Qian Liu
| Snapshot Date: 2026-05-08 13:45 -0400 (Fri, 08 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 2026-05-09 15:11 -0400 (Sat, 09 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" | 4890 |
| 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 1783/2374 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BIOCCHECK | BUILD BIN | ||||||||
| ReUseData 1.13.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | ERRORS | | ||||||||
| 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: 2026-05-09 03:37:36 -0400 (Sat, 09 May 2026) |
| EndedAt: 2026-05-09 03:40:26 -0400 (Sat, 09 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: 2026-05-09 07:37:36 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 5.901 0.216 6.121
* 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...
2a021f6a7f6b38_GRCh38.primary_assembly.genome.fa.1.bt2 added
2a021f733d06c6_GRCh38.primary_assembly.genome.fa.2.bt2 added
2a021f3994a9d9_GRCh38.primary_assembly.genome.fa.3.bt2 added
2a021f46008aa0_GRCh38.primary_assembly.genome.fa.4.bt2 added
2a021f744a30be_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2a021f78231840_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2a021f23e3698d_outfile.txt added
2a021f650f388b_GRCh37_to_GRCh38.chain added
2a021f415a6f2e_GRCh37_to_NCBI34.chain added
2a021f723ab53_GRCh37_to_NCBI35.chain added
2a021f99b7845_GRCh37_to_NCBI36.chain added
2a021f22f429cd_GRCh38_to_GRCh37.chain added
2a021f4c328fc8_GRCh38_to_NCBI34.chain added
2a021ffcb6da0_GRCh38_to_NCBI35.chain added
2a021fa329bd0_GRCh38_to_NCBI36.chain added
2a021f49f88568_NCBI34_to_GRCh37.chain added
2a021f478bf8cd_NCBI34_to_GRCh38.chain added
2a021f66d9bee6_NCBI35_to_GRCh37.chain added
2a021f3fdad0cd_NCBI35_to_GRCh38.chain added
2a021f386c6b10_NCBI36_to_GRCh37.chain added
2a021f4fc4cf8a_NCBI36_to_GRCh38.chain added
2a021f28c85244_GRCm38_to_NCBIM36.chain added
2a021f49b21f94_GRCm38_to_NCBIM37.chain added
2a021f37a71d_NCBIM36_to_GRCm38.chain added
2a021f494888c1_NCBIM37_to_GRCm38.chain added
2a021f34a89493_1000G_omni2.5.b37.vcf.gz added
2a021f7ff2bed6_1000G_omni2.5.b37.vcf.gz.tbi added
2a021f6a914936_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2a021f539c8eae_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2a021f545f6342_1000G_omni2.5.hg38.vcf.gz added
2a021f11063046_1000G_omni2.5.hg38.vcf.gz.tbi added
2a021f3e1bf9e7_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2a021f479c6a09_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2a021f4a9ada1f_af-only-gnomad.raw.sites.vcf added
2a021f41c8487_af-only-gnomad.raw.sites.vcf.idx added
2a021f3be69ac7_Mutect2-exome-panel.vcf.idx added
2a021f42bdf25f_Mutect2-WGS-panel-b37.vcf added
2a021f27ffee14_Mutect2-WGS-panel-b37.vcf.idx added
2a021f20f5d352_small_exac_common_3.vcf added
2a021f418618e_small_exac_common_3.vcf.idx added
2a021f2f239967_1000g_pon.hg38.vcf.gz added
2a021f2a914b98_1000g_pon.hg38.vcf.gz.tbi added
2a021f270c8b5b_af-only-gnomad.hg38.vcf.gz added
2a021f7b56292f_af-only-gnomad.hg38.vcf.gz.tbi added
2a021f3a5cb938_small_exac_common_3.hg38.vcf.gz added
2a021f313f272b_small_exac_common_3.hg38.vcf.gz.tbi added
2a021f454eae98_gencode.v41.annotation.gtf added
2a021f1e8b205_gencode.v42.annotation.gtf added
2a021f1818e611_gencode.vM30.annotation.gtf added
2a021f5297f65_gencode.vM31.annotation.gtf added
2a021f3a551d16_gencode.v41.transcripts.fa added
2a021f67ddb59b_gencode.v41.transcripts.fa.fai added
2a021f2df1d1a9_gencode.v42.transcripts.fa added
2a021f4073caa_gencode.v42.transcripts.fa.fai added
2a021f68155cb8_gencode.vM30.pc_transcripts.fa added
2a021f773a5a6a_gencode.vM30.pc_transcripts.fa.fai added
2a021f38afd13d_gencode.vM31.pc_transcripts.fa added
