Qian Liu
| Snapshot Date: 2026-02-11 13:40 -0500 (Wed, 11 Feb 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) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-12 11:32 -0500 (Thu, 12 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4864 |
| 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 1770/2352 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.11.0 (landing page) Qian Liu
| nebbiolo1 | 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: 1.11.0 |
| 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: 2026-02-12 03:25:41 -0500 (Thu, 12 Feb 2026) |
| EndedAt: 2026-02-12 03:28:24 -0500 (Thu, 12 Feb 2026) |
| EllapsedTime: 163.4 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 5.958 0.344 6.315
* 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 ‘1.11.0’ ** 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)
ReUseData.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-01-15 r89304) -- "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.)
}[1;30mINFO[0m Final process status is success
Updating data record...
outfile.txt added
Updating data record...
997fa5c575786_GRCh38.primary_assembly.genome.fa.1.bt2 added
997fa1341ff4d_GRCh38.primary_assembly.genome.fa.2.bt2 added
997fa6d93f2d8_GRCh38.primary_assembly.genome.fa.3.bt2 added
997fa30570937_GRCh38.primary_assembly.genome.fa.4.bt2 added
997fa5c50911a_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
997fa77754168_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
997fa16c8ae36_outfile.txt added
997fa45ff9772_GRCh37_to_GRCh38.chain added
997fad6f1ecc_GRCh37_to_NCBI34.chain added
997fa5ec3fb1_GRCh37_to_NCBI35.chain added
997fa1d25487d_GRCh37_to_NCBI36.chain added
997fa1a2bc6cb_GRCh38_to_GRCh37.chain added
997fa1ae3e26e_GRCh38_to_NCBI34.chain added
997fa3b061cfa_GRCh38_to_NCBI35.chain added
997fa365e73fc_GRCh38_to_NCBI36.chain added
997fa1f36ee65_NCBI34_to_GRCh37.chain added
997fa408f7d33_NCBI34_to_GRCh38.chain added
997fa2dcb678e_NCBI35_to_GRCh37.chain added
997fa43ef43c2_NCBI35_to_GRCh38.chain added
997fa39e30b44_NCBI36_to_GRCh37.chain added
997fa7b02ae1a_NCBI36_to_GRCh38.chain added
997fa355cf4ba_GRCm38_to_NCBIM36.chain added
997fa62b62fdc_GRCm38_to_NCBIM37.chain added
997fa67476e17_NCBIM36_to_GRCm38.chain added
997fa76486ab8_NCBIM37_to_GRCm38.chain added
997fa49d5bfdc_1000G_omni2.5.b37.vcf.gz added
997fa3b4b46a2_1000G_omni2.5.b37.vcf.gz.tbi added
997fa37f6e5dc_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
997fa2cda9c5_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
997fa67dcf297_1000G_omni2.5.hg38.vcf.gz added
997fa25dbb185_1000G_omni2.5.hg38.vcf.gz.tbi added
997fa5f25014b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
997fa7b1ef1e5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
997fa136fa45e_af-only-gnomad.raw.sites.vcf added
997faf7c0a82_af-only-gnomad.raw.sites.vcf.idx added
997fa576f82ff_Mutect2-exome-panel.vcf.idx added
997faae4e5c6_Mutect2-WGS-panel-b37.vcf added
997fa2644b8b9_Mutect2-WGS-panel-b37.vcf.idx added
997fa1d6f1a71_small_exac_common_3.vcf added
997fa18540493_small_exac_common_3.vcf.idx added
997fa2c30f86a_1000g_pon.hg38.vcf.gz added
997fa3a9462ee_1000g_pon.hg38.vcf.gz.tbi added
997fa327fcb5e_af-only-gnomad.hg38.vcf.gz added
997fa4714dad8_af-only-gnomad.hg38.vcf.gz.tbi added
997fa759a7fe8_small_exac_common_3.hg38.vcf.gz added
997fa68de3f5a_small_exac_common_3.hg38.vcf.gz.tbi added
997fa664bc93e_gencode.v41.annotation.gtf added
997fa3629fd1b_gencode.v42.annotation.gtf added
997fa16a9a6e8_gencode.vM30.annotation.gtf added
997fa2a3b0d00_gencode.vM31.annotation.gtf added
997fa700d0860_gencode.v41.transcripts.fa added
997fa11ac5502_gencode.v41.transcripts.fa.fai added
997fa5f9801ba_gencode.v42.transcripts.fa added
997fa52c3383c_gencode.v42.transcripts.fa.fai added
997fa78f3c319_gencode.vM30.pc_transcripts.fa added
997fa55e06c73_gencode.vM30.pc_transcripts.fa.fai added
997fa1c98f819_gencode.vM31.pc_transcripts.fa added
997fa343f09bc_gencode.vM31.pc_transcripts.fa.fai added
997fadd7524f_GRCh38.primary_assembly.genome.fa.1.ht2 added
997fa1f66a1de_GRCh38.primary_assembly.genome.fa.2.ht2 added
997fa1c1bfc53_GRCh38.primary_assembly.genome.fa.3.ht2 added
997fa33b303d5_GRCh38.primary_assembly.genome.fa.4.ht2 added
997fa7e8ba32a_GRCh38.primary_assembly.genome.fa.5.ht2 added
997fa173aee38_GRCh38.primary_assembly.genome.fa.6.ht2 added
997fa4722a833_GRCh38.primary_assembly.genome.fa.7.ht2 added
997fae07adac_GRCh38.primary_assembly.genome.fa.8.ht2 added
997fa6eaa7137_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
997fa52078df9_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
997fa344c6665_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
997fac198ba8_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
997fa6a5b928c_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
997fa607d5ed0_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
997fa46adee96_GRCh38_full_analysis_set_plus_decoy_hla.fa added
997fa1cdb5dea_GRCh38.primary_assembly.genome.fa.fai added
997fa279239a8_GRCh38.primary_assembly.genome.fa.amb added
997fa3c486e7e_GRCh38.primary_assembly.genome.fa.ann added
997fa5b99d44_GRCh38.primary_assembly.genome.fa.bwt added
997fadde02e6_GRCh38.primary_assembly.genome.fa.pac added
997fa72726b9a_GRCh38.primary_assembly.genome.fa.sa added
997fa1c63442c_GRCh38.primary_assembly.genome.fa added
997fa38190fe6_hs37d5.fa.fai added
997fa627f73fa_hs37d5.fa.amb added
997fa2e0f992e_hs37d5.fa.ann added
997fa17b111a1_hs37d5.fa.bwt added
997fa3542ac36_hs37d5.fa.pac added
997fa27035c48_hs37d5.fa.sa added
997fa6d917e14_hs37d5.fa added
997fa51dba44f_complete_ref_lens.bin added
997fa5b426604_ctable.bin added
997fa7b68d063_ctg_offsets.bin added
997fa7142462e_duplicate_clusters.tsv added
997fa775e6257_info.json added
997fa2f1bd438_mphf.bin added
997fa6fcde958_pos.bin added
997fae995090_pre_indexing.log added
997fa763e7c6b_rank.bin added
997fa7dd59704_ref_indexing.log added
997fa7d43c1c7_refAccumLengths.bin added
997fa48460a65_reflengths.bin added
997fa3221fd6a_refseq.bin added
997fa95d4d70_seq.bin added
997fa32a19cf1_versionInfo.json added
997fa129f5c3a_salmon_index added
997fa500b3c06_chrLength.txt added
997fa4f7cfadc_chrName.txt added
997fa3a3195e2_chrNameLength.txt added
997fac53aa85_chrStart.txt added
997fa55369820_exonGeTrInfo.tab added
997fa480f98c9_exonInfo.tab added
997fa7ec6161f_geneInfo.tab added
997fa7199dc4d_Genome added
997fa28a8af_genomeParameters.txt added
997fa61458a19_Log.out added
997fa1fa9757b_SA added
997fa17d9ba50_SAindex added
997fa1688364f_sjdbInfo.txt added
997fa46acd1c3_sjdbList.fromGTF.out.tab added
997fa56b3864_sjdbList.out.tab added
997fa6863da9f_transcriptInfo.tab added
997fa21ef37c7_GRCh38.GENCODE.v42_100 added
997fad408c8_knownGene_hg38.sql added
997fa59a620cd_knownGene_hg38.txt added
997fa194d9a1f_refGene_hg38.sql added
997fa2fefdd00_refGene_hg38.txt added
997fa49740a25_knownGene_mm39.sql added
997fa27e6eaaf_knownGene_mm39.txt added
997fa262e596c_refGene_mm39.sql added
997fa4749a129_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/RtmpBtmHjK/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 0 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
>
>
>
> proc.time()
user system elapsed
17.507 1.090 19.360
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.958 | 0.344 | 6.315 | |
| dataSearch | 1.144 | 0.014 | 1.159 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.671 | 0.121 | 3.797 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.123 | 0.001 | 0.125 | |
| recipeLoad | 1.268 | 0.021 | 1.290 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.542 | 0.008 | 0.551 | |
| recipeUpdate | 0 | 0 | 0 | |