Qian Liu
| Snapshot Date: 2026-02-23 13:45 -0500 (Mon, 23 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_22 |
| git_last_commit: 2d4066b |
| git_last_commit_date: 2025-10-29 11:20:44 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-24 11:58 -0500 (Tue, 24 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4891 |
| 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 1773/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.10.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 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: 1.10.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.10.0.tar.gz |
| StartedAt: 2026-02-24 03:04:49 -0500 (Tue, 24 Feb 2026) |
| EndedAt: 2026-02-24 03:07:31 -0500 (Tue, 24 Feb 2026) |
| EllapsedTime: 162.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.10.0’
* 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 5.605 0.249 5.857
* 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-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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)
ReUseData.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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.)
}[1;30mINFO[0m Final process status is success
Updating data record...
outfile.txt added
Updating data record...
3d274f2ba28ca9_GRCh38.primary_assembly.genome.fa.1.bt2 added
3d274f42b67be5_GRCh38.primary_assembly.genome.fa.2.bt2 added
3d274f4f67428e_GRCh38.primary_assembly.genome.fa.3.bt2 added
3d274f66f75da3_GRCh38.primary_assembly.genome.fa.4.bt2 added
3d274f1dda9a77_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3d274f43d46187_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3d274f528b55d8_outfile.txt added
3d274f504edffd_GRCh37_to_GRCh38.chain added
3d274f7ce66c11_GRCh37_to_NCBI34.chain added
3d274f1eeefb9e_GRCh37_to_NCBI35.chain added
3d274f634f37ec_GRCh37_to_NCBI36.chain added
3d274f1a1c4f3f_GRCh38_to_GRCh37.chain added
3d274f306d0894_GRCh38_to_NCBI34.chain added
3d274f76870faf_GRCh38_to_NCBI35.chain added
3d274f6ef75a7f_GRCh38_to_NCBI36.chain added
3d274f5ca10625_NCBI34_to_GRCh37.chain added
3d274f5c37142d_NCBI34_to_GRCh38.chain added
3d274f128f7316_NCBI35_to_GRCh37.chain added
3d274f19ff7010_NCBI35_to_GRCh38.chain added
3d274f17af5670_NCBI36_to_GRCh37.chain added
3d274f398db7ae_NCBI36_to_GRCh38.chain added
3d274f5e98428f_GRCm38_to_NCBIM36.chain added
3d274f50732aa_GRCm38_to_NCBIM37.chain added
3d274f556e14de_NCBIM36_to_GRCm38.chain added
3d274f59ca3bbb_NCBIM37_to_GRCm38.chain added
3d274f684456d1_1000G_omni2.5.b37.vcf.gz added
3d274f6ea7b174_1000G_omni2.5.b37.vcf.gz.tbi added
3d274f3baddc6b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3d274f31fe3690_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3d274f3b720fad_1000G_omni2.5.hg38.vcf.gz added
3d274f8c264b9_1000G_omni2.5.hg38.vcf.gz.tbi added
3d274f5da0c339_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3d274f7e288b93_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3d274f5829a747_af-only-gnomad.raw.sites.vcf added
3d274f449820dd_af-only-gnomad.raw.sites.vcf.idx added
3d274f1c03260a_Mutect2-exome-panel.vcf.idx added
3d274f1bfe08cf_Mutect2-WGS-panel-b37.vcf added
3d274f172376b5_Mutect2-WGS-panel-b37.vcf.idx added
3d274f6c520607_small_exac_common_3.vcf added
3d274f18e474e0_small_exac_common_3.vcf.idx added
3d274f36127253_1000g_pon.hg38.vcf.gz added
3d274f4fa13df3_1000g_pon.hg38.vcf.gz.tbi added
3d274f3300c41f_af-only-gnomad.hg38.vcf.gz added
3d274f667f7ae8_af-only-gnomad.hg38.vcf.gz.tbi added
3d274f46284da3_small_exac_common_3.hg38.vcf.gz added
3d274f21f81e9f_small_exac_common_3.hg38.vcf.gz.tbi added
3d274f4320810d_gencode.v41.annotation.gtf added
3d274f225f61d0_gencode.v42.annotation.gtf added
3d274f348791b5_gencode.vM30.annotation.gtf added
3d274f5d1ff11d_gencode.vM31.annotation.gtf added
3d274f3a0eb841_gencode.v41.transcripts.fa added
3d274f6e154963_gencode.v41.transcripts.fa.fai added
3d274f3bb833ac_gencode.v42.transcripts.fa added
3d274f3f15eaeb_gencode.v42.transcripts.fa.fai added
3d274f43835e42_gencode.vM30.pc_transcripts.fa added
3d274f15826f67_gencode.vM30.pc_transcripts.fa.fai added
3d274f275a41bc_gencode.vM31.pc_transcripts.fa added
3d274f322b0fb6_gencode.vM31.pc_transcripts.fa.fai added
3d274f51304bd2_GRCh38.primary_assembly.genome.fa.1.ht2 added
3d274f5958784d_GRCh38.primary_assembly.genome.fa.2.ht2 added
3d274f6d9d1f63_GRCh38.primary_assembly.genome.fa.3.ht2 added
3d274f59f2b08b_GRCh38.primary_assembly.genome.fa.4.ht2 added
3d274f36f93b86_GRCh38.primary_assembly.genome.fa.5.ht2 added
3d274f6bc5aaf6_GRCh38.primary_assembly.genome.fa.6.ht2 added
3d274f321c57d3_GRCh38.primary_assembly.genome.fa.7.ht2 added
3d274f7b915c63_GRCh38.primary_assembly.genome.fa.8.ht2 added
3d274f7c8d100_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3d274f4e1a60a2_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3d274f12b4d319_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3d274f741ad708_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3d274f66fed582_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3d274f48c7456c_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3d274f43bc14fb_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3d274f19ff99a1_GRCh38.primary_assembly.genome.fa.fai added
3d274f2f46c054_GRCh38.primary_assembly.genome.fa.amb added
3d274f9e4629e_GRCh38.primary_assembly.genome.fa.ann added
3d274f3bf7b840_GRCh38.primary_assembly.genome.fa.bwt added
3d274f72674161_GRCh38.primary_assembly.genome.fa.pac added
3d274f2c43c46f_GRCh38.primary_assembly.genome.fa.sa added
3d274f707f49f6_GRCh38.primary_assembly.genome.fa added
3d274f4f87327e_hs37d5.fa.fai added
3d274f66527cb0_hs37d5.fa.amb added
3d274f5e949359_hs37d5.fa.ann added
3d274fb3f662a_hs37d5.fa.bwt added
3d274f2568679b_hs37d5.fa.pac added
3d274f2217f19b_hs37d5.fa.sa added
3d274f20c1d591_hs37d5.fa added
3d274f4cc2a957_complete_ref_lens.bin added
3d274f54430151_ctable.bin added
3d274f71f22163_ctg_offsets.bin added
3d274f261b21a4_duplicate_clusters.tsv added
3d274f41e020b5_info.json added
3d274f4be4d1ef_mphf.bin added
3d274f5d145d2b_pos.bin added
3d274f2da5cbab_pre_indexing.log added
3d274f7e0129c2_rank.bin added
3d274f58a5b98e_ref_indexing.log added
3d274f356e9cac_refAccumLengths.bin added
3d274f4c1b8a64_reflengths.bin added
3d274f6b5a8ca7_refseq.bin added
3d274f298973b4_seq.bin added
3d274f331a5fe6_versionInfo.json added
3d274f3421d214_salmon_index added
3d274f6d4588af_chrLength.txt added
3d274f4d19f987_chrName.txt added
3d274f63689268_chrNameLength.txt added
3d274f7729eb4e_chrStart.txt added
3d274f911b1c8_exonGeTrInfo.tab added
3d274f55cfd3ca_exonInfo.tab added
3d274f236dafbd_geneInfo.tab added
3d274f7990fbbe_Genome added
3d274f25570648_genomeParameters.txt added
3d274f9c02c6d_Log.out added
3d274f58258f17_SA added
3d274f30966c73_SAindex added
3d274f2f289408_sjdbInfo.txt added
3d274f7a3d80b3_sjdbList.fromGTF.out.tab added
3d274f51584204_sjdbList.out.tab added
3d274f7beb3d5f_transcriptInfo.tab added
3d274f4e808204_GRCh38.GENCODE.v42_100 added
3d274f434a6368_knownGene_hg38.sql added
3d274f22065f04_knownGene_hg38.txt added
3d274f1060a2b9_refGene_hg38.sql added
3d274ff2f3557_refGene_hg38.txt added
3d274f7f1abc2f_knownGene_mm39.sql added
3d274f3e066e65_knownGene_mm39.txt added
3d274fd305f19_refGene_mm39.sql added
3d274f57c075bd_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/Rtmpd1mf6e/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
18.322 1.133 20.626
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.605 | 0.249 | 5.857 | |
| dataSearch | 1.081 | 0.006 | 1.087 | |
| dataUpdate | 0.001 | 0.000 | 0.001 | |
| getCloudData | 2.603 | 0.222 | 3.775 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.124 | 0.018 | 0.143 | |
| recipeLoad | 1.268 | 0.034 | 1.303 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.538 | 0.028 | 0.566 | |
| recipeUpdate | 0 | 0 | 0 | |