Qian Liu
| Snapshot Date: 2026-03-29 13:40 -0400 (Sun, 29 Mar 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-30 13:20 -0400 (Mon, 30 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4883 |
| 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 1784/2372 | 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: 2026-03-30 03:19:01 -0400 (Mon, 30 Mar 2026) |
| EndedAt: 2026-03-30 03:21:44 -0400 (Mon, 30 Mar 2026) |
| EllapsedTime: 163.5 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) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-30 07:19:01 UTC
* 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 5.875 0.423 6.3
* 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) (2026-03-05 r89546) -- "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...
394f2c4e5ee39e_GRCh38.primary_assembly.genome.fa.1.bt2 added
394f2cfee96a7_GRCh38.primary_assembly.genome.fa.2.bt2 added
394f2c54605623_GRCh38.primary_assembly.genome.fa.3.bt2 added
394f2ce0ec57f_GRCh38.primary_assembly.genome.fa.4.bt2 added
394f2c6e4f30e2_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
394f2c49d3be4b_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
394f2c76037c43_outfile.txt added
394f2c79e8eb11_GRCh37_to_GRCh38.chain added
394f2c5a53aca6_GRCh37_to_NCBI34.chain added
394f2c35983027_GRCh37_to_NCBI35.chain added
394f2c4cafec10_GRCh37_to_NCBI36.chain added
394f2c75abc5c8_GRCh38_to_GRCh37.chain added
394f2c56a4c67c_GRCh38_to_NCBI34.chain added
394f2c5d606e06_GRCh38_to_NCBI35.chain added
394f2c2dbd04fb_GRCh38_to_NCBI36.chain added
394f2c2f4b470f_NCBI34_to_GRCh37.chain added
394f2c4c677122_NCBI34_to_GRCh38.chain added
394f2c43f40eb8_NCBI35_to_GRCh37.chain added
394f2c3cd2ed2c_NCBI35_to_GRCh38.chain added
394f2c54cc1c0a_NCBI36_to_GRCh37.chain added
394f2c1b022851_NCBI36_to_GRCh38.chain added
394f2c986c12e_GRCm38_to_NCBIM36.chain added
394f2c6e4e9a21_GRCm38_to_NCBIM37.chain added
394f2c1fc2e5df_NCBIM36_to_GRCm38.chain added
394f2c489adc77_NCBIM37_to_GRCm38.chain added
394f2c331f4c20_1000G_omni2.5.b37.vcf.gz added
394f2c6cc6b8d0_1000G_omni2.5.b37.vcf.gz.tbi added
394f2c4fe8e35e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
394f2c7343f701_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
394f2c6be20355_1000G_omni2.5.hg38.vcf.gz added
394f2c21b783ab_1000G_omni2.5.hg38.vcf.gz.tbi added
394f2c41a2daa0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
394f2c7bd099fc_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
394f2c7617d9cf_af-only-gnomad.raw.sites.vcf added
394f2c4fb1a01f_af-only-gnomad.raw.sites.vcf.idx added
394f2c6a1fcadf_Mutect2-exome-panel.vcf.idx added
394f2c3feb981a_Mutect2-WGS-panel-b37.vcf added
394f2c45b51c62_Mutect2-WGS-panel-b37.vcf.idx added
394f2c6408b5f0_small_exac_common_3.vcf added
394f2c1a3f44c0_small_exac_common_3.vcf.idx added
394f2c7b4d4c8a_1000g_pon.hg38.vcf.gz added
394f2c30b8a201_1000g_pon.hg38.vcf.gz.tbi added
394f2cfeb0a88_af-only-gnomad.hg38.vcf.gz added
394f2c51f21306_af-only-gnomad.hg38.vcf.gz.tbi added
394f2ce191007_small_exac_common_3.hg38.vcf.gz added
394f2c3da80f83_small_exac_common_3.hg38.vcf.gz.tbi added
394f2c13d5a15_gencode.v41.annotation.gtf added
394f2c5a808129_gencode.v42.annotation.gtf added
394f2c19c1e3b_gencode.vM30.annotation.gtf added
394f2c3e104741_gencode.vM31.annotation.gtf added
394f2c2f4c9d33_gencode.v41.transcripts.fa added
394f2c1c9e468c_gencode.v41.transcripts.fa.fai added
394f2c47970870_gencode.v42.transcripts.fa added
394f2c1d9b3754_gencode.v42.transcripts.fa.fai added
394f2c3c612c6b_gencode.vM30.pc_transcripts.fa added
394f2c1031e4e7_gencode.vM30.pc_transcripts.fa.fai added
394f2c50ba8374_gencode.vM31.pc_transcripts.fa added
