Qian Liu
| Snapshot Date: 2026-04-14 13:40 -0400 (Tue, 14 Apr 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 2026-04-15 11:35 -0400 (Wed, 15 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4925 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4656 |
| 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 1796/2394 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.11.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.4 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: 2026-04-14 22:04:25 -0400 (Tue, 14 Apr 2026) |
| EndedAt: 2026-04-14 22:05:20 -0400 (Tue, 14 Apr 2026) |
| EllapsedTime: 55.5 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 version 4.6.0 alpha (2026-04-08 r89818)
* 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: 2026-04-15 02:04:25 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 version 4.6.0 alpha (2026-04-08 r89818)
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...
1c9b93b2e55_GRCh38.primary_assembly.genome.fa.1.bt2 added
1c9bc5ed32f_GRCh38.primary_assembly.genome.fa.2.bt2 added
1c9b257ab901_GRCh38.primary_assembly.genome.fa.3.bt2 added
1c9b1c0803e0_GRCh38.primary_assembly.genome.fa.4.bt2 added
1c9b52367580_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1c9b755c50aa_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1c9b7fb40517_outfile.txt added
1c9b3ba6a81_GRCh37_to_GRCh38.chain added
1c9b43a63d10_GRCh37_to_NCBI34.chain added
1c9b56f30822_GRCh37_to_NCBI35.chain added
1c9b6d9b1cc6_GRCh37_to_NCBI36.chain added
1c9b627e4361_GRCh38_to_GRCh37.chain added
1c9b4f79c7cb_GRCh38_to_NCBI34.chain added
1c9b442c0930_GRCh38_to_NCBI35.chain added
1c9b270f5147_GRCh38_to_NCBI36.chain added
1c9b5ea12059_NCBI34_to_GRCh37.chain added
1c9b2452e398_NCBI34_to_GRCh38.chain added
1c9b3ddc22c9_NCBI35_to_GRCh37.chain added
1c9b3f6fd9d9_NCBI35_to_GRCh38.chain added
1c9b48475618_NCBI36_to_GRCh37.chain added
1c9b436566ba_NCBI36_to_GRCh38.chain added
1c9b363b5fe7_GRCm38_to_NCBIM36.chain added
1c9b74155281_GRCm38_to_NCBIM37.chain added
1c9b23dbceb1_NCBIM36_to_GRCm38.chain added
1c9b33ded8db_NCBIM37_to_GRCm38.chain added
1c9b6b6f2c77_1000G_omni2.5.b37.vcf.gz added
1c9b4fd06fbb_1000G_omni2.5.b37.vcf.gz.tbi added
1c9b7d5786ec_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1c9b7d5b303d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1c9b6dbc3516_1000G_omni2.5.hg38.vcf.gz added
1c9b5f416fa2_1000G_omni2.5.hg38.vcf.gz.tbi added
1c9b41082589_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1c9b7dd866b9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1c9ba403c3b_af-only-gnomad.raw.sites.vcf added
1c9b7f324abe_af-only-gnomad.raw.sites.vcf.idx added
1c9b3ec9412f_Mutect2-exome-panel.vcf.idx added
1c9bed694dd_Mutect2-WGS-panel-b37.vcf added
1c9b29c740c7_Mutect2-WGS-panel-b37.vcf.idx added
1c9b586dde3e_small_exac_common_3.vcf added
1c9b1519e5cd_small_exac_common_3.vcf.idx added
1c9b573e008d_1000g_pon.hg38.vcf.gz added
1c9b279655ba_1000g_pon.hg38.vcf.gz.tbi added
1c9b7ed63aa3_af-only-gnomad.hg38.vcf.gz added
1c9b22a3e463_af-only-gnomad.hg38.vcf.gz.tbi added
1c9b35e73159_small_exac_common_3.hg38.vcf.gz added
1c9b5d58e5b4_small_exac_common_3.hg38.vcf.gz.tbi added
1c9b7750bc4c_gencode.v41.annotation.gtf added
1c9b557a5ec6_gencode.v42.annotation.gtf added
1c9b54e44501_gencode.vM30.annotation.gtf added
1c9b566e7031_gencode.vM31.annotation.gtf added
1c9b6c87cd4b_gencode.v41.transcripts.fa added
1c9b47b72e97_gencode.v41.transcripts.fa.fai added
1c9b4b53e049_gencode.v42.transcripts.fa added
1c9b6fa9ff41_gencode.v42.transcripts.fa.fai added
1c9b1b53dad_gencode.vM30.pc_transcripts.fa added
1c9b21e429bb_gencode.vM30.pc_transcripts.fa.fai added
1c9ba6fc55f_gencode.vM31.pc_transcripts.fa added
1c9b3006e553_gencode.vM31.pc_transcripts.fa.fai added
1c9b14b9c4c7_GRCh38.primary_assembly.genome.fa.1.ht2 added
1c9b3025ef72_GRCh38.primary_assembly.genome.fa.2.ht2 added
1c9ba8b3e10_GRCh38.primary_assembly.genome.fa.3.ht2 added
1c9b3b9791d8_GRCh38.primary_assembly.genome.fa.4.ht2 added
1c9b5be81a78_GRCh38.primary_assembly.genome.fa.5.ht2 added
1c9b6321eb6b_GRCh38.primary_assembly.genome.fa.6.ht2 added
1c9b47e6f0a5_GRCh38.primary_assembly.genome.fa.7.ht2 added
1c9bac10584_GRCh38.primary_assembly.genome.fa.8.ht2 added
1c9b65122a0_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1c9b38b8399d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1c9b46ce8f82_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1c9b232fc41f_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1c9b14f4e145_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1c9b58f183c2_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1c9b5801632c_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1c9b43160ad7_GRCh38.primary_assembly.genome.fa.fai added
1c9b5c21cba9_GRCh38.primary_assembly.genome.fa.amb added
1c9b2ec1f380_GRCh38.primary_assembly.genome.fa.ann added
1c9b3f59707b_GRCh38.primary_assembly.genome.fa.bwt added
1c9b8e7bbbb_GRCh38.primary_assembly.genome.fa.pac added
1c9b25d5f68e_GRCh38.primary_assembly.genome.fa.sa added
1c9b22df80a_GRCh38.primary_assembly.genome.fa added
1c9b17f759a4_hs37d5.fa.fai added
1c9b701e2a46_hs37d5.fa.amb added
1c9b4c69932b_hs37d5.fa.ann added
1c9b273d133e_hs37d5.fa.bwt added
1c9b1aba5f92_hs37d5.fa.pac added
1c9b41d877f3_hs37d5.fa.sa added
1c9b6aab144a_hs37d5.fa added
1c9b5c13cfc_complete_ref_lens.bin added
1c9b518ac757_ctable.bin added
1c9b6e254a93_ctg_offsets.bin added
1c9b52433163_duplicate_clusters.tsv added
1c9b395f84c6_info.json added
1c9b2e060097_mphf.bin added
1c9bc10d11c_pos.bin added
1c9b24108b74_pre_indexing.log added
1c9b3a337f2b_rank.bin added
1c9bae1fde7_ref_indexing.log added
1c9b7ae44e45_refAccumLengths.bin added
1c9b22ced30b_reflengths.bin added
1c9b38818907_refseq.bin added
1c9b404b478c_seq.bin added
1c9be46594e_versionInfo.json added
1c9b2c911734_salmon_index added
1c9b698a6dc7_chrLength.txt added
1c9b7f2d59f2_chrName.txt added
1c9b7a6c6018_chrNameLength.txt added
1c9b61190672_chrStart.txt added
1c9b31f6582b_exonGeTrInfo.tab added
1c9b241688ad_exonInfo.tab added
1c9b4367285d_geneInfo.tab added
1c9b298b143d_Genome added
1c9b69ddc619_genomeParameters.txt added
1c9b5ef8c99b_Log.out added
1c9b1f7c0fd3_SA added
1c9b9f2f5cb_SAindex added
1c9b2de6e787_sjdbInfo.txt added
1c9b126a679c_sjdbList.fromGTF.out.tab added
1c9b7b83c36_sjdbList.out.tab added
1c9b5079012f_transcriptInfo.tab added
1c9b383cddef_GRCh38.GENCODE.v42_100 added
1c9b240e92c1_knownGene_hg38.sql added
1c9b38c4cf65_knownGene_hg38.txt added
1c9b10c0d01_refGene_hg38.sql added
1c9b3e29bd30_refGene_hg38.txt added
1c9b2643ba32_knownGene_mm39.sql added
1c9b28753c3e_knownGene_mm39.txt added
1c9b28c61f32_refGene_mm39.sql added
1c9b672a2087_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//Rtmpd7etKQ/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
6.874 0.875 8.584
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 2.290 | 0.325 | 2.679 | |
| dataSearch | 0.387 | 0.024 | 0.416 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 0.898 | 0.061 | 1.668 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.050 | 0.005 | 0.057 | |
| recipeLoad | 0.458 | 0.034 | 0.524 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.158 | 0.012 | 0.169 | |
| recipeUpdate | 0 | 0 | 0 | |