Qian Liu
| Snapshot Date: 2026-04-02 13:40 -0400 (Thu, 02 Apr 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-03 11:38 -0400 (Fri, 03 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.6.0 alpha (2026-03-30 r89742) | 4894 |
| 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 1789/2381 | 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: 2026-04-03 03:08:39 -0400 (Fri, 03 Apr 2026) |
| EndedAt: 2026-04-03 03:11:23 -0400 (Fri, 03 Apr 2026) |
| EllapsedTime: 163.5 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 version 4.6.0 alpha (2026-03-30 r89742)
* 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: 2026-04-03 07:08:40 UTC
* 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 5.98 0.32 6.303
* 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 version 4.6.0 alpha (2026-03-30 r89742)
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...
423e074d41a7a_GRCh38.primary_assembly.genome.fa.1.bt2 added
423e051145734_GRCh38.primary_assembly.genome.fa.2.bt2 added
423e0c13d802_GRCh38.primary_assembly.genome.fa.3.bt2 added
423e036dd3c4f_GRCh38.primary_assembly.genome.fa.4.bt2 added
423e01939fa9e_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
423e04e333d61_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
423e018c71bc4_outfile.txt added
423e06e954c73_GRCh37_to_GRCh38.chain added
423e03cbc8287_GRCh37_to_NCBI34.chain added
423e01d6e43ca_GRCh37_to_NCBI35.chain added
423e0ff9b062_GRCh37_to_NCBI36.chain added
423e047a7964b_GRCh38_to_GRCh37.chain added
423e022ec1bd6_GRCh38_to_NCBI34.chain added
423e04c420d51_GRCh38_to_NCBI35.chain added
423e028fee5c0_GRCh38_to_NCBI36.chain added
423e05212e001_NCBI34_to_GRCh37.chain added
423e03881c05b_NCBI34_to_GRCh38.chain added
423e01bb422b5_NCBI35_to_GRCh37.chain added
423e07bd7f175_NCBI35_to_GRCh38.chain added
423e037451997_NCBI36_to_GRCh37.chain added
423e0415ed389_NCBI36_to_GRCh38.chain added
423e031870fb_GRCm38_to_NCBIM36.chain added
423e04a2c8eca_GRCm38_to_NCBIM37.chain added
423e010fefa13_NCBIM36_to_GRCm38.chain added
423e0295f5d8e_NCBIM37_to_GRCm38.chain added
423e063cc60d0_1000G_omni2.5.b37.vcf.gz added
423e02ad04a39_1000G_omni2.5.b37.vcf.gz.tbi added
423e035ccd7b0_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
423e0b6d7225_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
423e038bb130f_1000G_omni2.5.hg38.vcf.gz added
423e019345df0_1000G_omni2.5.hg38.vcf.gz.tbi added
423e0418c9f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
423e09cf6a44_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
423e0254835f2_af-only-gnomad.raw.sites.vcf added
423e0371ec8ee_af-only-gnomad.raw.sites.vcf.idx added
423e0230964e2_Mutect2-exome-panel.vcf.idx added
423e0737b7353_Mutect2-WGS-panel-b37.vcf added
423e04fe5e4b3_Mutect2-WGS-panel-b37.vcf.idx added
423e0119eb155_small_exac_common_3.vcf added
423e03037f5da_small_exac_common_3.vcf.idx added
423e06d54287d_1000g_pon.hg38.vcf.gz added
423e0219861b8_1000g_pon.hg38.vcf.gz.tbi added
423e077df8c26_af-only-gnomad.hg38.vcf.gz added
423e010404453_af-only-gnomad.hg38.vcf.gz.tbi added
423e06dda6f09_small_exac_common_3.hg38.vcf.gz added
423e020de71e6_small_exac_common_3.hg38.vcf.gz.tbi added
423e062532454_gencode.v41.annotation.gtf added
423e0265c2f65_gencode.v42.annotation.gtf added
423e03c92949c_gencode.vM30.annotation.gtf added
423e05e2b15c9_gencode.vM31.annotation.gtf added
423e05da148fc_gencode.v41.transcripts.fa added
423e07df16825_gencode.v41.transcripts.fa.fai added
423e0614386c4_gencode.v42.transcripts.fa added
423e027cdd7c6_gencode.v42.transcripts.fa.fai added
423e0ef06238_gencode.vM30.pc_transcripts.fa added
423e0aa2e452_gencode.vM30.pc_transcripts.fa.fai added
423e0b9a3896_gencode.vM31.pc_transcripts.fa added
423e039c0ac71_gencode.vM31.pc_transcripts.fa.fai added
423e0406fbc03_GRCh38.primary_assembly.genome.fa.1.ht2 added
423e01707aabb_GRCh38.primary_assembly.genome.fa.2.ht2 added
423e0727bbf81_GRCh38.primary_assembly.genome.fa.3.ht2 added
423e059a419f3_GRCh38.primary_assembly.genome.fa.4.ht2 added
423e01749375b_GRCh38.primary_assembly.genome.fa.5.ht2 added
423e07c4b29c5_GRCh38.primary_assembly.genome.fa.6.ht2 added
423e07eec4fe6_GRCh38.primary_assembly.genome.fa.7.ht2 added
423e04e680049_GRCh38.primary_assembly.genome.fa.8.ht2 added
423e01f548ea7_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
423e07267c339_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
423e01e4de4fc_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
423e030f33ffc_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
423e0229fb914_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
423e0ba20d79_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
423e0528ba1b4_GRCh38_full_analysis_set_plus_decoy_hla.fa added
423e01a7f453a_GRCh38.primary_assembly.genome.fa.fai added
423e01be251cc_GRCh38.primary_assembly.genome.fa.amb added
423e0406610be_GRCh38.primary_assembly.genome.fa.ann added
423e03b5db720_GRCh38.primary_assembly.genome.fa.bwt added
423e07e357620_GRCh38.primary_assembly.genome.fa.pac added
423e066c24023_GRCh38.primary_assembly.genome.fa.sa added
423e077f04bbc_GRCh38.primary_assembly.genome.fa added
423e05c608be9_hs37d5.fa.fai added
423e04463891f_hs37d5.fa.amb added
423e075e1b3e2_hs37d5.fa.ann added
423e03da412ad_hs37d5.fa.bwt added
423e06c3160e5_hs37d5.fa.pac added
423e04d2161a_hs37d5.fa.sa added
423e04846f700_hs37d5.fa added
423e077cb997b_complete_ref_lens.bin added
423e03e92c28c_ctable.bin added
423e08b6b303_ctg_offsets.bin added
423e0ed34437_duplicate_clusters.tsv added
423e0310e820d_info.json added
423e0625accf6_mphf.bin added
423e0261c7b92_pos.bin added
423e02d59abd2_pre_indexing.log added
423e061471cdc_rank.bin added
423e074847bdb_ref_indexing.log added
423e04cae3a79_refAccumLengths.bin added
423e053aee016_reflengths.bin added
423e012d260d8_refseq.bin added
423e07da17a75_seq.bin added
423e0764e992a_versionInfo.json added
423e01e746e51_salmon_index added
423e0502d1c2a_chrLength.txt added
423e010cdde64_chrName.txt added
423e03a56c01e_chrNameLength.txt added
423e010932ce8_chrStart.txt added
423e04c2b9584_exonGeTrInfo.tab added
423e0388c363e_exonInfo.tab added
423e077556d0b_geneInfo.tab added
423e0441be141_Genome added
423e014ecc228_genomeParameters.txt added
423e03bb8f62a_Log.out added
423e039fd9523_SA added
423e05290d4d5_SAindex added
423e027ea570f_sjdbInfo.txt added
423e03ecfab3d_sjdbList.fromGTF.out.tab added
423e01ad7cbd5_sjdbList.out.tab added
423e01fb5f08a_transcriptInfo.tab added
423e07d626dc9_GRCh38.GENCODE.v42_100 added
423e0238e7ed8_knownGene_hg38.sql added
423e02e8934c1_knownGene_hg38.txt added
423e02e70efd6_refGene_hg38.sql added
423e05e94bcf_refGene_hg38.txt added
423e054a5b053_knownGene_mm39.sql added
423e05bca9ba8_knownGene_mm39.txt added
423e0673068ab_refGene_mm39.sql added
423e0492a2c2f_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/RtmpDjqIa2/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
17.426 1.200 19.015
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.980 | 0.320 | 6.303 | |
| dataSearch | 1.039 | 0.019 | 1.058 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.558 | 0.087 | 3.239 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.001 | 0.001 | |
| recipeHub-class | 0.119 | 0.003 | 0.122 | |
| recipeLoad | 1.173 | 0.024 | 1.198 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.483 | 0.011 | 0.494 | |
| recipeUpdate | 0 | 0 | 0 | |