6.ht2 added
1324bf2461278c_GRCh38.primary_assembly.genome.fa.7.ht2 added
1324bf5e9d4dcd_GRCh38.primary_assembly.genome.fa.8.ht2 added
1324bf7ac368e5_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1324bf4a16a6d5_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1324bf2e1b3cdc_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1324bf5101c78f_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1324bf4708d81d_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1324bf44ab6e9a_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1324bf200b193_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1324bf728f5dc4_GRCh38.primary_assembly.genome.fa.fai added
1324bf5b3939b7_GRCh38.primary_assembly.genome.fa.amb added
1324bf331a36b1_GRCh38.primary_assembly.genome.fa.ann added
1324bf73a595a_GRCh38.primary_assembly.genome.fa.bwt added
1324bf26e0a091_GRCh38.primary_assembly.genome.fa.pac added
1324bf1a437254_GRCh38.primary_assembly.genome.fa.sa added
1324bf7b9873be_GRCh38.primary_assembly.genome.fa added
1324bf2f21e56c_hs37d5.fa.fai added
1324bf347b2fe1_hs37d5.fa.amb added
1324bf3d5cf696_hs37d5.fa.ann added
1324bf11212c4a_hs37d5.fa.bwt added
1324bf37caf6d7_hs37d5.fa.pac added
1324bf3d74a8c7_hs37d5.fa.sa added
1324bf5ac48bd4_hs37d5.fa added
1324bf1a752478_complete_ref_lens.bin added
1324bf391a1a5f_ctable.bin added
1324bf37bd7669_ctg_offsets.bin added
1324bf7afbac61_duplicate_clusters.tsv added
1324bf76fde74e_info.json added
1324bf5a3f14b0_mphf.bin added
1324bf30fbda81_pos.bin added
1324bf3ba04e09_pre_indexing.log added
1324bf7ea03c3c_rank.bin added
1324bff99284e_ref_indexing.log added
1324bf3663b6ee_refAccumLengths.bin added
1324bf48b6e311_reflengths.bin added
1324bf3db4652a_refseq.bin added
1324bf7657e7d_seq.bin added
1324bffbfbb2e_versionInfo.json added
1324bf25fd3c4_salmon_index added
1324bf9663010_chrLength.txt added
1324bf24f18f2_chrName.txt added
1324bf5d990d7c_chrNameLength.txt added
1324bf3c8066c2_chrStart.txt added
1324bf989724c_exonGeTrInfo.tab added
1324bf479ae0d_exonInfo.tab added
1324bf56c3d916_geneInfo.tab added
1324bf521e60a_Genome added
1324bf339b9379_genomeParameters.txt added
1324bfb3f08f7_Log.out added
1324bf427edca0_SA added
1324bf44bcbfc4_SAindex added
1324bf4309ffcf_sjdbInfo.txt added
1324bf7ff38568_sjdbList.fromGTF.out.tab added
1324bf1f814b98_sjdbList.out.tab added
1324bf5d7f2447_transcriptInfo.tab added
1324bf390d9fc7_GRCh38.GENCODE.v42_100 added
1324bf573ec202_knownGene_hg38.sql added
1324bf587ad0a8_knownGene_hg38.txt added
1324bf300b8715_refGene_hg38.sql added
1324bf317dd6b2_refGene_hg38.txt added
1324bf976ab29_knownGene_mm39.sql added
1324bf6babd51e_knownGene_mm39.txt added
1324bf301e12ee_refGene_mm39.sql added
1324bf190fd377_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/RtmprTl6yq/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 
 19.932   1.817  21.992