Qian Liu
| Snapshot Date: 2026-01-21 13:40 -0500 (Wed, 21 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 2026-01-22 11:35 -0500 (Thu, 22 Jan 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" | 4808 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4542 |
| 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 1764/2345 | 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: 2026-01-21 21:43:46 -0500 (Wed, 21 Jan 2026) |
| EndedAt: 2026-01-21 21:44:43 -0500 (Wed, 21 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) (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 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) (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...
ce03568f4944_GRCh38.primary_assembly.genome.fa.1.bt2 added
ce0359133bc1_GRCh38.primary_assembly.genome.fa.2.bt2 added
ce037db82996_GRCh38.primary_assembly.genome.fa.3.bt2 added
ce0345b27755_GRCh38.primary_assembly.genome.fa.4.bt2 added
ce0347b89132_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
ce0326448e67_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
ce035ee11fd1_outfile.txt added
ce03df00301_GRCh37_to_GRCh38.chain added
ce038553dcd_GRCh37_to_NCBI34.chain added
ce03144c6201_GRCh37_to_NCBI35.chain added
ce0322b63a10_GRCh37_to_NCBI36.chain added
ce03699e023d_GRCh38_to_GRCh37.chain added
ce034a528f7_GRCh38_to_NCBI34.chain added
ce0377247282_GRCh38_to_NCBI35.chain added
ce0379d9f1e9_GRCh38_to_NCBI36.chain added
ce035399367e_NCBI34_to_GRCh37.chain added
ce036fc8b512_NCBI34_to_GRCh38.chain added
ce0361e7ea13_NCBI35_to_GRCh37.chain added
ce0340b8b79c_NCBI35_to_GRCh38.chain added
ce031f1e83f6_NCBI36_to_GRCh37.chain added
ce03c699b70_NCBI36_to_GRCh38.chain added
ce03695bdc6d_GRCm38_to_NCBIM36.chain added
ce03de4ae25_GRCm38_to_NCBIM37.chain added
ce0320650643_NCBIM36_to_GRCm38.chain added
ce03487e2952_NCBIM37_to_GRCm38.chain added
ce0352caebac_1000G_omni2.5.b37.vcf.gz added
ce0383693ab_1000G_omni2.5.b37.vcf.gz.tbi added
ce033718c3c3_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
ce033adc5377_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
ce0356ebc7d1_1000G_omni2.5.hg38.vcf.gz added
ce03118b96ec_1000G_omni2.5.hg38.vcf.gz.tbi added
ce03636168f3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
ce0310315c7e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
ce0318af5c80_af-only-gnomad.raw.sites.vcf added
ce0320e1e429_af-only-gnomad.raw.sites.vcf.idx added
ce034e4a509c_Mutect2-exome-panel.vcf.idx added
ce0370f259eb_Mutect2-WGS-panel-b37.vcf added
ce0336ed8d3b_Mutect2-WGS-panel-b37.vcf.idx added
ce0325d338a9_small_exac_common_3.vcf added
ce034e2cf2a5_small_exac_common_3.vcf.idx added
ce0368ee56bb_1000g_pon.hg38.vcf.gz added
ce03778044ce_1000g_pon.hg38.vcf.gz.tbi added
ce036256dad_af-only-gnomad.hg38.vcf.gz added
ce033437c02_af-only-gnomad.hg38.vcf.gz.tbi added
ce03438268fa_small_exac_common_3.hg38.vcf.gz added
ce0326ba17b6_small_exac_common_3.hg38.vcf.gz.tbi added
ce0336ac197_gencode.v41.annotation.gtf added
ce0355cba241_gencode.v42.annotation.gtf added
ce032c098568_gencode.vM30.annotation.gtf added
ce032515856e_gencode.vM31.annotation.gtf added
ce0327eb0bc7_gencode.v41.transcripts.fa added
ce0338524a4a_gencode.v41.transcripts.fa.fai added
ce03228b5d29_gencode.v42.transcripts.fa added
ce036b914076_gencode.v42.transcripts.fa.fai added
ce03d1f3a26_gencode.vM30.pc_transcripts.fa added
ce037d229b84_gencode.vM30.pc_transcripts.fa.fai added
ce036b10374a_gencode.vM31.pc_transcripts.fa added
ce03759e122f_gencode.vM31.pc_transcripts.fa.fai added
