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###
### 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.10.0’
* 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 8.219  0.323   8.586
getCloudData  3.060  0.076   6.118
* 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-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ReUseData
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.10.0’
** 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 version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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...
e556d699d0aa_GRCh38.primary_assembly.genome.fa.1.bt2 added
e556d558e37b8_GRCh38.primary_assembly.genome.fa.2.bt2 added
e556dd137ea2_GRCh38.primary_assembly.genome.fa.3.bt2 added
e556d6c1158ad_GRCh38.primary_assembly.genome.fa.4.bt2 added
e556d7b843ce_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
e556d5523949c_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
e556d789fee91_outfile.txt added
e556d3c97529b_GRCh37_to_GRCh38.chain added
e556d16650373_GRCh37_to_NCBI34.chain added
e556d351da0c0_GRCh37_to_NCBI35.chain added
e556d7eef48aa_GRCh37_to_NCBI36.chain added
e556d1000f8fc_GRCh38_to_GRCh37.chain added
e556d27d4810c_GRCh38_to_NCBI34.chain added
e556d5edb2d2e_GRCh38_to_NCBI35.chain added
e556d4798d59d_GRCh38_to_NCBI36.chain added
e556d495f724c_NCBI34_to_GRCh37.chain added
e556d380b1e91_NCBI34_to_GRCh38.chain added
e556d6e1a423a_NCBI35_to_GRCh37.chain added
e556d7a13a66e_NCBI35_to_GRCh38.chain added
e556d3416bc5e_NCBI36_to_GRCh37.chain added
e556d1b26b7ce_NCBI36_to_GRCh38.chain added
e556d78a8f348_GRCm38_to_NCBIM36.chain added
e556d29101565_GRCm38_to_NCBIM37.chain added
e556d544ed7c0_NCBIM36_to_GRCm38.chain added
e556d7f7996bd_NCBIM37_to_GRCm38.chain added
e556d44f3df13_1000G_omni2.5.b37.vcf.gz added
e556d72910d5e_1000G_omni2.5.b37.vcf.gz.tbi added
e556d21e97b8b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
e556d15102c1c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
e556d45d77f_1000G_omni2.5.hg38.vcf.gz added
e556d5bb539a8_1000G_omni2.5.hg38.vcf.gz.tbi added
e556d1ba9fcc6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
e556d55d40f37_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
e556d68c8b84b_af-only-gnomad.raw.sites.vcf added
e556d7bb5574_af-only-gnomad.raw.sites.vcf.idx added
e556d5d8c5305_Mutect2-exome-panel.vcf.idx added
e556d3dec4ce7_Mutect2-WGS-panel-b37.vcf added
e556d5b4405_Mutect2-WGS-panel-b37.vcf.idx added
e556d1a23a5a1_small_exac_common_3.vcf added
e556d5451505a_small_exac_common_3.vcf.idx added
e556d3578e4c5_1000g_pon.hg38.vcf.gz added
e556d1912ee4b_1000g_pon.hg38.vcf.gz.tbi added
e556d64524956_af-only-gnomad.hg38.vcf.gz added
e556d5d4d65d2_af-only-gnomad.hg38.vcf.gz.tbi added
e556d77ee1b79_small_exac_common_3.hg38.vcf.gz added
e556d2beb1ef4_small_exac_common_3.hg38.vcf.gz.tbi added
e556d26acd81e_gencode.v41.annotation.gtf added
e556d2ff93a0a_gencode.v42.annotation.gtf added
e556d1a05612e_gencode.vM30.annotation.gtf added
e556d20c07e8c_gencode.vM31.annotation.gtf added
e556d640ff668_gencode.v41.transcripts.fa added
e556d352c18fc_gencode.v41.transcripts.fa.fai added
e556d196971d4_gencode.v42.transcripts.fa added
e556dd200bce_gencode.v42.transcripts.fa.fai added
e556d97af0bd_gencode.vM30.pc_transcripts.fa added
e556d18e30891_gencode.vM30.pc_transcripts.fa.fai added
e556d5213eae1_gencode.vM31.pc_transcripts.fa added
e556d7c0bfe1b_gencode.vM31.pc_transcripts.fa.fai added
e556d3acc841d_GRCh38.primary_assembly.genome.fa.1.ht2 added
e556d672416fe_GRCh38.primary_assembly.genome.fa.2.ht2 added
e556d7c51d59a_GRCh38.primary_assembly.genome.fa.3.ht2 added
e556d1681bdc5_GRCh38.primary_assembly.genome.fa.4.ht2 added
e556d2ce13c4_GRCh38.primary_assembly.genome.fa.5.ht2 added
e556d5225e4d1_GRCh38.primary_assembly.genome.fa.6.ht2 added
e556d7f4a7610_GRCh38.primary_assembly.genome.fa.7.ht2 added
e556da896938_GRCh38.primary_assembly.genome.fa.8.ht2 added
e556d2fb237d6_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
e556d3d36c2f7_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
e556dae4ad3e_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
e556d49d5dd77_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
e556d11881352_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
e556d405d9203_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
e556d62e8cbc2_GRCh38_full_analysis_set_plus_decoy_hla.fa added
e556d75da5ca8_GRCh38.primary_assembly.genome.fa.fai added
e556d1daaf7d5_GRCh38.primary_assembly.genome.fa.amb added
e556d5ad6e73b_GRCh38.primary_assembly.genome.fa.ann added
e556d21c57b9c_GRCh38.primary_assembly.genome.fa.bwt added
e556d4457cff3_GRCh38.primary_assembly.genome.fa.pac added
e556dad02145_GRCh38.primary_assembly.genome.fa.sa added
e556d3bcadcca_GRCh38.primary_assembly.genome.fa added
e556d65184e7f_hs37d5.fa.fai added
e556d6ee017ae_hs37d5.fa.amb added
e556d70f6f5c7_hs37d5.fa.ann added
e556d7e81c053_hs37d5.fa.bwt added
e556d7c00237c_hs37d5.fa.pac added
e556d7a71e684_hs37d5.fa.sa added
e556d1764c8e5_hs37d5.fa added
e556d4e140e5d_complete_ref_lens.bin added
e556d767de49f_ctable.bin added
e556d52314d02_ctg_offsets.bin added
e556d3538255b_duplicate_clusters.tsv added
e556d72cfba39_info.json added
e556d68b30ac7_mphf.bin added
e556d38063920_pos.bin added
e556d44f59f0a_pre_indexing.log added
e556d67fd80d8_rank.bin added
e556d428fa258_ref_indexing.log added
e556d74a7d6e0_refAccumLengths.bin added
e556d253443cf_reflengths.bin added
e556d4d744f96_refseq.bin added
e556d3e7db458_seq.bin added
e556d36bc5721_versionInfo.json added
e556ddd1e19a_salmon_index added
e556d2166801a_chrLength.txt added
e556d2c96b3ca_chrName.txt added
e556d2b7cd96f_chrNameLength.txt added
e556d7c3d6756_chrStart.txt added
e556d4e5c2f66_exonGeTrInfo.tab added
e556d6fd4a963_exonInfo.tab added
e556d70d889b_geneInfo.tab added
e556da270c31_Genome added
e556d54ecf7e2_genomeParameters.txt added
e556d75eda049_Log.out added
e556d7b1e01f8_SA added
e556d536eb836_SAindex added
e556d71edc3c5_sjdbInfo.txt added
e556d758fe87c_sjdbList.fromGTF.out.tab added
e556d6ad3811b_sjdbList.out.tab added
e556d4001d223_transcriptInfo.tab added
e556d6c0dcd1b_GRCh38.GENCODE.v42_100 added
e556d3d04ce1d_knownGene_hg38.sql added
e556d7539f77e_knownGene_hg38.txt added
e556d5edd8754_refGene_hg38.sql added
e556d25b7d8e4_refGene_hg38.txt added
e556d2d40309e_knownGene_mm39.sql added
e556d23d3265e_knownGene_mm39.txt added
e556ddb559bc_refGene_mm39.sql added
e556d6fcfd2f7_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/RtmpqbSYbH/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 
 24.389   1.905  29.631