394f2c2927e53c_gencode.vM31.pc_transcripts.fa.fai added
394f2c601ac846_GRCh38.primary_assembly.genome.fa.1.ht2 added
394f2c43fe7a75_GRCh38.primary_assembly.genome.fa.2.ht2 added
394f2c1509e891_GRCh38.primary_assembly.genome.fa.3.ht2 added
394f2c1d24bf1_GRCh38.primary_assembly.genome.fa.4.ht2 added
394f2c5a15515_GRCh38.primary_assembly.genome.fa.5.ht2 added
394f2c10da828d_GRCh38.primary_assembly.genome.fa.6.ht2 added
394f2c77ea25c0_GRCh38.primary_assembly.genome.fa.7.ht2 added
394f2c5552f534_GRCh38.primary_assembly.genome.fa.8.ht2 added
394f2c7afa4d6c_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
394f2c37d5bdda_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
394f2c1b081197_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
394f2c5f03035d_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
394f2c5215029a_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
394f2c16555e21_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
394f2cfbba55e_GRCh38_full_analysis_set_plus_decoy_hla.fa added
394f2c62000d22_GRCh38.primary_assembly.genome.fa.fai added
394f2c68477127_GRCh38.primary_assembly.genome.fa.amb added
394f2c1dd4b565_GRCh38.primary_assembly.genome.fa.ann added
394f2c1fa81ca6_GRCh38.primary_assembly.genome.fa.bwt added
394f2c6984cb3c_GRCh38.primary_assembly.genome.fa.pac added
394f2c7855368e_GRCh38.primary_assembly.genome.fa.sa added
394f2c21443ae1_GRCh38.primary_assembly.genome.fa added
394f2c2795127e_hs37d5.fa.fai added
394f2c27a1d3c1_hs37d5.fa.amb added
394f2c3de2816e_hs37d5.fa.ann added
394f2c6f2c1aee_hs37d5.fa.bwt added
394f2c453d0b15_hs37d5.fa.pac added
394f2c7a43add9_hs37d5.fa.sa added
394f2c7f5dffd5_hs37d5.fa added
394f2c15f78e89_complete_ref_lens.bin added
394f2c236b9315_ctable.bin added
394f2c5f78c81b_ctg_offsets.bin added
394f2c59f608fe_duplicate_clusters.tsv added
394f2c38757ba6_info.json added
394f2c614b140d_mphf.bin added
394f2c5f975e14_pos.bin added
394f2c494ffe34_pre_indexing.log added
394f2c593539cd_rank.bin added
394f2c34ea5348_ref_indexing.log added
394f2c444a4ba0_refAccumLengths.bin added
394f2c110af7a8_reflengths.bin added
394f2c4ff264df_refseq.bin added
394f2c234d4efd_seq.bin added
394f2c631ffa42_versionInfo.json added
394f2c6647c300_salmon_index added
394f2c3308f45b_chrLength.txt added
394f2c45200765_chrName.txt added
394f2c4e8f3427_chrNameLength.txt added
394f2c50dda9c0_chrStart.txt added
394f2c64c8240b_exonGeTrInfo.tab added
394f2c3813ff64_exonInfo.tab added
394f2c4932e04e_geneInfo.tab added
394f2c60c5eec_Genome added
394f2c5fa911e2_genomeParameters.txt added
394f2c70d4b40f_Log.out added
394f2c43eee05a_SA added
394f2c4ed52cd0_SAindex added
394f2c3611bf24_sjdbInfo.txt added
394f2c3e328e34_sjdbList.fromGTF.out.tab added
394f2c4e332ca5_sjdbList.out.tab added
394f2c4c094dad_transcriptInfo.tab added
394f2c619e2149_GRCh38.GENCODE.v42_100 added
394f2c2dabf4c1_knownGene_hg38.sql added
394f2c25ff56ac_knownGene_hg38.txt added
394f2c1a139cf0_refGene_hg38.sql added
394f2cef708ce_refGene_hg38.txt added
394f2c596b4c0_knownGene_mm39.sql added
394f2c63639b24_knownGene_mm39.txt added
394f2c682c429b_refGene_mm39.sql added
394f2c3a810808_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/RtmpkbgjrW/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
18.185 1.167 19.898
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.875 | 0.423 | 6.300 | |
| dataSearch | 1.182 | 0.045 | 1.229 | |
| dataUpdate | 0.001 | 0.000 | 0.000 | |
| getCloudData | 2.739 | 0.126 | 3.442 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.126 | 0.018 | 0.145 | |
| recipeLoad | 1.323 | 0.078 | 1.402 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.575 | 0.015 | 0.592 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |