Qian Liu
| Snapshot Date: 2026-03-27 13:45 -0400 (Fri, 27 Mar 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-28 11:57 -0400 (Sat, 28 Mar 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" | 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 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 | | ||||||||
| 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: 1.10.0 |
| 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: 2026-03-28 03:01:48 -0400 (Sat, 28 Mar 2026) |
| EndedAt: 2026-03-28 03:04:34 -0400 (Sat, 28 Mar 2026) |
| EllapsedTime: 165.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 24.04.4 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 5.774 0.254 6.033
* 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...
1b74cc56dacd9e_GRCh38.primary_assembly.genome.fa.1.bt2 added
1b74cc38176029_GRCh38.primary_assembly.genome.fa.2.bt2 added
1b74cc6306164e_GRCh38.primary_assembly.genome.fa.3.bt2 added
1b74cc48b660b_GRCh38.primary_assembly.genome.fa.4.bt2 added
1b74cc4677af3c_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1b74cc39fee12a_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1b74cc25fc83e3_outfile.txt added
1b74cc38552c22_GRCh37_to_GRCh38.chain added
1b74cc15545d7e_GRCh37_to_NCBI34.chain added
1b74cc7844c659_GRCh37_to_NCBI35.chain added
1b74cc394f93b9_GRCh37_to_NCBI36.chain added
1b74cc1f0a8c47_GRCh38_to_GRCh37.chain added
1b74cc7470941a_GRCh38_to_NCBI34.chain added
1b74cc9c9867d_GRCh38_to_NCBI35.chain added
1b74cc701f9a11_GRCh38_to_NCBI36.chain added
1b74cc465956b2_NCBI34_to_GRCh37.chain added
1b74cc1f7792d8_NCBI34_to_GRCh38.chain added
1b74cc666ab9f9_NCBI35_to_GRCh37.chain added
1b74cc7e3b5361_NCBI35_to_GRCh38.chain added
1b74cc118f4aad_NCBI36_to_GRCh37.chain added
1b74cc77b9ab1e_NCBI36_to_GRCh38.chain added
1b74cca2a353e_GRCm38_to_NCBIM36.chain added
1b74cc315ff1ab_GRCm38_to_NCBIM37.chain added
1b74cc13f94b9b_NCBIM36_to_GRCm38.chain added
1b74cc1cdbbc78_NCBIM37_to_GRCm38.chain added
1b74cc399cd183_1000G_omni2.5.b37.vcf.gz added
1b74cc1b97ecb1_1000G_omni2.5.b37.vcf.gz.tbi added
1b74cc71d05029_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1b74ccb324af5_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1b74ccd79c213_1000G_omni2.5.hg38.vcf.gz added
1b74cc11a95ad1_1000G_omni2.5.hg38.vcf.gz.tbi added
1b74cc620d1893_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1b74cc4591223c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1b74cc74af711f_af-only-gnomad.raw.sites.vcf added
1b74cc66987e9e_af-only-gnomad.raw.sites.vcf.idx added
1b74ccc08d178_Mutect2-exome-panel.vcf.idx added
1b74cc2eae5249_Mutect2-WGS-panel-b37.vcf added
1b74ccc950282_Mutect2-WGS-panel-b37.vcf.idx added
1b74cc445dfd9a_small_exac_common_3.vcf added
1b74cc4402afc8_small_exac_common_3.vcf.idx added
1b74cc4d9c8db_1000g_pon.hg38.vcf.gz added
1b74cc7dad9153_1000g_pon.hg38.vcf.gz.tbi added
1b74cc630d3c0f_af-only-gnomad.hg38.vcf.gz added
1b74cc794a5cf5_af-only-gnomad.hg38.vcf.gz.tbi added
1b74cc77717d1_small_exac_common_3.hg38.vcf.gz added
1b74cc532cd620_small_exac_common_3.hg38.vcf.gz.tbi added
1b74cc3fa3b3a7_gencode.v41.annotation.gtf added
1b74cc26eeaaa9_gencode.v42.annotation.gtf added
1b74cc39979019_gencode.vM30.annotation.gtf added
1b74cc3ddf0709_gencode.vM31.annotation.gtf added
1b74cc387df557_gencode.v41.transcripts.fa added
1b74cc31513b37_gencode.v41.transcripts.fa.fai added
1b74cc48093c47_gencode.v42.transcripts.fa added
1b74cc69dde702_gencode.v42.transcripts.fa.fai added
1b74cc454a86d2_gencode.vM30.pc_transcripts.fa added
1b74cc64e4f8bf_gencode.vM30.pc_transcripts.fa.fai added
1b74cc237ab885_gencode.vM31.pc_transcripts.fa added
