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This page was generated on 2026-01-03 11:34 -0500 (Sat, 03 Jan 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" 4809
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4593
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 1754/2332HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReUseData 1.11.0  (landing page)
Qian Liu
Snapshot Date: 2026-01-01 13:40 -0500 (Thu, 01 Jan 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 -0500 (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

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: 2026-01-02 02:58:03 -0500 (Fri, 02 Jan 2026)
EndedAt: 2026-01-02 03:00:50 -0500 (Fri, 02 Jan 2026)
EllapsedTime: 167.4 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) (2025-12-22 r89219)
* 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 24.04.3 LTS
* using session charset: UTF-8
* 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 5.838  0.379   6.218
getCloudData  2.556  0.129   5.225
* 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) (2025-12-22 r89219) -- "Unsuffered Consequences"
Copyright (C) 2025 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...
3b464d19304477_GRCh38.primary_assembly.genome.fa.1.bt2 added
3b464d3a2b03a2_GRCh38.primary_assembly.genome.fa.2.bt2 added
3b464d5a3113c9_GRCh38.primary_assembly.genome.fa.3.bt2 added
3b464d374996f7_GRCh38.primary_assembly.genome.fa.4.bt2 added
3b464d2711fa38_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3b464d3610e11a_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3b464d151c9ea9_outfile.txt added
3b464d1c85a458_GRCh37_to_GRCh38.chain added
3b464d71258c99_GRCh37_to_NCBI34.chain added
3b464d20cee113_GRCh37_to_NCBI35.chain added
3b464d6eca75c1_GRCh37_to_NCBI36.chain added
3b464d5483ed50_GRCh38_to_GRCh37.chain added
3b464d8a63ea6_GRCh38_to_NCBI34.chain added
3b464d24f124ce_GRCh38_to_NCBI35.chain added
3b464d1f9d9c07_GRCh38_to_NCBI36.chain added
3b464d24eda81d_NCBI34_to_GRCh37.chain added
3b464d1ea26d58_NCBI34_to_GRCh38.chain added
3b464d349abefc_NCBI35_to_GRCh37.chain added
3b464d4afe0e2f_NCBI35_to_GRCh38.chain added
3b464d70ff503c_NCBI36_to_GRCh37.chain added
3b464d1f0eb43c_NCBI36_to_GRCh38.chain added
3b464d5ee1aa73_GRCm38_to_NCBIM36.chain added
3b464d61e3ecd7_GRCm38_to_NCBIM37.chain added
3b464d3897fa2c_NCBIM36_to_GRCm38.chain added
3b464d24eb4fd7_NCBIM37_to_GRCm38.chain added
3b464d3784dd79_1000G_omni2.5.b37.vcf.gz added
3b464d720f5630_1000G_omni2.5.b37.vcf.gz.tbi added
3b464d4a264b33_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3b464df4cafb7_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3b464d5498872c_1000G_omni2.5.hg38.vcf.gz added
3b464d2ed18e69_1000G_omni2.5.hg38.vcf.gz.tbi added
3b464d287cf42f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3b464dec38acf_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3b464d902a232_af-only-gnomad.raw.sites.vcf added
3b464d5fc68b26_af-only-gnomad.raw.sites.vcf.idx added
3b464d35d58507_Mutect2-exome-panel.vcf.idx added
3b464d3f13834c_Mutect2-WGS-panel-b37.vcf added
3b464d74e329cf_Mutect2-WGS-panel-b37.vcf.idx added
3b464d525b295f_small_exac_common_3.vcf added
3b464d30390fe5_small_exac_common_3.vcf.idx added
3b464d15b20ae3_1000g_pon.hg38.vcf.gz added
3b464d41259f20_1000g_pon.hg38.vcf.gz.tbi added
3b464d4bcfd35_af-only-gnomad.hg38.vcf.gz added
3b464d1e584989_af-only-gnomad.hg38.vcf.gz.tbi added
3b464d6616c3ef_small_exac_common_3.hg38.vcf.gz added
3b464d245a993d_small_exac_common_3.hg38.vcf.gz.tbi added
3b464d4345f1a7_gencode.v41.annotation.gtf added
3b464d4b93147_gencode.v42.annotation.gtf added
3b464d58f55839_gencode.vM30.annotation.gtf added
3b464de43ffd6_gencode.vM31.annotation.gtf added
3b464d75b88183_gencode.v41.transcripts.fa added
3b464d78040c75_gencode.v41.transcripts.fa.fai added
3b464d6d25aa49_gencode.v42.transcripts.fa added
3b464d579c6e5b_gencode.v42.transcripts.fa.fai added
3b464d309c06a1_gencode.vM30.pc_transcripts.fa added
3b464d1210fa20_gencode.vM30.pc_transcripts.fa.fai added
3b464df214bd4_gencode.vM31.pc_transcripts.fa added
3b464d22ab5cd1_gencode.vM31.pc_transcripts.fa.fai added
3b464d5c374554_GRCh38.primary_assembly.genome.fa.1.ht2 added
3b464d1e6dfb8c_GRCh38.primary_assembly.genome.fa.2.ht2 added
3b464d7743e3fe_GRCh38.primary_assembly.genome.fa.3.ht2 added
3b464db08d3bd_GRCh38.primary_assembly.genome.fa.4.ht2 added
3b464d46eaefbb_GRCh38.primary_assembly.genome.fa.5.ht2 added
3b464d6076ecd_GRCh38.primary_assembly.genome.fa.6.ht2 added
3b464d140b75ef_GRCh38.primary_assembly.genome.fa.7.ht2 added
3b464d26b17ae1_GRCh38.primary_assembly.genome.fa.8.ht2 added
3b464d3bdcf3d4_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3b464d531ef93c_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3b464d1b94a4b1_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3b464de381d34_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3b464d3580921_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3b464d3146af94_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3b464d4f5dbc54_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3b464d8150657_GRCh38.primary_assembly.genome.fa.fai added
3b464d4f9ef91d_GRCh38.primary_assembly.genome.fa.amb added
3b464d35748043_GRCh38.primary_assembly.genome.fa.ann added
3b464d2c6f9f94_GRCh38.primary_assembly.genome.fa.bwt added
3b464d12e4eac4_GRCh38.primary_assembly.genome.fa.pac added
3b464d3a2db18a_GRCh38.primary_assembly.genome.fa.sa added
3b464d564f7cd_GRCh38.primary_assembly.genome.fa added
3b464d2128ea9a_hs37d5.fa.fai added
3b464d2fe6330e_hs37d5.fa.amb added
3b464d7d690442_hs37d5.fa.ann added
3b464de4e94e3_hs37d5.fa.bwt added
3b464d782a169_hs37d5.fa.pac added
3b464d2e050ae3_hs37d5.fa.sa added
3b464d205f8f04_hs37d5.fa added
3b464d16a3ed3d_complete_ref_lens.bin added
3b464d50b067b5_ctable.bin added
3b464d7c96d458_ctg_offsets.bin added
3b464d3511e8c9_duplicate_clusters.tsv added
3b464d47f44bb3_info.json added
3b464d79fa815_mphf.bin added
3b464d7bfcd884_pos.bin added
3b464d4dfbba80_pre_indexing.log added
3b464d1bab1e04_rank.bin added
3b464d22ae5366_ref_indexing.log added
3b464d9d8ae54_refAccumLengths.bin added
3b464d6eca1740_reflengths.bin added
3b464d3e42f817_refseq.bin added
3b464d1810cb88_seq.bin added
3b464d72222062_versionInfo.json added
3b464d6f89a7ab_salmon_index added
3b464d676e87dd_chrLength.txt added
3b464d7a3726b9_chrName.txt added
3b464d3f28a0c8_chrNameLength.txt added
3b464d1ce30820_chrStart.txt added
3b464d26a6c64d_exonGeTrInfo.tab added
3b464d520d8b8d_exonInfo.tab added
3b464d5710b9ab_geneInfo.tab added
3b464d2c0bbe1a_Genome added
3b464d73367627_genomeParameters.txt added
3b464d6f6ecb9_Log.out added
3b464d2974c25c_SA added
3b464d1850b0b_SAindex added
3b464de798e22_sjdbInfo.txt added
3b464d5779cd3f_sjdbList.fromGTF.out.tab added
3b464d21e49a0f_sjdbList.out.tab added
3b464d251d7b5f_transcriptInfo.tab added
3b464d282a34f4_GRCh38.GENCODE.v42_100 added
3b464d1e7b6e67_knownGene_hg38.sql added
3b464d5a2f6429_knownGene_hg38.txt added
3b464d701e80a7_refGene_hg38.sql added
3b464d261b167c_refGene_hg38.txt added
3b464d562c3cad_knownGene_mm39.sql added
3b464d3e1a3b27_knownGene_mm39.txt added
3b464d41c63480_refGene_mm39.sql added
3b464d78da9013_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/RtmpFywHzp/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 
 18.083   1.111  19.893

Example timings

ReUseData.Rcheck/ReUseData-Ex.timings

nameusersystemelapsed
dataHub-class5.8380.3796.218
dataSearch1.1110.0371.149
dataUpdate0.0010.0000.001
getCloudData2.5560.1295.225
getData0.0000.0000.001
meta_data0.0010.0000.001
recipeHub-class0.1280.0110.139
recipeLoad1.2960.0321.330
recipeMake0.0000.0010.000
recipeSearch0.5440.0100.554
recipeUpdate0.0000.0000.001