Qian Liu
| Snapshot Date: 2026-01-05 13:40 -0500 (Mon, 05 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 2026-01-06 11:35 -0500 (Tue, 06 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4815 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 1754/2332 | 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: 2026-01-05 21:57:12 -0500 (Mon, 05 Jan 2026) |
| EndedAt: 2026-01-05 21:58:09 -0500 (Mon, 05 Jan 2026) |
| EllapsedTime: 56.7 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) (2025-11-04 r88984)
* 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) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 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...
f8146852f609_GRCh38.primary_assembly.genome.fa.1.bt2 added
f8141e96fe61_GRCh38.primary_assembly.genome.fa.2.bt2 added
f8144b16a1f7_GRCh38.primary_assembly.genome.fa.3.bt2 added
f8143ae385a4_GRCh38.primary_assembly.genome.fa.4.bt2 added
f8142f5af030_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
f8147b4ef799_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
f8147d619d0d_outfile.txt added
f814138e00ca_GRCh37_to_GRCh38.chain added
f8144fd5d7cd_GRCh37_to_NCBI34.chain added
f814604afcad_GRCh37_to_NCBI35.chain added
f8145b12f33e_GRCh37_to_NCBI36.chain added
f814391f9a28_GRCh38_to_GRCh37.chain added
f81449c1d564_GRCh38_to_NCBI34.chain added
f81454a0be10_GRCh38_to_NCBI35.chain added
f81451e37d8_GRCh38_to_NCBI36.chain added
f8142e44888_NCBI34_to_GRCh37.chain added
f8145955da33_NCBI34_to_GRCh38.chain added
f81413687817_NCBI35_to_GRCh37.chain added
f8142fa437f5_NCBI35_to_GRCh38.chain added
f8144655ce42_NCBI36_to_GRCh37.chain added
f8142b587321_NCBI36_to_GRCh38.chain added
f8143bee91c2_GRCm38_to_NCBIM36.chain added
f8142ba3764b_GRCm38_to_NCBIM37.chain added
f81478ab4c4e_NCBIM36_to_GRCm38.chain added
f814361ed2c6_NCBIM37_to_GRCm38.chain added
f814219fe0ec_1000G_omni2.5.b37.vcf.gz added
f814767b733_1000G_omni2.5.b37.vcf.gz.tbi added
f8142a2c7911_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
f8144dc060b8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
f814110df7e9_1000G_omni2.5.hg38.vcf.gz added
f8142c0eeabe_1000G_omni2.5.hg38.vcf.gz.tbi added
f814755768b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
f8147bd9a36f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
f814d790bef_af-only-gnomad.raw.sites.vcf added
f8145fe7ed2_af-only-gnomad.raw.sites.vcf.idx added
f8147381011_Mutect2-exome-panel.vcf.idx added
f81471a6cfca_Mutect2-WGS-panel-b37.vcf added
f8147e941110_Mutect2-WGS-panel-b37.vcf.idx added
f8142aec725c_small_exac_common_3.vcf added
f8149480c08_small_exac_common_3.vcf.idx added
f814590de5fa_1000g_pon.hg38.vcf.gz added
f8141f75adc3_1000g_pon.hg38.vcf.gz.tbi added
f81466e2ed57_af-only-gnomad.hg38.vcf.gz added
f8143c4c1f86_af-only-gnomad.hg38.vcf.gz.tbi added
f81429a9b557_small_exac_common_3.hg38.vcf.gz added
f81444c0781f_small_exac_common_3.hg38.vcf.gz.tbi added
f814380e5e7c_gencode.v41.annotation.gtf added
f814375d3ba4_gencode.v42.annotation.gtf added
f81449f6a861_gencode.vM30.annotation.gtf added
f81460a89e36_gencode.vM31.annotation.gtf added
f8145e2b1ccd_gencode.v41.transcripts.fa added
f81460700707_gencode.v41.transcripts.fa.fai added
f8145add8e07_gencode.v42.transcripts.fa added
f8147979c2c_gencode.v42.transcripts.fa.fai added
f814728e1098_gencode.vM30.pc_transcripts.fa added
f8144ce3a5e9_gencode.vM30.pc_transcripts.fa.fai added
f81475a18b6e_gencode.vM31.pc_transcripts.fa added
f81440c91f17_gencode.vM31.pc_transcripts.fa.fai added
f8145418403b_GRCh38.primary_assembly.genome.fa.1.ht2 added
f8144210c9f_GRCh38.primary_assembly.genome.fa.2.ht2 added
f81415c39cd7_GRCh38.primary_assembly.genome.fa.3.ht2 added
f8145d6df26a_GRCh38.primary_assembly.genome.fa.4.ht2 added
f8145d463d11_GRCh38.primary_assembly.genome.fa.5.ht2 added
f8142e5356ee_GRCh38.primary_assembly.genome.fa.6.ht2 added
f81461703b04_GRCh38.primary_assembly.genome.fa.7.ht2 added
f814f32b596_GRCh38.primary_assembly.genome.fa.8.ht2 added
f8144a2f92a5_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
f8147944b4af_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
f814db28b5c_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
f81444db4c0a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
f814195d47d7_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
f8143b178143_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
f8144277404_GRCh38_full_analysis_set_plus_decoy_hla.fa added
f8143a31b4bd_GRCh38.primary_assembly.genome.fa.fai added
f81415510224_GRCh38.primary_assembly.genome.fa.amb added
f8147963946a_GRCh38.primary_assembly.genome.fa.ann added
f81478a4f968_GRCh38.primary_assembly.genome.fa.bwt added
f81416f258b9_GRCh38.primary_assembly.genome.fa.pac added
f8149ee574_GRCh38.primary_assembly.genome.fa.sa added
f8143fea22fd_GRCh38.primary_assembly.genome.fa added
f814249f30d3_hs37d5.fa.fai added
f8144f3e7f6d_hs37d5.fa.amb added
f814101ff5c0_hs37d5.fa.ann added
f814223f1885_hs37d5.fa.bwt added
f8145c62d553_hs37d5.fa.pac added
f8145ca36b87_hs37d5.fa.sa added
f8146ce89b94_hs37d5.fa added
f8141b3e4968_complete_ref_lens.bin added
f814164558d1_ctable.bin added
f81422ca0cc3_ctg_offsets.bin added
f8147f0be80c_duplicate_clusters.tsv added
f81466afacfd_info.json added
f81417864ab6_mphf.bin added
f8147192feca_pos.bin added
f8146995ba06_pre_indexing.log added
f81464e81611_rank.bin added
f8144100e9d8_ref_indexing.log added
f81422f8853f_refAccumLengths.bin added
f81469f3fd08_reflengths.bin added
f81411694e90_refseq.bin added
f81418a4d8de_seq.bin added
f8146e99e375_versionInfo.json added
f81439244f0d_salmon_index added
f8147ec1fbc9_chrLength.txt added
f81471798a22_chrName.txt added
f814625bf861_chrNameLength.txt added
f81440fdaba_chrStart.txt added
f8142ce0eb6b_exonGeTrInfo.tab added
f814627fd4d1_exonInfo.tab added
f814366d17dc_geneInfo.tab added
f8143439886e_Genome added
f8142d2c088b_genomeParameters.txt added
f81425e4f4d8_Log.out added
f8145a86a457_SA added
f8143d8f7a2f_SAindex added
f814169ec33c_sjdbInfo.txt added
f8141123a3be_sjdbList.fromGTF.out.tab added
f8143ad317bc_sjdbList.out.tab added
f81478bb55cf_transcriptInfo.tab added
f81452fec6f5_GRCh38.GENCODE.v42_100 added
f81454b82964_knownGene_hg38.sql added
f8146a58fb0_knownGene_hg38.txt added
f8145f7c6f38_refGene_hg38.sql added
f8146269f681_refGene_hg38.txt added
f8141ab6c1a1_knownGene_mm39.sql added
f81454623eba_knownGene_mm39.txt added
f8147e04509d_refGene_mm39.sql added
f8144d48b40d_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//RtmpEyRPLG/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
7.037 0.842 8.965
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.083 | 0.269 | 2.432 | |
| dataSearch | 0.357 | 0.018 | 0.380 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 0.908 | 0.067 | 2.021 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.001 | 0.000 | |
| recipeHub-class | 0.039 | 0.004 | 0.045 | |
| recipeLoad | 0.422 | 0.034 | 0.468 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.172 | 0.015 | 0.192 | |
| recipeUpdate | 0 | 0 | 0 | |