Qian Liu
| Snapshot Date: 2026-03-13 13:45 -0400 (Fri, 13 Mar 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-14 11:57 -0400 (Sat, 14 Mar 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" | 4892 |
| 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: 2026-03-14 03:07:32 -0400 (Sat, 14 Mar 2026) |
| EndedAt: 2026-03-14 03:10:19 -0400 (Sat, 14 Mar 2026) |
| EllapsedTime: 166.2 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 6.212 0.675 6.892
* 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...
389b051beaca28_GRCh38.primary_assembly.genome.fa.1.bt2 added
389b0519184468_GRCh38.primary_assembly.genome.fa.2.bt2 added
389b052cbc1619_GRCh38.primary_assembly.genome.fa.3.bt2 added
389b056c6db8d1_GRCh38.primary_assembly.genome.fa.4.bt2 added
389b053369fb0c_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
389b053bd97938_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
389b05434848c9_outfile.txt added
389b051eeecc33_GRCh37_to_GRCh38.chain added
389b05774d2bf2_GRCh37_to_NCBI34.chain added
389b05578af5e5_GRCh37_to_NCBI35.chain added
389b05bff6bca_GRCh37_to_NCBI36.chain added
389b0540b79e5d_GRCh38_to_GRCh37.chain added
389b056e4abb17_GRCh38_to_NCBI34.chain added
389b055a9d5ac7_GRCh38_to_NCBI35.chain added
389b055fd853_GRCh38_to_NCBI36.chain added
389b0531ed7266_NCBI34_to_GRCh37.chain added
389b054d991e8b_NCBI34_to_GRCh38.chain added
389b0522bb0f07_NCBI35_to_GRCh37.chain added
389b0552998f22_NCBI35_to_GRCh38.chain added
389b056a805ce5_NCBI36_to_GRCh37.chain added
389b056634b2c2_NCBI36_to_GRCh38.chain added
389b0523e7a240_GRCm38_to_NCBIM36.chain added
389b052d3853cf_GRCm38_to_NCBIM37.chain added
389b051832c553_NCBIM36_to_GRCm38.chain added
389b059c0127_NCBIM37_to_GRCm38.chain added
389b05e079734_1000G_omni2.5.b37.vcf.gz added
389b057ba5ac5c_1000G_omni2.5.b37.vcf.gz.tbi added
389b056f06ced_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
389b056bf5aa9e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
389b053e53c08f_1000G_omni2.5.hg38.vcf.gz added
389b05b3ada37_1000G_omni2.5.hg38.vcf.gz.tbi added
389b057e074c6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
389b05576c04f7_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
389b0537f6f050_af-only-gnomad.raw.sites.vcf added
389b05744e2d98_af-only-gnomad.raw.sites.vcf.idx added
389b05ad60003_Mutect2-exome-panel.vcf.idx added
389b0573d06988_Mutect2-WGS-panel-b37.vcf added
389b0537967661_Mutect2-WGS-panel-b37.vcf.idx added
389b0529c4cc36_small_exac_common_3.vcf added
389b056b1d957a_small_exac_common_3.vcf.idx added
389b05f216c46_1000g_pon.hg38.vcf.gz added
389b0535c43800_1000g_pon.hg38.vcf.gz.tbi added
389b052bd533d7_af-only-gnomad.hg38.vcf.gz added
389b057d6c275d_af-only-gnomad.hg38.vcf.gz.tbi added
389b05106192c8_small_exac_common_3.hg38.vcf.gz added
389b052c350c2b_small_exac_common_3.hg38.vcf.gz.tbi added
389b052f5999c3_gencode.v41.annotation.gtf added
389b055dfab153_gencode.v42.annotation.gtf added
389b054ef01b32_gencode.vM30.annotation.gtf added
389b051f328e5_gencode.vM31.annotation.gtf added
389b05487b0e38_gencode.v41.transcripts.fa added
389b053524cdf5_gencode.v41.transcripts.fa.fai added
389b0525dacb26_gencode.v42.transcripts.fa added
389b0575b36207_gencode.v42.transcripts.fa.fai added
389b054d579348_gencode.vM30.pc_transcripts.fa added
389b052676cc4d_gencode.vM30.pc_transcripts.fa.fai added
389b053baf93c_gencode.vM31.pc_transcripts.fa added
389b0548fd3fa4_gencode.vM31.pc_transcripts.fa.fai added
389b052d67393a_GRCh38.primary_assembly.genome.fa.1.ht2 added
389b056fb0a3da_GRCh38.primary_assembly.genome.fa.2.ht2 added
389b057510034_GRCh38.primary_assembly.genome.fa.3.ht2 added
389b0538a21371_GRCh38.primary_assembly.genome.fa.4.ht2 added
389b05779118a1_GRCh38.primary_assembly.genome.fa.5.ht2 added
389b055ebd052b_GRCh38.primary_assembly.genome.fa.6.ht2 added
389b05709903c1_GRCh38.primary_assembly.genome.fa.7.ht2 added
389b056bdf4639_GRCh38.primary_assembly.genome.fa.8.ht2 added
389b056993052f_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
389b0564696d49_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
389b052375bc9a_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
389b051357d165_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
389b054f8702c3_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
389b05329728e1_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
389b05491c0966_GRCh38_full_analysis_set_plus_decoy_hla.fa added
389b057b5c369b_GRCh38.primary_assembly.genome.fa.fai added
389b053003503e_GRCh38.primary_assembly.genome.fa.amb added
389b05597d9c2e_GRCh38.primary_assembly.genome.fa.ann added
389b05279142c6_GRCh38.primary_assembly.genome.fa.bwt added
389b055f5cea02_GRCh38.primary_assembly.genome.fa.pac added
389b0537784d81_GRCh38.primary_assembly.genome.fa.sa added
389b0576815df8_GRCh38.primary_assembly.genome.fa added
389b05615012e7_hs37d5.fa.fai added
389b057ff35bb9_hs37d5.fa.amb added
389b052ba62bed_hs37d5.fa.ann added
389b0572ade0d_hs37d5.fa.bwt added
389b0575a6bdc0_hs37d5.fa.pac added
389b0578fdbf36_hs37d5.fa.sa added
389b052da1aa5a_hs37d5.fa added
389b057961b6fc_complete_ref_lens.bin added
389b0541fafeda_ctable.bin added
389b055b08e395_ctg_offsets.bin added
389b0569125ad7_duplicate_clusters.tsv added
389b05494bff0e_info.json added
389b0513aaf706_mphf.bin added
389b0560a37378_pos.bin added
389b052809043a_pre_indexing.log added
389b05443fac8_rank.bin added
389b054c82b9b1_ref_indexing.log added
389b05119c0969_refAccumLengths.bin added
389b0568ad6811_reflengths.bin added
389b056ff8764b_refseq.bin added
389b0524f3dace_seq.bin added
389b0538346ad5_versionInfo.json added
389b05228f9f2c_salmon_index added
389b056e0fe434_chrLength.txt added
389b053390a170_chrName.txt added
389b055292ef6b_chrNameLength.txt added
389b05478d8062_chrStart.txt added
389b055b21e436_exonGeTrInfo.tab added
389b0531efd96d_exonInfo.tab added
389b057f05cde3_geneInfo.tab added
389b0551a3422e_Genome added
389b05133fec54_genomeParameters.txt added
389b057ef9299c_Log.out added
389b057d496e1c_SA added
389b051a6aca62_SAindex added
389b05749fe75d_sjdbInfo.txt added
389b0576472d52_sjdbList.fromGTF.out.tab added
389b05480c74bc_sjdbList.out.tab added
389b056e019e59_transcriptInfo.tab added
389b0538422c2c_GRCh38.GENCODE.v42_100 added
389b0523155851_knownGene_hg38.sql added
389b055713f930_knownGene_hg38.txt added
389b0518e2b3b_refGene_hg38.sql added
389b0536c04f58_refGene_hg38.txt added
389b0537b76ca8_knownGene_mm39.sql added
389b0529972f75_knownGene_mm39.txt added
389b053b044a20_refGene_mm39.sql added
389b0543a2659_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/RtmptbPaoR/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
18.901 1.448 21.091
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.212 | 0.675 | 6.892 | |
| dataSearch | 1.147 | 0.015 | 1.162 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.772 | 0.247 | 3.926 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.127 | 0.015 | 0.144 | |
| recipeLoad | 1.313 | 0.060 | 1.373 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.552 | 0.031 | 0.583 | |
| recipeUpdate | 0 | 0 | 0 | |