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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings ReUseData_1.3.2.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* 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 ‘1.3.2’
* 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 9.285  0.423   9.741
getCloudData  3.488  0.175   7.183
* 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-4.4-devel-2024.03.20/bin/R CMD INSTALL ReUseData
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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 Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
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...
25e2ef7be991e3_GRCh38.primary_assembly.genome.fa.1.bt2 added
25e2ef20a61eaf_GRCh38.primary_assembly.genome.fa.2.bt2 added
25e2ef62a3db86_GRCh38.primary_assembly.genome.fa.3.bt2 added
25e2ef778f5ff0_GRCh38.primary_assembly.genome.fa.4.bt2 added
25e2ef47a81a3b_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
25e2ef405f4986_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
25e2ef7d469a66_outfile.txt added
25e2ef31921b51_GRCh37_to_GRCh38.chain added
25e2ef3e7bf391_GRCh37_to_NCBI34.chain added
25e2ef385e6eb6_GRCh37_to_NCBI35.chain added
25e2efe8ea501_GRCh37_to_NCBI36.chain added
25e2ef1066e4a8_GRCh38_to_GRCh37.chain added
25e2ef28eb0bcc_GRCh38_to_NCBI34.chain added
25e2ef42a87363_GRCh38_to_NCBI35.chain added
25e2ef5545dc77_GRCh38_to_NCBI36.chain added
25e2ef3edd6ead_NCBI34_to_GRCh37.chain added
25e2ef427ed0db_NCBI34_to_GRCh38.chain added
25e2ef6729253_NCBI35_to_GRCh37.chain added
25e2ef66a043de_NCBI35_to_GRCh38.chain added
25e2ef2d722c32_NCBI36_to_GRCh37.chain added
25e2ef219079a3_NCBI36_to_GRCh38.chain added
25e2ef340ea15b_GRCm38_to_NCBIM36.chain added
25e2ef781b3f75_GRCm38_to_NCBIM37.chain added
25e2ef361c9b63_NCBIM36_to_GRCm38.chain added
25e2ef226ad623_NCBIM37_to_GRCm38.chain added
25e2ef68a9ef1e_1000G_omni2.5.b37.vcf.gz added
25e2ef3249cab9_1000G_omni2.5.b37.vcf.gz.tbi added
25e2ef76d090ea_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
25e2ef481855ca_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
25e2ef1fab6e9c_1000G_omni2.5.hg38.vcf.gz added
25e2ef7b0b1ca_1000G_omni2.5.hg38.vcf.gz.tbi added
25e2ef4401e7ae_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
25e2ef40518d4b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
25e2ef6a548d50_af-only-gnomad.raw.sites.vcf added
25e2ef3b91479e_af-only-gnomad.raw.sites.vcf.idx added
25e2ef7f9a786_Mutect2-exome-panel.vcf.idx added
25e2ef2ab3d6d7_Mutect2-WGS-panel-b37.vcf added
25e2ef38d7e204_Mutect2-WGS-panel-b37.vcf.idx added
25e2ef398bc2d8_small_exac_common_3.vcf added
25e2ef692fca68_small_exac_common_3.vcf.idx added
25e2ef713650bb_1000g_pon.hg38.vcf.gz added
25e2ef481a67d9_1000g_pon.hg38.vcf.gz.tbi added
25e2ef7996af10_af-only-gnomad.hg38.vcf.gz added
25e2ef1a215c87_af-only-gnomad.hg38.vcf.gz.tbi added
25e2efac2db3d_small_exac_common_3.hg38.vcf.gz added
25e2ef4edc8b88_small_exac_common_3.hg38.vcf.gz.tbi added
25e2ef58fecb35_gencode.v41.annotation.gtf added
25e2ef4d41ac18_gencode.v42.annotation.gtf added
25e2ef554f1ddb_gencode.vM30.annotation.gtf added
25e2ef3f9f0f13_gencode.vM31.annotation.gtf added
25e2ef7ab3d84a_gencode.v41.transcripts.fa added
25e2ef76df977f_gencode.v41.transcripts.fa.fai added
25e2ef73adb06e_gencode.v42.transcripts.fa added
25e2ef72cf17c0_gencode.v42.transcripts.fa.fai added
25e2ef2cfc32e2_gencode.vM30.pc_transcripts.fa added
25e2ef16188691_gencode.vM30.pc_transcripts.fa.fai added
25e2ef5b7906de_gencode.vM31.pc_transcripts.fa added
25e2ef5f45fd9c_gencode.vM31.pc_transcripts.fa.fai added
25e2efce9177b_GRCh38.primary_assembly.genome.fa.1.ht2 added
25e2ef23915ca9_GRCh38.primary_assembly.genome.fa.2.ht2 added
25e2ef7ef16c38_GRCh38.primary_assembly.genome.fa.3.ht2 added
25e2ef1499c945_GRCh38.primary_assembly.genome.fa.4.ht2 added
25e2ef67934457_GRCh38.primary_assembly.genome.fa.5.ht2 added
25e2ef3f42f983_GRCh38.primary_assembly.genome.fa.6.ht2 added
25e2ef7eee5696_GRCh38.primary_assembly.genome.fa.7.ht2 added
25e2ef23248bf5_GRCh38.primary_assembly.genome.fa.8.ht2 added
25e2ef473ca10a_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
25e2ef29a22d6d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
25e2ef5bfc6df9_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
25e2efc863e2_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
25e2ef12d1f7d5_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
25e2ef4d32beb4_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
25e2ef48e2cbbb_GRCh38_full_analysis_set_plus_decoy_hla.fa added
25e2efc68a6e6_GRCh38.primary_assembly.genome.fa.fai added
25e2ef67541b3c_GRCh38.primary_assembly.genome.fa.amb added
25e2ef53a5a6f8_GRCh38.primary_assembly.genome.fa.ann added
25e2ef5b45326e_GRCh38.primary_assembly.genome.fa.bwt added
25e2ef4052e671_GRCh38.primary_assembly.genome.fa.pac added
25e2ef20e75311_GRCh38.primary_assembly.genome.fa.sa added
25e2ef30945049_GRCh38.primary_assembly.genome.fa added
25e2ef7ff1f584_hs37d5.fa.fai added
25e2ef1b9b2b5b_hs37d5.fa.amb added
25e2ef2773e7c8_hs37d5.fa.ann added
25e2ef739fa5f2_hs37d5.fa.bwt added
25e2efe6a431b_hs37d5.fa.pac added
25e2ef54701aab_hs37d5.fa.sa added
25e2ef9b82c83_hs37d5.fa added
25e2ef69e349fa_complete_ref_lens.bin added
25e2ef33b61847_ctable.bin added
25e2ef16a143ff_ctg_offsets.bin added
25e2efd74a6a3_duplicate_clusters.tsv added
25e2ef32a7847f_info.json added
25e2ef2b3b0d44_mphf.bin added
25e2ef7507eafa_pos.bin added
25e2ef71ea7e02_pre_indexing.log added
25e2ef2a2963da_rank.bin added
25e2ef182c76ef_ref_indexing.log added
25e2ef39271f0c_refAccumLengths.bin added
25e2ef53cb9147_reflengths.bin added
25e2ef7428e4e8_refseq.bin added
25e2ef39ef82ee_seq.bin added
25e2ef669d891d_versionInfo.json added
25e2ef415ba39d_salmon_index added
25e2ef2d24eaa_chrLength.txt added
25e2ef73063003_chrName.txt added
25e2ef28afbed9_chrNameLength.txt added
25e2ef5677f5a2_chrStart.txt added
25e2ef4e4b6271_exonGeTrInfo.tab added
25e2ef6902a54a_exonInfo.tab added
25e2ef775f48b3_geneInfo.tab added
25e2ef7edfb2ba_Genome added
25e2ef68f49ace_genomeParameters.txt added
25e2ef12fa740f_Log.out added
25e2ef26539a83_SA added
25e2ef5c9440c0_SAindex added
25e2ef2164b72a_sjdbInfo.txt added
25e2ef7ac3b52e_sjdbList.fromGTF.out.tab added
25e2ef664c6d43_sjdbList.out.tab added
25e2efb480124_transcriptInfo.tab added
25e2ef2e79cd75_GRCh38.GENCODE.v42_100 added
25e2ef7cedb142_knownGene_hg38.sql added
25e2ef18bca7c7_knownGene_hg38.txt added
25e2ef612151f4_refGene_hg38.sql added
25e2ef2828be87_refGene_hg38.txt added
25e2efdc492c1_knownGene_mm39.sql added
25e2ef530bcff6_knownGene_mm39.txt added
25e2ef52522261_refGene_mm39.sql added
25e2ef25f109b0_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/Rtmp0a6GAi/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 
 29.661   1.663  34.629