Qian Liu
| Snapshot Date: 2026-03-09 13:40 -0400 (Mon, 09 Mar 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 Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-10 11:33 -0400 (Tue, 10 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4522 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 2847 |
| 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 1776/2360 | 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 | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 2026-03-10 02:40:40 -0400 (Tue, 10 Mar 2026) |
| EndedAt: 2026-03-10 02:43:26 -0400 (Tue, 10 Mar 2026) |
| EllapsedTime: 165.4 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) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-10 06:40:41 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 5.992 0.393 6.394
* 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) (2026-03-05 r89546) -- "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...
2682bac0302bb_GRCh38.primary_assembly.genome.fa.1.bt2 added
2682ba3026d0e6_GRCh38.primary_assembly.genome.fa.2.bt2 added
2682ba74f84517_GRCh38.primary_assembly.genome.fa.3.bt2 added
2682ba32add970_GRCh38.primary_assembly.genome.fa.4.bt2 added
2682ba172e643d_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2682ba178c63e1_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2682ba4731d362_outfile.txt added
2682ba7cb53c04_GRCh37_to_GRCh38.chain added
2682ba6f666b53_GRCh37_to_NCBI34.chain added
2682ba15282744_GRCh37_to_NCBI35.chain added
2682ba316cfbe7_GRCh37_to_NCBI36.chain added
2682ba57c91fbd_GRCh38_to_GRCh37.chain added
2682ba1f94a57a_GRCh38_to_NCBI34.chain added
2682ba1ae93fb9_GRCh38_to_NCBI35.chain added
2682ba23810068_GRCh38_to_NCBI36.chain added
2682ba185c1754_NCBI34_to_GRCh37.chain added
2682ba6ef623fe_NCBI34_to_GRCh38.chain added
2682ba46d2d8c9_NCBI35_to_GRCh37.chain added
2682ba63c95123_NCBI35_to_GRCh38.chain added
2682ba50a38ea5_NCBI36_to_GRCh37.chain added
2682ba5ddb5ba7_NCBI36_to_GRCh38.chain added
2682ba406f4635_GRCm38_to_NCBIM36.chain added
2682ba306ae68e_GRCm38_to_NCBIM37.chain added
2682ba6fb0341f_NCBIM36_to_GRCm38.chain added
2682ba91b356d_NCBIM37_to_GRCm38.chain added
2682ba32885de9_1000G_omni2.5.b37.vcf.gz added
2682ba953594b_1000G_omni2.5.b37.vcf.gz.tbi added
2682ba61f3e4f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2682ba2ee4894_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2682ba3ef88c41_1000G_omni2.5.hg38.vcf.gz added
2682ba1613192c_1000G_omni2.5.hg38.vcf.gz.tbi added
2682baef14b50_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2682ba6f1f5d27_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2682bab0b5e44_af-only-gnomad.raw.sites.vcf added
2682ba419f24c0_af-only-gnomad.raw.sites.vcf.idx added
2682ba64dc164_Mutect2-exome-panel.vcf.idx added
2682ba2297c225_Mutect2-WGS-panel-b37.vcf added
2682ba8d0f823_Mutect2-WGS-panel-b37.vcf.idx added
2682ba302fd68_small_exac_common_3.vcf added
2682ba11fe2d79_small_exac_common_3.vcf.idx added
2682ba1df91f67_1000g_pon.hg38.vcf.gz added
2682ba346ff950_1000g_pon.hg38.vcf.gz.tbi added
2682ba69c74d36_af-only-gnomad.hg38.vcf.gz added
2682ba3d8dc4e1_af-only-gnomad.hg38.vcf.gz.tbi added
2682ba4f593909_small_exac_common_3.hg38.vcf.gz added
2682bad484d9e_small_exac_common_3.hg38.vcf.gz.tbi added
2682ba55e9dc35_gencode.v41.annotation.gtf added
2682ba3e4f5d07_gencode.v42.annotation.gtf added
2682ba541b2667_gencode.vM30.annotation.gtf added
2682ba39b32d58_gencode.vM31.annotation.gtf added
2682baef2ebac_gencode.v41.transcripts.fa added
2682ba31f6820f_gencode.v41.transcripts.fa.fai added
2682ba7a22738e_gencode.v42.transcripts.fa added
2682ba3f5dd23b_gencode.v42.transcripts.fa.fai added
2682ba21a6b62e_gencode.vM30.pc_transcripts.fa added
2682ba33da8fb_gencode.vM30.pc_transcripts.fa.fai added
2682ba71e63024_gencode.vM31.pc_transcripts.fa added
2682ba2afa0f79_gencode.vM31.pc_transcripts.fa.fai added
2682ba95ce74b_GRCh38.primary_assembly.genome.fa.1.ht2 added
2682ba74d478b9_GRCh38.primary_assembly.genome.fa.2.ht2 added
2682ba69f29bbb_GRCh38.primary_assembly.genome.fa.3.ht2 added
2682ba1f700077_GRCh38.primary_assembly.genome.fa.4.ht2 added
2682ba3c5c409_GRCh38.primary_assembly.genome.fa.5.ht2 added
2682ba5911f8e2_GRCh38.primary_assembly.genome.fa.6.ht2 added
2682ba2a7b5ebb_GRCh38.primary_assembly.genome.fa.7.ht2 added
2682ba4564e8c9_GRCh38.primary_assembly.genome.fa.8.ht2 added
2682ba5f5fba47_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2682ba4d1320e1_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2682ba4e35e0ec_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2682ba6262b7af_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2682ba5f114e5a_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2682ba6c2f0053_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2682ba16d2b0ff_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2682ba48d89b90_GRCh38.primary_assembly.genome.fa.fai added
2682ba29bcc534_GRCh38.primary_assembly.genome.fa.amb added
2682ba662bea08_GRCh38.primary_assembly.genome.fa.ann added
2682ba5620e92e_GRCh38.primary_assembly.genome.fa.bwt added
2682ba7fa6a16a_GRCh38.primary_assembly.genome.fa.pac added
2682ba247b4710_GRCh38.primary_assembly.genome.fa.sa added
2682ba2a3c0f96_GRCh38.primary_assembly.genome.fa added
2682ba3959cec2_hs37d5.fa.fai added
2682ba336e32bc_hs37d5.fa.amb added
2682ba5c3291a5_hs37d5.fa.ann added
2682ba337c4250_hs37d5.fa.bwt added
2682ba72cc04f7_hs37d5.fa.pac added
2682ba7dd947d3_hs37d5.fa.sa added
2682ba36b9eb4c_hs37d5.fa added
2682ba64b2351c_complete_ref_lens.bin added
2682ba28d3574d_ctable.bin added
2682ba4016d297_ctg_offsets.bin added
2682ba5986add5_duplicate_clusters.tsv added
2682ba12c5f308_info.json added
2682ba5f86d30e_mphf.bin added
2682ba5d4c71de_pos.bin added
2682ba6bd7ebea_pre_indexing.log added
2682baa0231ca_rank.bin added
2682ba22b15aa7_ref_indexing.log added
2682ba4b37a631_refAccumLengths.bin added
2682ba571552ab_reflengths.bin added
2682ba70e73b94_refseq.bin added
2682ba2d9a5de1_seq.bin added
2682ba3626a105_versionInfo.json added
2682ba5d163be7_salmon_index added
2682ba446d0ee0_chrLength.txt added
2682ba7eff3c95_chrName.txt added
2682ba6d3011c_chrNameLength.txt added
2682ba2a98f8e9_chrStart.txt added
2682ba552025c3_exonGeTrInfo.tab added
2682ba679a286_exonInfo.tab added
2682ba4f143ff9_geneInfo.tab added
2682ba7f5c3559_Genome added
2682ba3fd37148_genomeParameters.txt added
2682ba28272b5_Log.out added
2682ba5b8ec6fe_SA added
2682ba734fb399_SAindex added
2682ba754e77ad_sjdbInfo.txt added
2682ba59680ed2_sjdbList.fromGTF.out.tab added
2682ba2a099ee5_sjdbList.out.tab added
2682ba5a00acc9_transcriptInfo.tab added
2682ba23b661f_GRCh38.GENCODE.v42_100 added
2682ba6a20717c_knownGene_hg38.sql added
2682ba33875a9e_knownGene_hg38.txt added
2682ba15015927_refGene_hg38.sql added
2682ba49a7448a_refGene_hg38.txt added
2682ba10d3cc7c_knownGene_mm39.sql added
2682bad94511_knownGene_mm39.txt added
2682ba53a97654_refGene_mm39.sql added
2682ba33852723_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/RtmpQTwagM/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
21.377 1.401 23.193
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.992 | 0.393 | 6.394 | |
| dataSearch | 1.155 | 0.041 | 1.196 | |
| dataUpdate | 0.000 | 0.001 | 0.000 | |
| getCloudData | 2.580 | 0.123 | 3.520 | |
| getData | 0.000 | 0.001 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.119 | 0.002 | 0.121 | |
| recipeLoad | 1.242 | 0.071 | 1.314 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.509 | 0.023 | 0.532 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |