##############################################################################
##############################################################################
###
### 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 8.596  0.402   9.045
getCloudData  3.497  0.410   6.536
* 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...
25134d34d6e1e4_GRCh38.primary_assembly.genome.fa.1.bt2 added
25134d2c3d88f1_GRCh38.primary_assembly.genome.fa.2.bt2 added
25134d4746c857_GRCh38.primary_assembly.genome.fa.3.bt2 added
25134d7602c4e1_GRCh38.primary_assembly.genome.fa.4.bt2 added
25134d42892d9f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
25134d685adfcb_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
25134d24e23231_outfile.txt added
25134d33cdd765_GRCh37_to_GRCh38.chain added
25134d3b6ba66c_GRCh37_to_NCBI34.chain added
25134daf6c425_GRCh37_to_NCBI35.chain added
25134d63fe9691_GRCh37_to_NCBI36.chain added
25134d1d16ccf9_GRCh38_to_GRCh37.chain added
25134d7bc7a206_GRCh38_to_NCBI34.chain added
25134d57fc7a63_GRCh38_to_NCBI35.chain added
25134d9614b73_GRCh38_to_NCBI36.chain added
25134d4cb65b8d_NCBI34_to_GRCh37.chain added
25134dd1b64ec_NCBI34_to_GRCh38.chain added
25134d418ed44e_NCBI35_to_GRCh37.chain added
25134d93b8a2_NCBI35_to_GRCh38.chain added
25134dc718e89_NCBI36_to_GRCh37.chain added
25134d4f820e04_NCBI36_to_GRCh38.chain added
25134d67eab652_GRCm38_to_NCBIM36.chain added
25134d7a61366e_GRCm38_to_NCBIM37.chain added
25134d3dbc1011_NCBIM36_to_GRCm38.chain added
25134d6da99397_NCBIM37_to_GRCm38.chain added
25134d3f8ee869_1000G_omni2.5.b37.vcf.gz added
25134d39d56ea6_1000G_omni2.5.b37.vcf.gz.tbi added
25134d248ecb0a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
25134d285dfdac_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
25134d636849b4_1000G_omni2.5.hg38.vcf.gz added
25134d6b8445fe_1000G_omni2.5.hg38.vcf.gz.tbi added
25134d5d34df90_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
25134dfa5d2a5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
25134d32cb0e55_af-only-gnomad.raw.sites.vcf added
25134d5337a471_af-only-gnomad.raw.sites.vcf.idx added
25134d522f0044_Mutect2-exome-panel.vcf.idx added
25134d1b25ee21_Mutect2-WGS-panel-b37.vcf added
25134d7819d6a3_Mutect2-WGS-panel-b37.vcf.idx added
25134d5fcd7a9_small_exac_common_3.vcf added
25134d5691948d_small_exac_common_3.vcf.idx added
25134d3109ac8_1000g_pon.hg38.vcf.gz added
25134d69fb6e3b_1000g_pon.hg38.vcf.gz.tbi added
25134d73a86186_af-only-gnomad.hg38.vcf.gz added
25134d7ed83cce_af-only-gnomad.hg38.vcf.gz.tbi added
25134d41f7e89e_small_exac_common_3.hg38.vcf.gz added
25134d7d09acfa_small_exac_common_3.hg38.vcf.gz.tbi added
25134d4b8e985c_gencode.v41.annotation.gtf added
25134d4f134d8a_gencode.v42.annotation.gtf added
25134d3e988148_gencode.vM30.annotation.gtf added
25134d4c2250fe_gencode.vM31.annotation.gtf added
25134d5b84dc13_gencode.v41.transcripts.fa added
25134de1a8f4c_gencode.v41.transcripts.fa.fai added
25134d340d0750_gencode.v42.transcripts.fa added
25134d55e61281_gencode.v42.transcripts.fa.fai added
25134d4bd69f5e_gencode.vM30.pc_transcripts.fa added
25134d21b69ae7_gencode.vM30.pc_transcripts.fa.fai added
25134d1574faea_gencode.vM31.pc_transcripts.fa added
25134d5ac0e04_gencode.vM31.pc_transcripts.fa.fai added
25134d464565f1_GRCh38.primary_assembly.genome.fa.1.ht2 added
25134d3dd2f897_GRCh38.primary_assembly.genome.fa.2.ht2 added
25134d691457b8_GRCh38.primary_assembly.genome.fa.3.ht2 added
25134d31c9abf0_GRCh38.primary_assembly.genome.fa.4.ht2 added
25134d1b07d827_GRCh38.primary_assembly.genome.fa.5.ht2 added
25134d78ba2a5d_GRCh38.primary_assembly.genome.fa.6.ht2 added
25134d6494ba45_GRCh38.primary_assembly.genome.fa.7.ht2 added
25134d6e3f7c99_GRCh38.primary_assembly.genome.fa.8.ht2 added
25134d4ae92aa1_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
25134d7fbaa866_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
25134d6659533c_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
25134d50e6024b_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
25134d564c3cf3_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
25134d6969ee04_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
25134d3ae17086_GRCh38_full_analysis_set_plus_decoy_hla.fa added
25134d49f49e7a_GRCh38.primary_assembly.genome.fa.fai added
25134d68422ad2_GRCh38.primary_assembly.genome.fa.amb added
25134d7cd95924_GRCh38.primary_assembly.genome.fa.ann added
25134d46fe4b74_GRCh38.primary_assembly.genome.fa.bwt added
25134d33d0c32e_GRCh38.primary_assembly.genome.fa.pac added
25134d4beca6ae_GRCh38.primary_assembly.genome.fa.sa added
25134d596ccbc_GRCh38.primary_assembly.genome.fa added
25134d7ff3142d_hs37d5.fa.fai added
25134d277182c1_hs37d5.fa.amb added
25134d13b15c09_hs37d5.fa.ann added
25134d34001b7d_hs37d5.fa.bwt added
25134d7d579542_hs37d5.fa.pac added
25134d5f87fb67_hs37d5.fa.sa added
25134d55b6b665_hs37d5.fa added
25134d12cc902c_complete_ref_lens.bin added
25134d6534096b_ctable.bin added
25134d1bfc1c56_ctg_offsets.bin added
25134d509f88c3_duplicate_clusters.tsv added
25134d4e486124_info.json added
25134d4dc5c846_mphf.bin added
25134d6ba760eb_pos.bin added
25134d47028b81_pre_indexing.log added
25134d325a828c_rank.bin added
25134d59e6dd84_ref_indexing.log added
25134d11ebb623_refAccumLengths.bin added
25134d32152af2_reflengths.bin added
25134d404030c0_refseq.bin added
25134d62d1b86e_seq.bin added
25134d86167e6_versionInfo.json added
25134d29aa1ec4_salmon_index added
25134d1db328f4_chrLength.txt added
25134d52560660_chrName.txt added
25134d11ec4996_chrNameLength.txt added
25134d1a8c8218_chrStart.txt added
25134d195451d4_exonGeTrInfo.tab added
25134d45bd0cc5_exonInfo.tab added
25134d667928c6_geneInfo.tab added
25134d1eeb1e90_Genome added
25134d45b020f2_genomeParameters.txt added
25134ddeaab87_Log.out added
25134d329c7a99_SA added
25134d79b03c6f_SAindex added
25134db4240c9_sjdbInfo.txt added
25134d12247600_sjdbList.fromGTF.out.tab added
25134d4f66f2d4_sjdbList.out.tab added
25134d1e0ed0f5_transcriptInfo.tab added
25134d77587f6c_GRCh38.GENCODE.v42_100 added
25134d6b630f2b_knownGene_hg38.sql added
25134d6eae59b9_knownGene_hg38.txt added
25134d45a0e090_refGene_hg38.sql added
25134d3928d771_refGene_hg38.txt added
25134d5a55baa4_knownGene_mm39.sql added
25134dca36c11_knownGene_mm39.txt added
25134d6b8359fd_refGene_mm39.sql added
25134d343c9828_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/RtmpSLyV8O/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 
 30.021   1.696  33.780