##############################################################################
##############################################################################
###
### 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 8.384  0.267   8.690
getCloudData  3.215  0.263   6.472
* 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
###
##############################################################################
##############################################################################


* 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...
25d75e42103278_GRCh38.primary_assembly.genome.fa.1.bt2 added
25d75e1e0026f_GRCh38.primary_assembly.genome.fa.2.bt2 added
25d75e65d18764_GRCh38.primary_assembly.genome.fa.3.bt2 added
25d75e401b6cf1_GRCh38.primary_assembly.genome.fa.4.bt2 added
25d75e34f2dbee_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
25d75e6a35b990_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
25d75e2ceedc86_outfile.txt added
25d75e798441d4_GRCh37_to_GRCh38.chain added
25d75e6f5af7b3_GRCh37_to_NCBI34.chain added
25d75e10b7dc2_GRCh37_to_NCBI35.chain added
25d75e4b0e8c7c_GRCh37_to_NCBI36.chain added
25d75e5cc33456_GRCh38_to_GRCh37.chain added
25d75e55475c1e_GRCh38_to_NCBI34.chain added
25d75eb4822b0_GRCh38_to_NCBI35.chain added
25d75e4b40293f_GRCh38_to_NCBI36.chain added
25d75e49cd6805_NCBI34_to_GRCh37.chain added
25d75e1c954387_NCBI34_to_GRCh38.chain added
25d75e10f8e11f_NCBI35_to_GRCh37.chain added
25d75e19e9c35d_NCBI35_to_GRCh38.chain added
25d75e2003d322_NCBI36_to_GRCh37.chain added
25d75e72e4f46b_NCBI36_to_GRCh38.chain added
25d75e16c3d4f3_GRCm38_to_NCBIM36.chain added
25d75e25932395_GRCm38_to_NCBIM37.chain added
25d75e2f69ef83_NCBIM36_to_GRCm38.chain added
25d75e42ffd750_NCBIM37_to_GRCm38.chain added
25d75ee58c33e_1000G_omni2.5.b37.vcf.gz added
25d75e6c85d8a2_1000G_omni2.5.b37.vcf.gz.tbi added
25d75e491d13e4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
25d75e486f975c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
25d75e4e9bb289_1000G_omni2.5.hg38.vcf.gz added
25d75e147f98f9_1000G_omni2.5.hg38.vcf.gz.tbi added
25d75ea7fc9d4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
25d75e507bb4f8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
25d75e7a51205d_af-only-gnomad.raw.sites.vcf added
25d75e4a9b36c5_af-only-gnomad.raw.sites.vcf.idx added
25d75e56e90e7_Mutect2-exome-panel.vcf.idx added
25d75e6486d9ee_Mutect2-WGS-panel-b37.vcf added
25d75e778a134b_Mutect2-WGS-panel-b37.vcf.idx added
25d75e7ef2d2bb_small_exac_common_3.vcf added
25d75e53e1d1a1_small_exac_common_3.vcf.idx added
25d75e7895910d_1000g_pon.hg38.vcf.gz added
25d75e4a015f37_1000g_pon.hg38.vcf.gz.tbi added
25d75e30a505f7_af-only-gnomad.hg38.vcf.gz added
25d75e4ddced2b_af-only-gnomad.hg38.vcf.gz.tbi added
25d75e554981e7_small_exac_common_3.hg38.vcf.gz added
25d75e7be52f36_small_exac_common_3.hg38.vcf.gz.tbi added
25d75e17aa5531_gencode.v41.annotation.gtf added
25d75e71dec56e_gencode.v42.annotation.gtf added
25d75ecde1055_gencode.vM30.annotation.gtf added
25d75e3194188e_gencode.vM31.annotation.gtf added
25d75e11e29891_gencode.v41.transcripts.fa added
25d75e7fc304c1_gencode.v41.transcripts.fa.fai added
25d75e4857ed81_gencode.v42.transcripts.fa added
25d75e3775bc26_gencode.v42.transcripts.fa.fai added
25d75e2f2cf444_gencode.vM30.pc_transcripts.fa added
25d75eb57c4d1_gencode.vM30.pc_transcripts.fa.fai added
25d75e45ce7f64_gencode.vM31.pc_transcripts.fa added
25d75e1bb2cce6_gencode.vM31.pc_transcripts.fa.fai added
25d75e5474d8b6_GRCh38.primary_assembly.genome.fa.1.ht2 added
25d75ee3e16c0_GRCh38.primary_assembly.genome.fa.2.ht2 added
25d75e6a4e7f6f_GRCh38.primary_assembly.genome.fa.3.ht2 added
25d75e68f471af_GRCh38.primary_assembly.genome.fa.4.ht2 added
25d75e18bde094_GRCh38.primary_assembly.genome.fa.5.ht2 added
25d75e3aca3468_GRCh38.primary_assembly.genome.fa.6.ht2 added
25d75e6345920d_GRCh38.primary_assembly.genome.fa.7.ht2 added
25d75e63591759_GRCh38.primary_assembly.genome.fa.8.ht2 added
25d75e4038c54f_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
25d75e47cc6bfb_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
25d75e5ae32aa5_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
25d75e3f2b980a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
25d75e1bae3d9c_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
25d75e5378bbb2_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
25d75e92cf741_GRCh38_full_analysis_set_plus_decoy_hla.fa added
25d75e4c534394_GRCh38.primary_assembly.genome.fa.fai added
25d75e2155a8de_GRCh38.primary_assembly.genome.fa.amb added
25d75e5e767929_GRCh38.primary_assembly.genome.fa.ann added
25d75e483872ca_GRCh38.primary_assembly.genome.fa.bwt added
25d75e38fffe0f_GRCh38.primary_assembly.genome.fa.pac added
25d75e50553e97_GRCh38.primary_assembly.genome.fa.sa added
25d75e55168320_GRCh38.primary_assembly.genome.fa added
25d75e6a94169d_hs37d5.fa.fai added
25d75e6237d728_hs37d5.fa.amb added
25d75e54d987e1_hs37d5.fa.ann added
25d75e32ec041e_hs37d5.fa.bwt added
25d75e19ad934e_hs37d5.fa.pac added
25d75e4067c25_hs37d5.fa.sa added
25d75e3e43c8f0_hs37d5.fa added
25d75e5f7c12b2_complete_ref_lens.bin added
25d75e1fb9490b_ctable.bin added
25d75e12b8a1a6_ctg_offsets.bin added
25d75e6dba2972_duplicate_clusters.tsv added
25d75ea07c87a_info.json added
25d75e7bad1355_mphf.bin added
25d75e6780a06_pos.bin added
25d75e44d1fce2_pre_indexing.log added
25d75e5ef2a562_rank.bin added
25d75e69d12160_ref_indexing.log added
25d75e50ac231_refAccumLengths.bin added
25d75e26bf115d_reflengths.bin added
25d75e44b44c05_refseq.bin added
25d75e44365a3b_seq.bin added
25d75e426d4efa_versionInfo.json added
25d75e182d07b7_salmon_index added
25d75e4d63517d_chrLength.txt added
25d75eec0928e_chrName.txt added
25d75e3982b095_chrNameLength.txt added
25d75e2bd9caa6_chrStart.txt added
25d75e56f90558_exonGeTrInfo.tab added
25d75e7282aea4_exonInfo.tab added
25d75e7c2f093d_geneInfo.tab added
25d75e2c0f8878_Genome added
25d75e5d16c541_genomeParameters.txt added
25d75e5e66e066_Log.out added
25d75ee91059_SA added
25d75e1002c960_SAindex added
25d75e781473b4_sjdbInfo.txt added
25d75e4ef8c7e_sjdbList.fromGTF.out.tab added
25d75e4e469250_sjdbList.out.tab added
25d75e57908667_transcriptInfo.tab added
25d75e24a8d589_GRCh38.GENCODE.v42_100 added
25d75e60ff33f6_knownGene_hg38.sql added
25d75e454aafd9_knownGene_hg38.txt added
25d75e2eb09e04_refGene_hg38.sql added
25d75e5cac474b_refGene_hg38.txt added
25d75e4bc2b9e0_knownGene_mm39.sql added
25d75e73829ae6_knownGene_mm39.txt added
25d75e3b9eecae_refGene_mm39.sql added
25d75e3593db40_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/Rtmpdl5th7/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 
 24.722   1.594  28.186