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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_1.8.0.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 9.108  0.606    9.76
getCloudData  3.418  0.227    5.42
* 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.

##############################################################################
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###
### 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...
1ffefa4e41cc41_GRCh38.primary_assembly.genome.fa.1.bt2 added
1ffefa66f88f66_GRCh38.primary_assembly.genome.fa.2.bt2 added
1ffefa35e4e625_GRCh38.primary_assembly.genome.fa.3.bt2 added
1ffefa242ae2d_GRCh38.primary_assembly.genome.fa.4.bt2 added
1ffefa4e421992_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1ffefa25a8693e_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1ffefa3216a05_outfile.txt added
1ffefa127232d3_GRCh37_to_GRCh38.chain added
1ffefa43f8f560_GRCh37_to_NCBI34.chain added
1ffefaa210297_GRCh37_to_NCBI35.chain added
1ffefa632bce20_GRCh37_to_NCBI36.chain added
1ffefa13430663_GRCh38_to_GRCh37.chain added
1ffefa6890091a_GRCh38_to_NCBI34.chain added
1ffefa9bf67d1_GRCh38_to_NCBI35.chain added
1ffefa609e433_GRCh38_to_NCBI36.chain added
1ffefa49893e62_NCBI34_to_GRCh37.chain added
1ffefa30fb0908_NCBI34_to_GRCh38.chain added
1ffefa4d1c6734_NCBI35_to_GRCh37.chain added
1ffefa8ee33a2_NCBI35_to_GRCh38.chain added
1ffefa148f409_NCBI36_to_GRCh37.chain added
1ffefa7df2643f_NCBI36_to_GRCh38.chain added
1ffefa41f1a138_GRCm38_to_NCBIM36.chain added
1ffefa3f57029d_GRCm38_to_NCBIM37.chain added
1ffefa656d647_NCBIM36_to_GRCm38.chain added
1ffefa185e783c_NCBIM37_to_GRCm38.chain added
1ffefa79e45f26_1000G_omni2.5.b37.vcf.gz added
1ffefa37940cdb_1000G_omni2.5.b37.vcf.gz.tbi added
1ffefa5d598f81_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1ffefa378a98e0_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1ffefa318d0a66_1000G_omni2.5.hg38.vcf.gz added
1ffefa7bd4e3e6_1000G_omni2.5.hg38.vcf.gz.tbi added
1ffefa5cc6522_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1ffefa188599cc_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1ffefa31b9ca0b_af-only-gnomad.raw.sites.vcf added
1ffefa80f134f_af-only-gnomad.raw.sites.vcf.idx added
1ffefa66c7b35e_Mutect2-exome-panel.vcf.idx added
1ffefa5762334a_Mutect2-WGS-panel-b37.vcf added
1ffefab307d54_Mutect2-WGS-panel-b37.vcf.idx added
1ffefa7939e631_small_exac_common_3.vcf added
1ffefa1b5b28aa_small_exac_common_3.vcf.idx added
1ffefa15517feb_1000g_pon.hg38.vcf.gz added
1ffefa5c65b451_1000g_pon.hg38.vcf.gz.tbi added
1ffefa2e9e2f0d_af-only-gnomad.hg38.vcf.gz added
1ffefa7de18905_af-only-gnomad.hg38.vcf.gz.tbi added
1ffefa66251c23_small_exac_common_3.hg38.vcf.gz added
1ffefa34a81340_small_exac_common_3.hg38.vcf.gz.tbi added
1ffefa476ac767_gencode.v41.annotation.gtf added
1ffefa1720252b_gencode.v42.annotation.gtf added
1ffefa1c47a75_gencode.vM30.annotation.gtf added
1ffefa5058fb0a_gencode.vM31.annotation.gtf added
1ffefa18691935_gencode.v41.transcripts.fa added
1ffefa7fb6deb4_gencode.v41.transcripts.fa.fai added
1ffefa124a9c42_gencode.v42.transcripts.fa added
1ffefa57c01bd2_gencode.v42.transcripts.fa.fai added
1ffefa60db4fc_gencode.vM30.pc_transcripts.fa added
1ffefa2aa9147e_gencode.vM30.pc_transcripts.fa.fai added
1ffefa51a47af8_gencode.vM31.pc_transcripts.fa added
1ffefa3da1c1d7_gencode.vM31.pc_transcripts.fa.fai added
1ffefa802a400_GRCh38.primary_assembly.genome.fa.1.ht2 added
1ffefa92f13d9_GRCh38.primary_assembly.genome.fa.2.ht2 added
1ffefa6f2ecc3d_GRCh38.primary_assembly.genome.fa.3.ht2 added
1ffefa3d787e6_GRCh38.primary_assembly.genome.fa.4.ht2 added
1ffefaefb78fb_GRCh38.primary_assembly.genome.fa.5.ht2 added
1ffefa7b46609_GRCh38.primary_assembly.genome.fa.6.ht2 added
1ffefa359151f1_GRCh38.primary_assembly.genome.fa.7.ht2 added
1ffefa170a8c4a_GRCh38.primary_assembly.genome.fa.8.ht2 added
1ffefa6e7c1968_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1ffefacf3853b_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1ffefa223b099e_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1ffefa67b5ff99_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1ffefa284eade5_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1ffefa378c898a_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1ffefa441bb3eb_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1ffefa56ecdcf3_GRCh38.primary_assembly.genome.fa.fai added
1ffefa356e128f_GRCh38.primary_assembly.genome.fa.amb added
1ffefa2a40d00e_GRCh38.primary_assembly.genome.fa.ann added
1ffefab94f033_GRCh38.primary_assembly.genome.fa.bwt added
1ffefa7cd8d9f7_GRCh38.primary_assembly.genome.fa.pac added
1ffefa4160f539_GRCh38.primary_assembly.genome.fa.sa added
1ffefad596aa8_GRCh38.primary_assembly.genome.fa added
1ffefa4d31d501_hs37d5.fa.fai added
1ffefa59ca0e6e_hs37d5.fa.amb added
1ffefad10495d_hs37d5.fa.ann added
1ffefa5f7c7143_hs37d5.fa.bwt added
1ffefa318a2a41_hs37d5.fa.pac added
1ffefa131dfe59_hs37d5.fa.sa added
1ffefaa2585c1_hs37d5.fa added
1ffefa32ea539_complete_ref_lens.bin added
1ffefa50bfc030_ctable.bin added
1ffefa122829c1_ctg_offsets.bin added
1ffefac5db912_duplicate_clusters.tsv added
1ffefa3fee8c6e_info.json added
1ffefa15ffb1a7_mphf.bin added
1ffefa1b59320d_pos.bin added
1ffefa47a2f277_pre_indexing.log added
1ffefa4b910399_rank.bin added
1ffefa3263be57_ref_indexing.log added
1ffefa361f0bdf_refAccumLengths.bin added
1ffefa588488d4_reflengths.bin added
1ffefa549ec7f6_refseq.bin added
1ffefa1dd50b79_seq.bin added
1ffefad336ba_versionInfo.json added
1ffefac2b5180_salmon_index added
1ffefa61f0bf64_chrLength.txt added
1ffefa57c013ad_chrName.txt added
1ffefa4199640f_chrNameLength.txt added
1ffefac318f72_chrStart.txt added
1ffefa635503e0_exonGeTrInfo.tab added
1ffefa3e723e06_exonInfo.tab added
1ffefa4d9284ab_geneInfo.tab added
1ffefa70ae6e89_Genome added
1ffefaba41307_genomeParameters.txt added
1ffefa275c931a_Log.out added
1ffefa7dbeb7e6_SA added
1ffefa6b20844a_SAindex added
1ffefa58e6bd5b_sjdbInfo.txt added
1ffefa10dcb63f_sjdbList.fromGTF.out.tab added
1ffefa75460a0c_sjdbList.out.tab added
1ffefa5c156294_transcriptInfo.tab added
1ffefa619c766f_GRCh38.GENCODE.v42_100 added
1ffefa76e33cd_knownGene_hg38.sql added
1ffefa68731ba7_knownGene_hg38.txt added
1ffefa218b02dd_refGene_hg38.sql added
1ffefa1d6de575_refGene_hg38.txt added
1ffefa3cc4db4_knownGene_mm39.sql added
1ffefa692df555_knownGene_mm39.txt added
1ffefa68fee90e_refGene_mm39.sql added
1ffefa36300c0c_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/RtmpgkpJNM/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 
 29.955   2.331  33.837