Qian Liu
| Snapshot Date: 2026-03-18 13:40 -0400 (Wed, 18 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 2026-03-19 11:34 -0400 (Thu, 19 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" | 4858 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4060 |
| 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 1782/2368 | 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.11.0.tar.gz |
| StartedAt: 2026-03-18 19:31:07 -0400 (Wed, 18 Mar 2026) |
| EndedAt: 2026-03-18 19:31:56 -0400 (Wed, 18 Mar 2026) |
| EllapsedTime: 48.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReUseData_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2026-03-01 r89506)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* current time: 2026-03-18 23:31:08 UTC
* using option ‘--no-vignettes’
* 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 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
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/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) (2026-03-01 r89506) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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...
5cbb246a252c_GRCh38.primary_assembly.genome.fa.1.bt2 added
5cbb34ae7e61_GRCh38.primary_assembly.genome.fa.2.bt2 added
5cbb2beb2d4c_GRCh38.primary_assembly.genome.fa.3.bt2 added
5cbb5ceaef1a_GRCh38.primary_assembly.genome.fa.4.bt2 added
5cbb43f7c39e_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
5cbb3f4bdcee_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
5cbbd95adb9_outfile.txt added
5cbb5dc053a6_GRCh37_to_GRCh38.chain added
5cbb7db3e75f_GRCh37_to_NCBI34.chain added
5cbb2e1b4e72_GRCh37_to_NCBI35.chain added
5cbb2bb3604_GRCh37_to_NCBI36.chain added
5cbb50d74202_GRCh38_to_GRCh37.chain added
5cbb642ebac4_GRCh38_to_NCBI34.chain added
5cbb37e7cd3e_GRCh38_to_NCBI35.chain added
5cbb5353be1e_GRCh38_to_NCBI36.chain added
5cbb1ee6ce4f_NCBI34_to_GRCh37.chain added
5cbb42f2b462_NCBI34_to_GRCh38.chain added
5cbb4c20b044_NCBI35_to_GRCh37.chain added
5cbb76146767_NCBI35_to_GRCh38.chain added
5cbb3590d7c1_NCBI36_to_GRCh37.chain added
5cbb3844db60_NCBI36_to_GRCh38.chain added
5cbb309e987c_GRCm38_to_NCBIM36.chain added
5cbb7c2d0dd3_GRCm38_to_NCBIM37.chain added
5cbb71e6d755_NCBIM36_to_GRCm38.chain added
5cbb6a4347de_NCBIM37_to_GRCm38.chain added
5cbb67237652_1000G_omni2.5.b37.vcf.gz added
5cbb492d3664_1000G_omni2.5.b37.vcf.gz.tbi added
5cbb374e04c4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
5cbb631afc39_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
5cbba53504_1000G_omni2.5.hg38.vcf.gz added
5cbb5e3b99f0_1000G_omni2.5.hg38.vcf.gz.tbi added
5cbb1af78be5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
5cbb72017537_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
5cbb3db6a85a_af-only-gnomad.raw.sites.vcf added
5cbb22e6cc5d_af-only-gnomad.raw.sites.vcf.idx added
5cbb5e72ff91_Mutect2-exome-panel.vcf.idx added
5cbb4fe8b908_Mutect2-WGS-panel-b37.vcf added
5cbb37cbe534_Mutect2-WGS-panel-b37.vcf.idx added
5cbb2b34d58a_small_exac_common_3.vcf added
5cbb19af6d2f_small_exac_common_3.vcf.idx added
5cbb4c2935d5_1000g_pon.hg38.vcf.gz added
5cbb258d5a03_1000g_pon.hg38.vcf.gz.tbi added
5cbb63108e37_af-only-gnomad.hg38.vcf.gz added
5cbb53e8efb0_af-only-gnomad.hg38.vcf.gz.tbi added
5cbb61d036d9_small_exac_common_3.hg38.vcf.gz added
5cbb2cc112ba_small_exac_common_3.hg38.vcf.gz.tbi added
5cbb37b4884a_gencode.v41.annotation.gtf added
5cbb2d5fced8_gencode.v42.annotation.gtf added
5cbb6d04de2d_gencode.vM30.annotation.gtf added
5cbb5a969445_gencode.vM31.annotation.gtf added
5cbb53e06c79_gencode.v41.transcripts.fa added
5cbb32f1a6f4_gencode.v41.transcripts.fa.fai added
5cbb1707f74d_gencode.v42.transcripts.fa added
5cbbbfcec0b_gencode.v42.transcripts.fa.fai added
5cbb9eccc53_gencode.vM30.pc_transcripts.fa added
5cbb195a623c_gencode.vM30.pc_transcripts.fa.fai added
5cbb7ce75e24_gencode.vM31.pc_transcripts.fa added
5cbb39d5cd8c_gencode.vM31.pc_transcripts.fa.fai added
5cbb3a9bffe_GRCh38.primary_assembly.genome.fa.1.ht2 added
5cbb7d7bbe92_GRCh38.primary_assembly.genome.fa.2.ht2 added
5cbb471ca39a_GRCh38.primary_assembly.genome.fa.3.ht2 added
5cbb2938f7ef_GRCh38.primary_assembly.genome.fa.4.ht2 added
5cbb5b1d810d_GRCh38.primary_assembly.genome.fa.5.ht2 added
5cbb6e03ab36_GRCh38.primary_assembly.genome.fa.6.ht2 added
5cbb32dd9ea7_GRCh38.primary_assembly.genome.fa.7.ht2 added
5cbb73db0007_GRCh38.primary_assembly.genome.fa.8.ht2 added
5cbb2edf06fd_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
5cbb3443e415_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
5cbb55333981_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
5cbb16046fda_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
5cbb7d4b5c80_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
5cbb5ea617c3_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
5cbb6a6233c0_GRCh38_full_analysis_set_plus_decoy_hla.fa added
5cbb5533b8d0_GRCh38.primary_assembly.genome.fa.fai added
5cbb36aa8b63_GRCh38.primary_assembly.genome.fa.amb added
5cbb76a52c9e_GRCh38.primary_assembly.genome.fa.ann added
5cbb561475ec_GRCh38.primary_assembly.genome.fa.bwt added
5cbb594a051a_GRCh38.primary_assembly.genome.fa.pac added
5cbba951bc2_GRCh38.primary_assembly.genome.fa.sa added
5cbb435162fb_GRCh38.primary_assembly.genome.fa added
5cbb14396f44_hs37d5.fa.fai added
5cbb46b7e3bb_hs37d5.fa.amb added
5cbb52c82e42_hs37d5.fa.ann added
5cbb54551983_hs37d5.fa.bwt added
5cbb1efe12b6_hs37d5.fa.pac added
5cbb3a7e7a9f_hs37d5.fa.sa added
5cbb45a47ab9_hs37d5.fa added
5cbb31752b67_complete_ref_lens.bin added
5cbb374908f_ctable.bin added
5cbb59be9e0e_ctg_offsets.bin added
5cbb717ad729_duplicate_clusters.tsv added
5cbb37c3fef3_info.json added
5cbb2497201f_mphf.bin added
5cbb3dbde5fd_pos.bin added
5cbb7e4664b5_pre_indexing.log added
5cbb3f7de7d7_rank.bin added
5cbb62fff4d1_ref_indexing.log added
5cbb1221f81e_refAccumLengths.bin added
5cbb742882de_reflengths.bin added
5cbbfa7f866_refseq.bin added
5cbb5ca4f891_seq.bin added
5cbb52bb271b_versionInfo.json added
5cbb7d04880b_salmon_index added
5cbb347fca4c_chrLength.txt added
5cbb31ba5e81_chrName.txt added
5cbb429280a8_chrNameLength.txt added
5cbb203cb7bd_chrStart.txt added
5cbb7242e9d3_exonGeTrInfo.tab added
5cbb7055640_exonInfo.tab added
5cbb6f618759_geneInfo.tab added
5cbb6bfd1d2f_Genome added
5cbb3687300c_genomeParameters.txt added
5cbb65637fcb_Log.out added
5cbb675b1c6d_SA added
5cbbea76d1e_SAindex added
5cbb11ecd416_sjdbInfo.txt added
5cbb5357f98b_sjdbList.fromGTF.out.tab added
5cbb34c03f6c_sjdbList.out.tab added
5cbb3983e682_transcriptInfo.tab added
5cbb2927e4e_GRCh38.GENCODE.v42_100 added
5cbb5fa23433_knownGene_hg38.sql added
5cbb12113152_knownGene_hg38.txt added
5cbb26bd07c2_refGene_hg38.sql added
5cbb4448656c_refGene_hg38.txt added
5cbb6cfab879_knownGene_mm39.sql added
5cbb406547d4_knownGene_mm39.txt added
5cbb394ed053_refGene_mm39.sql added
5cbb654f1689_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:
/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp9NRx5L/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
6.244 0.616 7.507
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.901 | 0.196 | 2.115 | |
| dataSearch | 0.341 | 0.013 | 0.358 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.846 | 0.048 | 2.088 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.038 | 0.004 | 0.042 | |
| recipeLoad | 0.393 | 0.022 | 0.418 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.159 | 0.008 | 0.167 | |
| recipeUpdate | 0 | 0 | 0 | |