Qian Liu
| Snapshot Date: 2026-03-02 13:40 -0500 (Mon, 02 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 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-03 11:35 -0500 (Tue, 03 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4877 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4570 |
| 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 1773/2357 | 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: 2026-03-02 21:48:15 -0500 (Mon, 02 Mar 2026) |
| EndedAt: 2026-03-02 21:49:11 -0500 (Mon, 02 Mar 2026) |
| EllapsedTime: 55.7 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) (2026-01-15 r89304)
* 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 Sonoma 14.8.3
* 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) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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...
122634a5aa0c2_GRCh38.primary_assembly.genome.fa.1.bt2 added
122633f046b1_GRCh38.primary_assembly.genome.fa.2.bt2 added
1226313b1107c_GRCh38.primary_assembly.genome.fa.3.bt2 added
122634db146fd_GRCh38.primary_assembly.genome.fa.4.bt2 added
1226331abb3e4_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
122637faf5735_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1226350869a10_outfile.txt added
1226334ecb9bd_GRCh37_to_GRCh38.chain added
1226321964270_GRCh37_to_NCBI34.chain added
12263fe3d84a_GRCh37_to_NCBI35.chain added
12263378cea6c_GRCh37_to_NCBI36.chain added
1226347274f2_GRCh38_to_GRCh37.chain added
12263765bbe25_GRCh38_to_NCBI34.chain added
12263120abd8_GRCh38_to_NCBI35.chain added
122637f1f27c_GRCh38_to_NCBI36.chain added
122631d66aef7_NCBI34_to_GRCh37.chain added
122634068e935_NCBI34_to_GRCh38.chain added
1226327a6b79c_NCBI35_to_GRCh37.chain added
122633260771a_NCBI35_to_GRCh38.chain added
122635b2b65cc_NCBI36_to_GRCh37.chain added
122637e2862d6_NCBI36_to_GRCh38.chain added
12263d71104f_GRCm38_to_NCBIM36.chain added
1226379e5b96d_GRCm38_to_NCBIM37.chain added
1226358f0e1a0_NCBIM36_to_GRCm38.chain added
122632e6cfcfe_NCBIM37_to_GRCm38.chain added
1226375559f81_1000G_omni2.5.b37.vcf.gz added
12263485b0a55_1000G_omni2.5.b37.vcf.gz.tbi added
122635103778f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
122633a9e76d6_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
12263798bf9aa_1000G_omni2.5.hg38.vcf.gz added
1226354b4463d_1000G_omni2.5.hg38.vcf.gz.tbi added
1226376f7a3d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1226327c23e9b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
12263419c4681_af-only-gnomad.raw.sites.vcf added
122637ad8e0cd_af-only-gnomad.raw.sites.vcf.idx added
12263348ef1bd_Mutect2-exome-panel.vcf.idx added
1226314a0ca40_Mutect2-WGS-panel-b37.vcf added
12263483e3a54_Mutect2-WGS-panel-b37.vcf.idx added
122636d6785d9_small_exac_common_3.vcf added
122632784a1ac_small_exac_common_3.vcf.idx added
1226374923778_1000g_pon.hg38.vcf.gz added
122632b77e312_1000g_pon.hg38.vcf.gz.tbi added
122634bdcc909_af-only-gnomad.hg38.vcf.gz added
12263c1294c8_af-only-gnomad.hg38.vcf.gz.tbi added
1226317e5dca9_small_exac_common_3.hg38.vcf.gz added
1226373f9e780_small_exac_common_3.hg38.vcf.gz.tbi added
122631bcdbffc_gencode.v41.annotation.gtf added
1226360f747a6_gencode.v42.annotation.gtf added
12263a811506_gencode.vM30.annotation.gtf added
12263208b424d_gencode.vM31.annotation.gtf added
1226316adddec_gencode.v41.transcripts.fa added
1226370c4bc95_gencode.v41.transcripts.fa.fai added
12263439140a_gencode.v42.transcripts.fa added
122633f529eb0_gencode.v42.transcripts.fa.fai added
122634930554a_gencode.vM30.pc_transcripts.fa added
1226342f92d0_gencode.vM30.pc_transcripts.fa.fai added
122634f4f97d5_gencode.vM31.pc_transcripts.fa added
12263727949a0_gencode.vM31.pc_transcripts.fa.fai added
1226378d0e216_GRCh38.primary_assembly.genome.fa.1.ht2 added
1226359ab5051_GRCh38.primary_assembly.genome.fa.2.ht2 added
122637e2623d4_GRCh38.primary_assembly.genome.fa.3.ht2 added
1226379fa73ff_GRCh38.primary_assembly.genome.fa.4.ht2 added
1226329d5a8e9_GRCh38.primary_assembly.genome.fa.5.ht2 added
12263a446e74_GRCh38.primary_assembly.genome.fa.6.ht2 added
1226312af86f0_GRCh38.primary_assembly.genome.fa.7.ht2 added
1226341c40025_GRCh38.primary_assembly.genome.fa.8.ht2 added
122632ae59ede_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
12263492116d2_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
122631b615a80_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
12263147c978b_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
122637fc1312e_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1226364840488_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
122631745b046_GRCh38_full_analysis_set_plus_decoy_hla.fa added
122636037cf99_GRCh38.primary_assembly.genome.fa.fai added
12263701e7728_GRCh38.primary_assembly.genome.fa.amb added
1226360211c99_GRCh38.primary_assembly.genome.fa.ann added
122631ddcb21d_GRCh38.primary_assembly.genome.fa.bwt added
122634319d3c_GRCh38.primary_assembly.genome.fa.pac added
122635549d04a_GRCh38.primary_assembly.genome.fa.sa added
122636109d604_GRCh38.primary_assembly.genome.fa added
122634cc1d261_hs37d5.fa.fai added
1226348db05a5_hs37d5.fa.amb added
12263234fb901_hs37d5.fa.ann added
1226346fb02c3_hs37d5.fa.bwt added
12263972749d_hs37d5.fa.pac added
122633945f443_hs37d5.fa.sa added
122631fa77815_hs37d5.fa added
122632bbcbaef_complete_ref_lens.bin added
122637394b757_ctable.bin added
122632890ec09_ctg_offsets.bin added
12263427857ad_duplicate_clusters.tsv added
122636ac440f2_info.json added
122637a8406a0_mphf.bin added
1226371cf3136_pos.bin added
1226359a80a99_pre_indexing.log added
12263274ff0cb_rank.bin added
122637149b396_ref_indexing.log added
122631dad76f5_refAccumLengths.bin added
12263675cde0b_reflengths.bin added
122631f5d931_refseq.bin added
12263338620f8_seq.bin added
122632ade9435_versionInfo.json added
122637ad4398f_salmon_index added
1226330f1a49_chrLength.txt added
122635486b030_chrName.txt added
1226356994aaa_chrNameLength.txt added
1226369f50b50_chrStart.txt added
1226356b9e788_exonGeTrInfo.tab added
12263470fbe33_exonInfo.tab added
122635a902ab7_geneInfo.tab added
122632ee482d4_Genome added
122631c494459_genomeParameters.txt added
12263e263d91_Log.out added
12263709401d8_SA added
1226350545a6_SAindex added
122631d1f97dd_sjdbInfo.txt added
1226352b3d1b_sjdbList.fromGTF.out.tab added
1226359b8ba43_sjdbList.out.tab added
122636eccb2b9_transcriptInfo.tab added
1226340e9c883_GRCh38.GENCODE.v42_100 added
12263346b31c0_knownGene_hg38.sql added
12263698f4f22_knownGene_hg38.txt added
122633f947752_refGene_hg38.sql added
122632c25c91a_refGene_hg38.txt added
1226364b5e09a_knownGene_mm39.sql added
1226360acd21d_knownGene_mm39.txt added
1226372169f80_refGene_mm39.sql added
122632b41c704_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//Rtmp4kOz26/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
6.981 0.777 8.798
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.079 | 0.239 | 2.399 | |
| dataSearch | 0.348 | 0.013 | 0.371 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.917 | 0.058 | 1.917 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.044 | 0.004 | 0.050 | |
| recipeLoad | 0.416 | 0.027 | 0.451 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.173 | 0.010 | 0.188 | |
| recipeUpdate | 0 | 0 | 0 | |