##############################################################################
##############################################################################
###
### 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 7.868  0.937   8.948
* 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.

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


* 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...
5c7e5e01bc3c_GRCh38.primary_assembly.genome.fa.1.bt2 added
5c7e43ed375b_GRCh38.primary_assembly.genome.fa.2.bt2 added
5c7eacd5a34_GRCh38.primary_assembly.genome.fa.3.bt2 added
5c7e2fdd1176_GRCh38.primary_assembly.genome.fa.4.bt2 added
5c7e5aa57286_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
5c7e2401e9e8_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
5c7e79a390cf_outfile.txt added
5c7e6178446c_GRCh37_to_GRCh38.chain added
5c7e1ed44072_GRCh37_to_NCBI34.chain added
5c7ed30c2e_GRCh37_to_NCBI35.chain added
5c7e1fc4a06e_GRCh37_to_NCBI36.chain added
5c7e2600a60d_GRCh38_to_GRCh37.chain added
5c7e7495b2f8_GRCh38_to_NCBI34.chain added
5c7e1018f394_GRCh38_to_NCBI35.chain added
5c7e561f81cd_GRCh38_to_NCBI36.chain added
5c7e2e82e5e7_NCBI34_to_GRCh37.chain added
5c7e13c3b88c_NCBI34_to_GRCh38.chain added
5c7e1688f977_NCBI35_to_GRCh37.chain added
5c7e7ab1ff2f_NCBI35_to_GRCh38.chain added
5c7e3be8a597_NCBI36_to_GRCh37.chain added
5c7e26cf7b3b_NCBI36_to_GRCh38.chain added
5c7e7fa37264_GRCm38_to_NCBIM36.chain added
5c7e43ab44b3_GRCm38_to_NCBIM37.chain added
5c7e212b667a_NCBIM36_to_GRCm38.chain added
5c7e2854e499_NCBIM37_to_GRCm38.chain added
5c7e5d6c0d7e_1000G_omni2.5.b37.vcf.gz added
5c7e60e9fb1c_1000G_omni2.5.b37.vcf.gz.tbi added
5c7e21651cf9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
5c7e7551308f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
5c7e254b3875_1000G_omni2.5.hg38.vcf.gz added
5c7e6d679c73_1000G_omni2.5.hg38.vcf.gz.tbi added
5c7e2d507a22_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
5c7e7e82656b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
5c7e22d094b0_af-only-gnomad.raw.sites.vcf added
5c7e2bd1c0ab_af-only-gnomad.raw.sites.vcf.idx added
5c7e57c03106_Mutect2-exome-panel.vcf.idx added
5c7ead2adec_Mutect2-WGS-panel-b37.vcf added
5c7ed986681_Mutect2-WGS-panel-b37.vcf.idx added
5c7e1071a620_small_exac_common_3.vcf added
5c7e1551874f_small_exac_common_3.vcf.idx added
5c7e1b8a5e78_1000g_pon.hg38.vcf.gz added
5c7e19402668_1000g_pon.hg38.vcf.gz.tbi added
5c7e429982cb_af-only-gnomad.hg38.vcf.gz added
5c7e6c59ff95_af-only-gnomad.hg38.vcf.gz.tbi added
5c7e89ac6c6_small_exac_common_3.hg38.vcf.gz added
5c7e696ff593_small_exac_common_3.hg38.vcf.gz.tbi added
5c7e3563bbf9_gencode.v41.annotation.gtf added
5c7e26c9f3d1_gencode.v42.annotation.gtf added
5c7e14a6323c_gencode.vM30.annotation.gtf added
5c7e2b2c0bbb_gencode.vM31.annotation.gtf added
5c7e58b63821_gencode.v41.transcripts.fa added
5c7e231f2c07_gencode.v41.transcripts.fa.fai added
5c7e53839194_gencode.v42.transcripts.fa added
5c7e62cab661_gencode.v42.transcripts.fa.fai added
5c7e6a8bccf2_gencode.vM30.pc_transcripts.fa added
5c7e3c5a84_gencode.vM30.pc_transcripts.fa.fai added
5c7e7a5a903a_gencode.vM31.pc_transcripts.fa added
5c7e4fb30e97_gencode.vM31.pc_transcripts.fa.fai added
5c7e74830461_GRCh38.primary_assembly.genome.fa.1.ht2 added
5c7e4594b809_GRCh38.primary_assembly.genome.fa.2.ht2 added
5c7e26be7a8f_GRCh38.primary_assembly.genome.fa.3.ht2 added
5c7e23605628_GRCh38.primary_assembly.genome.fa.4.ht2 added
5c7e9b86e3d_GRCh38.primary_assembly.genome.fa.5.ht2 added
5c7e2b4d6bc7_GRCh38.primary_assembly.genome.fa.6.ht2 added
5c7e67deec06_GRCh38.primary_assembly.genome.fa.7.ht2 added
5c7e5c59b330_GRCh38.primary_assembly.genome.fa.8.ht2 added
5c7e50343ae_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
5c7e19505714_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
5c7e6984ef07_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
5c7e1668eab0_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
5c7e4207d44e_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
5c7e10036ec0_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
5c7e515c0776_GRCh38_full_analysis_set_plus_decoy_hla.fa added
5c7e70edfdb4_GRCh38.primary_assembly.genome.fa.fai added
5c7e18ab6e58_GRCh38.primary_assembly.genome.fa.amb added
5c7e1ed9600f_GRCh38.primary_assembly.genome.fa.ann added
5c7e5131889b_GRCh38.primary_assembly.genome.fa.bwt added
5c7eaffa1c2_GRCh38.primary_assembly.genome.fa.pac added
5c7e14d4cd32_GRCh38.primary_assembly.genome.fa.sa added
5c7e1eeb984d_GRCh38.primary_assembly.genome.fa added
5c7e7d5bf716_hs37d5.fa.fai added
5c7e20bb05a6_hs37d5.fa.amb added
5c7e566fe613_hs37d5.fa.ann added
5c7e4c6a15ba_hs37d5.fa.bwt added
5c7e48b88d87_hs37d5.fa.pac added
5c7e4c53bf5d_hs37d5.fa.sa added
5c7ee3899d1_hs37d5.fa added
5c7e25fa6fa2_complete_ref_lens.bin added
5c7e5cb70828_ctable.bin added
5c7e7478a9a5_ctg_offsets.bin added
5c7e1dc9cb60_duplicate_clusters.tsv added
5c7e2b471ae7_info.json added
5c7e493749e3_mphf.bin added
5c7e4cd3fba2_pos.bin added
5c7e712d7015_pre_indexing.log added
5c7e5e19acbf_rank.bin added
5c7e679c5fdc_ref_indexing.log added
5c7e4b5999a8_refAccumLengths.bin added
5c7e67770b3d_reflengths.bin added
5c7e388306dc_refseq.bin added
5c7e22377280_seq.bin added
5c7e663e430c_versionInfo.json added
5c7e1a3fd45_salmon_index added
5c7e3548bdda_chrLength.txt added
5c7e3aa84e8a_chrName.txt added
5c7e7fbc641b_chrNameLength.txt added
5c7e29506a21_chrStart.txt added
5c7e5e67b1b7_exonGeTrInfo.tab added
5c7e69c495cc_exonInfo.tab added
5c7e6946ba53_geneInfo.tab added
5c7e2272d524_Genome added
5c7e21074027_genomeParameters.txt added
5c7e6304d161_Log.out added
5c7e514e6a10_SA added
5c7e73156a23_SAindex added
5c7e2eb5adc_sjdbInfo.txt added
5c7e299a2303_sjdbList.fromGTF.out.tab added
5c7e4670af4b_sjdbList.out.tab added
5c7e1004890e_transcriptInfo.tab added
5c7e19c1fe59_GRCh38.GENCODE.v42_100 added
5c7ef219245_knownGene_hg38.sql added
5c7e6509f7c5_knownGene_hg38.txt added
5c7e7169da55_refGene_hg38.sql added
5c7e5c7d3c9e_refGene_hg38.txt added
5c7e2216d882_knownGene_mm39.sql added
5c7e9e0504a_knownGene_mm39.txt added
5c7e65b72f56_refGene_mm39.sql added
5c7e5d84eb45_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/RtmpYe0BMO/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 
 23.372   2.839  27.226