2a021f68081b8e_gencode.vM31.pc_transcripts.fa.fai added
2a021f61cba3a0_GRCh38.primary_assembly.genome.fa.1.ht2 added
2a021fc4c5fec_GRCh38.primary_assembly.genome.fa.2.ht2 added
2a021f3c677ed1_GRCh38.primary_assembly.genome.fa.3.ht2 added
2a021f72d1d3e6_GRCh38.primary_assembly.genome.fa.4.ht2 added
2a021f4a6859d3_GRCh38.primary_assembly.genome.fa.5.ht2 added
2a021f403e8da_GRCh38.primary_assembly.genome.fa.6.ht2 added
2a021f3d6cae05_GRCh38.primary_assembly.genome.fa.7.ht2 added
2a021f4e84de5a_GRCh38.primary_assembly.genome.fa.8.ht2 added
2a021f3fea83a1_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2a021f2aa065_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2a021f7684cc6e_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2a021f60e056f3_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2a021f44301f3_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2a021f25a865d5_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2a021fb71a28b_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2a021f2b4f8d4e_GRCh38.primary_assembly.genome.fa.fai added
2a021f20fe8f04_GRCh38.primary_assembly.genome.fa.amb added
2a021f45ce5bc4_GRCh38.primary_assembly.genome.fa.ann added
2a021f5c8eb479_GRCh38.primary_assembly.genome.fa.bwt added
2a021f664d3d9c_GRCh38.primary_assembly.genome.fa.pac added
2a021f47b70dc9_GRCh38.primary_assembly.genome.fa.sa added
2a021f74a79a8a_GRCh38.primary_assembly.genome.fa added
2a021f6b76bd02_hs37d5.fa.fai added
2a021f20c2adf_hs37d5.fa.amb added
2a021f5c855025_hs37d5.fa.ann added
2a021f19688eab_hs37d5.fa.bwt added
2a021f6136789_hs37d5.fa.pac added
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2a021f2ca2c86b_ctable.bin added
2a021f726e8cb6_ctg_offsets.bin added
2a021f4b0f98b3_duplicate_clusters.tsv added
2a021f690a473c_info.json added
2a021f6540609d_mphf.bin added
2a021f1577f286_pos.bin added
2a021f6d0e3016_pre_indexing.log added
2a021f22ad0ea2_rank.bin added
2a021f63fcd0e0_ref_indexing.log added
2a021f2cf8b3b7_refAccumLengths.bin added
2a021f22d7af07_reflengths.bin added
2a021f5a819d4e_refseq.bin added
2a021fdd90aab_seq.bin added
2a021f271ab0fa_versionInfo.json added
2a021f2a0323_salmon_index added
2a021f194aad36_chrLength.txt added
2a021f526a3e48_chrName.txt added
2a021f21289227_chrNameLength.txt added
2a021f5f1908fa_chrStart.txt added
2a021f2ef8f2c1_exonGeTrInfo.tab added
2a021f775cfc4_exonInfo.tab added
2a021f26d016c4_geneInfo.tab added
2a021f23a08d4b_Genome added
2a021f72ec8cc6_genomeParameters.txt added
2a021f28dc41a3_Log.out added
2a021f25dd70_SA added
2a021fc551b71_SAindex added
2a021f2eefa92d_sjdbInfo.txt added
2a021f44c08a4d_sjdbList.fromGTF.out.tab added
2a021f1cf80487_sjdbList.out.tab added
2a021f6db2e1f4_transcriptInfo.tab added
2a021f716352b9_GRCh38.GENCODE.v42_100 added
2a021ff66913e_knownGene_hg38.sql added
2a021f38c27aa7_knownGene_hg38.txt added
2a021f5a6d99f5_refGene_hg38.sql added
2a021f74a6f1db_refGene_hg38.txt added
2a021f4e3a6d2d_knownGene_mm39.sql added
2a021f477bca0c_knownGene_mm39.txt added
2a021f1754007d_refGene_mm39.sql added
2a021f32373e0d_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/Rtmp1WHgGj/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
18.393 1.050 20.391
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.901 | 0.216 | 6.121 | |
| dataSearch | 1.074 | 0.004 | 1.079 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.594 | 0.109 | 3.628 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.001 | 0.001 | |
| recipeHub-class | 0.127 | 0.001 | 0.128 | |
| recipeLoad | 1.274 | 0.079 | 1.354 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.531 | 0.016 | 0.548 | |
| recipeUpdate | 0 | 0 | 0 | |