Qian Liu
| Snapshot Date: 2026-01-23 13:40 -0500 (Fri, 23 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 2026-01-24 11:35 -0500 (Sat, 24 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4811 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4545 |
| 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 1764/2345 | 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: 2026-01-23 21:54:34 -0500 (Fri, 23 Jan 2026) |
| EndedAt: 2026-01-23 21:55:32 -0500 (Fri, 23 Jan 2026) |
| EllapsedTime: 57.8 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) (2026-01-15 r89304)
* 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) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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...
fecfccd4f74_GRCh38.primary_assembly.genome.fa.1.bt2 added
fecf7b1b4f3c_GRCh38.primary_assembly.genome.fa.2.bt2 added
fecf3def2b48_GRCh38.primary_assembly.genome.fa.3.bt2 added
fecf2102a3bc_GRCh38.primary_assembly.genome.fa.4.bt2 added
fecf344b9c92_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
fecf50145010_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
fecf65947382_outfile.txt added
fecf752b8fe7_GRCh37_to_GRCh38.chain added
fecf7ef4c2c9_GRCh37_to_NCBI34.chain added
fecf77205b3c_GRCh37_to_NCBI35.chain added
fecf6d45fd3d_GRCh37_to_NCBI36.chain added
fecfdf4e7d7_GRCh38_to_GRCh37.chain added
fecf49a0db69_GRCh38_to_NCBI34.chain added
fecf5fa4f042_GRCh38_to_NCBI35.chain added
fecf4599ae1c_GRCh38_to_NCBI36.chain added
fecf6c75d3f6_NCBI34_to_GRCh37.chain added
fecf2baef31b_NCBI34_to_GRCh38.chain added
fecf6ada8804_NCBI35_to_GRCh37.chain added
fecf3117f56a_NCBI35_to_GRCh38.chain added
fecf1bf11b54_NCBI36_to_GRCh37.chain added
fecf72393620_NCBI36_to_GRCh38.chain added
fecfa10a976_GRCm38_to_NCBIM36.chain added
fecf4be58723_GRCm38_to_NCBIM37.chain added
fecf4a0b31c2_NCBIM36_to_GRCm38.chain added
fecf24efdd88_NCBIM37_to_GRCm38.chain added
fecf7fb91ea9_1000G_omni2.5.b37.vcf.gz added
fecf528c2ac1_1000G_omni2.5.b37.vcf.gz.tbi added
fecf704b0f3d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
fecf4fd5a763_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
fecf53e07d87_1000G_omni2.5.hg38.vcf.gz added
fecf37515516_1000G_omni2.5.hg38.vcf.gz.tbi added
fecf3ca933b9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
fecf882d5cc_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
fecf45a24871_af-only-gnomad.raw.sites.vcf added
fecf2142166e_af-only-gnomad.raw.sites.vcf.idx added
fecf79cea0d0_Mutect2-exome-panel.vcf.idx added
fecf6c9ff629_Mutect2-WGS-panel-b37.vcf added
fecf79da3575_Mutect2-WGS-panel-b37.vcf.idx added
fecf64ebd2d2_small_exac_common_3.vcf added
fecf365e0cc1_small_exac_common_3.vcf.idx added
fecf58976ec9_1000g_pon.hg38.vcf.gz added
fecf3dea7b8f_1000g_pon.hg38.vcf.gz.tbi added
fecf6d56090a_af-only-gnomad.hg38.vcf.gz added
fecf2b6ba79a_af-only-gnomad.hg38.vcf.gz.tbi added
fecf28c885bb_small_exac_common_3.hg38.vcf.gz added
fecf4c3cce8_small_exac_common_3.hg38.vcf.gz.tbi added
fecf52c195c9_gencode.v41.annotation.gtf added
fecf2350e991_gencode.v42.annotation.gtf added
fecf151640b4_gencode.vM30.annotation.gtf added
fecf67f1f43c_gencode.vM31.annotation.gtf added
fecf3dd9c474_gencode.v41.transcripts.fa added
fecf23f0bb65_gencode.v41.transcripts.fa.fai added
fecf119ef652_gencode.v42.transcripts.fa added
fecf5b3d8a87_gencode.v42.transcripts.fa.fai added
fecf2551d3dd_gencode.vM30.pc_transcripts.fa added
fecf1f2c654f_gencode.vM30.pc_transcripts.fa.fai added
fecf1baf3586_gencode.vM31.pc_transcripts.fa added
fecfbe2fe9d_gencode.vM31.pc_transcripts.fa.fai added
fecf63b9fb83_GRCh38.primary_assembly.genome.fa.1.ht2 added
fecf472f889b_GRCh38.primary_assembly.genome.fa.2.ht2 added
fecf1b19ca0_GRCh38.primary_assembly.genome.fa.3.ht2 added
fecf33a1cd3e_GRCh38.primary_assembly.genome.fa.4.ht2 added
fecf43a9bbed_GRCh38.primary_assembly.genome.fa.5.ht2 added
fecf3c70e74f_GRCh38.primary_assembly.genome.fa.6.ht2 added
fecf18621289_GRCh38.primary_assembly.genome.fa.7.ht2 added
fecf4eaeece0_GRCh38.primary_assembly.genome.fa.8.ht2 added
fecf3e418e7b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
fecf41f14d2b_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
fecf490163df_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
fecf7a43eaea_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
fecff3e75c_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
fecfcda4981_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
fecf4f0fbabe_GRCh38_full_analysis_set_plus_decoy_hla.fa added
fecf11ad387f_GRCh38.primary_assembly.genome.fa.fai added
fecf35822ea_GRCh38.primary_assembly.genome.fa.amb added
fecff5c325d_GRCh38.primary_assembly.genome.fa.ann added
fecf6dee7f8b_GRCh38.primary_assembly.genome.fa.bwt added
fecf44f7b70f_GRCh38.primary_assembly.genome.fa.pac added
fecf63135d28_GRCh38.primary_assembly.genome.fa.sa added
fecfc491fe9_GRCh38.primary_assembly.genome.fa added
fecf14ce004c_hs37d5.fa.fai added
fecf6075883f_hs37d5.fa.amb added
fecf44441192_hs37d5.fa.ann added
fecf50ddab41_hs37d5.fa.bwt added
fecf91661e1_hs37d5.fa.pac added
fecf1c73ff70_hs37d5.fa.sa added
fecf38720a8_hs37d5.fa added
fecf1c70f767_complete_ref_lens.bin added
fecf3c8299c7_ctable.bin added
fecf223df6da_ctg_offsets.bin added
fecf121973c6_duplicate_clusters.tsv added
fecf44ffd572_info.json added
fecf781652c1_mphf.bin added
fecf1933a7f_pos.bin added
fecf68e568a7_pre_indexing.log added
fecf2d39e1be_rank.bin added
fecf33139824_ref_indexing.log added
fecf4b697dae_refAccumLengths.bin added
fecf7aba512f_reflengths.bin added
fecf5e28239b_refseq.bin added
fecf1d39c568_seq.bin added
fecf3bcf3dd5_versionInfo.json added
fecf22e489a0_salmon_index added
fecf4a077945_chrLength.txt added
fecf30aac6fb_chrName.txt added
fecf1beda1b3_chrNameLength.txt added
fecfe12fd18_chrStart.txt added
fecfa639e0_exonGeTrInfo.tab added
fecf2121a175_exonInfo.tab added
fecf26ef1951_geneInfo.tab added
fecf1b6728cf_Genome added
fecf11a83c17_genomeParameters.txt added
fecf3c01130f_Log.out added
fecf6a8a5c8f_SA added
fecf21c2e6ee_SAindex added
fecf2c72493_sjdbInfo.txt added
fecf60323051_sjdbList.fromGTF.out.tab added
fecf7f02472d_sjdbList.out.tab added
fecf6e8f1c7f_transcriptInfo.tab added
fecf75980e8d_GRCh38.GENCODE.v42_100 added
fecf51e3874b_knownGene_hg38.sql added
fecf30c776ed_knownGene_hg38.txt added
fecf7750da9f_refGene_hg38.sql added
fecf5d4139eb_refGene_hg38.txt added
fecf6541a321_knownGene_mm39.sql added
fecf383cff76_knownGene_mm39.txt added
fecf2ca7b8d2_refGene_mm39.sql added
fecf3756f9e5_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//RtmpFEjxL9/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
6.995 0.886 9.067
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.072 | 0.270 | 2.490 | |
| dataSearch | 0.369 | 0.016 | 0.402 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.928 | 0.061 | 2.271 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.042 | 0.005 | 0.049 | |
| recipeLoad | 0.417 | 0.029 | 0.452 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.175 | 0.012 | 0.199 | |
| recipeUpdate | 0 | 0 | 0 | |