Qian Liu
| Snapshot Date: 2026-01-07 13:40 -0500 (Wed, 07 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 2026-01-08 11:35 -0500 (Thu, 08 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: 2026-01-08 03:02:19 -0500 (Thu, 08 Jan 2026) |
| EndedAt: 2026-01-08 03:05:04 -0500 (Thu, 08 Jan 2026) |
| EllapsedTime: 164.3 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 6.053 0.389 6.443
* 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...
7a09c5b3243e5_GRCh38.primary_assembly.genome.fa.1.bt2 added
7a09c33a667f1_GRCh38.primary_assembly.genome.fa.2.bt2 added
7a09c40a4ee1c_GRCh38.primary_assembly.genome.fa.3.bt2 added
7a09c47568841_GRCh38.primary_assembly.genome.fa.4.bt2 added
7a09c673a1386_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
7a09c669424f8_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
7a09c127d3178_outfile.txt added
7a09c23f1ffe9_GRCh37_to_GRCh38.chain added
7a09c3584adeb_GRCh37_to_NCBI34.chain added
7a09c785b5b34_GRCh37_to_NCBI35.chain added
7a09c240bf560_GRCh37_to_NCBI36.chain added
7a09c7fdb035e_GRCh38_to_GRCh37.chain added
7a09c36b80472_GRCh38_to_NCBI34.chain added
7a09c496e2060_GRCh38_to_NCBI35.chain added
7a09c29a6f949_GRCh38_to_NCBI36.chain added
7a09c4bf3cafc_NCBI34_to_GRCh37.chain added
7a09c243d23f0_NCBI34_to_GRCh38.chain added
7a09c1122d7e2_NCBI35_to_GRCh37.chain added
7a09c9349e50_NCBI35_to_GRCh38.chain added
7a09c5c5b4b44_NCBI36_to_GRCh37.chain added
7a09c5d3dc34c_NCBI36_to_GRCh38.chain added
7a09c13069c10_GRCm38_to_NCBIM36.chain added
7a09cde2d11c_GRCm38_to_NCBIM37.chain added
7a09ced8f859_NCBIM36_to_GRCm38.chain added
7a09c6e40cf5d_NCBIM37_to_GRCm38.chain added
7a09c50297776_1000G_omni2.5.b37.vcf.gz added
7a09cf7192a0_1000G_omni2.5.b37.vcf.gz.tbi added
7a09c76c8f7d9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
7a09c66a759dc_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
7a09c753ecaf9_1000G_omni2.5.hg38.vcf.gz added
7a09cbfcbe73_1000G_omni2.5.hg38.vcf.gz.tbi added
7a09c41d99dc1_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
7a09c28e532ea_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
7a09c4ca1ac8f_af-only-gnomad.raw.sites.vcf added
7a09c9302603_af-only-gnomad.raw.sites.vcf.idx added
7a09c101f4671_Mutect2-exome-panel.vcf.idx added
7a09c3335d188_Mutect2-WGS-panel-b37.vcf added
7a09c1bad577b_Mutect2-WGS-panel-b37.vcf.idx added
7a09c3411465a_small_exac_common_3.vcf added
7a09c68ba7f73_small_exac_common_3.vcf.idx added
7a09c1408b2af_1000g_pon.hg38.vcf.gz added
7a09c581d3bba_1000g_pon.hg38.vcf.gz.tbi added
7a09c689582d2_af-only-gnomad.hg38.vcf.gz added
7a09c4ac0b722_af-only-gnomad.hg38.vcf.gz.tbi added
7a09c218b5c1a_small_exac_common_3.hg38.vcf.gz added
7a09c123c7c1b_small_exac_common_3.hg38.vcf.gz.tbi added
7a09c16b4821e_gencode.v41.annotation.gtf added
7a09c45c8800b_gencode.v42.annotation.gtf added
7a09c235f53fe_gencode.vM30.annotation.gtf added
7a09c1fe9206f_gencode.vM31.annotation.gtf added
7a09c2223cb4f_gencode.v41.transcripts.fa added
7a09c9d174a_gencode.v41.transcripts.fa.fai added
7a09c32efbc7f_gencode.v42.transcripts.fa added
7a09c30069c6b_gencode.v42.transcripts.fa.fai added
7a09cf760fa4_gencode.vM30.pc_transcripts.fa added
7a09c21308bdc_gencode.vM30.pc_transcripts.fa.fai added
7a09c3013e1_gencode.vM31.pc_transcripts.fa added
7a09c1ee7a244_gencode.vM31.pc_transcripts.fa.fai added
7a09c17f983b5_GRCh38.primary_assembly.genome.fa.1.ht2 added
7a09c66d76dbd_GRCh38.primary_assembly.genome.fa.2.ht2 added
7a09c14266d3d_GRCh38.primary_assembly.genome.fa.3.ht2 added
7a09c23f64229_GRCh38.primary_assembly.genome.fa.4.ht2 added
7a09c28b10b7f_GRCh38.primary_assembly.genome.fa.5.ht2 added
7a09c3d0ba028_GRCh38.primary_assembly.genome.fa.6.ht2 added
7a09c7097eeb8_GRCh38.primary_assembly.genome.fa.7.ht2 added
7a09c31e13182_GRCh38.primary_assembly.genome.fa.8.ht2 added
7a09c4d2ae699_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
7a09c23cdc040_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
7a09c4d8e88fd_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
7a09c13c2cf3_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
7a09cc883fb4_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
7a09c61973bad_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
7a09c595968ad_GRCh38_full_analysis_set_plus_decoy_hla.fa added
7a09c751dc286_GRCh38.primary_assembly.genome.fa.fai added
7a09c2c57f2cf_GRCh38.primary_assembly.genome.fa.amb added
7a09c7ae4c4c7_GRCh38.primary_assembly.genome.fa.ann added
7a09c75a3ea1_GRCh38.primary_assembly.genome.fa.bwt added
7a09c430c74ed_GRCh38.primary_assembly.genome.fa.pac added
7a09c40ad44d2_GRCh38.primary_assembly.genome.fa.sa added
7a09c2ab9929f_GRCh38.primary_assembly.genome.fa added
7a09c62f5955c_hs37d5.fa.fai added
7a09c62d11021_hs37d5.fa.amb added
7a09c2b56a9ea_hs37d5.fa.ann added
7a09c15e551db_hs37d5.fa.bwt added
7a09c12d7ac8d_hs37d5.fa.pac added
7a09c3accb98e_hs37d5.fa.sa added
7a09c3715ddb7_hs37d5.fa added
7a09c1307c06e_complete_ref_lens.bin added
7a09c59b45bd2_ctable.bin added
7a09c4f0f616d_ctg_offsets.bin added
7a09c79df2e2c_duplicate_clusters.tsv added
7a09c6ddac910_info.json added
7a09c7305a396_mphf.bin added
7a09c229039ab_pos.bin added
7a09c2ae66938_pre_indexing.log added
7a09c639d924e_rank.bin added
7a09c54716b2d_ref_indexing.log added
7a09c78114fd1_refAccumLengths.bin added
7a09c76b528f_reflengths.bin added
7a09c21fff42a_refseq.bin added
7a09c794d7cc4_seq.bin added
7a09c13f39243_versionInfo.json added
7a09c3972fd7_salmon_index added
7a09c52a6e571_chrLength.txt added
7a09c91154c9_chrName.txt added
7a09c2fef22a6_chrNameLength.txt added
7a09c4d8baa38_chrStart.txt added
7a09c106b936a_exonGeTrInfo.tab added
7a09c72fb9794_exonInfo.tab added
7a09ce38ef0b_geneInfo.tab added
7a09c3b25260a_Genome added
7a09c55f12cf0_genomeParameters.txt added
7a09c7109ff2c_Log.out added
7a09c667bcff4_SA added
7a09c6bd67ecc_SAindex added
7a09c3e1abb9_sjdbInfo.txt added
7a09c21488982_sjdbList.fromGTF.out.tab added
7a09c22ec5c83_sjdbList.out.tab added
7a09c16e96c28_transcriptInfo.tab added
7a09c7afce554_GRCh38.GENCODE.v42_100 added
7a09c71fbbdf0_knownGene_hg38.sql added
7a09c10c89a54_knownGene_hg38.txt added
7a09c68d7ae64_refGene_hg38.sql added
7a09c65016186_refGene_hg38.txt added
7a09c3358d3ff_knownGene_mm39.sql added
7a09c13be179c_knownGene_mm39.txt added
7a09c489ef3d5_refGene_mm39.sql added
7a09c7ca3f2c_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/Rtmpe0P77t/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
18.207 1.126 19.663
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.053 | 0.389 | 6.443 | |
| dataSearch | 1.094 | 0.051 | 1.145 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 2.629 | 0.107 | 3.494 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.127 | 0.016 | 0.143 | |
| recipeLoad | 1.264 | 0.087 | 1.352 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.532 | 0.012 | 0.544 | |
| recipeUpdate | 0 | 0 | 0 | |