Qian Liu
| Snapshot Date: 2026-02-05 13:40 -0500 (Thu, 05 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 2026-02-06 11:32 -0500 (Fri, 06 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" | 4857 |
| 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 1766/2347 | 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: 2026-02-06 03:08:50 -0500 (Fri, 06 Feb 2026) |
| EndedAt: 2026-02-06 03:11:33 -0500 (Fri, 06 Feb 2026) |
| EllapsedTime: 163.3 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 5.996 0.399 6.397
* 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...
2a845202d74ed_GRCh38.primary_assembly.genome.fa.1.bt2 added
2a8451ab8b9df_GRCh38.primary_assembly.genome.fa.2.bt2 added
2a84553764e07_GRCh38.primary_assembly.genome.fa.3.bt2 added
2a845a9583c4_GRCh38.primary_assembly.genome.fa.4.bt2 added
2a8452d9deb15_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2a845462508f6_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2a8452bfd94f0_outfile.txt added
2a84535add71a_GRCh37_to_GRCh38.chain added
2a8457b6e6bfe_GRCh37_to_NCBI34.chain added
2a8453fffe693_GRCh37_to_NCBI35.chain added
2a84578ac8c29_GRCh37_to_NCBI36.chain added
2a8457bffb0e6_GRCh38_to_GRCh37.chain added
2a8455b713ab7_GRCh38_to_NCBI34.chain added
2a8451ababccd_GRCh38_to_NCBI35.chain added
2a8453f348c2a_GRCh38_to_NCBI36.chain added
2a8451d89e527_NCBI34_to_GRCh37.chain added
2a8456049f90c_NCBI34_to_GRCh38.chain added
2a845f9538a_NCBI35_to_GRCh37.chain added
2a8456bca5938_NCBI35_to_GRCh38.chain added
2a8456e0f4c35_NCBI36_to_GRCh37.chain added
2a84545233f23_NCBI36_to_GRCh38.chain added
2a84541b9134f_GRCm38_to_NCBIM36.chain added
2a8455a1e2c97_GRCm38_to_NCBIM37.chain added
2a8454e308b32_NCBIM36_to_GRCm38.chain added
2a8454953e846_NCBIM37_to_GRCm38.chain added
2a8459bdffa3_1000G_omni2.5.b37.vcf.gz added
2a8453783aefc_1000G_omni2.5.b37.vcf.gz.tbi added
2a8455b6824a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2a8455761458b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2a8453c66a847_1000G_omni2.5.hg38.vcf.gz added
2a8459d90d19_1000G_omni2.5.hg38.vcf.gz.tbi added
2a845778eba78_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2a845571f6227_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2a8455d4f5b20_af-only-gnomad.raw.sites.vcf added
2a8452243e3c_af-only-gnomad.raw.sites.vcf.idx added
2a8454bd4d3c_Mutect2-exome-panel.vcf.idx added
2a84523746416_Mutect2-WGS-panel-b37.vcf added
2a8452e21d32d_Mutect2-WGS-panel-b37.vcf.idx added
2a8453a6b2456_small_exac_common_3.vcf added
2a8451ee2d014_small_exac_common_3.vcf.idx added
2a8456e21b9c0_1000g_pon.hg38.vcf.gz added
2a8453317b07f_1000g_pon.hg38.vcf.gz.tbi added
2a8451ae280fb_af-only-gnomad.hg38.vcf.gz added
2a8454992f477_af-only-gnomad.hg38.vcf.gz.tbi added
2a8454dd26d4d_small_exac_common_3.hg38.vcf.gz added
2a8455a170d25_small_exac_common_3.hg38.vcf.gz.tbi added
2a845671cd99f_gencode.v41.annotation.gtf added
2a8452e1c6659_gencode.v42.annotation.gtf added
2a8455b1060af_gencode.vM30.annotation.gtf added
2a84552e732d7_gencode.vM31.annotation.gtf added
2a8451c2bb28e_gencode.v41.transcripts.fa added
2a84520339fd2_gencode.v41.transcripts.fa.fai added
2a84514a04626_gencode.v42.transcripts.fa added
2a8457649df25_gencode.v42.transcripts.fa.fai added
2a8456e642b05_gencode.vM30.pc_transcripts.fa added
2a8455df42e6d_gencode.vM30.pc_transcripts.fa.fai added
2a8457dec8_gencode.vM31.pc_transcripts.fa added
2a84525e7da01_gencode.vM31.pc_transcripts.fa.fai added
2a84563aab0b7_GRCh38.primary_assembly.genome.fa.1.ht2 added
2a84557692454_GRCh38.primary_assembly.genome.fa.2.ht2 added
2a845624e8249_GRCh38.primary_assembly.genome.fa.3.ht2 added
2a8456d83bdd1_GRCh38.primary_assembly.genome.fa.4.ht2 added
2a8454ef7decc_GRCh38.primary_assembly.genome.fa.5.ht2 added
2a845396de470_GRCh38.primary_assembly.genome.fa.6.ht2 added
2a8454ad318f1_GRCh38.primary_assembly.genome.fa.7.ht2 added
2a845511c1d09_GRCh38.primary_assembly.genome.fa.8.ht2 added
2a8453e2b31ac_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2a8456e477d08_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2a8457f3df036_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2a84578965602_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2a845d2a4d1c_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2a8456d5fa9f6_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2a8452bae0681_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2a845280cce17_GRCh38.primary_assembly.genome.fa.fai added
2a84536f29e6d_GRCh38.primary_assembly.genome.fa.amb added
2a845798073ce_GRCh38.primary_assembly.genome.fa.ann added
2a845223db3d_GRCh38.primary_assembly.genome.fa.bwt added
2a8451e0f780c_GRCh38.primary_assembly.genome.fa.pac added
2a845279cda28_GRCh38.primary_assembly.genome.fa.sa added
2a8455d343bec_GRCh38.primary_assembly.genome.fa added
2a84570f6aae4_hs37d5.fa.fai added
2a84543c88cb6_hs37d5.fa.amb added
2a8457d67dbbf_hs37d5.fa.ann added
2a845596f10a_hs37d5.fa.bwt added
2a8453a126bdc_hs37d5.fa.pac added
2a8456bcc06c4_hs37d5.fa.sa added
2a845638b1f77_hs37d5.fa added
2a8453a1a4aa4_complete_ref_lens.bin added
2a84511b3e0c5_ctable.bin added
2a8454735d02f_ctg_offsets.bin added
2a84511836ef8_duplicate_clusters.tsv added
2a8457402630e_info.json added
2a84534b98e00_mphf.bin added
2a845607b4dc5_pos.bin added
2a8452d70477e_pre_indexing.log added
2a8457f8ca6f1_rank.bin added
2a84531976ace_ref_indexing.log added
2a8456b9b792a_refAccumLengths.bin added
2a8456dd423f9_reflengths.bin added
2a84530d55b04_refseq.bin added
2a8456431cf2c_seq.bin added
2a8457afe7116_versionInfo.json added
2a8451e3504fa_salmon_index added
2a845fdfd5ae_chrLength.txt added
2a845230b3f2d_chrName.txt added
2a8455527a367_chrNameLength.txt added
2a845960497c_chrStart.txt added
2a845252f1a6a_exonGeTrInfo.tab added
2a84573371b74_exonInfo.tab added
2a84530fd23a4_geneInfo.tab added
2a8452635657_Genome added
2a845642dc658_genomeParameters.txt added
2a84574c5b05b_Log.out added
2a8457fcb3216_SA added
2a84569c4b762_SAindex added
2a8452ed81c37_sjdbInfo.txt added
2a8456b9738da_sjdbList.fromGTF.out.tab added
2a8454d4fd6da_sjdbList.out.tab added
2a84568f266db_transcriptInfo.tab added
2a8457d4b199f_GRCh38.GENCODE.v42_100 added
2a8451485a709_knownGene_hg38.sql added
2a8457a75d5d4_knownGene_hg38.txt added
2a845714d7cae_refGene_hg38.sql added
2a845493f3509_refGene_hg38.txt added
2a8455af12399_knownGene_mm39.sql added
2a8451ebdc42c_knownGene_mm39.txt added
2a84548cbdbfa_refGene_mm39.sql added
2a845c888e67_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/RtmpG0G5u3/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
18.416 1.455 20.705
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.996 | 0.399 | 6.397 | |
| dataSearch | 1.148 | 0.042 | 1.190 | |
| dataUpdate | 0.001 | 0.000 | 0.001 | |
| getCloudData | 2.598 | 0.093 | 3.522 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.121 | 0.010 | 0.132 | |
| recipeLoad | 1.296 | 0.052 | 1.354 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.523 | 0.007 | 0.530 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |