Qian Liu
| Snapshot Date: 2026-04-30 13:40 -0400 (Thu, 30 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_23 |
| git_last_commit: bb3489b |
| git_last_commit_date: 2026-04-28 08:59:39 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-01 11:36 -0400 (Fri, 01 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4988 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4718 |
| 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 1815/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.12.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.4 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: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2026-04-30 21:32:15 -0400 (Thu, 30 Apr 2026) |
| EndedAt: 2026-04-30 21:33:06 -0400 (Thu, 30 Apr 2026) |
| EllapsedTime: 51.6 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* 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: 2026-05-01 01:32:15 UTC
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.12.0’
* 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 ‘1.12.0’ ** 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 version 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"
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...
fbdf511d32_GRCh38.primary_assembly.genome.fa.1.bt2 added
fbdf4d53bdc7_GRCh38.primary_assembly.genome.fa.2.bt2 added
fbdf34d07b7a_GRCh38.primary_assembly.genome.fa.3.bt2 added
fbdf635aa1ac_GRCh38.primary_assembly.genome.fa.4.bt2 added
fbdf532c5629_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
fbdf3ccc868_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
fbdf797925ca_outfile.txt added
fbdfa02f14_GRCh37_to_GRCh38.chain added
fbdf1472ca5e_GRCh37_to_NCBI34.chain added
fbdf7c43ebce_GRCh37_to_NCBI35.chain added
fbdf4f2e611e_GRCh37_to_NCBI36.chain added
fbdf6dea212e_GRCh38_to_GRCh37.chain added
fbdf26288b62_GRCh38_to_NCBI34.chain added
fbdf2fd6e280_GRCh38_to_NCBI35.chain added
fbdf44b05a09_GRCh38_to_NCBI36.chain added
fbdf15e7281a_NCBI34_to_GRCh37.chain added
fbdf7af9ce31_NCBI34_to_GRCh38.chain added
fbdf2650320a_NCBI35_to_GRCh37.chain added
fbdf5b05422c_NCBI35_to_GRCh38.chain added
fbdf363b8563_NCBI36_to_GRCh37.chain added
fbdf7db24265_NCBI36_to_GRCh38.chain added
fbdf4225355b_GRCm38_to_NCBIM36.chain added
fbdf18d20b4a_GRCm38_to_NCBIM37.chain added
fbdf5e33401_NCBIM36_to_GRCm38.chain added
fbdf76b30ac_NCBIM37_to_GRCm38.chain added
fbdfe487002_1000G_omni2.5.b37.vcf.gz added
fbdf35b19aa1_1000G_omni2.5.b37.vcf.gz.tbi added
fbdf1f1edb91_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
fbdf22e11c8d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
fbdf69197ede_1000G_omni2.5.hg38.vcf.gz added
fbdf8d856ba_1000G_omni2.5.hg38.vcf.gz.tbi added
fbdf3325d1df_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
fbdf77f5a1b4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
fbdf1f4b6df3_af-only-gnomad.raw.sites.vcf added
fbdf111f7c92_af-only-gnomad.raw.sites.vcf.idx added
fbdf2a2b5e06_Mutect2-exome-panel.vcf.idx added
fbdf529f18b_Mutect2-WGS-panel-b37.vcf added
fbdf4b0df53_Mutect2-WGS-panel-b37.vcf.idx added
fbdf7815c48c_small_exac_common_3.vcf added
fbdf5d1b00eb_small_exac_common_3.vcf.idx added
fbdf17d9740e_1000g_pon.hg38.vcf.gz added
fbdf45524f5d_1000g_pon.hg38.vcf.gz.tbi added
fbdf1ed88639_af-only-gnomad.hg38.vcf.gz added
fbdf19541801_af-only-gnomad.hg38.vcf.gz.tbi added
fbdf5ff3f6a4_small_exac_common_3.hg38.vcf.gz added
fbdf9c5ba33_small_exac_common_3.hg38.vcf.gz.tbi added
fbdf14436f48_gencode.v41.annotation.gtf added
fbdf573eea5c_gencode.v42.annotation.gtf added
fbdf638c6ac3_gencode.vM30.annotation.gtf added
fbdf17b55b44_gencode.vM31.annotation.gtf added
fbdf37ad985_gencode.v41.transcripts.fa added
fbdf765eac8b_gencode.v41.transcripts.fa.fai added
fbdf41921663_gencode.v42.transcripts.fa added
