Qian Liu
| Snapshot Date: 2026-01-04 13:40 -0500 (Sun, 04 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 2026-01-05 11:35 -0500 (Mon, 05 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" | 4815 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 1754/2332 | 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: 2026-01-04 21:56:03 -0500 (Sun, 04 Jan 2026) |
| EndedAt: 2026-01-04 21:57:01 -0500 (Sun, 04 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...
1f861f31891d_GRCh38.primary_assembly.genome.fa.1.bt2 added
1f866d20deea_GRCh38.primary_assembly.genome.fa.2.bt2 added
1f8690b0c9f_GRCh38.primary_assembly.genome.fa.3.bt2 added
1f8634699f5c_GRCh38.primary_assembly.genome.fa.4.bt2 added
1f8625d6be6_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1f864356ca40_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1f8676f85249_outfile.txt added
1f8628e273a4_GRCh37_to_GRCh38.chain added
1f862b1628f4_GRCh37_to_NCBI34.chain added
1f863bdac145_GRCh37_to_NCBI35.chain added
1f8616c6b7b6_GRCh37_to_NCBI36.chain added
1f8650471968_GRCh38_to_GRCh37.chain added
1f866bd52404_GRCh38_to_NCBI34.chain added
1f86762fb9ea_GRCh38_to_NCBI35.chain added
1f863756ee44_GRCh38_to_NCBI36.chain added
1f862c34cebe_NCBI34_to_GRCh37.chain added
1f863ef1329e_NCBI34_to_GRCh38.chain added
1f864d32435a_NCBI35_to_GRCh37.chain added
1f861ee3f14e_NCBI35_to_GRCh38.chain added
1f866f747ba_NCBI36_to_GRCh37.chain added
1f86548607e8_NCBI36_to_GRCh38.chain added
1f862b713bb2_GRCm38_to_NCBIM36.chain added
1f8617063966_GRCm38_to_NCBIM37.chain added
1f8619a26359_NCBIM36_to_GRCm38.chain added
1f8674287534_NCBIM37_to_GRCm38.chain added
1f86c26e480_1000G_omni2.5.b37.vcf.gz added
1f864d6395bb_1000G_omni2.5.b37.vcf.gz.tbi added
1f8644fb4fae_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1f864f2c4be3_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1f86652a4cb0_1000G_omni2.5.hg38.vcf.gz added
1f863c10eab3_1000G_omni2.5.hg38.vcf.gz.tbi added
1f867aa0ac93_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1f864aa225ca_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1f865b5f170d_af-only-gnomad.raw.sites.vcf added
1f863fe28558_af-only-gnomad.raw.sites.vcf.idx added
1f8630a0752c_Mutect2-exome-panel.vcf.idx added
1f86766cb4a4_Mutect2-WGS-panel-b37.vcf added
1f865ac7b7b9_Mutect2-WGS-panel-b37.vcf.idx added
1f866def013e_small_exac_common_3.vcf added
1f86663ac5d4_small_exac_common_3.vcf.idx added
1f861c9215bb_1000g_pon.hg38.vcf.gz added
1f863ad0b6a4_1000g_pon.hg38.vcf.gz.tbi added
1f865c86e726_af-only-gnomad.hg38.vcf.gz added
1f861cb19f3f_af-only-gnomad.hg38.vcf.gz.tbi added
1f86514defd0_small_exac_common_3.hg38.vcf.gz added
1f8653bb6a63_small_exac_common_3.hg38.vcf.gz.tbi added
1f863545b487_gencode.v41.annotation.gtf added
1f86734f2663_gencode.v42.annotation.gtf added
1f86516168b9_gencode.vM30.annotation.gtf added
1f865222736c_gencode.vM31.annotation.gtf added
1f8653c7e194_gencode.v41.transcripts.fa added
1f8667aae684_gencode.v41.transcripts.fa.fai added
1f865041948_gencode.v42.transcripts.fa added
1f865017c88a_gencode.v42.transcripts.fa.fai added
1f86496f051a_gencode.vM30.pc_transcripts.fa added
1f8617b813a0_gencode.vM30.pc_transcripts.fa.fai added
1f863610798a_gencode.vM31.pc_transcripts.fa added
1f86739b6ec0_gencode.vM31.pc_transcripts.fa.fai added
1f8661843a8b_GRCh38.primary_assembly.genome.fa.1.ht2 added
1f86301fadb1_GRCh38.primary_assembly.genome.fa.2.ht2 added
