Qian Liu
| Snapshot Date: 2026-05-11 13:45 -0400 (Mon, 11 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 2026-05-12 11:33 -0400 (Tue, 12 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" | 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 1783/2374 | 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: 2026-05-12 03:36:54 -0400 (Tue, 12 May 2026) |
| EndedAt: 2026-05-12 03:39:39 -0400 (Tue, 12 May 2026) |
| EllapsedTime: 165.3 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: 2026-05-12 07:36:54 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 5.987 0.282 6.274
* 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...
254c885da65de7_GRCh38.primary_assembly.genome.fa.1.bt2 added
254c883c46c7ac_GRCh38.primary_assembly.genome.fa.2.bt2 added
254c8813582bb9_GRCh38.primary_assembly.genome.fa.3.bt2 added
254c88375883b8_GRCh38.primary_assembly.genome.fa.4.bt2 added
254c885593079f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
254c885e9b852_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
254c885aca2aec_outfile.txt added
254c88557726c0_GRCh37_to_GRCh38.chain added
254c8818e6b868_GRCh37_to_NCBI34.chain added
254c88272b5cd2_GRCh37_to_NCBI35.chain added
254c883fe5e075_GRCh37_to_NCBI36.chain added
254c882ce8a37d_GRCh38_to_GRCh37.chain added
254c8877e826ad_GRCh38_to_NCBI34.chain added
254c881b09365d_GRCh38_to_NCBI35.chain added
254c8851a876a5_GRCh38_to_NCBI36.chain added
254c88209151c0_NCBI34_to_GRCh37.chain added
254c883c51de96_NCBI34_to_GRCh38.chain added
254c885b955b1a_NCBI35_to_GRCh37.chain added
254c8827657ea6_NCBI35_to_GRCh38.chain added
254c886737f5c4_NCBI36_to_GRCh37.chain added
254c8819cdf50_NCBI36_to_GRCh38.chain added
254c886514b5f4_GRCm38_to_NCBIM36.chain added
254c8841cf90ed_GRCm38_to_NCBIM37.chain added
254c884cb5256c_NCBIM36_to_GRCm38.chain added
254c882cb7da48_NCBIM37_to_GRCm38.chain added
254c8817246d5b_1000G_omni2.5.b37.vcf.gz added
254c882f45e49b_1000G_omni2.5.b37.vcf.gz.tbi added
254c887631140_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
254c8843f209f1_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
254c885cbe2adf_1000G_omni2.5.hg38.vcf.gz added
254c8815db40e1_1000G_omni2.5.hg38.vcf.gz.tbi added
254c88219867d9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
254c881904f28b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
254c8829336c9a_af-only-gnomad.raw.sites.vcf added
254c8858f0eb91_af-only-gnomad.raw.sites.vcf.idx added
254c886e97fa2a_Mutect2-exome-panel.vcf.idx added
254c882f1d24ed_Mutect2-WGS-panel-b37.vcf added
254c8833bb167d_Mutect2-WGS-panel-b37.vcf.idx added
254c88440f20eb_small_exac_common_3.vcf added
254c884803dd55_small_exac_common_3.vcf.idx added
254c885ae67350_1000g_pon.hg38.vcf.gz added
254c883f50160_1000g_pon.hg38.vcf.gz.tbi added
254c8874ec80d3_af-only-gnomad.hg38.vcf.gz added
254c8852ce99fd_af-only-gnomad.hg38.vcf.gz.tbi added
254c881efe37bd_small_exac_common_3.hg38.vcf.gz added
254c884694f778_small_exac_common_3.hg38.vcf.gz.tbi added
254c88735febbe_gencode.v41.annotation.gtf added
254c885b501654_gencode.v42.annotation.gtf added
254c88222a5292_gencode.vM30.annotation.gtf added
254c881ac56a64_gencode.vM31.annotation.gtf added
254c8842880c18_gencode.v41.transcripts.fa added
254c8823c731e3_gencode.v41.transcripts.fa.fai added
254c887fda2059_gencode.v42.transcripts.fa added
254c884579d05_gencode.v42.transcripts.fa.fai added
254c88707c574f_gencode.vM30.pc_transcripts.fa added
254c882c91faa1_gencode.vM30.pc_transcripts.fa.fai added
254c881b7c0a60_gencode.vM31.pc_transcripts.fa added
254c881fc23bea_gencode.vM31.pc_transcripts.fa.fai added
254c8833f50be1_GRCh38.primary_assembly.genome.fa.1.ht2 added
254c885f6e1452_GRCh38.primary_assembly.genome.fa.2.ht2 added
254c887c8066c9_GRCh38.primary_assembly.genome.fa.3.ht2 added
254c8849d04cc2_GRCh38.primary_assembly.genome.fa.4.ht2 added
254c881067c2b_GRCh38.primary_assembly.genome.fa.5.ht2 added
254c8815855955_GRCh38.primary_assembly.genome.fa.6.ht2 added
254c887303b95d_GRCh38.primary_assembly.genome.fa.7.ht2 added
254c8859f767bc_GRCh38.primary_assembly.genome.fa.8.ht2 added
254c8841d537f_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
254c882220de4a_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
254c88db27e3a_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
254c88482c746a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
254c886a24bb9f_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
254c886898f18a_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
254c884c2175cb_GRCh38_full_analysis_set_plus_decoy_hla.fa added
254c885f113c72_GRCh38.primary_assembly.genome.fa.fai added
254c883b678b87_GRCh38.primary_assembly.genome.fa.amb added
254c886b1fad88_GRCh38.primary_assembly.genome.fa.ann added
254c8825a633ea_GRCh38.primary_assembly.genome.fa.bwt added
254c882ec77745_GRCh38.primary_assembly.genome.fa.pac added
254c88466fc3dc_GRCh38.primary_assembly.genome.fa.sa added
254c8847d0867d_GRCh38.primary_assembly.genome.fa added
254c88498ce1aa_hs37d5.fa.fai added
254c888f7cff5_hs37d5.fa.amb added
254c886b97b860_hs37d5.fa.ann added
254c8849670203_hs37d5.fa.bwt added
254c88d4f6cfa_hs37d5.fa.pac added
254c885c140faf_hs37d5.fa.sa added
254c8875f8fca4_hs37d5.fa added
254c8828cb775b_complete_ref_lens.bin added
254c887bd64b99_ctable.bin added
254c8829ee0885_ctg_offsets.bin added
254c888398bad_duplicate_clusters.tsv added
254c887856b263_info.json added
254c8873be5548_mphf.bin added
254c8894007d8_pos.bin added
254c88ddc0bb8_pre_indexing.log added
254c8866c20ea5_rank.bin added
254c8863376f94_ref_indexing.log added
254c8811f95f37_refAccumLengths.bin added
254c888e2ecef_reflengths.bin added
254c8870e9edce_refseq.bin added
254c885a25d3a2_seq.bin added
254c887307a88e_versionInfo.json added
254c885982df58_salmon_index added
254c882647496d_chrLength.txt added
254c885218e501_chrName.txt added
254c8814ea6ae0_chrNameLength.txt added
254c881166f6f5_chrStart.txt added
254c8877bf18eb_exonGeTrInfo.tab added
254c8843b1e225_exonInfo.tab added
254c8857d6bad2_geneInfo.tab added
254c883f8f9f68_Genome added
254c88d3ec3cf_genomeParameters.txt added
254c8860ce8ac7_Log.out added
254c882b2757c8_SA added
254c8856a5c5d2_SAindex added
254c886e1df7c1_sjdbInfo.txt added
254c8873b6777_sjdbList.fromGTF.out.tab added
254c884c9ec276_sjdbList.out.tab added
254c8816e96f1c_transcriptInfo.tab added
254c88311b311_GRCh38.GENCODE.v42_100 added
254c88768ccafc_knownGene_hg38.sql added
254c881f22fac9_knownGene_hg38.txt added
254c887b686574_refGene_hg38.sql added
254c886a4b2044_refGene_hg38.txt added
254c88286302a1_knownGene_mm39.sql added
254c88944712c_knownGene_mm39.txt added
254c88510d2ee9_refGene_mm39.sql added
254c88b9a7236_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/Rtmpw2Lvvx/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
17.848 1.005 19.572
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.987 | 0.282 | 6.274 | |
| dataSearch | 1.086 | 0.010 | 1.096 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.582 | 0.089 | 3.575 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.118 | 0.001 | 0.120 | |
| recipeLoad | 1.211 | 0.013 | 1.226 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.506 | 0.008 | 0.514 | |
| recipeUpdate | 0 | 0 | 0 | |