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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
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 5.639  0.392   6.032
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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...
3c7a5deba0640_GRCh38.primary_assembly.genome.fa.1.bt2 added
3c7a5d182b574b_GRCh38.primary_assembly.genome.fa.2.bt2 added
3c7a5d573bddc2_GRCh38.primary_assembly.genome.fa.3.bt2 added
3c7a5d374d49df_GRCh38.primary_assembly.genome.fa.4.bt2 added
3c7a5d64d159c9_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3c7a5d6726b07f_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3c7a5d72e608d1_outfile.txt added
3c7a5d677248f2_GRCh37_to_GRCh38.chain added
3c7a5d450abc46_GRCh37_to_NCBI34.chain added
3c7a5d3c86b6dd_GRCh37_to_NCBI35.chain added
3c7a5d5d08c480_GRCh37_to_NCBI36.chain added
3c7a5d6910130f_GRCh38_to_GRCh37.chain added
3c7a5d7d8cb9cc_GRCh38_to_NCBI34.chain added
3c7a5d5db15f44_GRCh38_to_NCBI35.chain added
3c7a5d193dbb4b_GRCh38_to_NCBI36.chain added
3c7a5d1c52c2df_NCBI34_to_GRCh37.chain added
3c7a5d250f2dac_NCBI34_to_GRCh38.chain added
3c7a5d5a59ef16_NCBI35_to_GRCh37.chain added
3c7a5d431876df_NCBI35_to_GRCh38.chain added
3c7a5d43b6038e_NCBI36_to_GRCh37.chain added
3c7a5d1d0eec3c_NCBI36_to_GRCh38.chain added
3c7a5d2da33f42_GRCm38_to_NCBIM36.chain added
3c7a5d6b84e94d_GRCm38_to_NCBIM37.chain added
3c7a5d20f36412_NCBIM36_to_GRCm38.chain added
3c7a5d5d6c01ca_NCBIM37_to_GRCm38.chain added
3c7a5d8e9d6ac_1000G_omni2.5.b37.vcf.gz added
3c7a5d57ae23d0_1000G_omni2.5.b37.vcf.gz.tbi added
3c7a5d66d6b58b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3c7a5d2ecab526_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3c7a5d37f796d8_1000G_omni2.5.hg38.vcf.gz added
3c7a5d2158f774_1000G_omni2.5.hg38.vcf.gz.tbi added
3c7a5d3d84bb67_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3c7a5d5022ee23_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3c7a5d7894d536_af-only-gnomad.raw.sites.vcf added
3c7a5d74d20546_af-only-gnomad.raw.sites.vcf.idx added
3c7a5d34f447ec_Mutect2-exome-panel.vcf.idx added
3c7a5d5fbb85b5_Mutect2-WGS-panel-b37.vcf added
3c7a5d67b80e17_Mutect2-WGS-panel-b37.vcf.idx added
3c7a5d1c6690de_small_exac_common_3.vcf added
3c7a5d24c641fb_small_exac_common_3.vcf.idx added
3c7a5d243ec4f5_1000g_pon.hg38.vcf.gz added
3c7a5d796f555e_1000g_pon.hg38.vcf.gz.tbi added
3c7a5ddd6550a_af-only-gnomad.hg38.vcf.gz added
3c7a5d21cb7ec1_af-only-gnomad.hg38.vcf.gz.tbi added
3c7a5d5720b4a2_small_exac_common_3.hg38.vcf.gz added
3c7a5d27141055_small_exac_common_3.hg38.vcf.gz.tbi added
3c7a5d3e1e41a0_gencode.v41.annotation.gtf added
3c7a5d7c2fe24e_gencode.v42.annotation.gtf added
3c7a5d16dff6b_gencode.vM30.annotation.gtf added
3c7a5d136b87f_gencode.vM31.annotation.gtf added
3c7a5d3fe5e5dd_gencode.v41.transcripts.fa added
3c7a5d1e7ceba7_gencode.v41.transcripts.fa.fai added
3c7a5d2ed9f7c1_gencode.v42.transcripts.fa added
3c7a5d2b6acf2a_gencode.v42.transcripts.fa.fai added
3c7a5d3f704fb9_gencode.vM30.pc_transcripts.fa added
3c7a5dc45f98b_gencode.vM30.pc_transcripts.fa.fai added
3c7a5d3454a5d7_gencode.vM31.pc_transcripts.fa added
3c7a5d171e738a_gencode.vM31.pc_transcripts.fa.fai added
3c7a5d731caf17_GRCh38.primary_assembly.genome.fa.1.ht2 added
3c7a5d631f5afd_GRCh38.primary_assembly.genome.fa.2.ht2 added
3c7a5d4f160a62_GRCh38.primary_assembly.genome.fa.3.ht2 added
3c7a5d1475a68b_GRCh38.primary_assembly.genome.fa.4.ht2 added
3c7a5d20a41664_GRCh38.primary_assembly.genome.fa.5.ht2 added
3c7a5d1f38f885_GRCh38.primary_assembly.genome.fa.6.ht2 added
3c7a5dd0a7bc1_GRCh38.primary_assembly.genome.fa.7.ht2 added
3c7a5d15761baa_GRCh38.primary_assembly.genome.fa.8.ht2 added
3c7a5d542d4071_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3c7a5d6cc60177_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3c7a5d7d2e29c2_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3c7a5d7093d14f_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3c7a5d118c4372_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3c7a5d216ceeb7_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3c7a5d6a0326ae_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3c7a5d1f62987d_GRCh38.primary_assembly.genome.fa.fai added
3c7a5d43386d78_GRCh38.primary_assembly.genome.fa.amb added
3c7a5d4123db50_GRCh38.primary_assembly.genome.fa.ann added
3c7a5d4676a8d2_GRCh38.primary_assembly.genome.fa.bwt added
3c7a5d156af18_GRCh38.primary_assembly.genome.fa.pac added
3c7a5d3d53bd9f_GRCh38.primary_assembly.genome.fa.sa added
3c7a5d47e4a83e_GRCh38.primary_assembly.genome.fa added
3c7a5d28d6798_hs37d5.fa.fai added
3c7a5d7d39a37c_hs37d5.fa.amb added
3c7a5d666193e5_hs37d5.fa.ann added
3c7a5d31675f59_hs37d5.fa.bwt added
3c7a5d28a472a6_hs37d5.fa.pac added
3c7a5d25d1e39f_hs37d5.fa.sa added
3c7a5d3dad58e5_hs37d5.fa added
3c7a5d5cf9187d_complete_ref_lens.bin added
3c7a5d3cf05729_ctable.bin added
3c7a5d30ca07fc_ctg_offsets.bin added
3c7a5d4018737b_duplicate_clusters.tsv added
3c7a5dc06618b_info.json added
3c7a5d453fae87_mphf.bin added
3c7a5d60bc89df_pos.bin added
3c7a5d2b3f5a10_pre_indexing.log added
3c7a5d524a2a48_rank.bin added
3c7a5d7632a58a_ref_indexing.log added
3c7a5d7f6c9a81_refAccumLengths.bin added
3c7a5d3f102bbf_reflengths.bin added
3c7a5d7360cf4c_refseq.bin added
3c7a5d70006bd0_seq.bin added
3c7a5d509c6f32_versionInfo.json added
3c7a5d14cdbe03_salmon_index added
3c7a5d5a03927e_chrLength.txt added
3c7a5d6fff07af_chrName.txt added
3c7a5d58062b7b_chrNameLength.txt added
3c7a5d1b276dcf_chrStart.txt added
3c7a5d3675b081_exonGeTrInfo.tab added
3c7a5d595cda93_exonInfo.tab added
3c7a5d587b2b6e_geneInfo.tab added
3c7a5d7e5a58bf_Genome added
3c7a5d5bea422b_genomeParameters.txt added
3c7a5d55b4ceea_Log.out added
3c7a5d64bbeca5_SA added
3c7a5dd51a185_SAindex added
3c7a5d7e594190_sjdbInfo.txt added
3c7a5da8dd044_sjdbList.fromGTF.out.tab added
3c7a5d4afefa6a_sjdbList.out.tab added
3c7a5d5b525a0e_transcriptInfo.tab added
3c7a5d477e276d_GRCh38.GENCODE.v42_100 added
3c7a5d7bc90266_knownGene_hg38.sql added
3c7a5d1b6acd89_knownGene_hg38.txt added
3c7a5d538488f8_refGene_hg38.sql added
3c7a5d4108b0ed_refGene_hg38.txt added
3c7a5d7c275768_knownGene_mm39.sql added
3c7a5d7ec3e308_knownGene_mm39.txt added
3c7a5d1352db35_refGene_mm39.sql added
3c7a5d7259fcf2_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/RtmpBoPd1N/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 
 20.050   1.535  22.147