Qian Liu
| Snapshot Date: 2026-03-09 13:40 -0400 (Mon, 09 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 2026-03-10 11:33 -0400 (Tue, 10 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" | 4522 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 2847 |
| 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 1776/2360 | 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: 2026-03-09 16:32:47 -0400 (Mon, 09 Mar 2026) |
| EndedAt: 2026-03-09 16:33:37 -0400 (Mon, 09 Mar 2026) |
| EllapsedTime: 50.8 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: 2026-03-09 20:32:47 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...
426a5534811d_GRCh38.primary_assembly.genome.fa.1.bt2 added
426a6a08c29e_GRCh38.primary_assembly.genome.fa.2.bt2 added
426a65214974_GRCh38.primary_assembly.genome.fa.3.bt2 added
426a6c5d928a_GRCh38.primary_assembly.genome.fa.4.bt2 added
426a733fd99a_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
426a64e74892_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
426ac4d9cff_outfile.txt added
426a3b7e2fa8_GRCh37_to_GRCh38.chain added
426a596add1b_GRCh37_to_NCBI34.chain added
426a76da4579_GRCh37_to_NCBI35.chain added
426a740747e4_GRCh37_to_NCBI36.chain added
426aa01053f_GRCh38_to_GRCh37.chain added
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426a7a211546_GRCh38_to_NCBI35.chain added
426a11fbe54e_GRCh38_to_NCBI36.chain added
426a308b6d1b_NCBI34_to_GRCh37.chain added
426a11a82083_NCBI34_to_GRCh38.chain added
426a34ee8183_NCBI35_to_GRCh37.chain added
426a1678da9b_NCBI35_to_GRCh38.chain added
426a585801a3_NCBI36_to_GRCh37.chain added
426a79d3a1a4_NCBI36_to_GRCh38.chain added
426a35195478_GRCm38_to_NCBIM36.chain added
426a11f8ad84_GRCm38_to_NCBIM37.chain added
426a5d47be53_NCBIM36_to_GRCm38.chain added
426a11206afd_NCBIM37_to_GRCm38.chain added
426a675010d3_1000G_omni2.5.b37.vcf.gz added
426a3980c1a2_1000G_omni2.5.b37.vcf.gz.tbi added
426a3428902c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
426a53115374_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
426a167e0f47_1000G_omni2.5.hg38.vcf.gz added
426a2e1d09da_1000G_omni2.5.hg38.vcf.gz.tbi added
426a7471dedc_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
426a5fde793d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
426a6e9c4f7_af-only-gnomad.raw.sites.vcf added
426a5d8237ac_af-only-gnomad.raw.sites.vcf.idx added
426a10152d2a_Mutect2-exome-panel.vcf.idx added
426a5e4828a5_Mutect2-WGS-panel-b37.vcf added
426a536498fe_Mutect2-WGS-panel-b37.vcf.idx added
426a71787677_small_exac_common_3.vcf added
426a1ba9b8d4_small_exac_common_3.vcf.idx added
426a23a5747c_1000g_pon.hg38.vcf.gz added
426a43828b2c_1000g_pon.hg38.vcf.gz.tbi added
426a2f7f1854_af-only-gnomad.hg38.vcf.gz added
426a41164b28_af-only-gnomad.hg38.vcf.gz.tbi added
426a1ea0507a_small_exac_common_3.hg38.vcf.gz added
426a2f03894b_small_exac_common_3.hg38.vcf.gz.tbi added
426a112ab30a_gencode.v41.annotation.gtf added
426aa505e54_gencode.v42.annotation.gtf added
426a2260e216_gencode.vM30.annotation.gtf added
426a69b23fc_gencode.vM31.annotation.gtf added
426a335778c7_gencode.v41.transcripts.fa added
426a33ba6b26_gencode.v41.transcripts.fa.fai added
426a13d0a652_gencode.v42.transcripts.fa added
426a67575ba7_gencode.v42.transcripts.fa.fai added
426a184265f2_gencode.vM30.pc_transcripts.fa added
426a2f32ff4f_gencode.vM30.pc_transcripts.fa.fai added
426a3d17b3be_gencode.vM31.pc_transcripts.fa added
426a5f199e47_gencode.vM31.pc_transcripts.fa.fai added
