Qian Liu
| Snapshot Date: 2026-01-26 13:45 -0500 (Mon, 26 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_22 |
| git_last_commit: 2d4066b |
| git_last_commit_date: 2025-10-29 11:20:44 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-01-29 11:58 -0500 (Thu, 29 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4886 |
| 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 1773/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.10.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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: 1.10.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.10.0.tar.gz |
| StartedAt: 2026-01-27 03:21:57 -0500 (Tue, 27 Jan 2026) |
| EndedAt: 2026-01-27 03:24:37 -0500 (Tue, 27 Jan 2026) |
| EllapsedTime: 160.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReUseData_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReUseData.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.10.0’
* 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 5.584 0.212 5.798
* 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-3.22-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.10.0’ ** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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...
11c7ff7aa6372f_GRCh38.primary_assembly.genome.fa.1.bt2 added
11c7ff6a2b55e1_GRCh38.primary_assembly.genome.fa.2.bt2 added
11c7ff857c6fd_GRCh38.primary_assembly.genome.fa.3.bt2 added
11c7ff57669ddc_GRCh38.primary_assembly.genome.fa.4.bt2 added
11c7ff23708722_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
11c7ff56daf5cc_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
11c7ff45d31d4a_outfile.txt added
11c7ff308245a8_GRCh37_to_GRCh38.chain added
11c7ff6edc3dc2_GRCh37_to_NCBI34.chain added
11c7ff42312ed6_GRCh37_to_NCBI35.chain added
11c7ff69117cba_GRCh37_to_NCBI36.chain added
11c7ff6e3cfdb2_GRCh38_to_GRCh37.chain added
11c7ff7fd27baf_GRCh38_to_NCBI34.chain added
11c7ff54ff8c0e_GRCh38_to_NCBI35.chain added
11c7ff7b57d4a8_GRCh38_to_NCBI36.chain added
11c7ff45abeebf_NCBI34_to_GRCh37.chain added
11c7ff2302b020_NCBI34_to_GRCh38.chain added
11c7ff790c4f3a_NCBI35_to_GRCh37.chain added
11c7ff5f06ae95_NCBI35_to_GRCh38.chain added
11c7ff5f6d4023_NCBI36_to_GRCh37.chain added
11c7ffe66f9c3_NCBI36_to_GRCh38.chain added
11c7ff78d69847_GRCm38_to_NCBIM36.chain added
11c7ff63acdd3a_GRCm38_to_NCBIM37.chain added
11c7ff7bd43c94_NCBIM36_to_GRCm38.chain added
11c7ff24d4c9a2_NCBIM37_to_GRCm38.chain added
11c7ff396f8b67_1000G_omni2.5.b37.vcf.gz added
11c7ff399482b7_1000G_omni2.5.b37.vcf.gz.tbi added
11c7ffdf9af8d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
11c7ff6e366400_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
11c7ff318af0c7_1000G_omni2.5.hg38.vcf.gz added
11c7ff3d41fc53_1000G_omni2.5.hg38.vcf.gz.tbi added
11c7ff68dc9b2f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
11c7ff1bb646a8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
11c7ff4599c351_af-only-gnomad.raw.sites.vcf added
11c7ff4043390c_af-only-gnomad.raw.sites.vcf.idx added
11c7ff3f26cdca_Mutect2-exome-panel.vcf.idx added
11c7ff1c74b91d_Mutect2-WGS-panel-b37.vcf added
11c7ff6165656_Mutect2-WGS-panel-b37.vcf.idx added
11c7ff6fa91372_small_exac_common_3.vcf added
11c7ffb50f6df_small_exac_common_3.vcf.idx added
11c7ff4847852c_1000g_pon.hg38.vcf.gz added
11c7ff58ba902d_1000g_pon.hg38.vcf.gz.tbi added
11c7ff798df491_af-only-gnomad.hg38.vcf.gz added
11c7ff481a00db_af-only-gnomad.hg38.vcf.gz.tbi added
11c7ff2dba1c3b_small_exac_common_3.hg38.vcf.gz added
11c7ff74e5c939_small_exac_common_3.hg38.vcf.gz.tbi added
11c7ffdc5ef9a_gencode.v41.annotation.gtf added
11c7ff50bccc5b_gencode.v42.annotation.gtf added
11c7ff6df21874_gencode.vM30.annotation.gtf added
11c7ff6ccc9e2f_gencode.vM31.annotation.gtf added
11c7ff302a0c7f_gencode.v41.transcripts.fa added
11c7ff7c591237_gencode.v41.transcripts.fa.fai added
11c7ff65a33677_gencode.v42.transcripts.fa added
