Qian Liu
| Snapshot Date: 2026-04-29 13:45 -0400 (Wed, 29 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: caf380d |
| git_last_commit_date: 2026-04-28 08:59:39 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-04-30 11:33 -0400 (Thu, 30 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4843 |
| 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 1775/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.13.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for ReUseData in R Universe. | ||||||||||||||
|
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. |
| Package: ReUseData |
| Version: 1.13.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings ReUseData_1.13.0.tar.gz |
| StartedAt: 2026-04-30 03:44:17 -0400 (Thu, 30 Apr 2026) |
| EndedAt: 2026-04-30 03:47:05 -0400 (Thu, 30 Apr 2026) |
| EllapsedTime: 168.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings ReUseData_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-30 07:44:17 UTC
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.13.0’
* 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 5.553 0.241 5.793
* 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-3.24-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.13.0’ ** 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)
ReUseData.Rcheck/tests/testthat.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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.)
}[1;30mINFO[0m Final process status is success
Updating data record...
outfile.txt added
Updating data record...
24c6625c4d0084_GRCh38.primary_assembly.genome.fa.1.bt2 added
24c662397071ad_GRCh38.primary_assembly.genome.fa.2.bt2 added
24c66218fae037_GRCh38.primary_assembly.genome.fa.3.bt2 added
24c662516a23c2_GRCh38.primary_assembly.genome.fa.4.bt2 added
24c662541fc4c9_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
24c6625f0ee5bf_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
24c6627d7890e2_outfile.txt added
24c6627f46edb0_GRCh37_to_GRCh38.chain added
24c662306f1dab_GRCh37_to_NCBI34.chain added
24c6621cf0ac10_GRCh37_to_NCBI35.chain added
24c66245843202_GRCh37_to_NCBI36.chain added
24c6622e2ef09b_GRCh38_to_GRCh37.chain added
24c662b96ac43_GRCh38_to_NCBI34.chain added
24c6622d53740b_GRCh38_to_NCBI35.chain added
24c6622b0f0f11_GRCh38_to_NCBI36.chain added
24c662570798d6_NCBI34_to_GRCh37.chain added
24c6623aab1c46_NCBI34_to_GRCh38.chain added
24c66250d6eaac_NCBI35_to_GRCh37.chain added
24c6627ff715c2_NCBI35_to_GRCh38.chain added
24c662c8affbb_NCBI36_to_GRCh37.chain added
24c66277f9142e_NCBI36_to_GRCh38.chain added
24c6629737c2a_GRCm38_to_NCBIM36.chain added
24c66244a46ff6_GRCm38_to_NCBIM37.chain added
24c66262280ec5_NCBIM36_to_GRCm38.chain added
24c66273738e6b_NCBIM37_to_GRCm38.chain added
24c662573377b5_1000G_omni2.5.b37.vcf.gz added
24c662ea723f4_1000G_omni2.5.b37.vcf.gz.tbi added
24c66224919a5c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
24c66210338806_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
24c6622a0ab47_1000G_omni2.5.hg38.vcf.gz added
24c66257be2575_1000G_omni2.5.hg38.vcf.gz.tbi added
24c6626c80888b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
24c6623c111cf5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
24c66270b905ad_af-only-gnomad.raw.sites.vcf added
24c6623deaac4d_af-only-gnomad.raw.sites.vcf.idx added
24c6621030e1be_Mutect2-exome-panel.vcf.idx added
24c6624fc7eb6c_Mutect2-WGS-panel-b37.vcf added
24c6623b633d2f_Mutect2-WGS-panel-b37.vcf.idx added
24c662f77cf6e_small_exac_common_3.vcf added
24c662370917_small_exac_common_3.vcf.idx added
24c6625853e93f_1000g_pon.hg38.vcf.gz added
24c66254fc0170_1000g_pon.hg38.vcf.gz.tbi added
24c6622e65f9b3_af-only-gnomad.hg38.vcf.gz added
24c66263ea9582_af-only-gnomad.hg38.vcf.gz.tbi added
24c66224f757b_small_exac_common_3.hg38.vcf.gz added
24c662597508c4_small_exac_common_3.hg38.vcf.gz.tbi added
24c6623af22e58_gencode.v41.annotation.gtf added
24c6623cfa91c1_gencode.v42.annotation.gtf added
24c6622a4bf370_gencode.vM30.annotation.gtf added
24c6623ae9441a_gencode.vM31.annotation.gtf added
24c6624985917c_gencode.v41.transcripts.fa added
24c6622245079e_gencode.v41.transcripts.fa.fai added
24c662445cc044_gencode.v42.transcripts.fa added
24c662e2a0172_gencode.v42.transcripts.fa.fai added
24c66246d1663_gencode.vM30.pc_transcripts.fa added
24c66237d04eb0_gencode.vM30.pc_transcripts.fa.fai added
24c662655d7927_gencode.vM31.pc_transcripts.fa added
24c66213143a57_gencode.vM31.pc_transcripts.fa.fai added
24c6625c61e90c_GRCh38.primary_assembly.genome.fa.1.ht2 added
24c6627591012e_GRCh38.primary_assembly.genome.fa.2.ht2 added
24c66215b4e59f_GRCh38.primary_assembly.genome.fa.3.ht2 added
24c66234200e81_GRCh38.primary_assembly.genome.fa.4.ht2 added
24c662621189b9_GRCh38.primary_assembly.genome.fa.5.ht2 added
24c66251c60294_GRCh38.primary_assembly.genome.fa.6.ht2 added
24c66224d9142e_GRCh38.primary_assembly.genome.fa.7.ht2 added
24c6621ffc3606_GRCh38.primary_assembly.genome.fa.8.ht2 added
24c66261f6e452_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
24c66274a0ff9b_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
24c6625b5f7335_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
24c662716eb3c0_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
24c66274d808b2_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
24c66233b35c74_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
24c662466ab531_GRCh38_full_analysis_set_plus_decoy_hla.fa added
24c662233e0265_GRCh38.primary_assembly.genome.fa.fai added
24c662179df1f7_GRCh38.primary_assembly.genome.fa.amb added
24c66248ba2aac_GRCh38.primary_assembly.genome.fa.ann added
24c6627cb30b29_GRCh38.primary_assembly.genome.fa.bwt added
24c6625290204f_GRCh38.primary_assembly.genome.fa.pac added
24c6625b4bc6e_GRCh38.primary_assembly.genome.fa.sa added
24c66226fefe99_GRCh38.primary_assembly.genome.fa added
24c662d79646a_hs37d5.fa.fai added
24c6624f3a4dea_hs37d5.fa.amb added
24c66249440637_hs37d5.fa.ann added
24c66251d624ae_hs37d5.fa.bwt added
24c6625d644f5d_hs37d5.fa.pac added
24c6624db11c9a_hs37d5.fa.sa added
24c6629a6735e_hs37d5.fa added
24c66242c1c884_complete_ref_lens.bin added
24c66260c556f2_ctable.bin added
24c66266085c6a_ctg_offsets.bin added
24c6623852c9b2_duplicate_clusters.tsv added
24c662767a3c91_info.json added
24c6621a286aec_mphf.bin added
24c6621a64536b_pos.bin added
24c66248403f25_pre_indexing.log added
24c6623f017f1a_rank.bin added
24c6623a608971_ref_indexing.log added
24c6622a372377_refAccumLengths.bin added
24c66233a27eb5_reflengths.bin added
24c66215bffca6_refseq.bin added
24c6621ba5d737_seq.bin added
24c662287a8768_versionInfo.json added
24c6624973591b_salmon_index added
24c66262108c68_chrLength.txt added
24c6624bb889cd_chrName.txt added
24c66261114b12_chrNameLength.txt added
24c6622acab715_chrStart.txt added
24c662486b94f7_exonGeTrInfo.tab added
24c66233a16b61_exonInfo.tab added
24c662307f7383_geneInfo.tab added
24c6626f6a9390_Genome added
24c662411acfcb_genomeParameters.txt added
24c6627fb9c16d_Log.out added
24c66238ae99c8_SA added
24c66212f0f47a_SAindex added
24c6625d1e10ca_sjdbInfo.txt added
24c66265fb662_sjdbList.fromGTF.out.tab added
24c6621c9767d8_sjdbList.out.tab added
24c6621fdfd94f_transcriptInfo.tab added
24c66267250d54_GRCh38.GENCODE.v42_100 added
24c66229fc443_knownGene_hg38.sql added
24c6625832a301_knownGene_hg38.txt added
24c6625d9f49e5_refGene_hg38.sql added
24c6621cc82f2f_refGene_hg38.txt added
24c6627296f66d_knownGene_mm39.sql added
24c66225df890a_knownGene_mm39.txt added
24c6625bc9ae49_refGene_mm39.sql added
24c6622cf77fde_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/RtmpIGjOPi/test_gcpData/outfile.txt
}[1;30mINFO[0m 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
18.658 1.152 20.239
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.553 | 0.241 | 5.793 | |
| dataSearch | 1.112 | 0.015 | 1.127 | |
| dataUpdate | 0.001 | 0.000 | 0.000 | |
| getCloudData | 2.998 | 0.106 | 3.871 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.142 | 0.001 | 0.144 | |
| recipeLoad | 2.066 | 0.032 | 2.100 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.533 | 0.017 | 0.549 | |
| recipeUpdate | 0 | 0 | 0 | |