Qian Liu
| Snapshot Date: 2026-05-20 13:40 -0400 (Wed, 20 May 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_23 |
| git_last_commit: bb3489b |
| git_last_commit_date: 2026-04-28 08:59:39 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-21 11:32 -0400 (Thu, 21 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4995 |
| 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 1815/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.12.0 (landing page) Qian Liu
| nebbiolo1 | 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: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2026-05-21 03:59:06 -0400 (Thu, 21 May 2026) |
| EndedAt: 2026-05-21 04:02:00 -0400 (Thu, 21 May 2026) |
| EllapsedTime: 174.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-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: 2026-05-21 07:59:06 UTC
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.12.0’
* 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 6.446 0.466 6.915
* 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.
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 ‘1.12.0’ ** 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...
2fc251644a95ae_GRCh38.primary_assembly.genome.fa.1.bt2 added
2fc251725b29cb_GRCh38.primary_assembly.genome.fa.2.bt2 added
2fc2516ec4183c_GRCh38.primary_assembly.genome.fa.3.bt2 added
2fc25173a5c80c_GRCh38.primary_assembly.genome.fa.4.bt2 added
2fc251703868e6_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2fc2511db42691_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2fc25171425832_outfile.txt added
2fc2514aa76503_GRCh37_to_GRCh38.chain added
2fc2516dc2d855_GRCh37_to_NCBI34.chain added
2fc251510b233_GRCh37_to_NCBI35.chain added
2fc251e1d927e_GRCh37_to_NCBI36.chain added
2fc2512f3b565e_GRCh38_to_GRCh37.chain added
2fc2511567478d_GRCh38_to_NCBI34.chain added
2fc2511684cb56_GRCh38_to_NCBI35.chain added
2fc2516808c419_GRCh38_to_NCBI36.chain added
2fc2512cd16176_NCBI34_to_GRCh37.chain added
2fc25116b04e06_NCBI34_to_GRCh38.chain added
2fc251697c31fa_NCBI35_to_GRCh37.chain added
2fc2514e7f96ee_NCBI35_to_GRCh38.chain added
2fc25166dd0746_NCBI36_to_GRCh37.chain added
2fc2514dc0d79e_NCBI36_to_GRCh38.chain added
2fc25115de659_GRCm38_to_NCBIM36.chain added
2fc25141b4956c_GRCm38_to_NCBIM37.chain added
2fc251e225c63_NCBIM36_to_GRCm38.chain added
2fc2511b5f341f_NCBIM37_to_GRCm38.chain added
2fc251b779a4_1000G_omni2.5.b37.vcf.gz added
2fc25114587ec6_1000G_omni2.5.b37.vcf.gz.tbi added
2fc2511f1ef59f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2fc2514b363251_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2fc2511ba38c33_1000G_omni2.5.hg38.vcf.gz added
2fc251598ab17d_1000G_omni2.5.hg38.vcf.gz.tbi added
2fc2512f80c7ff_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2fc251dfeb5fe_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2fc251484ec9b9_af-only-gnomad.raw.sites.vcf added
2fc2512326900c_af-only-gnomad.raw.sites.vcf.idx added
2fc2517e371ee5_Mutect2-exome-panel.vcf.idx added
2fc2516602f04a_Mutect2-WGS-panel-b37.vcf added
2fc2511468e83e_Mutect2-WGS-panel-b37.vcf.idx added
2fc25148de83e8_small_exac_common_3.vcf added
2fc25153c5c8a0_small_exac_common_3.vcf.idx added
2fc25119799a72_1000g_pon.hg38.vcf.gz added
2fc25156fc1666_1000g_pon.hg38.vcf.gz.tbi added
2fc2513011efe_af-only-gnomad.hg38.vcf.gz added
2fc2512ee0e1ff_af-only-gnomad.hg38.vcf.gz.tbi added
2fc2516d80e1bc_small_exac_common_3.hg38.vcf.gz added
2fc2516b09e317_small_exac_common_3.hg38.vcf.gz.tbi added
2fc2515bb24375_gencode.v41.annotation.gtf added
2fc2514312fc2_gencode.v42.annotation.gtf added
2fc25154861511_gencode.vM30.annotation.gtf added
2fc2512a31da64_gencode.vM31.annotation.gtf added
2fc2516b0e3708_gencode.v41.transcripts.fa added
2fc2512246ecaf_gencode.v41.transcripts.fa.fai added
2fc2512b8fc0bd_gencode.v42.transcripts.fa added
2fc2512cc2cc75_gencode.v42.transcripts.fa.fai added
2fc25130694912_gencode.vM30.pc_transcripts.fa added
2fc25146eef4dc_gencode.vM30.pc_transcripts.fa.fai added
2fc2512d7a4619_gencode.vM31.pc_transcripts.fa added
2fc25144c1c7d8_gencode.vM31.pc_transcripts.fa.fai added
2fc251660dea7b_GRCh38.primary_assembly.genome.fa.1.ht2 added
2fc25178b0786b_GRCh38.primary_assembly.genome.fa.2.ht2 added
2fc2516065540b_GRCh38.primary_assembly.genome.fa.3.ht2 added
2fc2513f989bf9_GRCh38.primary_assembly.genome.fa.4.ht2 added
2fc2512831406a_GRCh38.primary_assembly.genome.fa.5.ht2 added
2fc2516e640a0a_GRCh38.primary_assembly.genome.fa.6.ht2 added
2fc2517e765b2_GRCh38.primary_assembly.genome.fa.7.ht2 added
2fc2514b57d076_GRCh38.primary_assembly.genome.fa.8.ht2 added
2fc2516c9b28ef_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2fc2516dea55fd_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2fc2515fc0b8b5_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2fc2513579acd7_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2fc25141b01e9d_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2fc251793a5327_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2fc251c75c33d_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2fc25144b13d9b_GRCh38.primary_assembly.genome.fa.fai added
2fc251281b3526_GRCh38.primary_assembly.genome.fa.amb added
2fc25179f6a4fa_GRCh38.primary_assembly.genome.fa.ann added
2fc2512fbb20b2_GRCh38.primary_assembly.genome.fa.bwt added
2fc2513cd789c_GRCh38.primary_assembly.genome.fa.pac added
2fc2517e27d4bc_GRCh38.primary_assembly.genome.fa.sa added
2fc25144135c4_GRCh38.primary_assembly.genome.fa added
2fc2512dff5300_hs37d5.fa.fai added
2fc25169360bc5_hs37d5.fa.amb added
2fc25126882273_hs37d5.fa.ann added
2fc251598f13bd_hs37d5.fa.bwt added
2fc25115f8d83a_hs37d5.fa.pac added
2fc25156f16b86_hs37d5.fa.sa added
2fc251207e0899_hs37d5.fa added
2fc25143731e53_complete_ref_lens.bin added
2fc2511bb3335e_ctable.bin added
2fc25168bf314_ctg_offsets.bin added
2fc2513c2396be_duplicate_clusters.tsv added
2fc2517c18876a_info.json added
2fc25146248f0d_mphf.bin added
2fc2516454d729_pos.bin added
2fc2516a7c9174_pre_indexing.log added
2fc2514e0bf4c0_rank.bin added
2fc2512faca79f_ref_indexing.log added
2fc2515717ba63_refAccumLengths.bin added
2fc2513bf64abd_reflengths.bin added
2fc251f6d6054_refseq.bin added
2fc251c91673a_seq.bin added
2fc2517da6695a_versionInfo.json added
2fc2518a7b37b_salmon_index added
2fc25119072a77_chrLength.txt added
2fc2514257a6f5_chrName.txt added
2fc25130c2e8a2_chrNameLength.txt added
2fc25112fdcf71_chrStart.txt added
2fc2517212c7a7_exonGeTrInfo.tab added
2fc2513490613e_exonInfo.tab added
2fc2511125a42e_geneInfo.tab added
2fc2517653fd6b_Genome added
2fc251628fb43e_genomeParameters.txt added
2fc2517a5baff3_Log.out added
2fc2511cdc1fdf_SA added
2fc2513c1ec7fb_SAindex added
2fc2511054882d_sjdbInfo.txt added
2fc25173cd8b65_sjdbList.fromGTF.out.tab added
2fc2515c9cd094_sjdbList.out.tab added
2fc25153c7a680_transcriptInfo.tab added
2fc251f80bec3_GRCh38.GENCODE.v42_100 added
2fc2516328c3a8_knownGene_hg38.sql added
2fc251feb3d3f_knownGene_hg38.txt added
2fc251b99462d_refGene_hg38.sql added
2fc251294d52b6_refGene_hg38.txt added
2fc25174401468_knownGene_mm39.sql added
2fc2517615d7a1_knownGene_mm39.txt added
2fc25177594776_refGene_mm39.sql added
2fc25123ecbc07_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/RtmpgDpplZ/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
19.223 1.761 21.256
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.446 | 0.466 | 6.915 | |
| dataSearch | 1.214 | 0.032 | 1.246 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 3.008 | 0.225 | 3.752 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.000 | 0.001 | 0.001 | |
| recipeHub-class | 0.128 | 0.015 | 0.143 | |
| recipeLoad | 1.397 | 0.072 | 1.470 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.582 | 0.013 | 0.597 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |