Qian Liu
| Snapshot Date: 2026-02-26 13:40 -0500 (Thu, 26 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: 4a5d06b |
| git_last_commit_date: 2025-10-29 11:20:44 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-27 11:32 -0500 (Fri, 27 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4877 |
| 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 1773/2357 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.11.0 (landing page) Qian Liu
| nebbiolo1 | 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: 1.11.0 |
| 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_1.11.0.tar.gz |
| StartedAt: 2026-02-27 03:26:39 -0500 (Fri, 27 Feb 2026) |
| EndedAt: 2026-02-27 03:29:25 -0500 (Fri, 27 Feb 2026) |
| EllapsedTime: 166.5 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘1.11.0’
* 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 5.952 0.404 6.363
* 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 ‘1.11.0’ ** 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 Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
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...
2ed0f427504313_GRCh38.primary_assembly.genome.fa.1.bt2 added
2ed0f4126d7a5b_GRCh38.primary_assembly.genome.fa.2.bt2 added
2ed0f438a79c8a_GRCh38.primary_assembly.genome.fa.3.bt2 added
2ed0f44315af24_GRCh38.primary_assembly.genome.fa.4.bt2 added
2ed0f4481cb703_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2ed0f45d73097d_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2ed0f460de93cf_outfile.txt added
2ed0f46d9b0296_GRCh37_to_GRCh38.chain added
2ed0f4365f1ed9_GRCh37_to_NCBI34.chain added
2ed0f435b2ec91_GRCh37_to_NCBI35.chain added
2ed0f4945a4a8_GRCh37_to_NCBI36.chain added
2ed0f441a878b6_GRCh38_to_GRCh37.chain added
2ed0f4521fbe77_GRCh38_to_NCBI34.chain added
2ed0f4484f50a8_GRCh38_to_NCBI35.chain added
2ed0f42b67e34d_GRCh38_to_NCBI36.chain added
2ed0f421486b94_NCBI34_to_GRCh37.chain added
2ed0f47765c11a_NCBI34_to_GRCh38.chain added
2ed0f43522e516_NCBI35_to_GRCh37.chain added
2ed0f4159d00e5_NCBI35_to_GRCh38.chain added
2ed0f45c4437f2_NCBI36_to_GRCh37.chain added
2ed0f43ff34ad3_NCBI36_to_GRCh38.chain added
2ed0f4f2d2e54_GRCm38_to_NCBIM36.chain added
2ed0f44f67118_GRCm38_to_NCBIM37.chain added
2ed0f4427bd4e7_NCBIM36_to_GRCm38.chain added
2ed0f4117d0351_NCBIM37_to_GRCm38.chain added
2ed0f41592c495_1000G_omni2.5.b37.vcf.gz added
2ed0f42e56d7fc_1000G_omni2.5.b37.vcf.gz.tbi added
2ed0f42538a741_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2ed0f4581cfeeb_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2ed0f4117cc19c_1000G_omni2.5.hg38.vcf.gz added
2ed0f4f1f8a6_1000G_omni2.5.hg38.vcf.gz.tbi added
2ed0f47f6d41fe_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2ed0f423ea3bf7_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2ed0f439999530_af-only-gnomad.raw.sites.vcf added
2ed0f44282f122_af-only-gnomad.raw.sites.vcf.idx added
2ed0f46c06f2fa_Mutect2-exome-panel.vcf.idx added
2ed0f4170c9eae_Mutect2-WGS-panel-b37.vcf added
2ed0f4236184f1_Mutect2-WGS-panel-b37.vcf.idx added
2ed0f459a1f590_small_exac_common_3.vcf added
2ed0f44d6bbd87_small_exac_common_3.vcf.idx added
2ed0f459147182_1000g_pon.hg38.vcf.gz added
2ed0f462e79a38_1000g_pon.hg38.vcf.gz.tbi added
2ed0f4f14363d_af-only-gnomad.hg38.vcf.gz added
2ed0f42b342ff9_af-only-gnomad.hg38.vcf.gz.tbi added
2ed0f42b36eae0_small_exac_common_3.hg38.vcf.gz added
2ed0f43a7c198a_small_exac_common_3.hg38.vcf.gz.tbi added
2ed0f44c7c9b8d_gencode.v41.annotation.gtf added
2ed0f4229cabfa_gencode.v42.annotation.gtf added
2ed0f46f9efea1_gencode.vM30.annotation.gtf added
2ed0f462199c72_gencode.vM31.annotation.gtf added
2ed0f47ee0e3ec_gencode.v41.transcripts.fa added
2ed0f42f924974_gencode.v41.transcripts.fa.fai added
2ed0f47146cac6_gencode.v42.transcripts.fa added
2ed0f43d75504_gencode.v42.transcripts.fa.fai added