1f866fc45825_GRCh38.primary_assembly.genome.fa.3.ht2 added
1f8643771e76_GRCh38.primary_assembly.genome.fa.4.ht2 added
1f864170f794_GRCh38.primary_assembly.genome.fa.5.ht2 added
1f865f8e371c_GRCh38.primary_assembly.genome.fa.6.ht2 added
1f8671c44046_GRCh38.primary_assembly.genome.fa.7.ht2 added
1f86b57ee04_GRCh38.primary_assembly.genome.fa.8.ht2 added
1f8639cb4e6d_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1f865289f3bf_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1f865ee1aaee_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1f86319d1fec_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1f86429ad866_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1f8643f532b3_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1f8616d3a8a0_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1f8621e3ac15_GRCh38.primary_assembly.genome.fa.fai added
1f866a36a814_GRCh38.primary_assembly.genome.fa.amb added
1f862a54ef86_GRCh38.primary_assembly.genome.fa.ann added
1f862e395c20_GRCh38.primary_assembly.genome.fa.bwt added
1f8637cf5095_GRCh38.primary_assembly.genome.fa.pac added
1f86bb382d3_GRCh38.primary_assembly.genome.fa.sa added
1f863651f0a5_GRCh38.primary_assembly.genome.fa added
1f863d8dfc7f_hs37d5.fa.fai added
1f8634bc156b_hs37d5.fa.amb added
1f8628223ed9_hs37d5.fa.ann added
1f86604c2d24_hs37d5.fa.bwt added
1f862927c7e0_hs37d5.fa.pac added
1f8672b3583b_hs37d5.fa.sa added
1f865c65c451_hs37d5.fa added
1f861d3bd13b_complete_ref_lens.bin added
1f864225877b_ctable.bin added
1f862de1be2a_ctg_offsets.bin added
1f863f8bceee_duplicate_clusters.tsv added
1f8673be8bd9_info.json added
1f8662cf8eec_mphf.bin added
1f8628b05aa2_pos.bin added
1f86520e568c_pre_indexing.log added
1f862b542b6a_rank.bin added
1f8622ee525f_ref_indexing.log added
1f864c61ece3_refAccumLengths.bin added
1f8631075242_reflengths.bin added
1f8657a98433_refseq.bin added
1f863a265d3b_seq.bin added
1f862cb2ea50_versionInfo.json added
1f861635411d_salmon_index added
1f86245e24f_chrLength.txt added
1f863a0cb1b3_chrName.txt added
1f8617667c8b_chrNameLength.txt added
1f86497a95ad_chrStart.txt added
1f86ef8b68b_exonGeTrInfo.tab added
1f866a98675a_exonInfo.tab added
1f863ba97c62_geneInfo.tab added
1f8674252487_Genome added
1f86328156a3_genomeParameters.txt added
1f86495f013c_Log.out added
1f867c4a2fc5_SA added
1f866a866e42_SAindex added
1f861fb0e5b1_sjdbInfo.txt added
1f8616b7d7b8_sjdbList.fromGTF.out.tab added
1f867fb37cae_sjdbList.out.tab added
1f8660bec501_transcriptInfo.tab added
1f86c77f646_GRCh38.GENCODE.v42_100 added
1f8617c9740f_knownGene_hg38.sql added
1f862ae290fc_knownGene_hg38.txt added
1f869ca663_refGene_hg38.sql added
1f862c6fade5_refGene_hg38.txt added
1f865801ac2d_knownGene_mm39.sql added
1f8655ceeb7e_knownGene_mm39.txt added
1f863c6c935_refGene_mm39.sql added
1f866fc3b882_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//RtmpoXfDho/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
6.906 0.842 8.838
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.069 | 0.267 | 2.445 | |
| dataSearch | 0.356 | 0.020 | 0.402 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 0.920 | 0.062 | 2.045 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.043 | 0.005 | 0.048 | |
| recipeLoad | 0.427 | 0.031 | 0.498 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.173 | 0.012 | 0.193 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |