Qian Liu
| Snapshot Date: 2026-05-21 13:45 -0400 (Thu, 21 May 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: caf380d |
| git_last_commit_date: 2026-04-28 08:59:39 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-22 11:37 -0400 (Fri, 22 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4936 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There" | 4621 |
| 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 1787/2378 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.13.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | 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: 1.13.0 |
| 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_1.13.0.tar.gz |
| StartedAt: 2026-05-21 21:24:24 -0400 (Thu, 21 May 2026) |
| EndedAt: 2026-05-21 21:25:16 -0400 (Thu, 21 May 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_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* 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: 2026-05-22 01:24:24 UTC
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.13.0’
* 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-3.24-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 ‘1.13.0’ ** 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 (2026-05-01 r89994) -- "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...
108ab495f3476_GRCh38.primary_assembly.genome.fa.1.bt2 added
108ab96d549c_GRCh38.primary_assembly.genome.fa.2.bt2 added
108ab68cdd299_GRCh38.primary_assembly.genome.fa.3.bt2 added
108ab20bd7090_GRCh38.primary_assembly.genome.fa.4.bt2 added
108ab75290eba_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
108ab5a86116d_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
108ab17e23989_outfile.txt added
108ab52f5d9f_GRCh37_to_GRCh38.chain added
108ab68ab7461_GRCh37_to_NCBI34.chain added
108ab5065c1f6_GRCh37_to_NCBI35.chain added
108ab48a126b6_GRCh37_to_NCBI36.chain added
108ab4bf49bfa_GRCh38_to_GRCh37.chain added
108ab282c610b_GRCh38_to_NCBI34.chain added
108ab79972dc7_GRCh38_to_NCBI35.chain added
108ab343ea22e_GRCh38_to_NCBI36.chain added
108ab7c0994cd_NCBI34_to_GRCh37.chain added
108ab59085e59_NCBI34_to_GRCh38.chain added
108ab346a52b9_NCBI35_to_GRCh37.chain added
108ab305d0a91_NCBI35_to_GRCh38.chain added
108ab2c60ce65_NCBI36_to_GRCh37.chain added
108ab78e5fa6_NCBI36_to_GRCh38.chain added
108ab14298f2a_GRCm38_to_NCBIM36.chain added
108ab347618bd_GRCm38_to_NCBIM37.chain added
108ab35523b33_NCBIM36_to_GRCm38.chain added
108ab29acac9e_NCBIM37_to_GRCm38.chain added
108ab778ce72_1000G_omni2.5.b37.vcf.gz added
108abc39a233_1000G_omni2.5.b37.vcf.gz.tbi added
108ab1bc7c88a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
108ab593eea45_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
108ab318685c9_1000G_omni2.5.hg38.vcf.gz added
108ab76b96885_1000G_omni2.5.hg38.vcf.gz.tbi added
108ab67d30a8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
108ab50568ec_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
108ab262b6087_af-only-gnomad.raw.sites.vcf added
108ab69ce52a4_af-only-gnomad.raw.sites.vcf.idx added
108ab6893c340_Mutect2-exome-panel.vcf.idx added
108ab3cf7d463_Mutect2-WGS-panel-b37.vcf added
108ab3298ceda_Mutect2-WGS-panel-b37.vcf.idx added
108ab4e346429_small_exac_common_3.vcf added
108ab519be7db_small_exac_common_3.vcf.idx added
108ab529304b8_1000g_pon.hg38.vcf.gz added
108ab321af662_1000g_pon.hg38.vcf.gz.tbi added
108ab825b5a1_af-only-gnomad.hg38.vcf.gz added
108ab63b76134_af-only-gnomad.hg38.vcf.gz.tbi added
108ab1c4ed011_small_exac_common_3.hg38.vcf.gz added
108ab7a3e1a9b_small_exac_common_3.hg38.vcf.gz.tbi added
108ab344f4d0_gencode.v41.annotation.gtf added
108ab2424855d_gencode.v42.annotation.gtf added
108ab59afaf34_gencode.vM30.annotation.gtf added
108ab1d17acec_gencode.vM31.annotation.gtf added
108ab7d59c8df_gencode.v41.transcripts.fa added
108ab1192e8c4_gencode.v41.transcripts.fa.fai added
