Qian Liu
| Snapshot Date: 2026-05-20 13:45 -0400 (Wed, 20 May 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 2026-05-21 11:33 -0400 (Thu, 21 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" | 4936 |
| 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 1787/2378 | 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: 2026-05-21 03:40:51 -0400 (Thu, 21 May 2026) |
| EndedAt: 2026-05-21 03:43:41 -0400 (Thu, 21 May 2026) |
| EllapsedTime: 170.3 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: 2026-05-21 07:40:51 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 8.168 0.418 9.807
* 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...
d0c204e1a283d_GRCh38.primary_assembly.genome.fa.1.bt2 added
d0c20610b0e8_GRCh38.primary_assembly.genome.fa.2.bt2 added
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d0c202cf90d57_GRCh38.primary_assembly.genome.fa.4.bt2 added
d0c20fea78cf_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
d0c203623c29b_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
d0c203dc35a42_outfile.txt added
d0c202c327e9_GRCh37_to_GRCh38.chain added
d0c204c7c9604_GRCh37_to_NCBI34.chain added
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d0c20a6bfa4e_GRCh37_to_NCBI36.chain added
d0c2029cc2d79_GRCh38_to_GRCh37.chain added
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d0c202594c90e_NCBI34_to_GRCh37.chain added
d0c20608864ae_NCBI34_to_GRCh38.chain added
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d0c2011fe9288_NCBI35_to_GRCh38.chain added
d0c20719ee9aa_NCBI36_to_GRCh37.chain added
d0c20782d210_NCBI36_to_GRCh38.chain added
d0c20712f10a5_GRCm38_to_NCBIM36.chain added
d0c201ce6d314_GRCm38_to_NCBIM37.chain added
d0c201bfbedc0_NCBIM36_to_GRCm38.chain added
d0c206cd674df_NCBIM37_to_GRCm38.chain added
d0c20394b6622_1000G_omni2.5.b37.vcf.gz added
d0c206a010367_1000G_omni2.5.b37.vcf.gz.tbi added
d0c2073719cd_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
d0c2062e293a4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
d0c206b25e1a_1000G_omni2.5.hg38.vcf.gz added
d0c204c9b6176_1000G_omni2.5.hg38.vcf.gz.tbi added
d0c2030fcbbe1_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
d0c20cc30f02_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
d0c202ef9f638_af-only-gnomad.raw.sites.vcf added
d0c205df5c938_af-only-gnomad.raw.sites.vcf.idx added
d0c201cad87d1_Mutect2-exome-panel.vcf.idx added
d0c20651db8d3_Mutect2-WGS-panel-b37.vcf added
d0c201bb9237b_Mutect2-WGS-panel-b37.vcf.idx added
d0c201f70afba_small_exac_common_3.vcf added
d0c20319a4ed7_small_exac_common_3.vcf.idx added
d0c2025265527_1000g_pon.hg38.vcf.gz added
d0c2029dcaa08_1000g_pon.hg38.vcf.gz.tbi added
d0c205b667c50_af-only-gnomad.hg38.vcf.gz added
d0c205460af33_af-only-gnomad.hg38.vcf.gz.tbi added
d0c206032002c_small_exac_common_3.hg38.vcf.gz added
d0c201cf3e3d7_small_exac_common_3.hg38.vcf.gz.tbi added
d0c2079f57841_gencode.v41.annotation.gtf added
d0c2040ba64da_gencode.v42.annotation.gtf added
d0c202d3bf7d1_gencode.vM30.annotation.gtf added
d0c20bf40ac9_gencode.vM31.annotation.gtf added
d0c2032594e85_gencode.v41.transcripts.fa added
d0c2034bec9e2_gencode.v41.transcripts.fa.fai added
d0c207d231b6e_gencode.v42.transcripts.fa added
d0c204f402199_gencode.v42.transcripts.fa.fai added
d0c2050bab7a2_gencode.vM30.pc_transcripts.fa added
d0c2069f9904d_gencode.vM30.pc_transcripts.fa.fai added
d0c2088b87bb_gencode.vM31.pc_transcripts.fa added
