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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings ReUseData_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 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 9.811  0.515  10.365
getCloudData  3.511  0.224   8.517
* 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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...
55e572e7b0da_GRCh38.primary_assembly.genome.fa.1.bt2 added
55e5758574d34_GRCh38.primary_assembly.genome.fa.2.bt2 added
55e575a80bc69_GRCh38.primary_assembly.genome.fa.3.bt2 added
55e575f340310_GRCh38.primary_assembly.genome.fa.4.bt2 added
55e5756cd1cef_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
55e57cb1cb85_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
55e572db0ac3e_outfile.txt added
55e57711baa1e_GRCh37_to_GRCh38.chain added
55e5748090cc8_GRCh37_to_NCBI34.chain added
55e5720ade5bc_GRCh37_to_NCBI35.chain added
55e574a970062_GRCh37_to_NCBI36.chain added
55e576cf60090_GRCh38_to_GRCh37.chain added
55e574062a61d_GRCh38_to_NCBI34.chain added
55e57214f1038_GRCh38_to_NCBI35.chain added
55e572a72ccae_GRCh38_to_NCBI36.chain added
55e57452c2468_NCBI34_to_GRCh37.chain added
55e571dfc1dc9_NCBI34_to_GRCh38.chain added
55e577e920999_NCBI35_to_GRCh37.chain added
55e573d871a5e_NCBI35_to_GRCh38.chain added
55e572d7404f0_NCBI36_to_GRCh37.chain added
55e574bd6dd1d_NCBI36_to_GRCh38.chain added
55e577b8d3215_GRCm38_to_NCBIM36.chain added
55e5757f4945_GRCm38_to_NCBIM37.chain added
55e57725f5838_NCBIM36_to_GRCm38.chain added
55e5723ec7484_NCBIM37_to_GRCm38.chain added
55e573d545d54_1000G_omni2.5.b37.vcf.gz added
55e5773e8d6aa_1000G_omni2.5.b37.vcf.gz.tbi added
55e576936dcd2_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
55e57f1317bd_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
55e573dace108_1000G_omni2.5.hg38.vcf.gz added
55e5761e8d992_1000G_omni2.5.hg38.vcf.gz.tbi added
55e5711fac897_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
55e5716042e3d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
55e573c6995fb_af-only-gnomad.raw.sites.vcf added
55e57712ecba7_af-only-gnomad.raw.sites.vcf.idx added
55e576cd14b2c_Mutect2-exome-panel.vcf.idx added
55e57491b6181_Mutect2-WGS-panel-b37.vcf added
55e571edf77e6_Mutect2-WGS-panel-b37.vcf.idx added
55e575decf54a_small_exac_common_3.vcf added
55e5711246e49_small_exac_common_3.vcf.idx added
55e573f8d5da2_1000g_pon.hg38.vcf.gz added
55e572883f5ac_1000g_pon.hg38.vcf.gz.tbi added
55e577e1a6ed9_af-only-gnomad.hg38.vcf.gz added
55e577ff003bf_af-only-gnomad.hg38.vcf.gz.tbi added
55e5749d305e4_small_exac_common_3.hg38.vcf.gz added
55e57288d3b87_small_exac_common_3.hg38.vcf.gz.tbi added
55e57451c2828_gencode.v41.annotation.gtf added
55e5767cf23ad_gencode.v42.annotation.gtf added
55e57271f4520_gencode.vM30.annotation.gtf added
55e572a34286_gencode.vM31.annotation.gtf added
55e571543289d_gencode.v41.transcripts.fa added
55e5772f6223e_gencode.v41.transcripts.fa.fai added
55e577e30749c_gencode.v42.transcripts.fa added
55e571ac271e2_gencode.v42.transcripts.fa.fai added
55e5765557a76_gencode.vM30.pc_transcripts.fa added
55e57221ce920_gencode.vM30.pc_transcripts.fa.fai added
55e575816cf37_gencode.vM31.pc_transcripts.fa added
55e57593e5120_gencode.vM31.pc_transcripts.fa.fai added
55e57b53c5f2_GRCh38.primary_assembly.genome.fa.1.ht2 added
55e576729e6f4_GRCh38.primary_assembly.genome.fa.2.ht2 added
55e5716eb3229_GRCh38.primary_assembly.genome.fa.3.ht2 added
55e576d3c9f85_GRCh38.primary_assembly.genome.fa.4.ht2 added
55e577924af8b_GRCh38.primary_assembly.genome.fa.5.ht2 added
55e572cef6066_GRCh38.primary_assembly.genome.fa.6.ht2 added
55e5729a63580_GRCh38.primary_assembly.genome.fa.7.ht2 added
55e576a537b32_GRCh38.primary_assembly.genome.fa.8.ht2 added
55e5719c0ab92_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
55e5772c19701_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
55e57932f318_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
55e5777ada0dc_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
55e573e6054b_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
55e5748c050ba_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
55e5720319688_GRCh38_full_analysis_set_plus_decoy_hla.fa added
55e572007424_GRCh38.primary_assembly.genome.fa.fai added
55e5748b0547a_GRCh38.primary_assembly.genome.fa.amb added
55e576a049c6c_GRCh38.primary_assembly.genome.fa.ann added
55e572a8dafac_GRCh38.primary_assembly.genome.fa.bwt added
55e57dcc7ca2_GRCh38.primary_assembly.genome.fa.pac added
55e5751d3c019_GRCh38.primary_assembly.genome.fa.sa added
55e5751acf4cc_GRCh38.primary_assembly.genome.fa added
55e57106fbf28_hs37d5.fa.fai added
55e576716e8b7_hs37d5.fa.amb added
55e5744a3170a_hs37d5.fa.ann added
55e57ea033c4_hs37d5.fa.bwt added
55e571d95a99_hs37d5.fa.pac added
55e5729f89180_hs37d5.fa.sa added
55e5730bd1ce4_hs37d5.fa added
55e5759f029d0_complete_ref_lens.bin added
55e57336e2a1_ctable.bin added
55e573c10e2d7_ctg_offsets.bin added
55e57411a10c4_duplicate_clusters.tsv added
55e571a2214ca_info.json added
55e57294d825c_mphf.bin added
55e573a3ec04f_pos.bin added
55e5747117530_pre_indexing.log added
55e5752f3b7dc_rank.bin added
55e5724923b82_ref_indexing.log added
55e5760d220c2_refAccumLengths.bin added
55e5745b54ede_reflengths.bin added
55e572dc52e9a_refseq.bin added
55e57587fc19e_seq.bin added
55e57499b5429_versionInfo.json added
55e5776857f55_salmon_index added
55e5778b15826_chrLength.txt added
55e574b9bc84d_chrName.txt added
55e573f35d3cf_chrNameLength.txt added
55e5762b5f492_chrStart.txt added
55e57762977f9_exonGeTrInfo.tab added
55e574d025071_exonInfo.tab added
55e573489b4ab_geneInfo.tab added
55e5747d66cc6_Genome added
55e575d720f99_genomeParameters.txt added
55e571ba09d62_Log.out added
55e57c7983d0_SA added
55e576c12435e_SAindex added
55e571d79f7fc_sjdbInfo.txt added
55e5736721551_sjdbList.fromGTF.out.tab added
55e571ccf6042_sjdbList.out.tab added
55e57776a21cc_transcriptInfo.tab added
55e5739a8f7f2_GRCh38.GENCODE.v42_100 added
55e5758e04319_knownGene_hg38.sql added
55e5738843291_knownGene_hg38.txt added
55e5753cb0cbc_refGene_hg38.sql added
55e5722dc575_refGene_hg38.txt added
55e5772c2f2e0_knownGene_mm39.sql added
55e571adc81ec_knownGene_mm39.txt added
55e5755217d52_refGene_mm39.sql added
55e5717552e62_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: 
/home/biocbuild/tmp/RtmpLnJjUa/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 
 30.065   1.711  34.720