2ed0f4720e1e5b_gencode.vM30.pc_transcripts.fa added
2ed0f42c3ce18_gencode.vM30.pc_transcripts.fa.fai added
2ed0f4196a1999_gencode.vM31.pc_transcripts.fa added
2ed0f42064f657_gencode.vM31.pc_transcripts.fa.fai added
2ed0f427fc7559_GRCh38.primary_assembly.genome.fa.1.ht2 added
2ed0f471871884_GRCh38.primary_assembly.genome.fa.2.ht2 added
2ed0f431e1b7f3_GRCh38.primary_assembly.genome.fa.3.ht2 added
2ed0f428ee6dff_GRCh38.primary_assembly.genome.fa.4.ht2 added
2ed0f470f45a82_GRCh38.primary_assembly.genome.fa.5.ht2 added
2ed0f455cbf3ea_GRCh38.primary_assembly.genome.fa.6.ht2 added
2ed0f462880330_GRCh38.primary_assembly.genome.fa.7.ht2 added
2ed0f433774ba5_GRCh38.primary_assembly.genome.fa.8.ht2 added
2ed0f441d2e6e4_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2ed0f47994a1de_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2ed0f456d8d096_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2ed0f41b74dc74_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2ed0f447005f65_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2ed0f42fed4219_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2ed0f47e5c76ac_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2ed0f4561495a3_GRCh38.primary_assembly.genome.fa.fai added
2ed0f45b217212_GRCh38.primary_assembly.genome.fa.amb added
2ed0f42993618c_GRCh38.primary_assembly.genome.fa.ann added
2ed0f41090af2d_GRCh38.primary_assembly.genome.fa.bwt added
2ed0f4279e0da0_GRCh38.primary_assembly.genome.fa.pac added
2ed0f44c300d87_GRCh38.primary_assembly.genome.fa.sa added
2ed0f42fadce_GRCh38.primary_assembly.genome.fa added
2ed0f49b7aa12_hs37d5.fa.fai added
2ed0f44b10f173_hs37d5.fa.amb added
2ed0f42fc1f742_hs37d5.fa.ann added
2ed0f47afe74d9_hs37d5.fa.bwt added
2ed0f44ee84678_hs37d5.fa.pac added
2ed0f421d0159e_hs37d5.fa.sa added
2ed0f47dc242f1_hs37d5.fa added
2ed0f468526011_complete_ref_lens.bin added
2ed0f442350bf5_ctable.bin added
2ed0f425beb84a_ctg_offsets.bin added
2ed0f459d97896_duplicate_clusters.tsv added
2ed0f47416c3e9_info.json added
2ed0f44ead264a_mphf.bin added
2ed0f44acdd318_pos.bin added
2ed0f449e2b7d3_pre_indexing.log added
2ed0f43135297a_rank.bin added
2ed0f47e451ebd_ref_indexing.log added
2ed0f4bb59eb8_refAccumLengths.bin added
2ed0f42ac9cb58_reflengths.bin added
2ed0f4551def54_refseq.bin added
2ed0f4272a7b2c_seq.bin added
2ed0f471ca2abd_versionInfo.json added
2ed0f450b316d_salmon_index added
2ed0f42586f1d9_chrLength.txt added
2ed0f447dec060_chrName.txt added
2ed0f4602ca37f_chrNameLength.txt added
2ed0f44f1a5365_chrStart.txt added
2ed0f4586f6f8e_exonGeTrInfo.tab added
2ed0f47cab11f_exonInfo.tab added
2ed0f41b4a60ec_geneInfo.tab added
2ed0f4589f1d5c_Genome added
2ed0f411825b32_genomeParameters.txt added
2ed0f4665b5260_Log.out added
2ed0f4861149f_SA added
2ed0f4c80d00b_SAindex added
2ed0f4354398d8_sjdbInfo.txt added
2ed0f42a312a3d_sjdbList.fromGTF.out.tab added
2ed0f4a4312fc_sjdbList.out.tab added
2ed0f41d95f8e9_transcriptInfo.tab added
2ed0f46c663632_GRCh38.GENCODE.v42_100 added
2ed0f43001cb46_knownGene_hg38.sql added
2ed0f4776f717f_knownGene_hg38.txt added
2ed0f4607cfa1b_refGene_hg38.sql added
2ed0f47eaef190_refGene_hg38.txt added
2ed0f4423d4498_knownGene_mm39.sql added
2ed0f42a5fb1ef_knownGene_mm39.txt added
2ed0f42fe41b0a_refGene_mm39.sql added
2ed0f440826355_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/RtmphLDkqu/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
18.294 1.150 19.647
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.952 | 0.404 | 6.363 | |
| dataSearch | 1.109 | 0.040 | 1.149 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.846 | 0.132 | 3.741 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.137 | 0.016 | 0.153 | |
| recipeLoad | 1.282 | 0.091 | 1.374 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.551 | 0.013 | 0.564 | |
| recipeUpdate | 0 | 0 | 0 | |