1b74cc60e27384_gencode.vM31.pc_transcripts.fa.fai added
1b74cc56b548e8_GRCh38.primary_assembly.genome.fa.1.ht2 added
1b74cc2ead037a_GRCh38.primary_assembly.genome.fa.2.ht2 added
1b74cc6e5c3597_GRCh38.primary_assembly.genome.fa.3.ht2 added
1b74cc685ea3ba_GRCh38.primary_assembly.genome.fa.4.ht2 added
1b74cc10ba1c0e_GRCh38.primary_assembly.genome.fa.5.ht2 added
1b74cc33ed57d3_GRCh38.primary_assembly.genome.fa.6.ht2 added
1b74cc5d0e14d9_GRCh38.primary_assembly.genome.fa.7.ht2 added
1b74cc77529aac_GRCh38.primary_assembly.genome.fa.8.ht2 added
1b74cc3ff6294b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1b74ccbbc6723_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1b74cc3e79d2e_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1b74cc45426e6_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1b74cc4fbf16eb_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1b74cc8c16609_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1b74cc201b839_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1b74cc32cc52fa_GRCh38.primary_assembly.genome.fa.fai added
1b74cc20bc2fe_GRCh38.primary_assembly.genome.fa.amb added
1b74cc978d00a_GRCh38.primary_assembly.genome.fa.ann added
1b74cc5f9291b_GRCh38.primary_assembly.genome.fa.bwt added
1b74cc41af76a6_GRCh38.primary_assembly.genome.fa.pac added
1b74cc30677ab4_GRCh38.primary_assembly.genome.fa.sa added
1b74cc3f90b934_GRCh38.primary_assembly.genome.fa added
1b74cc7f8e7daf_hs37d5.fa.fai added
1b74cc68e5700b_hs37d5.fa.amb added
1b74cc70e1f46c_hs37d5.fa.ann added
1b74cc4797b9f6_hs37d5.fa.bwt added
1b74cc52c3570d_hs37d5.fa.pac added
1b74cc362c7b3e_hs37d5.fa.sa added
1b74cc2c7cb2b5_hs37d5.fa added
1b74cc763e0f92_complete_ref_lens.bin added
1b74cc170eeec2_ctable.bin added
1b74cc331fb9e_ctg_offsets.bin added
1b74cc24eb130d_duplicate_clusters.tsv added
1b74cc56b2459_info.json added
1b74cc6b909f58_mphf.bin added
1b74cc35a52f1b_pos.bin added
1b74cc39587c2c_pre_indexing.log added
1b74cc489eb431_rank.bin added
1b74cc2cf7c9c7_ref_indexing.log added
1b74cc794ea578_refAccumLengths.bin added
1b74cc545b1b54_reflengths.bin added
1b74cc30df66f6_refseq.bin added
1b74cc7da2cc5e_seq.bin added
1b74cc241a323f_versionInfo.json added
1b74cc39a0ccff_salmon_index added
1b74cc7fa48497_chrLength.txt added
1b74cc56e6853a_chrName.txt added
1b74cc3bac8ffe_chrNameLength.txt added
1b74cc91d54a2_chrStart.txt added
1b74cc5cdfae55_exonGeTrInfo.tab added
1b74cc7d5c06a4_exonInfo.tab added
1b74cc3984cf56_geneInfo.tab added
1b74cc1c706789_Genome added
1b74cc7cea8453_genomeParameters.txt added
1b74cc226a3f61_Log.out added
1b74ccd525bf5_SA added
1b74cc44823e49_SAindex added
1b74cc752d966e_sjdbInfo.txt added
1b74cc437ed734_sjdbList.fromGTF.out.tab added
1b74cc70fef0fe_sjdbList.out.tab added
1b74cc6b6ba600_transcriptInfo.tab added
1b74cc5a8dc5f6_GRCh38.GENCODE.v42_100 added
1b74cc7430ec9c_knownGene_hg38.sql added
1b74cc1056b90d_knownGene_hg38.txt added
1b74cc5ff8ea50_refGene_hg38.sql added
1b74cc5fc18bf4_refGene_hg38.txt added
1b74cc45fbe828_knownGene_mm39.sql added
1b74cc1951667c_knownGene_mm39.txt added
1b74cc28604026_refGene_mm39.sql added
1b74cc72f3b1f0_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/RtmpXwImR0/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
18.861 1.812 21.646
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.774 | 0.254 | 6.033 | |
| dataSearch | 1.14 | 0.02 | 1.16 | |
| dataUpdate | 0.001 | 0.000 | 0.000 | |
| getCloudData | 2.657 | 0.081 | 3.729 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.128 | 0.016 | 0.145 | |
| recipeLoad | 1.310 | 0.023 | 1.334 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.539 | 0.006 | 0.546 | |
| recipeUpdate | 0 | 0 | 0 | |