Qian Liu
| Snapshot Date: 2026-03-03 13:45 -0500 (Tue, 03 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 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-04 11:57 -0500 (Wed, 04 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: 2026-03-04 03:16:09 -0500 (Wed, 04 Mar 2026) |
| EndedAt: 2026-03-04 03:18:52 -0500 (Wed, 04 Mar 2026) |
| EllapsedTime: 162.2 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 5.617 0.246 5.865
* 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...
5bd703f9972a4_GRCh38.primary_assembly.genome.fa.1.bt2 added
5bd70774f8167_GRCh38.primary_assembly.genome.fa.2.bt2 added
5bd7052351f23_GRCh38.primary_assembly.genome.fa.3.bt2 added
5bd7040454c6f_GRCh38.primary_assembly.genome.fa.4.bt2 added
5bd70106cd3a8_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
5bd702c45093d_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
5bd706778e300_outfile.txt added
5bd70313b7d69_GRCh37_to_GRCh38.chain added
5bd7028aa3939_GRCh37_to_NCBI34.chain added
5bd70797b4008_GRCh37_to_NCBI35.chain added
5bd7025585465_GRCh37_to_NCBI36.chain added
5bd70799f17e_GRCh38_to_GRCh37.chain added
5bd702705cb7b_GRCh38_to_NCBI34.chain added
5bd702ee7bd8a_GRCh38_to_NCBI35.chain added
5bd7038bc1406_GRCh38_to_NCBI36.chain added
5bd7044dcb559_NCBI34_to_GRCh37.chain added
5bd701b2b7c9d_NCBI34_to_GRCh38.chain added
5bd706b91a797_NCBI35_to_GRCh37.chain added
5bd705ea97013_NCBI35_to_GRCh38.chain added
5bd70255610aa_NCBI36_to_GRCh37.chain added
5bd706e0b12f9_NCBI36_to_GRCh38.chain added
5bd7038efbc9b_GRCm38_to_NCBIM36.chain added
5bd705b904750_GRCm38_to_NCBIM37.chain added
5bd7049a4df1e_NCBIM36_to_GRCm38.chain added
5bd70407ef0ef_NCBIM37_to_GRCm38.chain added
5bd706a557589_1000G_omni2.5.b37.vcf.gz added
5bd704d2ec751_1000G_omni2.5.b37.vcf.gz.tbi added
5bd70607b5735_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
5bd705ad2553e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
5bd702ca4a880_1000G_omni2.5.hg38.vcf.gz added
5bd701f3d3412_1000G_omni2.5.hg38.vcf.gz.tbi added
5bd701a6bc7e2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
5bd7023f429e7_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
5bd7071725335_af-only-gnomad.raw.sites.vcf added
5bd705ab11451_af-only-gnomad.raw.sites.vcf.idx added
5bd703460fd90_Mutect2-exome-panel.vcf.idx added
5bd701db75c73_Mutect2-WGS-panel-b37.vcf added
5bd704229f751_Mutect2-WGS-panel-b37.vcf.idx added
5bd70659c7af9_small_exac_common_3.vcf added
5bd70466195ac_small_exac_common_3.vcf.idx added
5bd703ba53759_1000g_pon.hg38.vcf.gz added
5bd70af4cf5e_1000g_pon.hg38.vcf.gz.tbi added
5bd704dfb872a_af-only-gnomad.hg38.vcf.gz added
5bd7062ab02d4_af-only-gnomad.hg38.vcf.gz.tbi added
5bd7039dc8ce8_small_exac_common_3.hg38.vcf.gz added
5bd706b79b31_small_exac_common_3.hg38.vcf.gz.tbi added
5bd702787b82d_gencode.v41.annotation.gtf added
5bd7055080985_gencode.v42.annotation.gtf added
5bd70724942c8_gencode.vM30.annotation.gtf added
5bd706312840_gencode.vM31.annotation.gtf added
5bd707a5e1a2f_gencode.v41.transcripts.fa added
5bd70605455c2_gencode.v41.transcripts.fa.fai added
5bd703f20e4dc_gencode.v42.transcripts.fa added
5bd7055ee617f_gencode.v42.transcripts.fa.fai added
5bd7029f934e0_gencode.vM30.pc_transcripts.fa added
5bd707f9fd5cb_gencode.vM30.pc_transcripts.fa.fai added
5bd704043d709_gencode.vM31.pc_transcripts.fa added
5bd707727fc31_gencode.vM31.pc_transcripts.fa.fai added
5bd70601b2d01_GRCh38.primary_assembly.genome.fa.1.ht2 added
5bd701b162c47_GRCh38.primary_assembly.genome.fa.2.ht2 added
5bd7023cca4b2_GRCh38.primary_assembly.genome.fa.3.ht2 added
5bd707f586113_GRCh38.primary_assembly.genome.fa.4.ht2 added
5bd703581f429_GRCh38.primary_assembly.genome.fa.5.ht2 added
5bd7047c0ce99_GRCh38.primary_assembly.genome.fa.6.ht2 added
5bd7070cab448_GRCh38.primary_assembly.genome.fa.7.ht2 added
5bd701033087b_GRCh38.primary_assembly.genome.fa.8.ht2 added
5bd707c21cc29_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
5bd70e8210bb_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
5bd70525cffcc_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
5bd7061be4722_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
5bd7054e3a667_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
5bd70e023726_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
5bd706cb31680_GRCh38_full_analysis_set_plus_decoy_hla.fa added
5bd7022df2d92_GRCh38.primary_assembly.genome.fa.fai added
5bd7070ad39fa_GRCh38.primary_assembly.genome.fa.amb added
5bd70268fa368_GRCh38.primary_assembly.genome.fa.ann added
5bd702996c8c3_GRCh38.primary_assembly.genome.fa.bwt added
5bd701834f228_GRCh38.primary_assembly.genome.fa.pac added
5bd707b97acee_GRCh38.primary_assembly.genome.fa.sa added
5bd701be00b8b_GRCh38.primary_assembly.genome.fa added
5bd701e661a68_hs37d5.fa.fai added
5bd7075f5c71d_hs37d5.fa.amb added
5bd707c34614d_hs37d5.fa.ann added
5bd705d86ff44_hs37d5.fa.bwt added
5bd704be4289d_hs37d5.fa.pac added
5bd70262d962e_hs37d5.fa.sa added
5bd705d26d510_hs37d5.fa added
5bd70c27ffa6_complete_ref_lens.bin added
5bd701d55925f_ctable.bin added
5bd703d420211_ctg_offsets.bin added
5bd70273e2bed_duplicate_clusters.tsv added
5bd7041223711_info.json added
5bd703c9a6324_mphf.bin added
5bd705cc02016_pos.bin added
5bd708e305ab_pre_indexing.log added
5bd702d65176c_rank.bin added
5bd706cf32891_ref_indexing.log added
5bd70504d1d4_refAccumLengths.bin added
5bd703be72828_reflengths.bin added
5bd703f50285e_refseq.bin added
5bd7066c318f7_seq.bin added
5bd7010cace8f_versionInfo.json added
5bd704d525f84_salmon_index added
5bd7053762f77_chrLength.txt added
5bd7033a9fc21_chrName.txt added
5bd703dff997e_chrNameLength.txt added
5bd707a05d2e0_chrStart.txt added
5bd705d40c4e4_exonGeTrInfo.tab added
5bd7056348ba6_exonInfo.tab added
5bd70759d7fce_geneInfo.tab added
5bd707920d070_Genome added
5bd70749aa60f_genomeParameters.txt added
5bd706b9346eb_Log.out added
5bd70755531bd_SA added
5bd705221a553_SAindex added
5bd7037776f88_sjdbInfo.txt added
5bd701b82c7eb_sjdbList.fromGTF.out.tab added
5bd702f487a63_sjdbList.out.tab added
5bd70439f6f2e_transcriptInfo.tab added
5bd7038d85a4b_GRCh38.GENCODE.v42_100 added
5bd706c8a7c74_knownGene_hg38.sql added
5bd706add9b1b_knownGene_hg38.txt added
5bd7079fa915c_refGene_hg38.sql added
5bd702924df98_refGene_hg38.txt added
5bd70479dbb32_knownGene_mm39.sql added
5bd702dd9707_knownGene_mm39.txt added
5bd705689f705_refGene_mm39.sql added
5bd703490e3c3_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/Rtmp4mzOyX/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
17.727 1.359 19.579
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.617 | 0.246 | 5.865 | |
| dataSearch | 1.093 | 0.007 | 1.101 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.711 | 0.135 | 4.151 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.119 | 0.003 | 0.123 | |
| recipeLoad | 1.238 | 0.071 | 1.310 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.528 | 0.020 | 0.548 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |