Qian Liu
| Snapshot Date: 2026-04-30 13:45 -0400 (Thu, 30 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: caf380d |
| git_last_commit_date: 2026-04-28 08:59:39 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-01 11:32 -0400 (Fri, 01 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4843 |
| 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 1775/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.13.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.4 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: 1.13.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings ReUseData_1.13.0.tar.gz |
| StartedAt: 2026-05-01 03:38:32 -0400 (Fri, 01 May 2026) |
| EndedAt: 2026-05-01 03:41:17 -0400 (Fri, 01 May 2026) |
| EllapsedTime: 165.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings ReUseData_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-01 07:38:32 UTC
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.13.0’
* 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 5.978 0.251 6.23
* 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-3.24-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.13.0’ ** 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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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...
e8bc71dd9b5d8_GRCh38.primary_assembly.genome.fa.1.bt2 added
e8bc7f3d7289_GRCh38.primary_assembly.genome.fa.2.bt2 added
e8bc7157634a4_GRCh38.primary_assembly.genome.fa.3.bt2 added
e8bc77152efad_GRCh38.primary_assembly.genome.fa.4.bt2 added
e8bc723de9f88_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
e8bc75782a25c_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
e8bc776a3d43c_outfile.txt added
e8bc72c8b6800_GRCh37_to_GRCh38.chain added
e8bc720f93ae6_GRCh37_to_NCBI34.chain added
e8bc74f64fb89_GRCh37_to_NCBI35.chain added
e8bc74d7f607f_GRCh37_to_NCBI36.chain added
e8bc7172bc7b_GRCh38_to_GRCh37.chain added
e8bc75e17aae8_GRCh38_to_NCBI34.chain added
e8bc75d3ce4b3_GRCh38_to_NCBI35.chain added
e8bc7298a7508_GRCh38_to_NCBI36.chain added
e8bc779cf8c37_NCBI34_to_GRCh37.chain added
e8bc74e34050e_NCBI34_to_GRCh38.chain added
e8bc76bd81db9_NCBI35_to_GRCh37.chain added
e8bc716ebbaf1_NCBI35_to_GRCh38.chain added
e8bc755764e57_NCBI36_to_GRCh37.chain added
e8bc7121dad80_NCBI36_to_GRCh38.chain added
e8bc7520cf4de_GRCm38_to_NCBIM36.chain added
e8bc758708b44_GRCm38_to_NCBIM37.chain added
e8bc74587481b_NCBIM36_to_GRCm38.chain added
e8bc77df2a5aa_NCBIM37_to_GRCm38.chain added
e8bc7409f85fe_1000G_omni2.5.b37.vcf.gz added
e8bc773bcac29_1000G_omni2.5.b37.vcf.gz.tbi added
e8bc76d8bebcd_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
e8bc775443005_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
e8bc7737a5a69_1000G_omni2.5.hg38.vcf.gz added
e8bc75bc245be_1000G_omni2.5.hg38.vcf.gz.tbi added
e8bc7131de5dd_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
e8bc72b7ccf2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
e8bc771387a62_af-only-gnomad.raw.sites.vcf added
e8bc7470d58a_af-only-gnomad.raw.sites.vcf.idx added
e8bc726966c7a_Mutect2-exome-panel.vcf.idx added
e8bc748bb1cbf_Mutect2-WGS-panel-b37.vcf added
e8bc77b14a9c6_Mutect2-WGS-panel-b37.vcf.idx added
e8bc75321d47a_small_exac_common_3.vcf added
e8bc769b457a5_small_exac_common_3.vcf.idx added
e8bc74a79a54f_1000g_pon.hg38.vcf.gz added
e8bc720a134f9_1000g_pon.hg38.vcf.gz.tbi added
e8bc76b271420_af-only-gnomad.hg38.vcf.gz added
e8bc728915038_af-only-gnomad.hg38.vcf.gz.tbi added
e8bc77dde19ac_small_exac_common_3.hg38.vcf.gz added
e8bc714b18928_small_exac_common_3.hg38.vcf.gz.tbi added
e8bc72260dc6f_gencode.v41.annotation.gtf added
e8bc74c121ebb_gencode.v42.annotation.gtf added
e8bc789a6e1_gencode.vM30.annotation.gtf added
e8bc7394c9760_gencode.vM31.annotation.gtf added
e8bc721886d12_gencode.v41.transcripts.fa added
e8bc712a75462_gencode.v41.transcripts.fa.fai added
e8bc7b598c3e_gencode.v42.transcripts.fa added
e8bc779f8f856_gencode.v42.transcripts.fa.fai added
e8bc7582e9c7d_gencode.vM30.pc_transcripts.fa added
e8bc794c31e8_gencode.vM30.pc_transcripts.fa.fai added
e8bc73a987e55_gencode.vM31.pc_transcripts.fa added
e8bc74beb48a6_gencode.vM31.pc_transcripts.fa.fai added
e8bc776d81db5_GRCh38.primary_assembly.genome.fa.1.ht2 added
e8bc72fdcae5a_GRCh38.primary_assembly.genome.fa.2.ht2 added
e8bc73f65a30f_GRCh38.primary_assembly.genome.fa.3.ht2 added
e8bc7529a6374_GRCh38.primary_assembly.genome.fa.4.ht2 added
e8bc742fa9437_GRCh38.primary_assembly.genome.fa.5.ht2 added
e8bc7421d7001_GRCh38.primary_assembly.genome.fa.6.ht2 added
e8bc743d2ddd6_GRCh38.primary_assembly.genome.fa.7.ht2 added
e8bc7476b69c1_GRCh38.primary_assembly.genome.fa.8.ht2 added
e8bc768b3dc7c_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
e8bc7c8dfa95_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
e8bc742801387_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
e8bc73bd5b0f6_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
e8bc77642523a_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
e8bc7cf9b8d6_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
e8bc75c76e5f0_GRCh38_full_analysis_set_plus_decoy_hla.fa added
e8bc76169665a_GRCh38.primary_assembly.genome.fa.fai added
e8bc7358b090e_GRCh38.primary_assembly.genome.fa.amb added
e8bc75a54ff9c_GRCh38.primary_assembly.genome.fa.ann added
e8bc7761aef83_GRCh38.primary_assembly.genome.fa.bwt added
e8bc757ebe57d_GRCh38.primary_assembly.genome.fa.pac added
e8bc726671e57_GRCh38.primary_assembly.genome.fa.sa added
e8bc776a49664_GRCh38.primary_assembly.genome.fa added
e8bc711387cde_hs37d5.fa.fai added
e8bc747ef8b6a_hs37d5.fa.amb added
e8bc794beac6_hs37d5.fa.ann added
e8bc71c92091c_hs37d5.fa.bwt added
e8bc741e883c0_hs37d5.fa.pac added
e8bc7617a8743_hs37d5.fa.sa added
e8bc725de3b05_hs37d5.fa added
e8bc77c810215_complete_ref_lens.bin added
e8bc72d65cfea_ctable.bin added
e8bc71cb658ba_ctg_offsets.bin added
e8bc72c5db06f_duplicate_clusters.tsv added
e8bc76ccb72f9_info.json added
e8bc76f50bc2e_mphf.bin added
e8bc76f5844a6_pos.bin added
e8bc72ee8e2fb_pre_indexing.log added
e8bc733239a05_rank.bin added
e8bc736c3ae67_ref_indexing.log added
e8bc7179cbf77_refAccumLengths.bin added
e8bc73fb1949a_reflengths.bin added
e8bc77943c1ee_refseq.bin added
e8bc75372706d_seq.bin added
e8bc735f3e6d5_versionInfo.json added
e8bc763d7ac5_salmon_index added
e8bc72fe9565d_chrLength.txt added
e8bc7175d4d2f_chrName.txt added
e8bc73bc883d3_chrNameLength.txt added
e8bc7a3e55fa_chrStart.txt added
e8bc7d783cb2_exonGeTrInfo.tab added
e8bc713b46951_exonInfo.tab added
e8bc730a57451_geneInfo.tab added
e8bc741cd317_Genome added
e8bc724ece62f_genomeParameters.txt added
e8bc77894ffbb_Log.out added
e8bc7d68bddd_SA added
e8bc7417eef4b_SAindex added
e8bc73a7d837c_sjdbInfo.txt added
e8bc76ee34521_sjdbList.fromGTF.out.tab added
e8bc7675d2a50_sjdbList.out.tab added
e8bc736fe8591_transcriptInfo.tab added
e8bc71c49150b_GRCh38.GENCODE.v42_100 added
e8bc7413830b_knownGene_hg38.sql added
e8bc7635c3601_knownGene_hg38.txt added
e8bc79148804_refGene_hg38.sql added
e8bc773643f39_refGene_hg38.txt added
e8bc752b47aa7_knownGene_mm39.sql added
e8bc737fd6aff_knownGene_mm39.txt added
e8bc72687d93e_refGene_mm39.sql added
e8bc7978290f_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/RtmpfbZjwS/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
18.739 1.011 20.194
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.978 | 0.251 | 6.230 | |
| dataSearch | 1.080 | 0.008 | 1.088 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.724 | 0.083 | 3.525 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.121 | 0.003 | 0.124 | |
| recipeLoad | 1.313 | 0.013 | 1.326 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.564 | 0.007 | 0.571 | |
| recipeUpdate | 0 | 0 | 0 | |