Qian Liu
| Snapshot Date: 2026-05-13 13:45 -0400 (Wed, 13 May 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: caf380d |
| git_last_commit_date: 2026-04-28 08:59:39 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-14 11:33 -0400 (Thu, 14 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4893 |
| 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 1783/2374 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.13.0 (landing page) Qian Liu
| nebbiolo2 | Linux (Ubuntu 24.04.4 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: 1.13.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings ReUseData_1.13.0.tar.gz |
| StartedAt: 2026-05-14 03:39:40 -0400 (Thu, 14 May 2026) |
| EndedAt: 2026-05-14 03:42:29 -0400 (Thu, 14 May 2026) |
| EllapsedTime: 169.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings ReUseData_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-14 07:39:40 UTC
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.13.0’
* 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 6.001 0.264 6.268
* 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-3.24-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.13.0’ ** 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 RC (2026-04-17 r89917) -- "Because it was There"
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...
19693977bd7552_GRCh38.primary_assembly.genome.fa.1.bt2 added
1969394c80c73b_GRCh38.primary_assembly.genome.fa.2.bt2 added
1969394fee3a86_GRCh38.primary_assembly.genome.fa.3.bt2 added
19693933d37ddf_GRCh38.primary_assembly.genome.fa.4.bt2 added
19693913e9488a_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1969393d0474c8_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
19693944c23e62_outfile.txt added
19693914844e6_GRCh37_to_GRCh38.chain added
1969397aaa683_GRCh37_to_NCBI34.chain added
19693979a2cb7a_GRCh37_to_NCBI35.chain added
19693959e710bb_GRCh37_to_NCBI36.chain added
19693932f70d49_GRCh38_to_GRCh37.chain added
19693958d88b4c_GRCh38_to_NCBI34.chain added
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19693947c7ba15_GRCh38_to_NCBI36.chain added
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1969394cc6b491_NCBI34_to_GRCh38.chain added
1969393b14f18a_NCBI35_to_GRCh37.chain added
1969396afbeb33_NCBI35_to_GRCh38.chain added
19693972ac0ac3_NCBI36_to_GRCh37.chain added
1969391dd18f21_NCBI36_to_GRCh38.chain added
1969392f6d2ab7_GRCm38_to_NCBIM36.chain added
1969397b909f5c_GRCm38_to_NCBIM37.chain added
1969394de24ea0_NCBIM36_to_GRCm38.chain added
19693942e63a6f_NCBIM37_to_GRCm38.chain added
19693967931d35_1000G_omni2.5.b37.vcf.gz added
1969396c404c3b_1000G_omni2.5.b37.vcf.gz.tbi added
196939461a308_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1969394f5ad0bd_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
19693941690c74_1000G_omni2.5.hg38.vcf.gz added
196939460c31be_1000G_omni2.5.hg38.vcf.gz.tbi added
1969394718460f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
196939de9d3b0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
19693915fa6c44_af-only-gnomad.raw.sites.vcf added
1969397aebc3ee_af-only-gnomad.raw.sites.vcf.idx added
19693921d31c3a_Mutect2-exome-panel.vcf.idx added
19693952fee10c_Mutect2-WGS-panel-b37.vcf added
1969393fae0251_Mutect2-WGS-panel-b37.vcf.idx added
196939231b6120_small_exac_common_3.vcf added
1969395aa9878f_small_exac_common_3.vcf.idx added
1969393950cdcb_1000g_pon.hg38.vcf.gz added
1969397d0271db_1000g_pon.hg38.vcf.gz.tbi added
196939da094d8_af-only-gnomad.hg38.vcf.gz added
19693912295917_af-only-gnomad.hg38.vcf.gz.tbi added
1969393d00b8ac_small_exac_common_3.hg38.vcf.gz added
19693955684eed_small_exac_common_3.hg38.vcf.gz.tbi added
1969397df80206_gencode.v41.annotation.gtf added
1969399c76d3d_gencode.v42.annotation.gtf added
196939107d4078_gencode.vM30.annotation.gtf added
19693968f3ed39_gencode.vM31.annotation.gtf added
1969397c737800_gencode.v41.transcripts.fa added
1969392e4ecf99_gencode.v41.transcripts.fa.fai added
196939186117f0_gencode.v42.transcripts.fa added
1969397804175c_gencode.v42.transcripts.fa.fai added
1969397c311e3a_gencode.vM30.pc_transcripts.fa added
1969395b47525f_gencode.vM30.pc_transcripts.fa.fai added
1969395f973491_gencode.vM31.pc_transcripts.fa added
19693968716a75_gencode.vM31.pc_transcripts.fa.fai added
1969395fa8f567_GRCh38.primary_assembly.genome.fa.1.ht2 added
1969392ef2054e_GRCh38.primary_assembly.genome.fa.2.ht2 added
19693929da76e9_GRCh38.primary_assembly.genome.fa.3.ht2 added
19693925b52725_GRCh38.primary_assembly.genome.fa.4.ht2 added
196939760a4b5d_GRCh38.primary_assembly.genome.fa.5.ht2 added
19693937c44a99_GRCh38.primary_assembly.genome.fa.6.ht2 added
1969393baf9369_GRCh38.primary_assembly.genome.fa.7.ht2 added
19693970f60f4c_GRCh38.primary_assembly.genome.fa.8.ht2 added
196939599766d3_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
196939eae7475_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
19693930a4119d_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1969397cb2c7f4_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1969396957fc04_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
19693969f4df68_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
19693979b539cf_GRCh38_full_analysis_set_plus_decoy_hla.fa added
19693976f890dd_GRCh38.primary_assembly.genome.fa.fai added
1969397c1e387f_GRCh38.primary_assembly.genome.fa.amb added
19693936b5f27b_GRCh38.primary_assembly.genome.fa.ann added
1969394c60dfca_GRCh38.primary_assembly.genome.fa.bwt added
1969397a163a85_GRCh38.primary_assembly.genome.fa.pac added
196939407d5fb8_GRCh38.primary_assembly.genome.fa.sa added
1969395cde2042_GRCh38.primary_assembly.genome.fa added
196939630a27be_hs37d5.fa.fai added
1969393cf0d7b8_hs37d5.fa.amb added
196939b2cefdc_hs37d5.fa.ann added
1969397b6b3fae_hs37d5.fa.bwt added
19693934f4ef14_hs37d5.fa.pac added
19693975e0e16_hs37d5.fa.sa added
19693956b2920d_hs37d5.fa added
196939148c23a6_complete_ref_lens.bin added
1969396fcf788b_ctable.bin added
196939365b8775_ctg_offsets.bin added
196939437e28f4_duplicate_clusters.tsv added
19693919a9ef74_info.json added
1969395c10ae9a_mphf.bin added
19693939887452_pos.bin added
196939516e3a0e_pre_indexing.log added
19693917c04204_rank.bin added
1969392a7e839e_ref_indexing.log added
1969392b05a0e1_refAccumLengths.bin added
196939266eb679_reflengths.bin added
1969395b22953b_refseq.bin added
19693927b868d5_seq.bin added
196939fc6b27e_versionInfo.json added
196939451774a3_salmon_index added
196939216da2a5_chrLength.txt added
1969396bf435b_chrName.txt added
1969394135ad22_chrNameLength.txt added
19693958239520_chrStart.txt added
19693953202325_exonGeTrInfo.tab added
1969393b4be7a8_exonInfo.tab added
19693918a0f4d9_geneInfo.tab added
1969392ffe4368_Genome added
1969391e560f66_genomeParameters.txt added
1969395591cc91_Log.out added
1969393b2b3344_SA added
19693919c14f15_SAindex added
196939a86bba6_sjdbInfo.txt added
1969394289415a_sjdbList.fromGTF.out.tab added
1969397073e122_sjdbList.out.tab added
1969391f12df4c_transcriptInfo.tab added
1969393258b9e5_GRCh38.GENCODE.v42_100 added
19693926cf6897_knownGene_hg38.sql added
19693962910840_knownGene_hg38.txt added
1969394c02a959_refGene_hg38.sql added
1969392e01732_refGene_hg38.txt added
1969391c197c92_knownGene_mm39.sql added
1969391d70e367_knownGene_mm39.txt added
1969391aa05936_refGene_mm39.sql added
19693946980030_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/RtmpeBuJ5A/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
18.336 1.043 20.197
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.001 | 0.264 | 6.268 | |
| dataSearch | 1.109 | 0.030 | 1.140 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.822 | 0.145 | 3.940 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.137 | 0.011 | 0.149 | |
| recipeLoad | 1.281 | 0.024 | 1.306 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.533 | 0.009 | 0.541 | |
| recipeUpdate | 0 | 0 | 0 | |