Qian Liu
| Snapshot Date: 2026-05-18 13:40 -0400 (Mon, 18 May 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_23 |
| git_last_commit: bb3489b |
| git_last_commit_date: 2026-04-28 08:59:39 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-19 11:33 -0400 (Tue, 19 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4995 |
| 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 1815/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.12.0 (landing page) Qian Liu
| nebbiolo1 | 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: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2026-05-19 03:58:40 -0400 (Tue, 19 May 2026) |
| EndedAt: 2026-05-19 04:01:30 -0400 (Tue, 19 May 2026) |
| EllapsedTime: 169.3 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-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: 2026-05-19 07:58:41 UTC
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.12.0’
* 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 6.857 0.7 7.557
* 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 ‘1.12.0’ ** 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...
1a7416290a27d4_GRCh38.primary_assembly.genome.fa.1.bt2 added
1a7416658ead95_GRCh38.primary_assembly.genome.fa.2.bt2 added
1a741653f0a69_GRCh38.primary_assembly.genome.fa.3.bt2 added
1a741649f7b031_GRCh38.primary_assembly.genome.fa.4.bt2 added
1a74161f09b0cf_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1a741669fe69b0_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1a741638eac9b7_outfile.txt added
1a741642c8060b_GRCh37_to_GRCh38.chain added
1a7416627fb13c_GRCh37_to_NCBI34.chain added
1a74166ab04095_GRCh37_to_NCBI35.chain added
1a74164ec2f622_GRCh37_to_NCBI36.chain added
1a741675eacf1e_GRCh38_to_GRCh37.chain added
1a74167f47d94a_GRCh38_to_NCBI34.chain added
1a74166b3006b9_GRCh38_to_NCBI35.chain added
1a7416634b45e9_GRCh38_to_NCBI36.chain added
1a741612434973_NCBI34_to_GRCh37.chain added
1a74162faf0ee2_NCBI34_to_GRCh38.chain added
1a74165d0cc0c3_NCBI35_to_GRCh37.chain added
1a7416b772d36_NCBI35_to_GRCh38.chain added
1a74166c5679e7_NCBI36_to_GRCh37.chain added
1a741660682f95_NCBI36_to_GRCh38.chain added
1a74162d95131c_GRCm38_to_NCBIM36.chain added
1a7416290734e9_GRCm38_to_NCBIM37.chain added
1a7416745d5d03_NCBIM36_to_GRCm38.chain added
1a7416307d4f4c_NCBIM37_to_GRCm38.chain added
1a741621c92983_1000G_omni2.5.b37.vcf.gz added
1a741625216c63_1000G_omni2.5.b37.vcf.gz.tbi added
1a74166d077d6_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1a74167efeea18_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1a74161fe52bd1_1000G_omni2.5.hg38.vcf.gz added
1a741623585b3_1000G_omni2.5.hg38.vcf.gz.tbi added
1a7416280911ec_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1a7416573d966_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1a7416774901c_af-only-gnomad.raw.sites.vcf added
1a74167200c21d_af-only-gnomad.raw.sites.vcf.idx added
1a7416247d8a36_Mutect2-exome-panel.vcf.idx added
1a74167172f9cd_Mutect2-WGS-panel-b37.vcf added
1a74162aeb8bd4_Mutect2-WGS-panel-b37.vcf.idx added
1a741667459041_small_exac_common_3.vcf added
1a741653f2ab09_small_exac_common_3.vcf.idx added
1a7416159bcc69_1000g_pon.hg38.vcf.gz added
1a741636088663_1000g_pon.hg38.vcf.gz.tbi added
1a741649dd7a27_af-only-gnomad.hg38.vcf.gz added
1a741614e3a5b3_af-only-gnomad.hg38.vcf.gz.tbi added
1a741621388d1c_small_exac_common_3.hg38.vcf.gz added
1a74162d28c010_small_exac_common_3.hg38.vcf.gz.tbi added
1a74162726ef26_gencode.v41.annotation.gtf added
1a741650e79bfe_gencode.v42.annotation.gtf added
1a7416a3580d3_gencode.vM30.annotation.gtf added
1a7416329e1c5d_gencode.vM31.annotation.gtf added
1a74163d3e15e5_gencode.v41.transcripts.fa added
1a74166a9db068_gencode.v41.transcripts.fa.fai added
1a741660332f79_gencode.v42.transcripts.fa added
1a741666454ace_gencode.v42.transcripts.fa.fai added
1a74165efb0d6b_gencode.vM30.pc_transcripts.fa added
1a741610b07ec5_gencode.vM30.pc_transcripts.fa.fai added
1a741680e7451_gencode.vM31.pc_transcripts.fa added
1a741641c79cf_gencode.vM31.pc_transcripts.fa.fai added
1a74161780f69b_GRCh38.primary_assembly.genome.fa.1.ht2 added
1a741670d5e69_GRCh38.primary_assembly.genome.fa.2.ht2 added
1a74162401a5a0_GRCh38.primary_assembly.genome.fa.3.ht2 added
1a741619b67c4e_GRCh38.primary_assembly.genome.fa.4.ht2 added
1a74162f167055_GRCh38.primary_assembly.genome.fa.5.ht2 added
1a741629757f06_GRCh38.primary_assembly.genome.fa.6.ht2 added
1a7416212b0c6b_GRCh38.primary_assembly.genome.fa.7.ht2 added
1a741621173272_GRCh38.primary_assembly.genome.fa.8.ht2 added
1a74164df3093c_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1a7416129e0638_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1a74164c02be46_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1a74163538997d_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1a74166690b141_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1a7416619e8aaf_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1a74166b411fe0_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1a7416306e2b69_GRCh38.primary_assembly.genome.fa.fai added
1a741676823063_GRCh38.primary_assembly.genome.fa.amb added
1a7416c79acfc_GRCh38.primary_assembly.genome.fa.ann added
1a74165d96eb79_GRCh38.primary_assembly.genome.fa.bwt added
1a74161da91f89_GRCh38.primary_assembly.genome.fa.pac added
1a74165d6148fb_GRCh38.primary_assembly.genome.fa.sa added
1a741667cc6c4d_GRCh38.primary_assembly.genome.fa added
1a741650473be6_hs37d5.fa.fai added
1a74161a9f5ee0_hs37d5.fa.amb added
1a7416526a1cb5_hs37d5.fa.ann added
1a7416307a6b5f_hs37d5.fa.bwt added
1a7416e4a9af_hs37d5.fa.pac added
1a741631652a21_hs37d5.fa.sa added
1a7416412aea25_hs37d5.fa added
1a74168f31e00_complete_ref_lens.bin added
1a74163581a3f0_ctable.bin added
1a741658abe0c0_ctg_offsets.bin added
1a741610007c6a_duplicate_clusters.tsv added
1a741659834990_info.json added
1a741672625d0f_mphf.bin added
1a74163f16ecbf_pos.bin added
1a74162f8c896_pre_indexing.log added
1a7416138d697a_rank.bin added
1a7416602e1f32_ref_indexing.log added
1a741650ebd1d3_refAccumLengths.bin added
1a7416262b6fb2_reflengths.bin added
1a74162c30dd78_refseq.bin added
1a74166246b50_seq.bin added
1a7416cbc20f3_versionInfo.json added
1a7416dcf6828_salmon_index added
1a741671658b31_chrLength.txt added
1a74163d2a4c5c_chrName.txt added
1a7416451988b_chrNameLength.txt added
1a74167ddf382d_chrStart.txt added
1a74161ac137d6_exonGeTrInfo.tab added
1a741621fab814_exonInfo.tab added
1a74165b408128_geneInfo.tab added
1a741628da423_Genome added
1a74167241f3fb_genomeParameters.txt added
1a741675dfe009_Log.out added
1a741654f7c0d8_SA added
1a741622bc5f5a_SAindex added
1a741676c489b8_sjdbInfo.txt added
1a741665ceaf9_sjdbList.fromGTF.out.tab added
1a741663e7497f_sjdbList.out.tab added
1a74167fb7a7b8_transcriptInfo.tab added
1a74163bde8ee9_GRCh38.GENCODE.v42_100 added
1a74163c932a40_knownGene_hg38.sql added
1a7416fb82422_knownGene_hg38.txt added
1a74161561d879_refGene_hg38.sql added
1a74162ef5874f_refGene_hg38.txt added
1a74164ecf10e2_knownGene_mm39.sql added
1a7416185aa110_knownGene_mm39.txt added
1a74164282f0c9_refGene_mm39.sql added
1a74162efd3014_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/RtmpceZGLY/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
18.575 1.223 19.916
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.857 | 0.700 | 7.557 | |
| dataSearch | 1.173 | 0.046 | 1.220 | |
| dataUpdate | 0.001 | 0.000 | 0.001 | |
| getCloudData | 2.721 | 0.196 | 3.246 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.001 | 0.001 | |
| recipeHub-class | 0.129 | 0.009 | 0.139 | |
| recipeLoad | 1.277 | 0.077 | 1.355 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.558 | 0.017 | 0.576 | |
| recipeUpdate | 0 | 0 | 0 | |