426aae67818_GRCh38.primary_assembly.genome.fa.1.ht2 added
426a20d6753f_GRCh38.primary_assembly.genome.fa.2.ht2 added
426a5fab8bf0_GRCh38.primary_assembly.genome.fa.3.ht2 added
426a77706aa1_GRCh38.primary_assembly.genome.fa.4.ht2 added
426a7568ad49_GRCh38.primary_assembly.genome.fa.5.ht2 added
426a2b48cfd7_GRCh38.primary_assembly.genome.fa.6.ht2 added
426a39454274_GRCh38.primary_assembly.genome.fa.7.ht2 added
426a720deb0b_GRCh38.primary_assembly.genome.fa.8.ht2 added
426a6fc259ac_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
426a408d6486_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
426a2c2ba86_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
426a3e63b4d4_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
426a3f4ea4c_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
426a4442259b_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
426a52b3061f_GRCh38_full_analysis_set_plus_decoy_hla.fa added
426a675707a3_GRCh38.primary_assembly.genome.fa.fai added
426a2b69356_GRCh38.primary_assembly.genome.fa.amb added
426a2082f47e_GRCh38.primary_assembly.genome.fa.ann added
426a75818cde_GRCh38.primary_assembly.genome.fa.bwt added
426ac477f17_GRCh38.primary_assembly.genome.fa.pac added
426a29e8c54d_GRCh38.primary_assembly.genome.fa.sa added
426a70f157b9_GRCh38.primary_assembly.genome.fa added
426a74b66c9c_hs37d5.fa.fai added
426a7494b1a0_hs37d5.fa.amb added
426a4e19bb2b_hs37d5.fa.ann added
426a7b4f2c1b_hs37d5.fa.bwt added
426aad8dfdc_hs37d5.fa.pac added
426a2450ea14_hs37d5.fa.sa added
426a3c37d9ac_hs37d5.fa added
426a76b3ca16_complete_ref_lens.bin added
426a1598a73c_ctable.bin added
426a590b5f37_ctg_offsets.bin added
426a7998418c_duplicate_clusters.tsv added
426a7af78cb1_info.json added
426a1235f789_mphf.bin added
426a150e4cb6_pos.bin added
426a5dce4b86_pre_indexing.log added
426a12c07a87_rank.bin added
426a1aac3eaf_ref_indexing.log added
426a224760d7_refAccumLengths.bin added
426a7c26d4d5_reflengths.bin added
426a595f2ba0_refseq.bin added
426a77294336_seq.bin added
426a35fbcb58_versionInfo.json added
426a25e31a18_salmon_index added
426a60c63116_chrLength.txt added
426a73c0ccfc_chrName.txt added
426a76d1efc2_chrNameLength.txt added
426a50d3e67f_chrStart.txt added
426a7c1c54e_exonGeTrInfo.tab added
426a428087dc_exonInfo.tab added
426a4579ea0_geneInfo.tab added
426a146f1c9a_Genome added
426aabeccf1_genomeParameters.txt added
426a7480e7b9_Log.out added
426a3aed5e70_SA added
426a35d32949_SAindex added
426a3a3b933a_sjdbInfo.txt added
426a1d3ee2b4_sjdbList.fromGTF.out.tab added
426ab95a66c_sjdbList.out.tab added
426ade10265_transcriptInfo.tab added
426a2f643c01_GRCh38.GENCODE.v42_100 added
426a5d9f7df5_knownGene_hg38.sql added
426a12068fd8_knownGene_hg38.txt added
426a6ccdb726_refGene_hg38.sql added
426a35b35798_refGene_hg38.txt added
426a113bd7b3_knownGene_mm39.sql added
426a6fce319b_knownGene_mm39.txt added
426a4a1af075_refGene_mm39.sql added
426a2ea0b755_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//RtmpIM1C0J/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
6.666 0.699 8.195
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 1.939 | 0.214 | 2.200 | |
| dataSearch | 0.339 | 0.013 | 0.356 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.810 | 0.046 | 2.334 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.036 | 0.004 | 0.042 | |
| recipeLoad | 0.386 | 0.023 | 0.417 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.161 | 0.008 | 0.169 | |
| recipeUpdate | 0 | 0 | 0 | |