Qian Liu
| Snapshot Date: 2026-03-13 13:40 -0400 (Fri, 13 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 2026-03-14 11:34 -0400 (Sat, 14 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" | 4837 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4050 |
| 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 1777/2361 | 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: 2026-03-13 19:56:44 -0400 (Fri, 13 Mar 2026) |
| EndedAt: 2026-03-13 19:57:40 -0400 (Fri, 13 Mar 2026) |
| EllapsedTime: 55.8 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) (2026-03-01 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: 2026-03-13 23:56:45 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...
1675126b385e6_GRCh38.primary_assembly.genome.fa.1.bt2 added
16751541bd2e3_GRCh38.primary_assembly.genome.fa.2.bt2 added
167516eb26038_GRCh38.primary_assembly.genome.fa.3.bt2 added
16751cb354f_GRCh38.primary_assembly.genome.fa.4.bt2 added
167511d18d5f1_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
167514985d023_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
167517023cf8a_outfile.txt added
167513f0ea68a_GRCh37_to_GRCh38.chain added
167515ad7ce5d_GRCh37_to_NCBI34.chain added
16751e2d6a43_GRCh37_to_NCBI35.chain added
16751479b5bfa_GRCh37_to_NCBI36.chain added
1675128b39ed0_GRCh38_to_GRCh37.chain added
16751287f7e90_GRCh38_to_NCBI34.chain added
167514a4e34b5_GRCh38_to_NCBI35.chain added
1675154667d2f_GRCh38_to_NCBI36.chain added
1675114a4c3f3_NCBI34_to_GRCh37.chain added
167514d3c911b_NCBI34_to_GRCh38.chain added
16751435aab3a_NCBI35_to_GRCh37.chain added
16751759f8f61_NCBI35_to_GRCh38.chain added
167513e7e659b_NCBI36_to_GRCh37.chain added
167515c40c32a_NCBI36_to_GRCh38.chain added
167511fcd29b7_GRCm38_to_NCBIM36.chain added
16751566dbdb0_GRCm38_to_NCBIM37.chain added
167513ec09a24_NCBIM36_to_GRCm38.chain added
1675156c7d1ab_NCBIM37_to_GRCm38.chain added
1675158965e0f_1000G_omni2.5.b37.vcf.gz added
1675177f95838_1000G_omni2.5.b37.vcf.gz.tbi added
16751130f0211_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
167513e50b3dd_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1675124509221_1000G_omni2.5.hg38.vcf.gz added
1675125a9c727_1000G_omni2.5.hg38.vcf.gz.tbi added
167512d51e4c2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
167515b8193cc_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
16751180e6503_af-only-gnomad.raw.sites.vcf added
167515909b44b_af-only-gnomad.raw.sites.vcf.idx added
16751c1bd598_Mutect2-exome-panel.vcf.idx added
167517763f45d_Mutect2-WGS-panel-b37.vcf added
16751434042e7_Mutect2-WGS-panel-b37.vcf.idx added
167512fe86e2f_small_exac_common_3.vcf added
167514499e83b_small_exac_common_3.vcf.idx added
16751545d9cac_1000g_pon.hg38.vcf.gz added
167514dd90b79_1000g_pon.hg38.vcf.gz.tbi added
1675164805cdc_af-only-gnomad.hg38.vcf.gz added
167512750a310_af-only-gnomad.hg38.vcf.gz.tbi added
167511f01839a_small_exac_common_3.hg38.vcf.gz added
167511c67035d_small_exac_common_3.hg38.vcf.gz.tbi added
167512f0ddd3c_gencode.v41.annotation.gtf added
167513737a646_gencode.v42.annotation.gtf added
16751268559fc_gencode.vM30.annotation.gtf added
167517cd6c325_gencode.vM31.annotation.gtf added
1675177a5f22a_gencode.v41.transcripts.fa added
167512fbde0c4_gencode.v41.transcripts.fa.fai added
167515aef7c58_gencode.v42.transcripts.fa added
1675120cca40c_gencode.v42.transcripts.fa.fai added
167515b2620a6_gencode.vM30.pc_transcripts.fa added
167512429a10a_gencode.vM30.pc_transcripts.fa.fai added
16751290baa12_gencode.vM31.pc_transcripts.fa added
167513cca98cb_gencode.vM31.pc_transcripts.fa.fai added
1675118f5569b_GRCh38.primary_assembly.genome.fa.1.ht2 added
167511308e6ea_GRCh38.primary_assembly.genome.fa.2.ht2 added
167512d701669_GRCh38.primary_assembly.genome.fa.3.ht2 added
1675119cf5ecd_GRCh38.primary_assembly.genome.fa.4.ht2 added
167517d58f1f7_GRCh38.primary_assembly.genome.fa.5.ht2 added
167515a75cf6b_GRCh38.primary_assembly.genome.fa.6.ht2 added
167516c84a832_GRCh38.primary_assembly.genome.fa.7.ht2 added
16751793ea246_GRCh38.primary_assembly.genome.fa.8.ht2 added
167517f0fdfd9_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
167516b3160ba_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1675176c58a50_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1675122fbc71b_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
167513fcccf8e_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
167511f4e945b_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
167515fedf26b_GRCh38_full_analysis_set_plus_decoy_hla.fa added
167517ec68000_GRCh38.primary_assembly.genome.fa.fai added
1675119fdc106_GRCh38.primary_assembly.genome.fa.amb added
16751628b7e3e_GRCh38.primary_assembly.genome.fa.ann added
16751340d4afd_GRCh38.primary_assembly.genome.fa.bwt added
1675154b642bd_GRCh38.primary_assembly.genome.fa.pac added
167519d7b1be_GRCh38.primary_assembly.genome.fa.sa added
167512fd635fe_GRCh38.primary_assembly.genome.fa added
167511872cf3b_hs37d5.fa.fai added
1675119833707_hs37d5.fa.amb added
167517591b9a6_hs37d5.fa.ann added
1675132337d97_hs37d5.fa.bwt added
16751527a5e40_hs37d5.fa.pac added
167515fc1e60d_hs37d5.fa.sa added
1675132e69098_hs37d5.fa added
167513f1f0543_complete_ref_lens.bin added
16751d929215_ctable.bin added
1675111b4a7a9_ctg_offsets.bin added
167516b6b5153_duplicate_clusters.tsv added
1675152a8573d_info.json added
1675129f79030_mphf.bin added
167513c1b54d6_pos.bin added
16751265ecc6e_pre_indexing.log added
1675119bf5d70_rank.bin added
16751628f7144_ref_indexing.log added
16751375559e9_refAccumLengths.bin added
167514481ec60_reflengths.bin added
167512dc5b5c3_refseq.bin added
16751f202caf_seq.bin added
167519559ceb_versionInfo.json added
1675153b10d16_salmon_index added
16751cd24a47_chrLength.txt added
16751420a81e4_chrName.txt added
167513fd5c19b_chrNameLength.txt added
167516a99c7da_chrStart.txt added
16751160fefe3_exonGeTrInfo.tab added
16751704e2b65_exonInfo.tab added
167511c032d7d_geneInfo.tab added
16751149f77e9_Genome added
1675171796c92_genomeParameters.txt added
167515ac71f71_Log.out added
1675146e16246_SA added
1675176fb0604_SAindex added
167515a482da2_sjdbInfo.txt added
1675138ac14fc_sjdbList.fromGTF.out.tab added
167512995c975_sjdbList.out.tab added
1675128dd35a7_transcriptInfo.tab added
1675152ed7be6_GRCh38.GENCODE.v42_100 added
1675165616392_knownGene_hg38.sql added
167515cd03a3d_knownGene_hg38.txt added
167516a9faa65_refGene_hg38.sql added
16751186c0393_refGene_hg38.txt added
167515b5eb46b_knownGene_mm39.sql added
1675126970baa_knownGene_mm39.txt added
1675167ed9b1_refGene_mm39.sql added
167517205f6cb_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//Rtmpd0Hw2B/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
7.048 0.766 8.683
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.112 | 0.242 | 2.458 | |
| dataSearch | 0.378 | 0.015 | 0.407 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.951 | 0.056 | 1.914 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.046 | 0.006 | 0.053 | |
| recipeLoad | 0.445 | 0.026 | 0.491 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.185 | 0.010 | 0.199 | |
| recipeUpdate | 0 | 0 | 0 | |