Qian Liu
| Snapshot Date: 2026-03-26 13:40 -0400 (Thu, 26 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 2026-03-27 11:33 -0400 (Fri, 27 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" | 4880 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" | 4577 |
| 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 1784/2372 | 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: 2026-03-26 21:19:43 -0400 (Thu, 26 Mar 2026) |
| EndedAt: 2026-03-26 21:20:35 -0400 (Thu, 26 Mar 2026) |
| EllapsedTime: 52.5 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: 2026-03-27 01:19:43 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...
11aa626105e2f_GRCh38.primary_assembly.genome.fa.1.bt2 added
11aa67c97732e_GRCh38.primary_assembly.genome.fa.2.bt2 added
11aa63b0b10e9_GRCh38.primary_assembly.genome.fa.3.bt2 added
11aa653834f47_GRCh38.primary_assembly.genome.fa.4.bt2 added
11aa651c9e926_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
11aa61ee9e7bd_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
11aa6e6d3926_outfile.txt added
11aa624c2f530_GRCh37_to_GRCh38.chain added
11aa67b6f352a_GRCh37_to_NCBI34.chain added
11aa6420b97b5_GRCh37_to_NCBI35.chain added
11aa67150df3_GRCh37_to_NCBI36.chain added
11aa67746d026_GRCh38_to_GRCh37.chain added
11aa64a0babf7_GRCh38_to_NCBI34.chain added
11aa644470b1b_GRCh38_to_NCBI35.chain added
11aa6142a3ca2_GRCh38_to_NCBI36.chain added
11aa660f2ba05_NCBI34_to_GRCh37.chain added
11aa65f92cffc_NCBI34_to_GRCh38.chain added
11aa61f94da69_NCBI35_to_GRCh37.chain added
11aa6658f33b1_NCBI35_to_GRCh38.chain added
11aa61c8add8e_NCBI36_to_GRCh37.chain added
11aa660d7a445_NCBI36_to_GRCh38.chain added
11aa66d61dfae_GRCm38_to_NCBIM36.chain added
11aa634a4509c_GRCm38_to_NCBIM37.chain added
11aa6fa84cc4_NCBIM36_to_GRCm38.chain added
11aa67247dfe3_NCBIM37_to_GRCm38.chain added
11aa64cbbeab2_1000G_omni2.5.b37.vcf.gz added
11aa6452d7379_1000G_omni2.5.b37.vcf.gz.tbi added
11aa62af8306a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
11aa6c329530_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
11aa64ce08891_1000G_omni2.5.hg38.vcf.gz added
11aa629260f05_1000G_omni2.5.hg38.vcf.gz.tbi added
11aa61a4265e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
11aa63fd2e629_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
11aa62f04ae7b_af-only-gnomad.raw.sites.vcf added
11aa65c5b255a_af-only-gnomad.raw.sites.vcf.idx added
11aa663f16714_Mutect2-exome-panel.vcf.idx added
11aa67da6854e_Mutect2-WGS-panel-b37.vcf added
11aa63f7a0454_Mutect2-WGS-panel-b37.vcf.idx added
11aa663b2475a_small_exac_common_3.vcf added
11aa64d6a98d8_small_exac_common_3.vcf.idx added
11aa61158b49d_1000g_pon.hg38.vcf.gz added
11aa656b9b850_1000g_pon.hg38.vcf.gz.tbi added
11aa63af3b8ab_af-only-gnomad.hg38.vcf.gz added
11aa656e100c9_af-only-gnomad.hg38.vcf.gz.tbi added
11aa64dfab8ae_small_exac_common_3.hg38.vcf.gz added
11aa6772cf81_small_exac_common_3.hg38.vcf.gz.tbi added
11aa629521f9_gencode.v41.annotation.gtf added
11aa6ce963c2_gencode.v42.annotation.gtf added
11aa62e945c2d_gencode.vM30.annotation.gtf added
11aa6e2fa63f_gencode.vM31.annotation.gtf added
11aa65a4b795f_gencode.v41.transcripts.fa added
11aa6110d7a49_gencode.v41.transcripts.fa.fai added
11aa6bd7575e_gencode.v42.transcripts.fa added
11aa666a8e264_gencode.v42.transcripts.fa.fai added
11aa659a747e3_gencode.vM30.pc_transcripts.fa added
11aa67560b610_gencode.vM30.pc_transcripts.fa.fai added
11aa6205110a4_gencode.vM31.pc_transcripts.fa added
11aa62a1b8f8f_gencode.vM31.pc_transcripts.fa.fai added
11aa6776e0ae1_GRCh38.primary_assembly.genome.fa.1.ht2 added
11aa6598c7708_GRCh38.primary_assembly.genome.fa.2.ht2 added
11aa614dadc26_GRCh38.primary_assembly.genome.fa.3.ht2 added
11aa62cab4d7c_GRCh38.primary_assembly.genome.fa.4.ht2 added
11aa6226c1ecd_GRCh38.primary_assembly.genome.fa.5.ht2 added
11aa6685a3662_GRCh38.primary_assembly.genome.fa.6.ht2 added
11aa67aa89173_GRCh38.primary_assembly.genome.fa.7.ht2 added
11aa650e553ee_GRCh38.primary_assembly.genome.fa.8.ht2 added
11aa67fe957bf_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
11aa6307ffe34_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
11aa6230a20cc_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
11aa66def430c_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
11aa6771b0136_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
11aa6decbd51_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
11aa6318117fb_GRCh38_full_analysis_set_plus_decoy_hla.fa added
11aa6124d7921_GRCh38.primary_assembly.genome.fa.fai added
11aa61c4b6eea_GRCh38.primary_assembly.genome.fa.amb added
11aa61c5ed329_GRCh38.primary_assembly.genome.fa.ann added
11aa61579374c_GRCh38.primary_assembly.genome.fa.bwt added
11aa6491d6997_GRCh38.primary_assembly.genome.fa.pac added
11aa629ff5e01_GRCh38.primary_assembly.genome.fa.sa added
11aa63c74a931_GRCh38.primary_assembly.genome.fa added
11aa6f0feef9_hs37d5.fa.fai added
11aa65f122528_hs37d5.fa.amb added
11aa6204595db_hs37d5.fa.ann added
11aa638716d6a_hs37d5.fa.bwt added
11aa61ec66719_hs37d5.fa.pac added
11aa6739aaa17_hs37d5.fa.sa added
11aa62f15074c_hs37d5.fa added
11aa6d9226ba_complete_ref_lens.bin added
11aa6762c844b_ctable.bin added
11aa664a19489_ctg_offsets.bin added
11aa62c1ee1fc_duplicate_clusters.tsv added
11aa61f867e05_info.json added
11aa636bb8a6e_mphf.bin added
11aa6527d57d4_pos.bin added
11aa62311499b_pre_indexing.log added
11aa643f77119_rank.bin added
11aa62a22432b_ref_indexing.log added
11aa62f67d1a9_refAccumLengths.bin added
11aa648f5c68f_reflengths.bin added
11aa67fbefbb4_refseq.bin added
11aa6537f27f1_seq.bin added
11aa641176a0a_versionInfo.json added
11aa66832d7e8_salmon_index added
11aa661fcf5c9_chrLength.txt added
11aa6266c9161_chrName.txt added
11aa621bc8afc_chrNameLength.txt added
11aa66148b7b1_chrStart.txt added
11aa66d13f75c_exonGeTrInfo.tab added
11aa639d4f0f6_exonInfo.tab added
11aa64b17c423_geneInfo.tab added
11aa654dfc59_Genome added
11aa642f239c7_genomeParameters.txt added
11aa62caf5a27_Log.out added
11aa62c47cd5c_SA added
11aa61dfb69ba_SAindex added
11aa664da41b6_sjdbInfo.txt added
11aa635104774_sjdbList.fromGTF.out.tab added
11aa63fc32be3_sjdbList.out.tab added
11aa6267664c9_transcriptInfo.tab added
11aa626d2dbd9_GRCh38.GENCODE.v42_100 added
11aa65d5f9778_knownGene_hg38.sql added
11aa62ed1772c_knownGene_hg38.txt added
11aa639e701b7_refGene_hg38.sql added
11aa66d21b313_refGene_hg38.txt added
11aa63f73dc5e_knownGene_mm39.sql added
11aa64f88bfdd_knownGene_mm39.txt added
11aa61aec6ef6_refGene_mm39.sql added
11aa61868e649_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//RtmpVTxO2n/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
6.565 0.844 7.931
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.130 | 0.336 | 2.535 | |
| dataSearch | 0.376 | 0.028 | 0.423 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.853 | 0.057 | 1.532 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.040 | 0.003 | 0.043 | |
| recipeLoad | 0.424 | 0.033 | 0.464 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.158 | 0.012 | 0.171 | |
| recipeUpdate | 0 | 0 | 0 | |