Qian Liu
| Snapshot Date: 2026-03-15 13:40 -0400 (Sun, 15 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 2026-03-16 11:34 -0400 (Mon, 16 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" | 4053 |
| 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: 2026-03-15 19:31:32 -0400 (Sun, 15 Mar 2026) |
| EndedAt: 2026-03-15 19:32:21 -0400 (Sun, 15 Mar 2026) |
| EllapsedTime: 48.6 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: 2026-03-15 23:31:33 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...
c786794d200c_GRCh38.primary_assembly.genome.fa.1.bt2 added
c7863673320b_GRCh38.primary_assembly.genome.fa.2.bt2 added
c78644da8c1a_GRCh38.primary_assembly.genome.fa.3.bt2 added
c78668242246_GRCh38.primary_assembly.genome.fa.4.bt2 added
c7861c465714_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
c7864dfef08c_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
c7861c629f55_outfile.txt added
c786eca9402_GRCh37_to_GRCh38.chain added
c78615bb16e4_GRCh37_to_NCBI34.chain added
c7862ddbdde1_GRCh37_to_NCBI35.chain added
c7863dc3f64c_GRCh37_to_NCBI36.chain added
c786c5f1742_GRCh38_to_GRCh37.chain added
c78636eff466_GRCh38_to_NCBI34.chain added
c786439670b7_GRCh38_to_NCBI35.chain added
c78649c2210b_GRCh38_to_NCBI36.chain added
c78668077f01_NCBI34_to_GRCh37.chain added
c78644235002_NCBI34_to_GRCh38.chain added
c7866a59d640_NCBI35_to_GRCh37.chain added
c78630013a4c_NCBI35_to_GRCh38.chain added
c786209a6c33_NCBI36_to_GRCh37.chain added
c7867a3598fd_NCBI36_to_GRCh38.chain added
c78654cf48b9_GRCm38_to_NCBIM36.chain added
c78674af952e_GRCm38_to_NCBIM37.chain added
c786336b3adb_NCBIM36_to_GRCm38.chain added
c78644e51a3c_NCBIM37_to_GRCm38.chain added
c7861d1d7c7a_1000G_omni2.5.b37.vcf.gz added
c7867ad73c84_1000G_omni2.5.b37.vcf.gz.tbi added
c78648c63d1d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
c7864ed6603e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
c7865c48aee1_1000G_omni2.5.hg38.vcf.gz added
c78627d1651c_1000G_omni2.5.hg38.vcf.gz.tbi added
c786244525b0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
c78637ad586a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
c7865587b3b4_af-only-gnomad.raw.sites.vcf added
c78640271a4a_af-only-gnomad.raw.sites.vcf.idx added
c786472f112d_Mutect2-exome-panel.vcf.idx added
c7866310c5dd_Mutect2-WGS-panel-b37.vcf added
c786622e62fa_Mutect2-WGS-panel-b37.vcf.idx added
c78653643d71_small_exac_common_3.vcf added
c78659fdf07c_small_exac_common_3.vcf.idx added
c7862eb78b0c_1000g_pon.hg38.vcf.gz added
c7861409d8ca_1000g_pon.hg38.vcf.gz.tbi added
c7861277c00d_af-only-gnomad.hg38.vcf.gz added
c78673e19ef3_af-only-gnomad.hg38.vcf.gz.tbi added
c786618a9ef4_small_exac_common_3.hg38.vcf.gz added
c78653c9d733_small_exac_common_3.hg38.vcf.gz.tbi added
c786684f803e_gencode.v41.annotation.gtf added
c7863b6c9bf2_gencode.v42.annotation.gtf added
c78657724b58_gencode.vM30.annotation.gtf added
c78610b0ab42_gencode.vM31.annotation.gtf added
c7863ebb829d_gencode.v41.transcripts.fa added
c78687c3198_gencode.v41.transcripts.fa.fai added
c786119bf682_gencode.v42.transcripts.fa added
c7861654d9d6_gencode.v42.transcripts.fa.fai added
c7861ca97c0e_gencode.vM30.pc_transcripts.fa added
c7863b0f89d5_gencode.vM30.pc_transcripts.fa.fai added
c78679221d3d_gencode.vM31.pc_transcripts.fa added
c7862eadcdec_gencode.vM31.pc_transcripts.fa.fai added
c78614aa58e5_GRCh38.primary_assembly.genome.fa.1.ht2 added
c7863bb22cfc_GRCh38.primary_assembly.genome.fa.2.ht2 added
c7862ea77302_GRCh38.primary_assembly.genome.fa.3.ht2 added
c786736fa03b_GRCh38.primary_assembly.genome.fa.4.ht2 added
c7862580bcb2_GRCh38.primary_assembly.genome.fa.5.ht2 added
c78626e45d5a_GRCh38.primary_assembly.genome.fa.6.ht2 added
c7865aacd3a8_GRCh38.primary_assembly.genome.fa.7.ht2 added
c78687be91a_GRCh38.primary_assembly.genome.fa.8.ht2 added
c7867f04ae4f_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
c786c5005af_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
c78659a52a79_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
c7866a879be9_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
c7866d0d14a2_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
c78675c5cf9c_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
c786dc1472c_GRCh38_full_analysis_set_plus_decoy_hla.fa added
c786c27a0c2_GRCh38.primary_assembly.genome.fa.fai added
c7867dab26c9_GRCh38.primary_assembly.genome.fa.amb added
c7866f7f9693_GRCh38.primary_assembly.genome.fa.ann added
c7862176c615_GRCh38.primary_assembly.genome.fa.bwt added
c7867cc69ddc_GRCh38.primary_assembly.genome.fa.pac added
c78653a61683_GRCh38.primary_assembly.genome.fa.sa added
c7863d101d5c_GRCh38.primary_assembly.genome.fa added
c7866cf7a255_hs37d5.fa.fai added
c78675c2b256_hs37d5.fa.amb added
c786414a6880_hs37d5.fa.ann added
c7867c12ccfc_hs37d5.fa.bwt added
c786364ff407_hs37d5.fa.pac added
c7863b1e136c_hs37d5.fa.sa added
c786338d35c6_hs37d5.fa added
c7867bc5749a_complete_ref_lens.bin added
c786606a69f1_ctable.bin added
c7866a517eaa_ctg_offsets.bin added
c786c53016e_duplicate_clusters.tsv added
c7861d82e314_info.json added
c7867c0a452e_mphf.bin added
c7866440ea1_pos.bin added
c7865e1c6f3d_pre_indexing.log added
c7861ccb3e10_rank.bin added
c78663579b34_ref_indexing.log added
c786c8ea5e0_refAccumLengths.bin added
c786692c1b90_reflengths.bin added
c7864ec5c0e1_refseq.bin added
c78618fa1c2e_seq.bin added
c7864c501cd1_versionInfo.json added
c7861f94047b_salmon_index added
c7862eb2376f_chrLength.txt added
c7863655705c_chrName.txt added
c7862343c3e2_chrNameLength.txt added
c78635f13c84_chrStart.txt added
c78670bc19c6_exonGeTrInfo.tab added
c7864d404ffc_exonInfo.tab added
c78639435103_geneInfo.tab added
c786727bb953_Genome added
c78618c432dd_genomeParameters.txt added
c78678e757de_Log.out added
c7861c39edd5_SA added
c7861f2d496d_SAindex added
c786562fa318_sjdbInfo.txt added
c786517ca8dc_sjdbList.fromGTF.out.tab added
c7864f322d4f_sjdbList.out.tab added
c786673cc627_transcriptInfo.tab added
c78646f55f64_GRCh38.GENCODE.v42_100 added
c7861749c2a1_knownGene_hg38.sql added
c7866b88e3f8_knownGene_hg38.txt added
c786682ee5ef_refGene_hg38.sql added
c7865ef9e358_refGene_hg38.txt added
c78667bcd71e_knownGene_mm39.sql added
c7861ecf27c7_knownGene_mm39.txt added
c786323c899e_refGene_mm39.sql added
c786246efdd6_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//Rtmp4kdj45/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
6.181 0.631 7.771
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.793 | 0.198 | 1.996 | |
| dataSearch | 0.319 | 0.011 | 0.331 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.871 | 0.054 | 1.773 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.038 | 0.004 | 0.043 | |
| recipeLoad | 0.389 | 0.023 | 0.415 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.159 | 0.009 | 0.168 | |
| recipeUpdate | 0 | 0 | 0 | |