Qian Liu
| Snapshot Date: 2026-02-09 13:45 -0500 (Mon, 09 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 2026-02-12 11:58 -0500 (Thu, 12 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" | 4889 |
| 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: 2026-02-10 03:40:01 -0500 (Tue, 10 Feb 2026) |
| EndedAt: 2026-02-10 03:42:42 -0500 (Tue, 10 Feb 2026) |
| EllapsedTime: 161.2 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 5.658 0.21 5.871
* 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...
337e2860e0567d_GRCh38.primary_assembly.genome.fa.1.bt2 added
337e2810b0a9a3_GRCh38.primary_assembly.genome.fa.2.bt2 added
337e283493ffe9_GRCh38.primary_assembly.genome.fa.3.bt2 added
337e2831852626_GRCh38.primary_assembly.genome.fa.4.bt2 added
337e283acd8078_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
337e2849421822_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
337e285c780bf2_outfile.txt added
337e2830ff4971_GRCh37_to_GRCh38.chain added
337e287f41c564_GRCh37_to_NCBI34.chain added
337e28ede2e3e_GRCh37_to_NCBI35.chain added
337e287a74cbcb_GRCh37_to_NCBI36.chain added
337e286cfa46a8_GRCh38_to_GRCh37.chain added
337e285dd689f6_GRCh38_to_NCBI34.chain added
337e285bfbbcf8_GRCh38_to_NCBI35.chain added
337e28658bb0e4_GRCh38_to_NCBI36.chain added
337e2867f53aed_NCBI34_to_GRCh37.chain added
337e281c80b9db_NCBI34_to_GRCh38.chain added
337e281d46840f_NCBI35_to_GRCh37.chain added
337e28736b3eaf_NCBI35_to_GRCh38.chain added
337e286af8198c_NCBI36_to_GRCh37.chain added
337e2877f286c9_NCBI36_to_GRCh38.chain added
337e285361c930_GRCm38_to_NCBIM36.chain added
337e284fb4ab1d_GRCm38_to_NCBIM37.chain added
337e2852cf89e6_NCBIM36_to_GRCm38.chain added
337e2816d73256_NCBIM37_to_GRCm38.chain added
337e282f9d0065_1000G_omni2.5.b37.vcf.gz added
337e28784e22e3_1000G_omni2.5.b37.vcf.gz.tbi added
337e28110678e1_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
337e28494ec059_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
337e2835a416ee_1000G_omni2.5.hg38.vcf.gz added
337e281de08b34_1000G_omni2.5.hg38.vcf.gz.tbi added
337e282a2f16d6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
337e284654c091_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
337e2852748b1d_af-only-gnomad.raw.sites.vcf added
337e285bb43cfd_af-only-gnomad.raw.sites.vcf.idx added
337e281224109_Mutect2-exome-panel.vcf.idx added
337e281bb6a33f_Mutect2-WGS-panel-b37.vcf added
337e28382c48ef_Mutect2-WGS-panel-b37.vcf.idx added
337e2832218a7a_small_exac_common_3.vcf added
337e281af868a4_small_exac_common_3.vcf.idx added
337e28470a772d_1000g_pon.hg38.vcf.gz added
337e282c965646_1000g_pon.hg38.vcf.gz.tbi added
337e287f2af4c_af-only-gnomad.hg38.vcf.gz added
337e2824e10123_af-only-gnomad.hg38.vcf.gz.tbi added
337e28892133e_small_exac_common_3.hg38.vcf.gz added
337e286d7e6030_small_exac_common_3.hg38.vcf.gz.tbi added
337e28cd63c11_gencode.v41.annotation.gtf added
337e282512cd1a_gencode.v42.annotation.gtf added
337e28ac4e43f_gencode.vM30.annotation.gtf added
337e28417ac0_gencode.vM31.annotation.gtf added
337e28100ae6a6_gencode.v41.transcripts.fa added
337e282b76b09_gencode.v41.transcripts.fa.fai added
337e2853a343f0_gencode.v42.transcripts.fa added
337e285fbf91c3_gencode.v42.transcripts.fa.fai added
337e285586f4ef_gencode.vM30.pc_transcripts.fa added
337e286a7a7646_gencode.vM30.pc_transcripts.fa.fai added
337e28f5c9229_gencode.vM31.pc_transcripts.fa added
337e284dd517d2_gencode.vM31.pc_transcripts.fa.fai added
337e287b80ef28_GRCh38.primary_assembly.genome.fa.1.ht2 added
