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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 7.979  0.903   9.028
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReUseData
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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-apple-darwin20

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...
1067f12eeb05c_GRCh38.primary_assembly.genome.fa.1.bt2 added
1067f747c71b9_GRCh38.primary_assembly.genome.fa.2.bt2 added
1067f160e646e_GRCh38.primary_assembly.genome.fa.3.bt2 added
1067fae37d12_GRCh38.primary_assembly.genome.fa.4.bt2 added
1067f5d282e53_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1067f78f97aec_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1067f42f55a00_outfile.txt added
1067f79e7d857_GRCh37_to_GRCh38.chain added
1067f642c7647_GRCh37_to_NCBI34.chain added
1067f230962b2_GRCh37_to_NCBI35.chain added
1067f3d2ea616_GRCh37_to_NCBI36.chain added
1067f419a0dbb_GRCh38_to_GRCh37.chain added
1067f68fb91a2_GRCh38_to_NCBI34.chain added
1067f5c165886_GRCh38_to_NCBI35.chain added
1067f3f0df4a5_GRCh38_to_NCBI36.chain added
1067f2d389cfa_NCBI34_to_GRCh37.chain added
1067f5fc9f847_NCBI34_to_GRCh38.chain added
1067f44cb2e72_NCBI35_to_GRCh37.chain added
1067f775661a6_NCBI35_to_GRCh38.chain added
1067f4825167f_NCBI36_to_GRCh37.chain added
1067f7ae810d9_NCBI36_to_GRCh38.chain added
1067f19aa5599_GRCm38_to_NCBIM36.chain added
1067f7dd9bcf8_GRCm38_to_NCBIM37.chain added
1067f62057e54_NCBIM36_to_GRCm38.chain added
1067f56a8ef12_NCBIM37_to_GRCm38.chain added
1067f6ce7b330_1000G_omni2.5.b37.vcf.gz added
1067f5fa54c2b_1000G_omni2.5.b37.vcf.gz.tbi added
1067f5d2bcc1b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1067f66653066_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1067f7d4cad0e_1000G_omni2.5.hg38.vcf.gz added
1067f34f5b266_1000G_omni2.5.hg38.vcf.gz.tbi added
1067f6e9361b3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1067fdf3677c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1067f670f050b_af-only-gnomad.raw.sites.vcf added
1067fb144a09_af-only-gnomad.raw.sites.vcf.idx added
1067f61089a8d_Mutect2-exome-panel.vcf.idx added
1067f7bdad0bf_Mutect2-WGS-panel-b37.vcf added
1067f5abeeb1f_Mutect2-WGS-panel-b37.vcf.idx added
1067f2c3e6ec4_small_exac_common_3.vcf added
1067f36da1c8d_small_exac_common_3.vcf.idx added
1067f2988891d_1000g_pon.hg38.vcf.gz added
1067f42e1e438_1000g_pon.hg38.vcf.gz.tbi added
1067f7c4e3ad5_af-only-gnomad.hg38.vcf.gz added
1067f73f8b5b4_af-only-gnomad.hg38.vcf.gz.tbi added
1067f4d6177e7_small_exac_common_3.hg38.vcf.gz added
1067f3a070661_small_exac_common_3.hg38.vcf.gz.tbi added
1067f2333e80a_gencode.v41.annotation.gtf added
1067f24c6fa94_gencode.v42.annotation.gtf added
1067f36d1d69_gencode.vM30.annotation.gtf added
1067f70a5da40_gencode.vM31.annotation.gtf added
1067f189bd987_gencode.v41.transcripts.fa added
1067f1fe63ab0_gencode.v41.transcripts.fa.fai added
1067f4417092c_gencode.v42.transcripts.fa added
1067f445b4aa0_gencode.v42.transcripts.fa.fai added
1067f4580716f_gencode.vM30.pc_transcripts.fa added
1067f7397520e_gencode.vM30.pc_transcripts.fa.fai added
1067f538c506b_gencode.vM31.pc_transcripts.fa added
1067f20f3cba7_gencode.vM31.pc_transcripts.fa.fai added
1067f65bf51d7_GRCh38.primary_assembly.genome.fa.1.ht2 added
1067f73962e70_GRCh38.primary_assembly.genome.fa.2.ht2 added
1067f8c2f659_GRCh38.primary_assembly.genome.fa.3.ht2 added
1067f37bb518d_GRCh38.primary_assembly.genome.fa.4.ht2 added
1067f6ae71c90_GRCh38.primary_assembly.genome.fa.5.ht2 added
1067f6b0468c4_GRCh38.primary_assembly.genome.fa.6.ht2 added
1067f6e7a52bf_GRCh38.primary_assembly.genome.fa.7.ht2 added
1067f20ceb243_GRCh38.primary_assembly.genome.fa.8.ht2 added
1067f62195d88_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1067f6f4bbe08_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1067f55a9384d_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1067f58af732a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1067f66b1f7e2_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1067f2e094b1a_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1067f6421af92_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1067f5f8dcd99_GRCh38.primary_assembly.genome.fa.fai added
1067f56b528d1_GRCh38.primary_assembly.genome.fa.amb added
1067ff8addd0_GRCh38.primary_assembly.genome.fa.ann added
1067f65e88aa8_GRCh38.primary_assembly.genome.fa.bwt added
1067f5e74fdd_GRCh38.primary_assembly.genome.fa.pac added
1067f152c3932_GRCh38.primary_assembly.genome.fa.sa added
1067fa5f0c7a_GRCh38.primary_assembly.genome.fa added
1067f662c22e7_hs37d5.fa.fai added
1067f5ba7a018_hs37d5.fa.amb added
1067f59ffb6aa_hs37d5.fa.ann added
1067f2331810f_hs37d5.fa.bwt added
1067f71011d6_hs37d5.fa.pac added
1067f3002fc39_hs37d5.fa.sa added
1067f13fd1acf_hs37d5.fa added
1067f4deb1649_complete_ref_lens.bin added
1067f5043a96_ctable.bin added
1067f58a2506c_ctg_offsets.bin added
1067f84e0fea_duplicate_clusters.tsv added
1067f3cf6cfe8_info.json added
1067f6fcba79c_mphf.bin added
1067f23692c1b_pos.bin added
1067f4dceb2c6_pre_indexing.log added
1067f3d3b0d12_rank.bin added
1067f6fd73825_ref_indexing.log added
1067f1aa73e80_refAccumLengths.bin added
1067f59f8532b_reflengths.bin added
1067f3e1c5a32_refseq.bin added
1067f3765a879_seq.bin added
1067f7317bc58_versionInfo.json added
1067f1b4e7070_salmon_index added
1067f3ab7d711_chrLength.txt added
1067f7b88bb34_chrName.txt added
1067f4dba9248_chrNameLength.txt added
1067f13d9dcd6_chrStart.txt added
1067f44316fc8_exonGeTrInfo.tab added
1067f9a1d672_exonInfo.tab added
1067f6005db4e_geneInfo.tab added
1067f20810f22_Genome added
1067f790891d9_genomeParameters.txt added
1067f219f7ba3_Log.out added
1067f6d6e1b93_SA added
1067f57d48805_SAindex added
1067f422e2d4f_sjdbInfo.txt added
1067f65a0bf7a_sjdbList.fromGTF.out.tab added
1067f1c7b16b6_sjdbList.out.tab added
1067f55101555_transcriptInfo.tab added
1067f12e8ab14_GRCh38.GENCODE.v42_100 added
1067f6937b7be_knownGene_hg38.sql added
1067f490050e9_knownGene_hg38.txt added
1067f33c01670_refGene_hg38.sql added
1067f8012d9b_refGene_hg38.txt added
1067f5591f38_knownGene_mm39.sql added
1067f1e109846_knownGene_mm39.txt added
1067f537d2b15_refGene_mm39.sql added
1067f3e979a85_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/RtmpmRn3A3/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 
 26.293   3.402  30.675