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 11:34 -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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz |
| StartedAt: 2026-01-06 03:05:28 -0500 (Tue, 06 Jan 2026) |
| EndedAt: 2026-01-06 03:08:19 -0500 (Tue, 06 Jan 2026) |
| EllapsedTime: 170.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-12-22 r89219)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataHub-class 6.423 0.754 7.179
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-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) (2025-12-22 r89219) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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...
b8f887ff41770_GRCh38.primary_assembly.genome.fa.1.bt2 added
b8f886474be59_GRCh38.primary_assembly.genome.fa.2.bt2 added
b8f88569dad4f_GRCh38.primary_assembly.genome.fa.3.bt2 added
b8f8829982a21_GRCh38.primary_assembly.genome.fa.4.bt2 added
b8f88469e510b_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
b8f88781da02a_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
b8f8852654402_outfile.txt added
b8f8824012a50_GRCh37_to_GRCh38.chain added
b8f88589836c9_GRCh37_to_NCBI34.chain added
b8f88676949ed_GRCh37_to_NCBI35.chain added
b8f8833e80a43_GRCh37_to_NCBI36.chain added
b8f885bba7b1f_GRCh38_to_GRCh37.chain added
b8f8821856526_GRCh38_to_NCBI34.chain added
b8f88567f31e8_GRCh38_to_NCBI35.chain added
b8f88368449f7_GRCh38_to_NCBI36.chain added
b8f88217e869c_NCBI34_to_GRCh37.chain added
b8f8849a6bf02_NCBI34_to_GRCh38.chain added
b8f887fff98a_NCBI35_to_GRCh37.chain added
b8f8827ce810d_NCBI35_to_GRCh38.chain added
b8f884787b3a1_NCBI36_to_GRCh37.chain added
b8f88763cd583_NCBI36_to_GRCh38.chain added
b8f887110501d_GRCm38_to_NCBIM36.chain added
b8f88259cd6ee_GRCm38_to_NCBIM37.chain added
b8f8865fd7f2f_NCBIM36_to_GRCm38.chain added
b8f8854b9acf3_NCBIM37_to_GRCm38.chain added
b8f8819bf558c_1000G_omni2.5.b37.vcf.gz added
b8f88638eb6d5_1000G_omni2.5.b37.vcf.gz.tbi added
b8f8866d271ca_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
b8f8878a1854b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
b8f883d0771b4_1000G_omni2.5.hg38.vcf.gz added
b8f881a4dbb9_1000G_omni2.5.hg38.vcf.gz.tbi added
b8f8878959cbc_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
b8f88217c300d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
b8f8858428908_af-only-gnomad.raw.sites.vcf added
b8f88222dc6dd_af-only-gnomad.raw.sites.vcf.idx added
b8f88681a8119_Mutect2-exome-panel.vcf.idx added
b8f8850602932_Mutect2-WGS-panel-b37.vcf added
b8f8874930adf_Mutect2-WGS-panel-b37.vcf.idx added
b8f88c1bab69_small_exac_common_3.vcf added
b8f8828f85ffb_small_exac_common_3.vcf.idx added
b8f885bfc54cd_1000g_pon.hg38.vcf.gz added
b8f884003b5ad_1000g_pon.hg38.vcf.gz.tbi added
b8f884b2db1a_af-only-gnomad.hg38.vcf.gz added
b8f887d81b9f3_af-only-gnomad.hg38.vcf.gz.tbi added
b8f881682e795_small_exac_common_3.hg38.vcf.gz added
b8f883b372512_small_exac_common_3.hg38.vcf.gz.tbi added
b8f881f004090_gencode.v41.annotation.gtf added
b8f886029a697_gencode.v42.annotation.gtf added
b8f8843371e9c_gencode.vM30.annotation.gtf added
b8f8846cec19d_gencode.vM31.annotation.gtf added
b8f8827b15a38_gencode.v41.transcripts.fa added
b8f883973f41f_gencode.v41.transcripts.fa.fai added
b8f8837df11bb_gencode.v42.transcripts.fa added
b8f884d4e3126_gencode.v42.transcripts.fa.fai added
b8f881f71734e_gencode.vM30.pc_transcripts.fa added
b8f88c98beae_gencode.vM30.pc_transcripts.fa.fai added
b8f88670d86b3_gencode.vM31.pc_transcripts.fa added
b8f883002a23_gencode.vM31.pc_transcripts.fa.fai added
b8f88736b3078_GRCh38.primary_assembly.genome.fa.1.ht2 added
b8f885faf0bfe_GRCh38.primary_assembly.genome.fa.2.ht2 added
b8f8840079bd8_GRCh38.primary_assembly.genome.fa.3.ht2 added
b8f8875100c31_GRCh38.primary_assembly.genome.fa.4.ht2 added
b8f885844a8ba_GRCh38.primary_assembly.genome.fa.5.ht2 added
b8f886183cbe5_GRCh38.primary_assembly.genome.fa.6.ht2 added
b8f884d529539_GRCh38.primary_assembly.genome.fa.7.ht2 added
b8f887a726f98_GRCh38.primary_assembly.genome.fa.8.ht2 added
b8f88499e4cfe_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
b8f881db2be6b_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
b8f886f057a77_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
b8f8855b9f868_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
b8f8846ab1e66_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
b8f884b01cf44_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
b8f8815bdae15_GRCh38_full_analysis_set_plus_decoy_hla.fa added
b8f884b5df981_GRCh38.primary_assembly.genome.fa.fai added
b8f8848838938_GRCh38.primary_assembly.genome.fa.amb added
b8f882c4095aa_GRCh38.primary_assembly.genome.fa.ann added
b8f886951e93_GRCh38.primary_assembly.genome.fa.bwt added
b8f886783c9c8_GRCh38.primary_assembly.genome.fa.pac added
b8f88c6a3c41_GRCh38.primary_assembly.genome.fa.sa added
b8f8849cc3d2f_GRCh38.primary_assembly.genome.fa added
b8f882e528b65_hs37d5.fa.fai added
b8f88341b9679_hs37d5.fa.amb added
b8f88340314e_hs37d5.fa.ann added
b8f8866319d20_hs37d5.fa.bwt added
b8f88169c7a0_hs37d5.fa.pac added
b8f8822b1a49c_hs37d5.fa.sa added
b8f8872ca5bce_hs37d5.fa added
b8f8868774e53_complete_ref_lens.bin added
b8f8825b1cebf_ctable.bin added
b8f8866358c46_ctg_offsets.bin added
b8f8848265a51_duplicate_clusters.tsv added
b8f8865b96a97_info.json added
b8f885b459877_mphf.bin added
b8f88206b030c_pos.bin added
b8f88473d367d_pre_indexing.log added
b8f8828982db0_rank.bin added
b8f881add72a4_ref_indexing.log added
b8f8810db837b_refAccumLengths.bin added
b8f88464aec1b_reflengths.bin added
b8f889e2ed1b_refseq.bin added
b8f8866957be3_seq.bin added
b8f88cf60a82_versionInfo.json added
b8f8854e4bc60_salmon_index added
b8f887c5329f8_chrLength.txt added
b8f8858540403_chrName.txt added
b8f881d684598_chrNameLength.txt added
b8f882893bfa2_chrStart.txt added
b8f885ee92296_exonGeTrInfo.tab added
b8f884ec0f60_exonInfo.tab added
b8f8834fdfbe3_geneInfo.tab added
b8f8828b55fc5_Genome added
b8f88333e9ac5_genomeParameters.txt added
b8f886919925d_Log.out added
b8f882bf59113_SA added
b8f88197037e6_SAindex added
b8f886a8359fd_sjdbInfo.txt added
b8f884ea735af_sjdbList.fromGTF.out.tab added
b8f88c3a93b4_sjdbList.out.tab added
b8f8852faa850_transcriptInfo.tab added
b8f887459046e_GRCh38.GENCODE.v42_100 added
b8f8872701ffb_knownGene_hg38.sql added
b8f881b2102a1_knownGene_hg38.txt added
b8f885a126f06_refGene_hg38.sql added
b8f884db5b872_refGene_hg38.txt added
b8f883b8c05ad_knownGene_mm39.sql added
b8f88214fa583_knownGene_mm39.txt added
b8f88764de623_refGene_mm39.sql added
b8f8856697851_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:
/tmp/RtmpLtVVsy/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
18.487 1.250 20.428
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.423 | 0.754 | 7.179 | |
| dataSearch | 1.262 | 0.063 | 1.325 | |
| dataUpdate | 0.001 | 0.000 | 0.001 | |
| getCloudData | 2.789 | 0.416 | 4.500 | |
| getData | 0.000 | 0.001 | 0.001 | |
| meta_data | 0.000 | 0.001 | 0.001 | |
| recipeHub-class | 0.134 | 0.003 | 0.138 | |
| recipeLoad | 1.377 | 0.059 | 1.438 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.529 | 0.012 | 0.541 | |
| recipeUpdate | 0 | 0 | 0 | |