d0c203abbbb09_gencode.vM31.pc_transcripts.fa.fai added
d0c207130aa1a_GRCh38.primary_assembly.genome.fa.1.ht2 added
d0c206b6e1b5f_GRCh38.primary_assembly.genome.fa.2.ht2 added
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d0c201c6ad740_GRCh38.primary_assembly.genome.fa.5.ht2 added
d0c204e312826_GRCh38.primary_assembly.genome.fa.6.ht2 added
d0c206cc601c8_GRCh38.primary_assembly.genome.fa.7.ht2 added
d0c207a60a079_GRCh38.primary_assembly.genome.fa.8.ht2 added
d0c206adeaff7_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
d0c2051e3ba9c_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
d0c201619c3f4_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
d0c20a4f5fb2_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
d0c2037e0973_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
d0c203b40191b_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
d0c20342c09ba_GRCh38_full_analysis_set_plus_decoy_hla.fa added
d0c205ee485c4_GRCh38.primary_assembly.genome.fa.fai added
d0c20fa0c84f_GRCh38.primary_assembly.genome.fa.amb added
d0c20145e09e7_GRCh38.primary_assembly.genome.fa.ann added
d0c207bd8699b_GRCh38.primary_assembly.genome.fa.bwt added
d0c209964090_GRCh38.primary_assembly.genome.fa.pac added
d0c2055186ec1_GRCh38.primary_assembly.genome.fa.sa added
d0c202914616d_GRCh38.primary_assembly.genome.fa added
d0c20158a4b5a_hs37d5.fa.fai added
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d0c2012ad66c8_hs37d5.fa.bwt added
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d0c206dd7a130_ctg_offsets.bin added
d0c204aab81fa_duplicate_clusters.tsv added
d0c202ab7b71e_info.json added
d0c202ba3acc1_mphf.bin added
d0c206716593b_pos.bin added
d0c2078e8df44_pre_indexing.log added
d0c201869ae89_rank.bin added
d0c206176f9b4_ref_indexing.log added
d0c2063c78f3b_refAccumLengths.bin added
d0c206a4d6925_reflengths.bin added
d0c207790bda8_refseq.bin added
d0c206e16eeed_seq.bin added
d0c206dcb7299_versionInfo.json added
d0c2032d0d6c3_salmon_index added
d0c202242f8a8_chrLength.txt added
d0c204caff85d_chrName.txt added
d0c2042719f12_chrNameLength.txt added
d0c2036a1028f_chrStart.txt added
d0c20488861f8_exonGeTrInfo.tab added
d0c204c07dfa3_exonInfo.tab added
d0c20bb97150_geneInfo.tab added
d0c20719cc365_Genome added
d0c2061922afd_genomeParameters.txt added
d0c20132b2e97_Log.out added
d0c204f6feeb4_SA added
d0c20743f91c5_SAindex added
d0c2069dd0d76_sjdbInfo.txt added
d0c207dfdd1a5_sjdbList.fromGTF.out.tab added
d0c2070e688db_sjdbList.out.tab added
d0c20491a7411_transcriptInfo.tab added
d0c2067476fa0_GRCh38.GENCODE.v42_100 added
d0c205ebe2a0c_knownGene_hg38.sql added
d0c2013c5f60c_knownGene_hg38.txt added
d0c2011ff26be_refGene_hg38.sql added
d0c20a61d6cd_refGene_hg38.txt added
d0c207adc4f47_knownGene_mm39.sql added
d0c20ae80602_knownGene_mm39.txt added
d0c2022cb8556_refGene_mm39.sql added
d0c205c5348fb_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/RtmpBd53jH/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
18.611 1.027 20.357
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 8.168 | 0.418 | 9.807 | |
| dataSearch | 1.108 | 0.006 | 1.114 | |
| dataUpdate | 0.001 | 0.000 | 0.001 | |
| getCloudData | 2.920 | 0.289 | 4.014 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.151 | 0.009 | 0.160 | |
| recipeLoad | 1.368 | 0.078 | 1.448 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.548 | 0.029 | 0.577 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |