Qian Liu
| Snapshot Date: 2026-02-18 13:40 -0500 (Wed, 18 Feb 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 Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-19 11:32 -0500 (Thu, 19 Feb 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" | 4868 |
| 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 1772/2354 | 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 | | ||||||||
| 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: /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: 2026-02-19 03:38:33 -0500 (Thu, 19 Feb 2026) |
| EndedAt: 2026-02-19 03:41:20 -0500 (Thu, 19 Feb 2026) |
| EllapsedTime: 166.5 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) (2026-01-15 r89304)
* 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 5.836 0.373 6.21
* 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) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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...
1c6c5b171f98a7_GRCh38.primary_assembly.genome.fa.1.bt2 added
1c6c5b72b1dce5_GRCh38.primary_assembly.genome.fa.2.bt2 added
1c6c5b2d49d910_GRCh38.primary_assembly.genome.fa.3.bt2 added
1c6c5b1f892501_GRCh38.primary_assembly.genome.fa.4.bt2 added
1c6c5b5bebaf5_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1c6c5b30483e1e_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1c6c5b723b8469_outfile.txt added
1c6c5b55ce3644_GRCh37_to_GRCh38.chain added
1c6c5b23755f57_GRCh37_to_NCBI34.chain added
1c6c5b4e30c6dc_GRCh37_to_NCBI35.chain added
1c6c5b5bcebc9b_GRCh37_to_NCBI36.chain added
1c6c5b79a3e055_GRCh38_to_GRCh37.chain added
1c6c5b5ff379dc_GRCh38_to_NCBI34.chain added
1c6c5b399aa47d_GRCh38_to_NCBI35.chain added
1c6c5b145e62c6_GRCh38_to_NCBI36.chain added
1c6c5b4397b2f7_NCBI34_to_GRCh37.chain added
1c6c5b1ae92512_NCBI34_to_GRCh38.chain added
1c6c5b35119b3_NCBI35_to_GRCh37.chain added
1c6c5b5320c733_NCBI35_to_GRCh38.chain added
1c6c5b79c2b206_NCBI36_to_GRCh37.chain added
1c6c5b39b94194_NCBI36_to_GRCh38.chain added
1c6c5b31aca727_GRCm38_to_NCBIM36.chain added
1c6c5b67d17a40_GRCm38_to_NCBIM37.chain added
1c6c5b13d57015_NCBIM36_to_GRCm38.chain added
1c6c5b245a706_NCBIM37_to_GRCm38.chain added
1c6c5b19ce8296_1000G_omni2.5.b37.vcf.gz added
1c6c5be25ba51_1000G_omni2.5.b37.vcf.gz.tbi added
1c6c5b67d5aeed_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1c6c5b6bf2ff42_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1c6c5b1a494b65_1000G_omni2.5.hg38.vcf.gz added
1c6c5b35b86608_1000G_omni2.5.hg38.vcf.gz.tbi added
1c6c5b31297e9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1c6c5bcfb284a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1c6c5b63023f18_af-only-gnomad.raw.sites.vcf added
1c6c5b229bbceb_af-only-gnomad.raw.sites.vcf.idx added
1c6c5b12b9e33f_Mutect2-exome-panel.vcf.idx added
1c6c5b134a7d37_Mutect2-WGS-panel-b37.vcf added
1c6c5b14d74154_Mutect2-WGS-panel-b37.vcf.idx added
1c6c5b68881983_small_exac_common_3.vcf added
1c6c5b36bfdc8e_small_exac_common_3.vcf.idx added
1c6c5b63080831_1000g_pon.hg38.vcf.gz added
1c6c5b4456d61e_1000g_pon.hg38.vcf.gz.tbi added
1c6c5b3063bce3_af-only-gnomad.hg38.vcf.gz added
1c6c5b42fb820d_af-only-gnomad.hg38.vcf.gz.tbi added
1c6c5b7df17a9c_small_exac_common_3.hg38.vcf.gz added
1c6c5b44c21fa9_small_exac_common_3.hg38.vcf.gz.tbi added
1c6c5b6933504_gencode.v41.annotation.gtf added
1c6c5b18da9fae_gencode.v42.annotation.gtf added
1c6c5b4813395d_gencode.vM30.annotation.gtf added
1c6c5b59b3fc38_gencode.vM31.annotation.gtf added
1c6c5b129d51b4_gencode.v41.transcripts.fa added
1c6c5b1cc7af1_gencode.v41.transcripts.fa.fai added
1c6c5bb60a35f_gencode.v42.transcripts.fa added
1c6c5b7a6ecbf4_gencode.v42.transcripts.fa.fai added
1c6c5b15a1eb06_gencode.vM30.pc_transcripts.fa added
1c6c5bda64a65_gencode.vM30.pc_transcripts.fa.fai added
1c6c5b143d4e8a_gencode.vM31.pc_transcripts.fa added
1c6c5b23c7a558_gencode.vM31.pc_transcripts.fa.fai added
1c6c5b757bf953_GRCh38.primary_assembly.genome.fa.1.ht2 added
1c6c5b304dcd_GRCh38.primary_assembly.genome.fa.2.ht2 added
1c6c5b3e10f0bd_GRCh38.primary_assembly.genome.fa.3.ht2 added
1c6c5b2b345f5b_GRCh38.primary_assembly.genome.fa.4.ht2 added
1c6c5b342e5b6_GRCh38.primary_assembly.genome.fa.5.ht2 added
1c6c5b4b0c1907_GRCh38.primary_assembly.genome.fa.6.ht2 added
1c6c5be369e73_GRCh38.primary_assembly.genome.fa.7.ht2 added
1c6c5b25dea2a1_GRCh38.primary_assembly.genome.fa.8.ht2 added
1c6c5b5dc5fc46_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1c6c5b21811baa_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1c6c5b3ab5e3f6_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1c6c5b464e15c9_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1c6c5b5840f838_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1c6c5b1dbdec27_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1c6c5baa4ebe7_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1c6c5b8a4b51c_GRCh38.primary_assembly.genome.fa.fai added
1c6c5b60b96e34_GRCh38.primary_assembly.genome.fa.amb added
1c6c5b8966683_GRCh38.primary_assembly.genome.fa.ann added
1c6c5b4d66d4c5_GRCh38.primary_assembly.genome.fa.bwt added
1c6c5b674ca338_GRCh38.primary_assembly.genome.fa.pac added
1c6c5b21710631_GRCh38.primary_assembly.genome.fa.sa added
1c6c5b157a0e22_GRCh38.primary_assembly.genome.fa added
1c6c5b41009f70_hs37d5.fa.fai added
1c6c5b340e57e5_hs37d5.fa.amb added
1c6c5b17468914_hs37d5.fa.ann added
1c6c5b4c6142cf_hs37d5.fa.bwt added
1c6c5b2e7d23d9_hs37d5.fa.pac added
1c6c5b2ce8741a_hs37d5.fa.sa added
1c6c5b5a078d35_hs37d5.fa added
1c6c5b42ba7264_complete_ref_lens.bin added
1c6c5b50b01972_ctable.bin added
1c6c5b4f838688_ctg_offsets.bin added
1c6c5b42eac031_duplicate_clusters.tsv added
1c6c5bec10a2f_info.json added
1c6c5b7ab7e5e3_mphf.bin added
1c6c5b462da5e7_pos.bin added
1c6c5b59cd2336_pre_indexing.log added
1c6c5b8ee8456_rank.bin added
1c6c5b6c0c4889_ref_indexing.log added
1c6c5b37931f7c_refAccumLengths.bin added
1c6c5b2a6fa001_reflengths.bin added
1c6c5b26c22c7f_refseq.bin added
1c6c5b7de13545_seq.bin added
1c6c5b2b09839_versionInfo.json added
1c6c5b448018a6_salmon_index added
1c6c5b886212d_chrLength.txt added
1c6c5bb554d55_chrName.txt added
1c6c5b253986da_chrNameLength.txt added
1c6c5b111c87b0_chrStart.txt added
1c6c5b58bc221b_exonGeTrInfo.tab added
1c6c5bc862a12_exonInfo.tab added
1c6c5b328d8de2_geneInfo.tab added
1c6c5b6e36303d_Genome added
1c6c5b4d86c983_genomeParameters.txt added
1c6c5b669be5c7_Log.out added
1c6c5b57cb951_SA added
1c6c5b19e80c52_SAindex added
1c6c5b151909a1_sjdbInfo.txt added
1c6c5b32652d6c_sjdbList.fromGTF.out.tab added
1c6c5b73ef9987_sjdbList.out.tab added
1c6c5b57d37c05_transcriptInfo.tab added
1c6c5b31546de_GRCh38.GENCODE.v42_100 added
1c6c5b4373200f_knownGene_hg38.sql added
1c6c5b1abe3c36_knownGene_hg38.txt added
1c6c5b11d6510e_refGene_hg38.sql added
1c6c5b3e2b05f2_refGene_hg38.txt added
1c6c5b60ebe21d_knownGene_mm39.sql added
1c6c5b6ba37444_knownGene_mm39.txt added
1c6c5b47198a49_refGene_mm39.sql added
1c6c5b4cf82aa6_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/Rtmp4ObQ5l/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
17.694 1.108 19.315
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.836 | 0.373 | 6.210 | |
| dataSearch | 1.130 | 0.012 | 1.141 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 2.578 | 0.112 | 3.969 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.001 | 0.000 | |
| recipeHub-class | 0.117 | 0.002 | 0.119 | |
| recipeLoad | 1.235 | 0.025 | 1.261 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.522 | 0.009 | 0.531 | |
| recipeUpdate | 0 | 0 | 0 | |