Qian Liu
| Snapshot Date: 2026-01-15 13:40 -0500 (Thu, 15 Jan 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 Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-16 11:12 -0500 (Fri, 16 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4849 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4628 |
| 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 1762/2343 | 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 | | ||||||||
|
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: 2026-01-15 22:09:56 -0500 (Thu, 15 Jan 2026) |
| EndedAt: 2026-01-15 22:10:54 -0500 (Thu, 15 Jan 2026) |
| EllapsedTime: 57.7 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) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* 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-arm64/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) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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...
1414e68c6a686_GRCh38.primary_assembly.genome.fa.1.bt2 added
1414e49dedd27_GRCh38.primary_assembly.genome.fa.2.bt2 added
1414e46895154_GRCh38.primary_assembly.genome.fa.3.bt2 added
1414e613a85f9_GRCh38.primary_assembly.genome.fa.4.bt2 added
1414e4931d04d_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1414e656294c5_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1414e2b154583_outfile.txt added
1414e186b18e_GRCh37_to_GRCh38.chain added
1414e31f2e26a_GRCh37_to_NCBI34.chain added
1414e40eeb6c4_GRCh37_to_NCBI35.chain added
1414e78211f29_GRCh37_to_NCBI36.chain added
1414e4684fa5c_GRCh38_to_GRCh37.chain added
1414e4450d22f_GRCh38_to_NCBI34.chain added
1414e16172eb3_GRCh38_to_NCBI35.chain added
1414e4bfaf519_GRCh38_to_NCBI36.chain added
1414e48f16347_NCBI34_to_GRCh37.chain added
1414e5facefba_NCBI34_to_GRCh38.chain added
1414e52aecd68_NCBI35_to_GRCh37.chain added
1414e522f9140_NCBI35_to_GRCh38.chain added
1414e30e92ae7_NCBI36_to_GRCh37.chain added
1414e1bffbcc7_NCBI36_to_GRCh38.chain added
1414e32c2bb2d_GRCm38_to_NCBIM36.chain added
1414ee8ea164_GRCm38_to_NCBIM37.chain added
1414e3605b3b3_NCBIM36_to_GRCm38.chain added
1414e3058c87a_NCBIM37_to_GRCm38.chain added
1414e14d1da62_1000G_omni2.5.b37.vcf.gz added
1414e5d58629b_1000G_omni2.5.b37.vcf.gz.tbi added
1414e55b1ddfd_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1414e106538ff_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1414e6580f5c1_1000G_omni2.5.hg38.vcf.gz added
1414e758685f6_1000G_omni2.5.hg38.vcf.gz.tbi added
1414e52c515c1_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1414e9175c5b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1414e5cb05f06_af-only-gnomad.raw.sites.vcf added
1414e3f2eb274_af-only-gnomad.raw.sites.vcf.idx added
1414e12c5fe14_Mutect2-exome-panel.vcf.idx added
1414e4abdcad_Mutect2-WGS-panel-b37.vcf added
1414e2f24e440_Mutect2-WGS-panel-b37.vcf.idx added
1414e1f053dee_small_exac_common_3.vcf added
1414e1124e42b_small_exac_common_3.vcf.idx added
1414ecffcbd8_1000g_pon.hg38.vcf.gz added
1414e6d9fd892_1000g_pon.hg38.vcf.gz.tbi added
1414e19439178_af-only-gnomad.hg38.vcf.gz added
1414e23036a3d_af-only-gnomad.hg38.vcf.gz.tbi added
1414e3533dcc0_small_exac_common_3.hg38.vcf.gz added
1414e5fe1dc89_small_exac_common_3.hg38.vcf.gz.tbi added
1414e6555d78c_gencode.v41.annotation.gtf added
1414e66ba5c4d_gencode.v42.annotation.gtf added
1414e5501f7eb_gencode.vM30.annotation.gtf added
1414e743b90e6_gencode.vM31.annotation.gtf added
1414e72a627a7_gencode.v41.transcripts.fa added
1414e7a757fbe_gencode.v41.transcripts.fa.fai added
1414e3815d1c1_gencode.v42.transcripts.fa added
1414e207df2ab_gencode.v42.transcripts.fa.fai added
1414e2cc6c937_gencode.vM30.pc_transcripts.fa added
1414e2ec450d8_gencode.vM30.pc_transcripts.fa.fai added
1414e5a97ace4_gencode.vM31.pc_transcripts.fa added
1414e1bd7db33_gencode.vM31.pc_transcripts.fa.fai added
1414e7877ff8c_GRCh38.primary_assembly.genome.fa.1.ht2 added
1414ee2a7e1e_GRCh38.primary_assembly.genome.fa.2.ht2 added
1414e7bdead6_GRCh38.primary_assembly.genome.fa.3.ht2 added
1414e45848b92_GRCh38.primary_assembly.genome.fa.4.ht2 added
1414ee741e6_GRCh38.primary_assembly.genome.fa.5.ht2 added
1414e4e976380_GRCh38.primary_assembly.genome.fa.6.ht2 added
1414e350590cf_GRCh38.primary_assembly.genome.fa.7.ht2 added
1414e66213b_GRCh38.primary_assembly.genome.fa.8.ht2 added
1414e310fa8b1_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1414e7b0c15a0_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1414e565ffa7c_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1414e37360f31_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1414e3e1f7648_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1414e38e90d5_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1414e4c691c6_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1414e88c609d_GRCh38.primary_assembly.genome.fa.fai added
1414e381ae7cd_GRCh38.primary_assembly.genome.fa.amb added
1414e6e686081_GRCh38.primary_assembly.genome.fa.ann added
1414e697edc8_GRCh38.primary_assembly.genome.fa.bwt added
1414e607be8d9_GRCh38.primary_assembly.genome.fa.pac added
1414e66f4300b_GRCh38.primary_assembly.genome.fa.sa added
1414e297e56fb_GRCh38.primary_assembly.genome.fa added
1414e25808e05_hs37d5.fa.fai added
1414e1aebfd7f_hs37d5.fa.amb added
1414e7b4faaa7_hs37d5.fa.ann added
1414e2b4cf930_hs37d5.fa.bwt added
1414e4a7bd485_hs37d5.fa.pac added
1414e7bd8df7_hs37d5.fa.sa added
1414e2db35719_hs37d5.fa added
1414e591b41bf_complete_ref_lens.bin added
1414ec79904d_ctable.bin added
1414ef0b5a1_ctg_offsets.bin added
1414e3b245d82_duplicate_clusters.tsv added
1414e50772023_info.json added
1414e3cdf031a_mphf.bin added
1414e5544bf2e_pos.bin added
1414e146390be_pre_indexing.log added
1414e14b3b467_rank.bin added
1414e2208e0cf_ref_indexing.log added
1414e74df477d_refAccumLengths.bin added
1414e6ece9b7c_reflengths.bin added
1414e3e4222b9_refseq.bin added
1414e67f5bf9d_seq.bin added
1414e36f711bd_versionInfo.json added
1414e16adab7c_salmon_index added
1414e63d56585_chrLength.txt added
1414e4efc31f7_chrName.txt added
1414ef3477a4_chrNameLength.txt added
1414e3d9ab7c8_chrStart.txt added
1414e7897cb10_exonGeTrInfo.tab added
1414e3594c54a_exonInfo.tab added
1414e3a2498c1_geneInfo.tab added
1414e38a8c4b9_Genome added
1414e500b6abe_genomeParameters.txt added
1414e1d8d0900_Log.out added
1414e1649ee28_SA added
1414e4fb28f86_SAindex added
1414e53eccf4a_sjdbInfo.txt added
1414e601d2e51_sjdbList.fromGTF.out.tab added
1414e1bcbf923_sjdbList.out.tab added
1414e6c517716_transcriptInfo.tab added
1414e58617ce8_GRCh38.GENCODE.v42_100 added
1414e684f90ac_knownGene_hg38.sql added
1414e3fa341b4_knownGene_hg38.txt added
1414e772eb10f_refGene_hg38.sql added
1414e1a6a8cea_refGene_hg38.txt added
1414e49496432_knownGene_mm39.sql added
1414e71513434_knownGene_mm39.txt added
1414ea3a7c0b_refGene_mm39.sql added
1414e5a5bb6c_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//RtmptMgY3k/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 0 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
>
>
>
> proc.time()
user system elapsed
7.036 0.870 9.259
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.073 | 0.258 | 2.432 | |
| dataSearch | 0.352 | 0.016 | 0.396 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.957 | 0.058 | 1.985 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.038 | 0.005 | 0.043 | |
| recipeLoad | 0.424 | 0.030 | 0.469 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.181 | 0.015 | 0.210 | |
| recipeUpdate | 0 | 0 | 0 | |