##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReUseData_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.8.0’
* 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 9.243  0.456   9.744
getCloudData  3.585  0.171   7.650
* 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-3.21-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.8.0’
** 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) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 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...
8c084ab6076a_GRCh38.primary_assembly.genome.fa.1.bt2 added
8c087d6ff515_GRCh38.primary_assembly.genome.fa.2.bt2 added
8c081989cdaf_GRCh38.primary_assembly.genome.fa.3.bt2 added
8c0813a0aa6b_GRCh38.primary_assembly.genome.fa.4.bt2 added
8c083ea4eef2_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
8c08722fc2b7_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
8c082c229f0d_outfile.txt added
8c0822b6ba8e_GRCh37_to_GRCh38.chain added
8c086451df59_GRCh37_to_NCBI34.chain added
8c085feeedc7_GRCh37_to_NCBI35.chain added
8c08208df681_GRCh37_to_NCBI36.chain added
8c08356b6662_GRCh38_to_GRCh37.chain added
8c083d7ef363_GRCh38_to_NCBI34.chain added
8c08792f99_GRCh38_to_NCBI35.chain added
8c0811a71fd6_GRCh38_to_NCBI36.chain added
8c0835336811_NCBI34_to_GRCh37.chain added
8c0866af9e6b_NCBI34_to_GRCh38.chain added
8c0826224575_NCBI35_to_GRCh37.chain added
8c0832f721fc_NCBI35_to_GRCh38.chain added
8c0819e992df_NCBI36_to_GRCh37.chain added
8c08607d219b_NCBI36_to_GRCh38.chain added
8c084b3e7353_GRCm38_to_NCBIM36.chain added
8c087b292648_GRCm38_to_NCBIM37.chain added
8c084aa483d_NCBIM36_to_GRCm38.chain added
8c0817814b6_NCBIM37_to_GRCm38.chain added
8c087d7039bf_1000G_omni2.5.b37.vcf.gz added
8c0815007566_1000G_omni2.5.b37.vcf.gz.tbi added
8c087cea7ad3_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
8c082de095af_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
8c08213034cc_1000G_omni2.5.hg38.vcf.gz added
8c08701c9579_1000G_omni2.5.hg38.vcf.gz.tbi added
8c0878969d19_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
8c081ea029e1_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
8c089a66329_af-only-gnomad.raw.sites.vcf added
8c08c374784_af-only-gnomad.raw.sites.vcf.idx added
8c085d4518d3_Mutect2-exome-panel.vcf.idx added
8c087bd625e0_Mutect2-WGS-panel-b37.vcf added
8c083859e691_Mutect2-WGS-panel-b37.vcf.idx added
8c087ffbd362_small_exac_common_3.vcf added
8c0860280539_small_exac_common_3.vcf.idx added
8c081848d459_1000g_pon.hg38.vcf.gz added
8c082089c9e3_1000g_pon.hg38.vcf.gz.tbi added
8c0815936b9c_af-only-gnomad.hg38.vcf.gz added
8c0855c7c7bc_af-only-gnomad.hg38.vcf.gz.tbi added
8c082102f97c_small_exac_common_3.hg38.vcf.gz added
8c08273a8b72_small_exac_common_3.hg38.vcf.gz.tbi added
8c08afb2fcd_gencode.v41.annotation.gtf added
8c087b297e7_gencode.v42.annotation.gtf added
8c084d5cd0e7_gencode.vM30.annotation.gtf added
8c083df251c9_gencode.vM31.annotation.gtf added
8c08219c2ac6_gencode.v41.transcripts.fa added
8c082dd9f282_gencode.v41.transcripts.fa.fai added
8c08930c51d_gencode.v42.transcripts.fa added
8c081cc5510f_gencode.v42.transcripts.fa.fai added
8c0832843abf_gencode.vM30.pc_transcripts.fa added
8c08aa8d9d3_gencode.vM30.pc_transcripts.fa.fai added
8c081a358ace_gencode.vM31.pc_transcripts.fa added
8c084784b026_gencode.vM31.pc_transcripts.fa.fai added
8c0879354a6_GRCh38.primary_assembly.genome.fa.1.ht2 added
8c084816207d_GRCh38.primary_assembly.genome.fa.2.ht2 added
8c0868b4e4f2_GRCh38.primary_assembly.genome.fa.3.ht2 added
8c0877afea20_GRCh38.primary_assembly.genome.fa.4.ht2 added
8c0840acbd96_GRCh38.primary_assembly.genome.fa.5.ht2 added
8c087550ed3_GRCh38.primary_assembly.genome.fa.6.ht2 added
8c081564d49_GRCh38.primary_assembly.genome.fa.7.ht2 added
8c084ce4051a_GRCh38.primary_assembly.genome.fa.8.ht2 added
8c08649a27a7_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
8c087d2c7329_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
8c0853debac_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
8c086495fb09_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
8c085d547862_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
8c081d86c005_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
8c0851fc4ec_GRCh38_full_analysis_set_plus_decoy_hla.fa added
8c0872e7e3fe_GRCh38.primary_assembly.genome.fa.fai added
8c08734e87c1_GRCh38.primary_assembly.genome.fa.amb added
8c082622be68_GRCh38.primary_assembly.genome.fa.ann added
8c081a226f70_GRCh38.primary_assembly.genome.fa.bwt added
8c087e49b78e_GRCh38.primary_assembly.genome.fa.pac added
8c082dd55650_GRCh38.primary_assembly.genome.fa.sa added
8c08677f4058_GRCh38.primary_assembly.genome.fa added
8c083c3c0957_hs37d5.fa.fai added
8c084f718116_hs37d5.fa.amb added
8c08155932da_hs37d5.fa.ann added
8c08456cce74_hs37d5.fa.bwt added
8c086c36d225_hs37d5.fa.pac added
8c0847dd6d9a_hs37d5.fa.sa added
8c085015a847_hs37d5.fa added
8c0866c5cf4_complete_ref_lens.bin added
8c08f621dc0_ctable.bin added
8c0857a8fcee_ctg_offsets.bin added
8c084e827d71_duplicate_clusters.tsv added
8c08781702b2_info.json added
8c084f58e70e_mphf.bin added
8c08f2f3b08_pos.bin added
8c087f6c1185_pre_indexing.log added
8c0850af3457_rank.bin added
8c085c134022_ref_indexing.log added
8c086406392c_refAccumLengths.bin added
8c084ddba780_reflengths.bin added
8c0861512bce_refseq.bin added
8c08489c3435_seq.bin added
8c082b301fe2_versionInfo.json added
8c087ed7ebd3_salmon_index added
8c084dbbf921_chrLength.txt added
8c081e1803e1_chrName.txt added
8c0872267394_chrNameLength.txt added
8c0873deb78a_chrStart.txt added
8c08383a7351_exonGeTrInfo.tab added
8c0870702b22_exonInfo.tab added
8c0821b40dda_geneInfo.tab added
8c081fb9b3a9_Genome added
8c082cac347a_genomeParameters.txt added
8c0871258ef0_Log.out added
8c083512e684_SA added
8c08721902ee_SAindex added
8c085d5c6116_sjdbInfo.txt added
8c087cf0541e_sjdbList.fromGTF.out.tab added
8c08422eab36_sjdbList.out.tab added
8c0863c8be0a_transcriptInfo.tab added
8c08c5271de_GRCh38.GENCODE.v42_100 added
8c0819d7a824_knownGene_hg38.sql added
8c08324b3b7b_knownGene_hg38.txt added
8c084697490_refGene_hg38.sql added
8c0869308f32_refGene_hg38.txt added
8c08417a7683_knownGene_mm39.sql added
8c083d58615_knownGene_mm39.txt added
8c0839dfc389_refGene_mm39.sql added
8c081d8db6a6_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/RtmpT5x5YQ/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 
 30.088   2.685  36.175