ce035cbc07fc_GRCh38.primary_assembly.genome.fa.1.ht2 added
ce033cb060f4_GRCh38.primary_assembly.genome.fa.2.ht2 added
ce035fad524c_GRCh38.primary_assembly.genome.fa.3.ht2 added
ce036bf62ca6_GRCh38.primary_assembly.genome.fa.4.ht2 added
ce036eed7da9_GRCh38.primary_assembly.genome.fa.5.ht2 added
ce0329d51b24_GRCh38.primary_assembly.genome.fa.6.ht2 added
ce0365e8edf0_GRCh38.primary_assembly.genome.fa.7.ht2 added
ce031f5d5bd5_GRCh38.primary_assembly.genome.fa.8.ht2 added
ce032a380d09_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
ce0345dfdf86_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
ce036ccbfa40_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
ce03439ab78d_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
ce036288aca7_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
ce037aff3a7a_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
ce03a585eac_GRCh38_full_analysis_set_plus_decoy_hla.fa added
ce032faf7382_GRCh38.primary_assembly.genome.fa.fai added
ce0327c87443_GRCh38.primary_assembly.genome.fa.amb added
ce035948ef1c_GRCh38.primary_assembly.genome.fa.ann added
ce03434a450f_GRCh38.primary_assembly.genome.fa.bwt added
ce0340fbfe4c_GRCh38.primary_assembly.genome.fa.pac added
ce035ff450e8_GRCh38.primary_assembly.genome.fa.sa added
ce0320ebe08f_GRCh38.primary_assembly.genome.fa added
ce035de3dd2b_hs37d5.fa.fai added
ce031acd6235_hs37d5.fa.amb added
ce0321ea9352_hs37d5.fa.ann added
ce032f6dfde3_hs37d5.fa.bwt added
ce035e375a68_hs37d5.fa.pac added
ce03410922b_hs37d5.fa.sa added
ce035bec4722_hs37d5.fa added
ce0375323853_complete_ref_lens.bin added
ce0334100d41_ctable.bin added
ce039d6411b_ctg_offsets.bin added
ce03514c58a8_duplicate_clusters.tsv added
ce036b50a74a_info.json added
ce037c172250_mphf.bin added
ce0352cdf1d5_pos.bin added
ce034ec0016b_pre_indexing.log added
ce031f9d4031_rank.bin added
ce03ce1612e_ref_indexing.log added
ce0320b3199d_refAccumLengths.bin added
ce034e56a330_reflengths.bin added
ce0319f3cc7e_refseq.bin added
ce0354f67181_seq.bin added
ce037f95f7ba_versionInfo.json added
ce034ebb15c6_salmon_index added
ce035c92a28b_chrLength.txt added
ce031eed8328_chrName.txt added
ce037b3dc6f4_chrNameLength.txt added
ce0314d0fc62_chrStart.txt added
ce032469909b_exonGeTrInfo.tab added
ce03e94c2ca_exonInfo.tab added
ce0348806340_geneInfo.tab added
ce0364f423ef_Genome added
ce03586353b0_genomeParameters.txt added
ce03610b7525_Log.out added
ce03373801e9_SA added
ce033e058451_SAindex added
ce035c3201a6_sjdbInfo.txt added
ce03570a6893_sjdbList.fromGTF.out.tab added
ce036c57b789_sjdbList.out.tab added
ce0372d2baf0_transcriptInfo.tab added
ce0368ef1d74_GRCh38.GENCODE.v42_100 added
ce032a76e07e_knownGene_hg38.sql added
ce03628c85f9_knownGene_hg38.txt added
ce0377afd0fa_refGene_hg38.sql added
ce0337c10a79_refGene_hg38.txt added
ce036296aa87_knownGene_mm39.sql added
ce031195b7a2_knownGene_mm39.txt added
ce037c4af5b2_refGene_mm39.sql added
ce031d48b8de_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//Rtmp8qLnI3/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
7.027 0.854 8.874
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.021 | 0.259 | 2.393 | |
| dataSearch | 0.365 | 0.016 | 0.387 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.908 | 0.079 | 2.207 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.038 | 0.005 | 0.045 | |
| recipeLoad | 0.439 | 0.029 | 0.481 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.181 | 0.014 | 0.205 | |
| recipeUpdate | 0 | 0 | 0 | |