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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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 6.98  0.753   7.784
* 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-3.19-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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: aarch64-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...
14eef1189bef_GRCh38.primary_assembly.genome.fa.1.bt2 added
14eef76a56878_GRCh38.primary_assembly.genome.fa.2.bt2 added
14eef656ddb22_GRCh38.primary_assembly.genome.fa.3.bt2 added
14eeff4dc934_GRCh38.primary_assembly.genome.fa.4.bt2 added
14eef3bd47cc5_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
14eef7b4b8832_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
14eef1bdac9db_outfile.txt added
14eef38fa5726_GRCh37_to_GRCh38.chain added
14eef3b6f9d03_GRCh37_to_NCBI34.chain added
14eef1cad4e71_GRCh37_to_NCBI35.chain added
14eef35f8eb6c_GRCh37_to_NCBI36.chain added
14eef69281b22_GRCh38_to_GRCh37.chain added
14eef480d8b1d_GRCh38_to_NCBI34.chain added
14eef712841df_GRCh38_to_NCBI35.chain added
14eef9fcd183_GRCh38_to_NCBI36.chain added
14eef351ef494_NCBI34_to_GRCh37.chain added
14eef34b3bcb_NCBI34_to_GRCh38.chain added
14eef40428e1d_NCBI35_to_GRCh37.chain added
14eef518032e0_NCBI35_to_GRCh38.chain added
14eef378c39ed_NCBI36_to_GRCh37.chain added
14eef572f1318_NCBI36_to_GRCh38.chain added
14eef538eb95f_GRCm38_to_NCBIM36.chain added
14eef3f2c36d4_GRCm38_to_NCBIM37.chain added
14eef6fc3b8b2_NCBIM36_to_GRCm38.chain added
14eef1a92e771_NCBIM37_to_GRCm38.chain added
14eef2298b958_1000G_omni2.5.b37.vcf.gz added
14eef58b05226_1000G_omni2.5.b37.vcf.gz.tbi added
14eef1fe16a47_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
14eef8086bab_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
14eef60d4abab_1000G_omni2.5.hg38.vcf.gz added
14eef2a529937_1000G_omni2.5.hg38.vcf.gz.tbi added
14eef14c8ff96_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
14eef1803db83_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
14eef254081c6_af-only-gnomad.raw.sites.vcf added
14eef2e080145_af-only-gnomad.raw.sites.vcf.idx added
14eeff8b709f_Mutect2-exome-panel.vcf.idx added
14eefb8edeb2_Mutect2-WGS-panel-b37.vcf added
14eef50be7e0b_Mutect2-WGS-panel-b37.vcf.idx added
14eefa452d97_small_exac_common_3.vcf added
14eef43b419c5_small_exac_common_3.vcf.idx added
14eef6507f73c_1000g_pon.hg38.vcf.gz added
14eef6df8b7f5_1000g_pon.hg38.vcf.gz.tbi added
14eef63f56e3a_af-only-gnomad.hg38.vcf.gz added
14eef617d51b_af-only-gnomad.hg38.vcf.gz.tbi added
14eef6a7e2bd_small_exac_common_3.hg38.vcf.gz added
14eef7816e9b4_small_exac_common_3.hg38.vcf.gz.tbi added
14eef28496604_gencode.v41.annotation.gtf added
14eef6ac8a545_gencode.v42.annotation.gtf added
14eef1ada8bc8_gencode.vM30.annotation.gtf added
14eef20f053e_gencode.vM31.annotation.gtf added
14eef28212a80_gencode.v41.transcripts.fa added
14eef196d4e15_gencode.v41.transcripts.fa.fai added
14eef572151bd_gencode.v42.transcripts.fa added
14eef4c7d7bfb_gencode.v42.transcripts.fa.fai added
14eef4256c2f8_gencode.vM30.pc_transcripts.fa added
14eef4e1a49ce_gencode.vM30.pc_transcripts.fa.fai added
14eef1fe39b71_gencode.vM31.pc_transcripts.fa added
14eef17f22812_gencode.vM31.pc_transcripts.fa.fai added
14eef1b24c206_GRCh38.primary_assembly.genome.fa.1.ht2 added
14eefa3e25d6_GRCh38.primary_assembly.genome.fa.2.ht2 added
14eef762609da_GRCh38.primary_assembly.genome.fa.3.ht2 added
14eef3b5103cf_GRCh38.primary_assembly.genome.fa.4.ht2 added
14eef43d12975_GRCh38.primary_assembly.genome.fa.5.ht2 added
14eef58f8e31b_GRCh38.primary_assembly.genome.fa.6.ht2 added
14eef3c062f3f_GRCh38.primary_assembly.genome.fa.7.ht2 added
14eef3a07efe2_GRCh38.primary_assembly.genome.fa.8.ht2 added
14eef5f15fc31_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
14eef1c6025bc_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
14eef6c4d6831_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
14eef4df3a083_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
14eef35af2070_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
14eef7c7ab498_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
14eef5be6a700_GRCh38_full_analysis_set_plus_decoy_hla.fa added
14eef3de2023_GRCh38.primary_assembly.genome.fa.fai added
14eef6c0fdbd0_GRCh38.primary_assembly.genome.fa.amb added
14eef5286c1d_GRCh38.primary_assembly.genome.fa.ann added
14eef20d1e690_GRCh38.primary_assembly.genome.fa.bwt added
14eef347808c5_GRCh38.primary_assembly.genome.fa.pac added
14eef3487d86c_GRCh38.primary_assembly.genome.fa.sa added
14eef4291b565_GRCh38.primary_assembly.genome.fa added
14eef6c1c1c07_hs37d5.fa.fai added
14eef29744704_hs37d5.fa.amb added
14eef10e26cdf_hs37d5.fa.ann added
14eef159ad22_hs37d5.fa.bwt added
14eef267593df_hs37d5.fa.pac added
14eef713f2932_hs37d5.fa.sa added
14eef69a9cbb3_hs37d5.fa added
14eefa7c8af7_complete_ref_lens.bin added
14eef76876381_ctable.bin added
14eef3295e6f2_ctg_offsets.bin added
14eeff6d33d0_duplicate_clusters.tsv added
14eef4a64a499_info.json added
14eef15725ef7_mphf.bin added
14eef7b8b521_pos.bin added
14eef6f7b8d7c_pre_indexing.log added
14eef18860112_rank.bin added
14eef5b05152_ref_indexing.log added
14eef7aaae168_refAccumLengths.bin added
14eef68b4b1c2_reflengths.bin added
14eef2f026d42_refseq.bin added
14eef4853202a_seq.bin added
14eef4964ca7e_versionInfo.json added
14eef782a3bd6_salmon_index added
14eef1cbe9c3c_chrLength.txt added
14eef260335e2_chrName.txt added
14eef1cc69bed_chrNameLength.txt added
14eef3326f35d_chrStart.txt added
14eef423378e7_exonGeTrInfo.tab added
14eef4146a7a5_exonInfo.tab added
14eef5a8631e_geneInfo.tab added
14eef72034978_Genome added
14eef35cc9fc2_genomeParameters.txt added
14eefd0c9526_Log.out added
14eef3513f87b_SA added
14eef321e6e76_SAindex added
14eef6be61eae_sjdbInfo.txt added
14eef50e868d9_sjdbList.fromGTF.out.tab added
14eef4a3ba80e_sjdbList.out.tab added
14eef12965535_transcriptInfo.tab added
14eef4bb4141b_GRCh38.GENCODE.v42_100 added
14eef1b941f71_knownGene_hg38.sql added
14eef199c41dc_knownGene_hg38.txt added
14eef61a7dfa6_refGene_hg38.sql added
14eef544c3d60_refGene_hg38.txt added
14eef595194dc_knownGene_mm39.sql added
14eef7b042553_knownGene_mm39.txt added
14eef4d2eab3d_refGene_mm39.sql added
14eef32ec5961_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/RtmphBXZhy/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 
 24.272   2.944  28.634