108ab43efa4df_gencode.v42.transcripts.fa added
108ab2a314f51_gencode.v42.transcripts.fa.fai added
108abb4e647b_gencode.vM30.pc_transcripts.fa added
108ab47a6cd09_gencode.vM30.pc_transcripts.fa.fai added
108ab17df2e9f_gencode.vM31.pc_transcripts.fa added
108ab3d6dd4f7_gencode.vM31.pc_transcripts.fa.fai added
108ab75b8c3a2_GRCh38.primary_assembly.genome.fa.1.ht2 added
108ab3533fd0f_GRCh38.primary_assembly.genome.fa.2.ht2 added
108ab682aff12_GRCh38.primary_assembly.genome.fa.3.ht2 added
108ab5ed02c2b_GRCh38.primary_assembly.genome.fa.4.ht2 added
108ab3503ebae_GRCh38.primary_assembly.genome.fa.5.ht2 added
108ab146607b3_GRCh38.primary_assembly.genome.fa.6.ht2 added
108ab3683833b_GRCh38.primary_assembly.genome.fa.7.ht2 added
108ab741cb272_GRCh38.primary_assembly.genome.fa.8.ht2 added
108ab80795ec_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
108ab2a03bd12_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
108ab5b71fe4a_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
108ab18eddb2d_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
108ab27d07424_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
108ab6678fbe7_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
108ab10e22f40_GRCh38_full_analysis_set_plus_decoy_hla.fa added
108ab718c1b68_GRCh38.primary_assembly.genome.fa.fai added
108ab255b8315_GRCh38.primary_assembly.genome.fa.amb added
108ab1afaeadc_GRCh38.primary_assembly.genome.fa.ann added
108ab4f511f5a_GRCh38.primary_assembly.genome.fa.bwt added
108ab56e17664_GRCh38.primary_assembly.genome.fa.pac added
108ab6c23cbcb_GRCh38.primary_assembly.genome.fa.sa added
108ab2218b3e4_GRCh38.primary_assembly.genome.fa added
108ab3ca4f39_hs37d5.fa.fai added
108ab57172920_hs37d5.fa.amb added
108ab318d208b_hs37d5.fa.ann added
108ab28539f17_hs37d5.fa.bwt added
108ab9f1b3b0_hs37d5.fa.pac added
108ab5b4bece9_hs37d5.fa.sa added
108ab55aee3d2_hs37d5.fa added
108ab4cef1bf0_complete_ref_lens.bin added
108ab66135105_ctable.bin added
108ab7e2c539d_ctg_offsets.bin added
108ab1025a922_duplicate_clusters.tsv added
108ab1882ff76_info.json added
108ab4051a88c_mphf.bin added
108ab3110a051_pos.bin added
108ab3a8d3f01_pre_indexing.log added
108abf2378af_rank.bin added
108ab61c830ec_ref_indexing.log added
108ab1e04081b_refAccumLengths.bin added
108ab1ab03402_reflengths.bin added
108ab26267cfe_refseq.bin added
108ab28d81b43_seq.bin added
108ab3e5e0a8_versionInfo.json added
108ab69003797_salmon_index added
108abd41d05c_chrLength.txt added
108ab5bd64ed0_chrName.txt added
108ab52d068ca_chrNameLength.txt added
108ab708fd03f_chrStart.txt added
108ab71b111d4_exonGeTrInfo.tab added
108ab2009af9c_exonInfo.tab added
108ab5be83b32_geneInfo.tab added
108ab6b867ec1_Genome added
108ab4aebe80d_genomeParameters.txt added
108ab45cfd3e8_Log.out added
108ab4f614826_SA added
108ab7bc7df80_SAindex added
108ab7f228bfc_sjdbInfo.txt added
108ab35148e99_sjdbList.fromGTF.out.tab added
108ab589dfa08_sjdbList.out.tab added
108ab6b8a50ab_transcriptInfo.tab added
108ab45b641b5_GRCh38.GENCODE.v42_100 added
108ab4093f5d4_knownGene_hg38.sql added
108ab31f0526b_knownGene_hg38.txt added
108ab18b3086a_refGene_hg38.sql added
108ab11ed73d1_refGene_hg38.txt added
108ab7c4ea788_knownGene_mm39.sql added
108abfd9117a_knownGene_mm39.txt added
108ab740a68b6_refGene_mm39.sql added
108ab5760c03e_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//RtmpGVXm43/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
6.665 0.822 8.069
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.974 | 0.262 | 2.245 | |
| dataSearch | 0.341 | 0.017 | 0.359 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 0.837 | 0.049 | 1.701 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.039 | 0.003 | 0.043 | |
| recipeLoad | 0.395 | 0.027 | 0.423 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.164 | 0.012 | 0.175 | |
| recipeUpdate | 0 | 0 | 0 | |