337e2858ab5282_GRCh38.primary_assembly.genome.fa.2.ht2 added
337e283792ec1_GRCh38.primary_assembly.genome.fa.3.ht2 added
337e2819617a5c_GRCh38.primary_assembly.genome.fa.4.ht2 added
337e282da6958_GRCh38.primary_assembly.genome.fa.5.ht2 added
337e2849cdef52_GRCh38.primary_assembly.genome.fa.6.ht2 added
337e286bd6057a_GRCh38.primary_assembly.genome.fa.7.ht2 added
337e285e8ea655_GRCh38.primary_assembly.genome.fa.8.ht2 added
337e284af0305c_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
337e2878ca8b9_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
337e2816baef44_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
337e287d11bad6_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
337e282285115d_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
337e285dc56671_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
337e2829a8111c_GRCh38_full_analysis_set_plus_decoy_hla.fa added
337e282a77c0a9_GRCh38.primary_assembly.genome.fa.fai added
337e282a66795_GRCh38.primary_assembly.genome.fa.amb added
337e28323a245b_GRCh38.primary_assembly.genome.fa.ann added
337e2817f620d9_GRCh38.primary_assembly.genome.fa.bwt added
337e28f7ca3a6_GRCh38.primary_assembly.genome.fa.pac added
337e28574cf175_GRCh38.primary_assembly.genome.fa.sa added
337e2822bb0519_GRCh38.primary_assembly.genome.fa added
337e28fbe1e66_hs37d5.fa.fai added
337e286757d81b_hs37d5.fa.amb added
337e2825727022_hs37d5.fa.ann added
337e2863616256_hs37d5.fa.bwt added
337e28471769df_hs37d5.fa.pac added
337e287af96511_hs37d5.fa.sa added
337e284ddbd89d_hs37d5.fa added
337e285673fc08_complete_ref_lens.bin added
337e2848ce7ce3_ctable.bin added
337e28495cc7c5_ctg_offsets.bin added
337e282f1f4e8a_duplicate_clusters.tsv added
337e284c47aba4_info.json added
337e2862be4221_mphf.bin added
337e2831f9b7e2_pos.bin added
337e2816159af7_pre_indexing.log added
337e284e94479b_rank.bin added
337e2810885e38_ref_indexing.log added
337e286105cb53_refAccumLengths.bin added
337e285620f055_reflengths.bin added
337e2827434d7c_refseq.bin added
337e285e178629_seq.bin added
337e2878a601b2_versionInfo.json added
337e28508b3ee_salmon_index added
337e287bf9746_chrLength.txt added
337e28231dc25c_chrName.txt added
337e287af1b83_chrNameLength.txt added
337e2839f9bba1_chrStart.txt added
337e283b13e335_exonGeTrInfo.tab added
337e28172bbf29_exonInfo.tab added
337e281146ad16_geneInfo.tab added
337e285dcee84e_Genome added
337e2826e9dd8f_genomeParameters.txt added
337e28789e8531_Log.out added
337e283415870_SA added
337e28a4b3fe5_SAindex added
337e283fb5ef10_sjdbInfo.txt added
337e287e3abd81_sjdbList.fromGTF.out.tab added
337e2858271882_sjdbList.out.tab added
337e281629eb18_transcriptInfo.tab added
337e2847093a65_GRCh38.GENCODE.v42_100 added
337e282183e047_knownGene_hg38.sql added
337e28454939a2_knownGene_hg38.txt added
337e281350e609_refGene_hg38.sql added
337e284422269_refGene_hg38.txt added
337e287742f185_knownGene_mm39.sql added
337e2829668100_knownGene_mm39.txt added
337e2852d66a04_refGene_mm39.sql added
337e287cb4fbd_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/RtmpynPpGJ/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
18.192 1.504 20.412
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.658 | 0.210 | 5.871 | |
| dataSearch | 1.078 | 0.009 | 1.087 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.593 | 0.126 | 3.760 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.116 | 0.003 | 0.120 | |
| recipeLoad | 1.253 | 0.011 | 1.265 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.522 | 0.003 | 0.525 | |
| recipeUpdate | 0 | 0 | 0 | |