Qian Liu
| Snapshot Date: 2025-12-03 13:40 -0500 (Wed, 03 Dec 2025) |
| 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 2025-12-04 11:35 -0500 (Thu, 04 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 1753/2331 | 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: 2025-12-04 02:38:58 -0500 (Thu, 04 Dec 2025) |
| EndedAt: 2025-12-04 02:39:57 -0500 (Thu, 04 Dec 2025) |
| EllapsedTime: 58.6 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...
cec74b140cf2_GRCh38.primary_assembly.genome.fa.1.bt2 added
cec7115e0a60_GRCh38.primary_assembly.genome.fa.2.bt2 added
cec734fb2d88_GRCh38.primary_assembly.genome.fa.3.bt2 added
cec7566a56e4_GRCh38.primary_assembly.genome.fa.4.bt2 added
cec75f6ebf0e_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
cec75fc16114_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
cec710cc9929_outfile.txt added
cec7685b5b5c_GRCh37_to_GRCh38.chain added
cec745cb2a8a_GRCh37_to_NCBI34.chain added
cec71d55edd2_GRCh37_to_NCBI35.chain added
cec774708509_GRCh37_to_NCBI36.chain added
cec772e4d98_GRCh38_to_GRCh37.chain added
cec770e839d6_GRCh38_to_NCBI34.chain added
cec71e2d4a83_GRCh38_to_NCBI35.chain added
cec72f76edef_GRCh38_to_NCBI36.chain added
cec728fefe41_NCBI34_to_GRCh37.chain added
cec77ce6726d_NCBI34_to_GRCh38.chain added
cec77d62922a_NCBI35_to_GRCh37.chain added
cec7526a43b5_NCBI35_to_GRCh38.chain added
cec73e834a58_NCBI36_to_GRCh37.chain added
cec71d85f778_NCBI36_to_GRCh38.chain added
cec74639f66c_GRCm38_to_NCBIM36.chain added
cec77615079_GRCm38_to_NCBIM37.chain added
cec75ea3bb8_NCBIM36_to_GRCm38.chain added
cec754f6b010_NCBIM37_to_GRCm38.chain added
cec7fa11604_1000G_omni2.5.b37.vcf.gz added
cec718ac68a0_1000G_omni2.5.b37.vcf.gz.tbi added
cec75f08ed07_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
cec74301974f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
cec71d74e5e7_1000G_omni2.5.hg38.vcf.gz added
cec765a1afcc_1000G_omni2.5.hg38.vcf.gz.tbi added
cec75a1cae34_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
cec710f10624_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
cec73fca2e2c_af-only-gnomad.raw.sites.vcf added
cec7729d6b6b_af-only-gnomad.raw.sites.vcf.idx added
cec73cf77896_Mutect2-exome-panel.vcf.idx added
cec71b0ddf1f_Mutect2-WGS-panel-b37.vcf added
cec72bb37a19_Mutect2-WGS-panel-b37.vcf.idx added
cec7141515b9_small_exac_common_3.vcf added
cec774452efb_small_exac_common_3.vcf.idx added
cec76a0f9c5f_1000g_pon.hg38.vcf.gz added
cec726e3575f_1000g_pon.hg38.vcf.gz.tbi added
cec7177d31eb_af-only-gnomad.hg38.vcf.gz added
cec71c584759_af-only-gnomad.hg38.vcf.gz.tbi added
cec767b43298_small_exac_common_3.hg38.vcf.gz added
cec76765ce58_small_exac_common_3.hg38.vcf.gz.tbi added
cec74cce2870_gencode.v41.annotation.gtf added
cec772c0f874_gencode.v42.annotation.gtf added
cec75af7c287_gencode.vM30.annotation.gtf added
cec740045bb9_gencode.vM31.annotation.gtf added
cec75e21ef84_gencode.v41.transcripts.fa added
cec75f3f364_gencode.v41.transcripts.fa.fai added
cec752f02d49_gencode.v42.transcripts.fa added
cec7162d3e29_gencode.v42.transcripts.fa.fai added
cec7744c011e_gencode.vM30.pc_transcripts.fa added
cec729dd9438_gencode.vM30.pc_transcripts.fa.fai added
cec7122dfe01_gencode.vM31.pc_transcripts.fa added
cec797efcfa_gencode.vM31.pc_transcripts.fa.fai added
cec7701285f4_GRCh38.primary_assembly.genome.fa.1.ht2 added
cec750188fa7_GRCh38.primary_assembly.genome.fa.2.ht2 added
cec77c7f4605_GRCh38.primary_assembly.genome.fa.3.ht2 added
cec77ce321e_GRCh38.primary_assembly.genome.fa.4.ht2 added
cec7723c5392_GRCh38.primary_assembly.genome.fa.5.ht2 added
cec75692d0d5_GRCh38.primary_assembly.genome.fa.6.ht2 added
cec740cc7c5a_GRCh38.primary_assembly.genome.fa.7.ht2 added
cec730f819f2_GRCh38.primary_assembly.genome.fa.8.ht2 added
cec7706f77fb_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
cec7262e3968_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
cec724baee6d_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
cec76c7b48f1_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
cec711f1fddb_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
cec726513e11_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
cec71fc1e1be_GRCh38_full_analysis_set_plus_decoy_hla.fa added
cec771cb913b_GRCh38.primary_assembly.genome.fa.fai added
cec76babf2da_GRCh38.primary_assembly.genome.fa.amb added
cec765d4fd6f_GRCh38.primary_assembly.genome.fa.ann added
cec724ab6a4_GRCh38.primary_assembly.genome.fa.bwt added
cec7771cca28_GRCh38.primary_assembly.genome.fa.pac added
cec731c4530_GRCh38.primary_assembly.genome.fa.sa added
cec7350253e8_GRCh38.primary_assembly.genome.fa added
cec72bd2bf88_hs37d5.fa.fai added
cec7191c9032_hs37d5.fa.amb added
cec7223ecf7f_hs37d5.fa.ann added
cec749a8ac69_hs37d5.fa.bwt added
cec760cf4746_hs37d5.fa.pac added
cec748507651_hs37d5.fa.sa added
cec71a87e4ee_hs37d5.fa added
cec74fc6d2dd_complete_ref_lens.bin added
cec763dd416_ctable.bin added
cec7452ef38d_ctg_offsets.bin added
cec7d77d177_duplicate_clusters.tsv added
cec73558e289_info.json added
cec75e80abbb_mphf.bin added
cec7518ab275_pos.bin added
cec768ca4925_pre_indexing.log added
cec7388851e2_rank.bin added
cec77db7e96c_ref_indexing.log added
cec7353df1ef_refAccumLengths.bin added
cec775d69d37_reflengths.bin added
cec75cebc251_refseq.bin added
cec77a22837f_seq.bin added
cec76fe7457d_versionInfo.json added
cec738834af0_salmon_index added
cec733acef8c_chrLength.txt added
cec71ea2ead5_chrName.txt added
cec759e755a9_chrNameLength.txt added
cec762a8f85b_chrStart.txt added
cec7434950f7_exonGeTrInfo.tab added
cec7262aaa4_exonInfo.tab added
cec71bb0f635_geneInfo.tab added
cec77ef41fc6_Genome added
cec74d524147_genomeParameters.txt added
cec7533bc3f9_Log.out added
cec778bf3b1f_SA added
cec752c2ae27_SAindex added
cec76b37ace3_sjdbInfo.txt added
cec71437a213_sjdbList.fromGTF.out.tab added
cec7507197c3_sjdbList.out.tab added
cec751a2ac77_transcriptInfo.tab added
cec7ee8e280_GRCh38.GENCODE.v42_100 added
cec75b6e4925_knownGene_hg38.sql added
cec725844b08_knownGene_hg38.txt added
cec7105a0d76_refGene_hg38.sql added
cec7829c65d_refGene_hg38.txt added
cec76e9e07da_knownGene_mm39.sql added
cec74915b1f2_knownGene_mm39.txt added
cec72f55ac5a_refGene_mm39.sql added
cec721a660fd_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//RtmpcOg0s2/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
6.870 0.783 9.057
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.043 | 0.238 | 2.318 | |
| dataSearch | 0.349 | 0.018 | 0.366 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 0.930 | 0.063 | 4.042 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.042 | 0.006 | 0.052 | |
| recipeLoad | 0.427 | 0.031 | 0.479 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.180 | 0.011 | 0.194 | |
| recipeUpdate | 0 | 0 | 0 | |