11c7ff13d6e9b9_gencode.v42.transcripts.fa.fai added
11c7ff782d4ecb_gencode.vM30.pc_transcripts.fa added
11c7ffa780019_gencode.vM30.pc_transcripts.fa.fai added
11c7ff4d467520_gencode.vM31.pc_transcripts.fa added
11c7ff31c1d182_gencode.vM31.pc_transcripts.fa.fai added
11c7ff1871afa6_GRCh38.primary_assembly.genome.fa.1.ht2 added
11c7ff3b7cd920_GRCh38.primary_assembly.genome.fa.2.ht2 added
11c7ff634cc249_GRCh38.primary_assembly.genome.fa.3.ht2 added
11c7ff55b3abf9_GRCh38.primary_assembly.genome.fa.4.ht2 added
11c7ff24597450_GRCh38.primary_assembly.genome.fa.5.ht2 added
11c7ff7f0308f1_GRCh38.primary_assembly.genome.fa.6.ht2 added
11c7ff1b4d6f4a_GRCh38.primary_assembly.genome.fa.7.ht2 added
11c7ff649cad5c_GRCh38.primary_assembly.genome.fa.8.ht2 added
11c7ff3e29d6bb_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
11c7ff37c22867_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
11c7ff6ab303b2_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
11c7ff2dd2ea2e_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
11c7ff43131f47_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
11c7ff32fa88de_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
11c7ff68d7a5b_GRCh38_full_analysis_set_plus_decoy_hla.fa added
11c7ff3ca113d8_GRCh38.primary_assembly.genome.fa.fai added
11c7ff7b1489ba_GRCh38.primary_assembly.genome.fa.amb added
11c7ff34479696_GRCh38.primary_assembly.genome.fa.ann added
11c7ff3186dd12_GRCh38.primary_assembly.genome.fa.bwt added
11c7ff8da7954_GRCh38.primary_assembly.genome.fa.pac added
11c7ff50462f2_GRCh38.primary_assembly.genome.fa.sa added
11c7ff1f78f586_GRCh38.primary_assembly.genome.fa added
11c7ff75a71784_hs37d5.fa.fai added
11c7ff352e6f71_hs37d5.fa.amb added
11c7ff1bd207bd_hs37d5.fa.ann added
11c7ff5b4a4dfb_hs37d5.fa.bwt added
11c7ff4905592a_hs37d5.fa.pac added
11c7ff13ff5688_hs37d5.fa.sa added
11c7ff65c24e14_hs37d5.fa added
11c7ff164bce4a_complete_ref_lens.bin added
11c7ff45c1280a_ctable.bin added
11c7ff7e33fdba_ctg_offsets.bin added
11c7ff51c8a76a_duplicate_clusters.tsv added
11c7ff290dea54_info.json added
11c7ff53e7a9b3_mphf.bin added
11c7ff76221bba_pos.bin added
11c7ff2810f345_pre_indexing.log added
11c7ff6f3518fe_rank.bin added
11c7ff5abec916_ref_indexing.log added
11c7ff663aca01_refAccumLengths.bin added
11c7ff26f74165_reflengths.bin added
11c7ff4571ccc8_refseq.bin added
11c7ff140db42f_seq.bin added
11c7ff6a0a60ac_versionInfo.json added
11c7ff786c55a7_salmon_index added
11c7ff1a9b2e8a_chrLength.txt added
11c7ff26ab7485_chrName.txt added
11c7ff7380df61_chrNameLength.txt added
11c7ff4ee2c520_chrStart.txt added
11c7ff58325197_exonGeTrInfo.tab added
11c7ff7c5b58b5_exonInfo.tab added
11c7ff53e72812_geneInfo.tab added
11c7ff77ab471d_Genome added
11c7ff72027039_genomeParameters.txt added
11c7ff9159783_Log.out added
11c7ff137d4eda_SA added
11c7ff4d4cbe34_SAindex added
11c7ff521af0ad_sjdbInfo.txt added
11c7ff277ca562_sjdbList.fromGTF.out.tab added
11c7ff330f0c48_sjdbList.out.tab added
11c7ff6866bef7_transcriptInfo.tab added
11c7ff6d3dcd6c_GRCh38.GENCODE.v42_100 added
11c7ff31430a02_knownGene_hg38.sql added
11c7ff3a2f6662_knownGene_hg38.txt added
11c7ff164bb7c0_refGene_hg38.sql added
11c7ff52ab3b6_refGene_hg38.txt added
11c7ff3051821c_knownGene_mm39.sql added
11c7ff3e5cab06_knownGene_mm39.txt added
11c7ff745fccb4_refGene_mm39.sql added
11c7ffb104b33_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/RtmpBcRLDF/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
17.885 0.927 19.567
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.584 | 0.212 | 5.798 | |
| dataSearch | 1.079 | 0.011 | 1.090 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.644 | 0.108 | 4.092 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.118 | 0.003 | 0.122 | |
| recipeLoad | 1.270 | 0.046 | 1.317 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.522 | 0.002 | 0.525 | |
| recipeUpdate | 0 | 0 | 0 | |