Qian Liu
| Snapshot Date: 2026-03-23 13:40 -0400 (Mon, 23 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 2026-03-24 11:35 -0400 (Tue, 24 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" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" | 4567 |
| 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: 2026-03-23 22:10:51 -0400 (Mon, 23 Mar 2026) |
| EndedAt: 2026-03-23 22:11:54 -0400 (Mon, 23 Mar 2026) |
| EllapsedTime: 62.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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) (2026-03-20 r89666)
* 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 Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-03-24 02:10:51 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) (2026-03-20 r89666) -- "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...
547e338bc262_GRCh38.primary_assembly.genome.fa.1.bt2 added
547e1c86ca5e_GRCh38.primary_assembly.genome.fa.2.bt2 added
547e554feff3_GRCh38.primary_assembly.genome.fa.3.bt2 added
547e73126646_GRCh38.primary_assembly.genome.fa.4.bt2 added
547e3cf8b8af_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
547e6d25086e_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
547e1a4ca5bd_outfile.txt added
547e1e1528c8_GRCh37_to_GRCh38.chain added
547e7f2871e5_GRCh37_to_NCBI34.chain added
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547e41805fdc_NCBI35_to_GRCh38.chain added
547e5315861c_NCBI36_to_GRCh37.chain added
547e2a17c2e1_NCBI36_to_GRCh38.chain added
547e7dfb575d_GRCm38_to_NCBIM36.chain added
547e24db49_GRCm38_to_NCBIM37.chain added
547e73b895b1_NCBIM36_to_GRCm38.chain added
547e5b6bd2d1_NCBIM37_to_GRCm38.chain added
547e3ddc63b_1000G_omni2.5.b37.vcf.gz added
547e55014d78_1000G_omni2.5.b37.vcf.gz.tbi added
547e48852ce1_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
547e1f458cf9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
547ef2a3f79_1000G_omni2.5.hg38.vcf.gz added
547e1ead28b6_1000G_omni2.5.hg38.vcf.gz.tbi added
547e7a4bd475_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
547e8698c0d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
547e4969adcb_af-only-gnomad.raw.sites.vcf added
547e39111014_af-only-gnomad.raw.sites.vcf.idx added
547ef36ae51_Mutect2-exome-panel.vcf.idx added
547e4eee4fa4_Mutect2-WGS-panel-b37.vcf added
547e7faec077_Mutect2-WGS-panel-b37.vcf.idx added
547e29de061e_small_exac_common_3.vcf added
547e2f63b10b_small_exac_common_3.vcf.idx added
547e39fc617b_1000g_pon.hg38.vcf.gz added
547e6863effa_1000g_pon.hg38.vcf.gz.tbi added
547e79203ba0_af-only-gnomad.hg38.vcf.gz added
547e332ac380_af-only-gnomad.hg38.vcf.gz.tbi added
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547e4f4806fe_small_exac_common_3.hg38.vcf.gz.tbi added
547e1c3365c_gencode.v41.annotation.gtf added
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547e143a5e96_gencode.vM30.annotation.gtf added
547e417d43a_gencode.vM31.annotation.gtf added
547e386e2def_gencode.v41.transcripts.fa added
547e4989c2da_gencode.v41.transcripts.fa.fai added
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547e7cbe1fc3_gencode.v42.transcripts.fa.fai added
547e26177b30_gencode.vM30.pc_transcripts.fa added
547e4f989fd9_gencode.vM30.pc_transcripts.fa.fai added
547e2d268862_gencode.vM31.pc_transcripts.fa added
547e3cc3f116_gencode.vM31.pc_transcripts.fa.fai added
547e6408fa84_GRCh38.primary_assembly.genome.fa.1.ht2 added
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547e45b43b28_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
547e3b97e2d8_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
547e70adf178_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
547e2bc83713_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
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547e63f19359_GRCh38.primary_assembly.genome.fa.fai added
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547e6e94b4b_GRCh38.primary_assembly.genome.fa.bwt added
547e3e4e2c78_GRCh38.primary_assembly.genome.fa.pac added
547e7e499a3c_GRCh38.primary_assembly.genome.fa.sa added
547e122d19ea_GRCh38.primary_assembly.genome.fa added
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547e4b0693fc_ctable.bin added
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547e1d3ecc47_duplicate_clusters.tsv added
547e5d55851_info.json added
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547e3854ecaa_pos.bin added
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547e56e4a603_versionInfo.json added
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547e2f44e34c_chrNameLength.txt added
547e53a6aad2_chrStart.txt added
547e6318ebe5_exonGeTrInfo.tab added
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547e7e5eed5d_geneInfo.tab added
547ea31b57c_Genome added
547e4581e51e_genomeParameters.txt added
547e52e93838_Log.out added
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547e1e84cc54_sjdbList.fromGTF.out.tab added
547e2082ae73_sjdbList.out.tab added
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547e3ef50785_GRCh38.GENCODE.v42_100 added
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547e60768bb2_refGene_hg38.txt added
547e6cd8498_knownGene_mm39.sql added
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547e4f795666_refGene_mm39.sql added
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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//RtmpoKPdSk/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
7.261 1.054 9.412
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.165 | 0.308 | 2.549 | |
| dataSearch | 0.386 | 0.023 | 0.416 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.847 | 0.062 | 1.745 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.036 | 0.003 | 0.040 | |
| recipeLoad | 0.482 | 0.046 | 0.543 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.160 | 0.016 | 0.178 | |
| recipeUpdate | 0 | 0 | 0 | |