##############################################################################
##############################################################################
###
### 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 8.779  0.406   9.227
getCloudData  3.237  0.371   6.645
* 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...
15176c724e51df_GRCh38.primary_assembly.genome.fa.1.bt2 added
15176c20726944_GRCh38.primary_assembly.genome.fa.2.bt2 added
15176c1913629e_GRCh38.primary_assembly.genome.fa.3.bt2 added
15176c5e7c6578_GRCh38.primary_assembly.genome.fa.4.bt2 added
15176c22f8657f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
15176c7cc4066_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
15176c24fa156b_outfile.txt added
15176c4fdf8397_GRCh37_to_GRCh38.chain added
15176c56fdcaa0_GRCh37_to_NCBI34.chain added
15176c68504271_GRCh37_to_NCBI35.chain added
15176c67536ed1_GRCh37_to_NCBI36.chain added
15176c7cd15b17_GRCh38_to_GRCh37.chain added
15176c5f786a8f_GRCh38_to_NCBI34.chain added
15176c742a0245_GRCh38_to_NCBI35.chain added
15176c33a395ac_GRCh38_to_NCBI36.chain added
15176c13469169_NCBI34_to_GRCh37.chain added
15176c3afad5ba_NCBI34_to_GRCh38.chain added
15176c3734add8_NCBI35_to_GRCh37.chain added
15176c2df331_NCBI35_to_GRCh38.chain added
15176c713f2b74_NCBI36_to_GRCh37.chain added
15176c595cf9a3_NCBI36_to_GRCh38.chain added
15176c4c3d8991_GRCm38_to_NCBIM36.chain added
15176c26b5922d_GRCm38_to_NCBIM37.chain added
15176c7a9f2ac8_NCBIM36_to_GRCm38.chain added
15176c4789127f_NCBIM37_to_GRCm38.chain added
15176c3bb27662_1000G_omni2.5.b37.vcf.gz added
15176c419c8af0_1000G_omni2.5.b37.vcf.gz.tbi added
15176c5d24dc1d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
15176c52a1dd17_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
15176c34190085_1000G_omni2.5.hg38.vcf.gz added
15176c39b8c8e8_1000G_omni2.5.hg38.vcf.gz.tbi added
15176c44f02ef6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
15176c548b69c9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
15176c52cc2b86_af-only-gnomad.raw.sites.vcf added
15176c236c946f_af-only-gnomad.raw.sites.vcf.idx added
15176c7783cf48_Mutect2-exome-panel.vcf.idx added
15176c5a986bec_Mutect2-WGS-panel-b37.vcf added
15176c4866a9da_Mutect2-WGS-panel-b37.vcf.idx added
15176c476352df_small_exac_common_3.vcf added
15176c3196368d_small_exac_common_3.vcf.idx added
15176c30b6ec4c_1000g_pon.hg38.vcf.gz added
15176c2eb6c1b0_1000g_pon.hg38.vcf.gz.tbi added
15176c2e6791a4_af-only-gnomad.hg38.vcf.gz added
15176c102f56db_af-only-gnomad.hg38.vcf.gz.tbi added
15176c22e0c3f5_small_exac_common_3.hg38.vcf.gz added
15176c620b2750_small_exac_common_3.hg38.vcf.gz.tbi added
15176c2375e844_gencode.v41.annotation.gtf added
15176c5ddb99b0_gencode.v42.annotation.gtf added
15176c193fd528_gencode.vM30.annotation.gtf added
15176c23a3db76_gencode.vM31.annotation.gtf added
15176c4f1ac524_gencode.v41.transcripts.fa added
15176c729ccecb_gencode.v41.transcripts.fa.fai added
15176c6fe16507_gencode.v42.transcripts.fa added
15176c75d05751_gencode.v42.transcripts.fa.fai added
15176c6d3bf993_gencode.vM30.pc_transcripts.fa added
15176c376a7787_gencode.vM30.pc_transcripts.fa.fai added
15176c3182cdb3_gencode.vM31.pc_transcripts.fa added
15176c2ed88483_gencode.vM31.pc_transcripts.fa.fai added
15176c148f53a4_GRCh38.primary_assembly.genome.fa.1.ht2 added
15176c424aacb_GRCh38.primary_assembly.genome.fa.2.ht2 added
15176c62f18508_GRCh38.primary_assembly.genome.fa.3.ht2 added
15176c4e481c8c_GRCh38.primary_assembly.genome.fa.4.ht2 added
15176c4914d9c1_GRCh38.primary_assembly.genome.fa.5.ht2 added
15176c377ceed1_GRCh38.primary_assembly.genome.fa.6.ht2 added
15176c21144812_GRCh38.primary_assembly.genome.fa.7.ht2 added
15176c6c816e30_GRCh38.primary_assembly.genome.fa.8.ht2 added
15176c2f00be19_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
15176c7bacb3ff_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
15176c34e8180b_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
15176c766410f9_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
15176c2d42ea8c_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
15176c659f0457_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
15176c251ad2a9_GRCh38_full_analysis_set_plus_decoy_hla.fa added
15176c5baa7c30_GRCh38.primary_assembly.genome.fa.fai added
15176c75ce5b32_GRCh38.primary_assembly.genome.fa.amb added
15176c47fb969f_GRCh38.primary_assembly.genome.fa.ann added
15176c3db5a381_GRCh38.primary_assembly.genome.fa.bwt added
15176c19444376_GRCh38.primary_assembly.genome.fa.pac added
15176c25d7304f_GRCh38.primary_assembly.genome.fa.sa added
15176c56f578a9_GRCh38.primary_assembly.genome.fa added
15176c3ce81eec_hs37d5.fa.fai added
15176c74f1f573_hs37d5.fa.amb added
15176c49924775_hs37d5.fa.ann added
15176c2cc983f4_hs37d5.fa.bwt added
15176c6ac24cc5_hs37d5.fa.pac added
15176c36ce4108_hs37d5.fa.sa added
15176c6433fb7b_hs37d5.fa added
15176c1c451a78_complete_ref_lens.bin added
15176c65a6c58c_ctable.bin added
15176c78c34f1f_ctg_offsets.bin added
15176c2069c543_duplicate_clusters.tsv added
15176c48984a94_info.json added
15176c470b6bab_mphf.bin added
15176c697e9f05_pos.bin added
15176c153966_pre_indexing.log added
15176c681fb3bd_rank.bin added
15176c56000d35_ref_indexing.log added
15176c2f15f77f_refAccumLengths.bin added
15176c63cc67bc_reflengths.bin added
15176cae82540_refseq.bin added
15176c257a0878_seq.bin added
15176c110f5248_versionInfo.json added
15176c70872997_salmon_index added
15176c4a94db22_chrLength.txt added
15176c6cb9ce79_chrName.txt added
15176c665584c9_chrNameLength.txt added
15176c129071c1_chrStart.txt added
15176c2a6f71fa_exonGeTrInfo.tab added
15176c7f99c840_exonInfo.tab added
15176c3867a210_geneInfo.tab added
15176c164eaa3_Genome added
15176c3c81e72c_genomeParameters.txt added
15176c2d599783_Log.out added
15176c4af73218_SA added
15176c694b6b20_SAindex added
15176c181be448_sjdbInfo.txt added
15176c1c57321_sjdbList.fromGTF.out.tab added
15176c4d7f669b_sjdbList.out.tab added
15176c3460fec1_transcriptInfo.tab added
15176c676c38ad_GRCh38.GENCODE.v42_100 added
15176c4642b5ba_knownGene_hg38.sql added
15176c54cac404_knownGene_hg38.txt added
15176c30048341_refGene_hg38.sql added
15176cd4e2165_refGene_hg38.txt added
15176c3e496309_knownGene_mm39.sql added
15176c3019bca7_knownGene_mm39.txt added
15176c756dd523_refGene_mm39.sql added
15176c1449703f_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/RtmpufQRzE/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 
 24.735   1.040  27.752