fbdf5dfbdf36_gencode.v42.transcripts.fa.fai added
fbdf42fb826e_gencode.vM30.pc_transcripts.fa added
fbdfe30261d_gencode.vM30.pc_transcripts.fa.fai added
fbdf7b164131_gencode.vM31.pc_transcripts.fa added
fbdf72123718_gencode.vM31.pc_transcripts.fa.fai added
fbdf9df432a_GRCh38.primary_assembly.genome.fa.1.ht2 added
fbdf20b27f76_GRCh38.primary_assembly.genome.fa.2.ht2 added
fbdf26ce2cbf_GRCh38.primary_assembly.genome.fa.3.ht2 added
fbdf29dbc380_GRCh38.primary_assembly.genome.fa.4.ht2 added
fbdf1b001df8_GRCh38.primary_assembly.genome.fa.5.ht2 added
fbdf24af92a1_GRCh38.primary_assembly.genome.fa.6.ht2 added
fbdf2c39ad8_GRCh38.primary_assembly.genome.fa.7.ht2 added
fbdf77eadc52_GRCh38.primary_assembly.genome.fa.8.ht2 added
fbdf5c26c8ff_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
fbdf76560c9c_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
fbdfb561276_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
fbdf3fd606ca_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
fbdf7c57d883_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
fbdf6b47c03b_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
fbdf339d9883_GRCh38_full_analysis_set_plus_decoy_hla.fa added
fbdf2f87daee_GRCh38.primary_assembly.genome.fa.fai added
fbdf3657a3_GRCh38.primary_assembly.genome.fa.amb added
fbdf6fb38e70_GRCh38.primary_assembly.genome.fa.ann added
fbdf754c945a_GRCh38.primary_assembly.genome.fa.bwt added
fbdf769fdcdf_GRCh38.primary_assembly.genome.fa.pac added
fbdf795df150_GRCh38.primary_assembly.genome.fa.sa added
fbdf68df970_GRCh38.primary_assembly.genome.fa added
fbdf52f32b6c_hs37d5.fa.fai added
fbdf5aa7e9ff_hs37d5.fa.amb added
fbdf45f392d8_hs37d5.fa.ann added
fbdf7a2dc6c8_hs37d5.fa.bwt added
fbdf5355b322_hs37d5.fa.pac added
fbdf1f63a7ec_hs37d5.fa.sa added
fbdf47a5870d_hs37d5.fa added
fbdf44458b3a_complete_ref_lens.bin added
fbdf31b7afda_ctable.bin added
fbdf127a2ab6_ctg_offsets.bin added
fbdf128a1c34_duplicate_clusters.tsv added
fbdf2941a36e_info.json added
fbdf14509feb_mphf.bin added
fbdf393307b8_pos.bin added
fbdf453fde5e_pre_indexing.log added
fbdf642010d6_rank.bin added
fbdf753184f4_ref_indexing.log added
fbdf60feb48_refAccumLengths.bin added
fbdf7f1fc713_reflengths.bin added
fbdf7f46f198_refseq.bin added
fbdfa9f7370_seq.bin added
fbdf6a53c382_versionInfo.json added
fbdf2148c257_salmon_index added
fbdf2fceeed3_chrLength.txt added
fbdf3aa1772a_chrName.txt added
fbdf3e968478_chrNameLength.txt added
fbdfbd30262_chrStart.txt added
fbdf4a4175fe_exonGeTrInfo.tab added
fbdffa99cc8_exonInfo.tab added
fbdf48741680_geneInfo.tab added
fbdf3d7152a9_Genome added
fbdf5ae9f4c2_genomeParameters.txt added
fbdf35c41b2f_Log.out added
fbdf5dd4c63c_SA added
fbdf3c22bd44_SAindex added
fbdfcb7da34_sjdbInfo.txt added
fbdf7a569271_sjdbList.fromGTF.out.tab added
fbdf49a87776_sjdbList.out.tab added
fbdf533b09c1_transcriptInfo.tab added
fbdf48fd8897_GRCh38.GENCODE.v42_100 added
fbdf7d1296f0_knownGene_hg38.sql added
fbdf4f73a6b6_knownGene_hg38.txt added
fbdf31c61f7a_refGene_hg38.sql added
fbdf463c9c1d_refGene_hg38.txt added
fbdf352d57f1_knownGene_mm39.sql added
fbdf33e8aa7d_knownGene_mm39.txt added
fbdf70110f2a_refGene_mm39.sql added
fbdf6ffac7e0_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//RtmpFBMjNh/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
6.650 0.823 8.307
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.982 | 0.282 | 2.274 | |
| dataSearch | 0.333 | 0.016 | 0.349 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.863 | 0.056 | 1.596 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.001 | 0.000 | |
| recipeHub-class | 0.040 | 0.003 | 0.043 | |
| recipeLoad | 0.397 | 0.028 | 0.426 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.163 | 0.014 | 0.176 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |