Back to Multiple platform build/check report for BioC 3.23:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2026-03-16 11:34 -0400 (Mon, 16 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" 4837
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" 4053
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1777/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReUseData 1.11.0  (landing page)
Qian Liu
Snapshot Date: 2026-03-15 13:40 -0400 (Sun, 15 Mar 2026)
git_url: https://git.bioconductor.org/packages/ReUseData
git_branch: devel
git_last_commit: 4a5d06b
git_last_commit_date: 2025-10-29 11:20:44 -0400 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
See other builds for ReUseData in R Universe.

CHECK results for ReUseData on nebbiolo1

To the developers/maintainers of the ReUseData package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReUseData.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ReUseData
Version: 1.11.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz
StartedAt: 2026-03-16 03:55:05 -0400 (Mon, 16 Mar 2026)
EndedAt: 2026-03-16 03:57:48 -0400 (Mon, 16 Mar 2026)
EllapsedTime: 162.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ReUseData.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-16 07:55:05 UTC
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.11.0’
* 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 5.847  0.382   6.235
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

Installation output

ReUseData.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.11.0’
** 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)

Tests output

ReUseData.Rcheck/tests/testthat.Rout


R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-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...
1ef27518ef571e_GRCh38.primary_assembly.genome.fa.1.bt2 added
1ef27522b569a0_GRCh38.primary_assembly.genome.fa.2.bt2 added
1ef2753f0c580c_GRCh38.primary_assembly.genome.fa.3.bt2 added
1ef27544629c47_GRCh38.primary_assembly.genome.fa.4.bt2 added
1ef2755e7c7245_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1ef2757d120145_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1ef27568fd21d6_outfile.txt added
1ef2754f1e315a_GRCh37_to_GRCh38.chain added
1ef2755bb5c507_GRCh37_to_NCBI34.chain added
1ef27554a305db_GRCh37_to_NCBI35.chain added
1ef27577c9c8e0_GRCh37_to_NCBI36.chain added
1ef275569e845a_GRCh38_to_GRCh37.chain added
1ef275794a9148_GRCh38_to_NCBI34.chain added
1ef2758f1b36f_GRCh38_to_NCBI35.chain added
1ef2755ea622f6_GRCh38_to_NCBI36.chain added
1ef2755630a3a8_NCBI34_to_GRCh37.chain added
1ef2751d0c8d90_NCBI34_to_GRCh38.chain added
1ef275230c0e16_NCBI35_to_GRCh37.chain added
1ef275515d56b7_NCBI35_to_GRCh38.chain added
1ef27534c10677_NCBI36_to_GRCh37.chain added
1ef2752e88867_NCBI36_to_GRCh38.chain added
1ef275371e5ab5_GRCm38_to_NCBIM36.chain added
1ef27565d6739f_GRCm38_to_NCBIM37.chain added
1ef275faef8aa_NCBIM36_to_GRCm38.chain added
1ef2751080d759_NCBIM37_to_GRCm38.chain added
1ef2753d182843_1000G_omni2.5.b37.vcf.gz added
1ef275c83a08f_1000G_omni2.5.b37.vcf.gz.tbi added
1ef2756886b76e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1ef2756e35a322_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1ef275408dac78_1000G_omni2.5.hg38.vcf.gz added
1ef275547465f4_1000G_omni2.5.hg38.vcf.gz.tbi added
1ef275724fa41_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1ef27563431618_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1ef2751380be00_af-only-gnomad.raw.sites.vcf added
1ef2754b879688_af-only-gnomad.raw.sites.vcf.idx added
1ef27541bf885e_Mutect2-exome-panel.vcf.idx added
1ef2751092bf45_Mutect2-WGS-panel-b37.vcf added
1ef2753484b85f_Mutect2-WGS-panel-b37.vcf.idx added
1ef27510ddb9b8_small_exac_common_3.vcf added
1ef2756c48844c_small_exac_common_3.vcf.idx added
1ef275927be3a_1000g_pon.hg38.vcf.gz added
1ef2758a78298_1000g_pon.hg38.vcf.gz.tbi added
1ef27542e708a7_af-only-gnomad.hg38.vcf.gz added
1ef2752724f82_af-only-gnomad.hg38.vcf.gz.tbi added
1ef27511993607_small_exac_common_3.hg38.vcf.gz added
1ef275218d2b9d_small_exac_common_3.hg38.vcf.gz.tbi added
1ef27558a2f32b_gencode.v41.annotation.gtf added
1ef2752ea5c397_gencode.v42.annotation.gtf added
1ef275449939b3_gencode.vM30.annotation.gtf added
1ef2752a0049e2_gencode.vM31.annotation.gtf added
1ef2756366ca0f_gencode.v41.transcripts.fa added
1ef2754781c21a_gencode.v41.transcripts.fa.fai added
1ef275611ea498_gencode.v42.transcripts.fa added
1ef275493d3dae_gencode.v42.transcripts.fa.fai added
1ef2755730bac5_gencode.vM30.pc_transcripts.fa added
1ef275719f7bf1_gencode.vM30.pc_transcripts.fa.fai added
1ef27565565f1_gencode.vM31.pc_transcripts.fa added
1ef27563b45b54_gencode.vM31.pc_transcripts.fa.fai added
1ef2755a263360_GRCh38.primary_assembly.genome.fa.1.ht2 added
1ef275748b0913_GRCh38.primary_assembly.genome.fa.2.ht2 added
1ef275244207cc_GRCh38.primary_assembly.genome.fa.3.ht2 added
1ef2752e9a9954_GRCh38.primary_assembly.genome.fa.4.ht2 added
1ef2757bb00354_GRCh38.primary_assembly.genome.fa.5.ht2 added
1ef2757851de5_GRCh38.primary_assembly.genome.fa.6.ht2 added
1ef275421b5754_GRCh38.primary_assembly.genome.fa.7.ht2 added
1ef275473799dd_GRCh38.primary_assembly.genome.fa.8.ht2 added
1ef2754944a643_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1ef27552ae1699_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1ef2757bbc523c_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1ef2755a225ffb_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1ef2753ef69ae5_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1ef2754e41076_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1ef27562c9e294_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1ef2751dda38c_GRCh38.primary_assembly.genome.fa.fai added
1ef2757565ff8_GRCh38.primary_assembly.genome.fa.amb added
1ef2757463189b_GRCh38.primary_assembly.genome.fa.ann added
1ef275236acf2a_GRCh38.primary_assembly.genome.fa.bwt added
1ef2755ff95323_GRCh38.primary_assembly.genome.fa.pac added
1ef2752308dc33_GRCh38.primary_assembly.genome.fa.sa added
1ef275680408dd_GRCh38.primary_assembly.genome.fa added
1ef2759f99d06_hs37d5.fa.fai added
1ef27566fa642_hs37d5.fa.amb added
1ef2752f85caf8_hs37d5.fa.ann added
1ef2756b18419e_hs37d5.fa.bwt added
1ef2754face3f0_hs37d5.fa.pac added
1ef2756b685bd_hs37d5.fa.sa added
1ef2755cb7bd8f_hs37d5.fa added
1ef275560249e1_complete_ref_lens.bin added
1ef2756a6ae111_ctable.bin added
1ef27536ddf0ef_ctg_offsets.bin added
1ef2754a8d52f4_duplicate_clusters.tsv added
1ef275eace8de_info.json added
1ef27565788a43_mphf.bin added
1ef275463d5649_pos.bin added
1ef275163206c3_pre_indexing.log added
1ef2752793e197_rank.bin added
1ef275d74f026_ref_indexing.log added
1ef2755f76ad06_refAccumLengths.bin added
1ef2757a41f830_reflengths.bin added
1ef2759314262_refseq.bin added
1ef27539990d01_seq.bin added
1ef27539389316_versionInfo.json added
1ef275e1552d8_salmon_index added
1ef2751c62ef95_chrLength.txt added
1ef2753b1636a2_chrName.txt added
1ef275156bb2d0_chrNameLength.txt added
1ef27510c60831_chrStart.txt added
1ef2755e8105cc_exonGeTrInfo.tab added
1ef275756505f4_exonInfo.tab added
1ef27533cee464_geneInfo.tab added
1ef27546850eaa_Genome added
1ef2757f5ea2fa_genomeParameters.txt added
1ef2753a3e8aa6_Log.out added
1ef275760ad9a2_SA added
1ef2756a76e498_SAindex added
1ef2759eb6e96_sjdbInfo.txt added
1ef2757cc15f5f_sjdbList.fromGTF.out.tab added
1ef275472ea227_sjdbList.out.tab added
1ef2755fedb877_transcriptInfo.tab added
1ef275672c4070_GRCh38.GENCODE.v42_100 added
1ef2757e0c9317_knownGene_hg38.sql added
1ef2752a7b0b6b_knownGene_hg38.txt added
1ef27575d9294e_refGene_hg38.sql added
1ef27563851d5a_refGene_hg38.txt added
1ef27570b861b4_knownGene_mm39.sql added
1ef275c0b3011_knownGene_mm39.txt added
1ef275b18fef2_refGene_mm39.sql added
1ef2757e2d51da_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: 
/tmp/Rtmp7N4OqN/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 1 | SKIP 0 | PASS 44 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
> 
> 
> 
> proc.time()
   user  system elapsed 
 18.186   1.449  20.305

Example timings

ReUseData.Rcheck/ReUseData-Ex.timings

nameusersystemelapsed
dataHub-class5.8470.3826.235
dataSearch1.1210.0301.150
dataUpdate0.0010.0000.000
getCloudData2.6080.0893.561
getData0.0010.0000.000
meta_data0.0000.0010.001
recipeHub-class0.1250.0070.133
recipeLoad1.2230.0521.276
recipeMake000
recipeSearch0.5100.0110.521
recipeUpdate000