Qian Liu
| Snapshot Date: 2026-03-11 13:40 -0400 (Wed, 11 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 2026-03-12 11:34 -0400 (Thu, 12 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" | 4806 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4049 |
| 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: 2026-03-11 20:07:08 -0400 (Wed, 11 Mar 2026) |
| EndedAt: 2026-03-11 20:08:02 -0400 (Wed, 11 Mar 2026) |
| EllapsedTime: 54.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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: 2026-03-12 00:07:08 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...
bcc9744c63d4_GRCh38.primary_assembly.genome.fa.1.bt2 added
bcc9432e2ef2_GRCh38.primary_assembly.genome.fa.2.bt2 added
bcc9d0c3453_GRCh38.primary_assembly.genome.fa.3.bt2 added
bcc91c3f3bd6_GRCh38.primary_assembly.genome.fa.4.bt2 added
bcc97b716d16_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
bcc953b0feaa_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
bcc991f75d3_outfile.txt added
bcc970707452_GRCh37_to_GRCh38.chain added
bcc966e4ed29_GRCh37_to_NCBI34.chain added
bcc93f8e5385_GRCh37_to_NCBI35.chain added
bcc9190d615c_GRCh37_to_NCBI36.chain added
bcc93d72ebdd_GRCh38_to_GRCh37.chain added
bcc943db19af_GRCh38_to_NCBI34.chain added
bcc9657352f6_GRCh38_to_NCBI35.chain added
bcc9764bc882_GRCh38_to_NCBI36.chain added
bcc969590b7a_NCBI34_to_GRCh37.chain added
bcc95500ac9e_NCBI34_to_GRCh38.chain added
bcc91f44e4ab_NCBI35_to_GRCh37.chain added
bcc96400a696_NCBI35_to_GRCh38.chain added
bcc966b8f524_NCBI36_to_GRCh37.chain added
bcc978e6432b_NCBI36_to_GRCh38.chain added
bcc95543fa0f_GRCm38_to_NCBIM36.chain added
bcc961d61a84_GRCm38_to_NCBIM37.chain added
bcc92f67024a_NCBIM36_to_GRCm38.chain added
bcc913c76096_NCBIM37_to_GRCm38.chain added
bcc969621ff_1000G_omni2.5.b37.vcf.gz added
bcc96a91efb9_1000G_omni2.5.b37.vcf.gz.tbi added
bcc913119158_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
bcc9665d322f_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
bcc97089e029_1000G_omni2.5.hg38.vcf.gz added
bcc96bdbdd77_1000G_omni2.5.hg38.vcf.gz.tbi added
bcc92fa8e6f3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
bcc979d273f6_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
bcc967bb59f5_af-only-gnomad.raw.sites.vcf added
bcc93d0f1907_af-only-gnomad.raw.sites.vcf.idx added
bcc92a3439e2_Mutect2-exome-panel.vcf.idx added
bcc94ac43a13_Mutect2-WGS-panel-b37.vcf added
bcc918c0dbbe_Mutect2-WGS-panel-b37.vcf.idx added
bcc91d9aa3a4_small_exac_common_3.vcf added
bcc9136d732b_small_exac_common_3.vcf.idx added
bcc976a41603_1000g_pon.hg38.vcf.gz added
bcc9ea15bcf_1000g_pon.hg38.vcf.gz.tbi added
bcc93927a8a_af-only-gnomad.hg38.vcf.gz added
bcc95aafbdb_af-only-gnomad.hg38.vcf.gz.tbi added
bcc91c7ce9c5_small_exac_common_3.hg38.vcf.gz added
bcc94cd7931f_small_exac_common_3.hg38.vcf.gz.tbi added
bcc95cfbffa2_gencode.v41.annotation.gtf added
bcc9244c145f_gencode.v42.annotation.gtf added
bcc97ecd7b96_gencode.vM30.annotation.gtf added
bcc9646cf5e3_gencode.vM31.annotation.gtf added
bcc92d833d97_gencode.v41.transcripts.fa added
bcc93409bd9_gencode.v41.transcripts.fa.fai added
bcc96b7c53a_gencode.v42.transcripts.fa added
bcc9af56648_gencode.v42.transcripts.fa.fai added
bcc9750e0696_gencode.vM30.pc_transcripts.fa added
bcc96bd29de3_gencode.vM30.pc_transcripts.fa.fai added
bcc9507bd962_gencode.vM31.pc_transcripts.fa added
bcc972fcda35_gencode.vM31.pc_transcripts.fa.fai added
bcc9365a088d_GRCh38.primary_assembly.genome.fa.1.ht2 added
bcc950e77cdb_GRCh38.primary_assembly.genome.fa.2.ht2 added
bcc9db6375c_GRCh38.primary_assembly.genome.fa.3.ht2 added
bcc935ec800c_GRCh38.primary_assembly.genome.fa.4.ht2 added
bcc939caaf7c_GRCh38.primary_assembly.genome.fa.5.ht2 added
bcc929c71388_GRCh38.primary_assembly.genome.fa.6.ht2 added
bcc94cd35b25_GRCh38.primary_assembly.genome.fa.7.ht2 added
bcc94805018a_GRCh38.primary_assembly.genome.fa.8.ht2 added
bcc940a82ff6_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
bcc961e4e0a3_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
bcc979581f8a_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
bcc987edb43_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
bcc9406d1010_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
bcc93839ab7b_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
bcc952293513_GRCh38_full_analysis_set_plus_decoy_hla.fa added
bcc9f5b9c89_GRCh38.primary_assembly.genome.fa.fai added
bcc94781ee3f_GRCh38.primary_assembly.genome.fa.amb added
bcc923408ec6_GRCh38.primary_assembly.genome.fa.ann added
bcc9635d7b3e_GRCh38.primary_assembly.genome.fa.bwt added
bcc9e465669_GRCh38.primary_assembly.genome.fa.pac added
bcc92bd30ed1_GRCh38.primary_assembly.genome.fa.sa added
bcc92d71d1d1_GRCh38.primary_assembly.genome.fa added
bcc9b8607a6_hs37d5.fa.fai added
bcc9c602933_hs37d5.fa.amb added
bcc97d30d99d_hs37d5.fa.ann added
bcc9121f12a1_hs37d5.fa.bwt added
bcc936001152_hs37d5.fa.pac added
bcc93e713a30_hs37d5.fa.sa added
bcc97ba34556_hs37d5.fa added
bcc91c1d5084_complete_ref_lens.bin added
bcc948911887_ctable.bin added
bcc92de16c49_ctg_offsets.bin added
bcc92a8c4427_duplicate_clusters.tsv added
bcc95ece7243_info.json added
bcc943afbd55_mphf.bin added
bcc946b73a2a_pos.bin added
bcc9274bbfab_pre_indexing.log added
bcc95e1487b4_rank.bin added
bcc915d96aad_ref_indexing.log added
bcc974ea8f0f_refAccumLengths.bin added
bcc953565dc0_reflengths.bin added
bcc94b2512fe_refseq.bin added
bcc96f02083c_seq.bin added
bcc96e6ad413_versionInfo.json added
bcc927896407_salmon_index added
bcc92d061bd8_chrLength.txt added
bcc96c0e18ff_chrName.txt added
bcc9118b44c5_chrNameLength.txt added
bcc94e4fea82_chrStart.txt added
bcc960ad24f8_exonGeTrInfo.tab added
bcc9756475e_exonInfo.tab added
bcc931677015_geneInfo.tab added
bcc97def8c09_Genome added
bcc979d2e376_genomeParameters.txt added
bcc94539676_Log.out added
bcc9bbb1f32_SA added
bcc929fd11a2_SAindex added
bcc92590b837_sjdbInfo.txt added
bcc9402e3625_sjdbList.fromGTF.out.tab added
bcc919e4d80e_sjdbList.out.tab added
bcc97f248c69_transcriptInfo.tab added
bcc9387e82b5_GRCh38.GENCODE.v42_100 added
bcc979b7560c_knownGene_hg38.sql added
bcc973726c41_knownGene_hg38.txt added
bcc95d215a9d_refGene_hg38.sql added
bcc938c4292f_refGene_hg38.txt added
bcc9566be9c6_knownGene_mm39.sql added
bcc946c0f27d_knownGene_mm39.txt added
bcc9257010d5_refGene_mm39.sql added
bcc960612326_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//RtmpsORAW4/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
6.828 0.715 8.092
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.089 | 0.252 | 2.396 | |
| dataSearch | 0.370 | 0.015 | 0.393 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 0.911 | 0.053 | 1.899 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.045 | 0.006 | 0.051 | |
| recipeLoad | 0.414 | 0.026 | 0.447 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.169 | 0.010 | 0.178 | |
| recipeUpdate | 0 | 0 | 0 | |