Qian Liu
| Snapshot Date: 2026-02-23 13:40 -0500 (Mon, 23 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 2026-02-24 11:32 -0500 (Tue, 24 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" | 4872 |
| 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: 2026-02-24 03:21:12 -0500 (Tue, 24 Feb 2026) |
| EndedAt: 2026-02-24 03:23:56 -0500 (Tue, 24 Feb 2026) |
| EllapsedTime: 163.4 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 5.832 0.32 6.155
* 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...
1d26f425be1c10_GRCh38.primary_assembly.genome.fa.1.bt2 added
1d26f43dcb07cd_GRCh38.primary_assembly.genome.fa.2.bt2 added
1d26f4698520e5_GRCh38.primary_assembly.genome.fa.3.bt2 added
1d26f41cb5445b_GRCh38.primary_assembly.genome.fa.4.bt2 added
1d26f437866eb2_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1d26f43ea7abc5_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1d26f42c2b7c72_outfile.txt added
1d26f43e429ce8_GRCh37_to_GRCh38.chain added
1d26f4285776fd_GRCh37_to_NCBI34.chain added
1d26f4ead4923_GRCh37_to_NCBI35.chain added
1d26f44bfaead1_GRCh37_to_NCBI36.chain added
1d26f42a902b00_GRCh38_to_GRCh37.chain added
1d26f45875f0a1_GRCh38_to_NCBI34.chain added
1d26f47d456803_GRCh38_to_NCBI35.chain added
1d26f49fd5e21_GRCh38_to_NCBI36.chain added
1d26f4537a11cf_NCBI34_to_GRCh37.chain added
1d26f45b790bcd_NCBI34_to_GRCh38.chain added
1d26f46205beb1_NCBI35_to_GRCh37.chain added
1d26f4ef991eb_NCBI35_to_GRCh38.chain added
1d26f44fcb96ca_NCBI36_to_GRCh37.chain added
1d26f41d2bc381_NCBI36_to_GRCh38.chain added
1d26f453731aa2_GRCm38_to_NCBIM36.chain added
1d26f4425915f3_GRCm38_to_NCBIM37.chain added
1d26f41f3b0427_NCBIM36_to_GRCm38.chain added
1d26f443de013e_NCBIM37_to_GRCm38.chain added
1d26f4531f642_1000G_omni2.5.b37.vcf.gz added
1d26f430773796_1000G_omni2.5.b37.vcf.gz.tbi added
1d26f4472235b6_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1d26f433a5742b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1d26f4454f414a_1000G_omni2.5.hg38.vcf.gz added
1d26f42e32306d_1000G_omni2.5.hg38.vcf.gz.tbi added
1d26f45963903b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1d26f431a4918_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1d26f417b75153_af-only-gnomad.raw.sites.vcf added
1d26f47618d496_af-only-gnomad.raw.sites.vcf.idx added
1d26f43aa0b7ca_Mutect2-exome-panel.vcf.idx added
1d26f4565efd18_Mutect2-WGS-panel-b37.vcf added
1d26f422445108_Mutect2-WGS-panel-b37.vcf.idx added
1d26f478e354b3_small_exac_common_3.vcf added
1d26f47eb67415_small_exac_common_3.vcf.idx added
1d26f430f19a2b_1000g_pon.hg38.vcf.gz added
1d26f444de3f84_1000g_pon.hg38.vcf.gz.tbi added
1d26f429469f16_af-only-gnomad.hg38.vcf.gz added
1d26f49678acc_af-only-gnomad.hg38.vcf.gz.tbi added
1d26f44223a787_small_exac_common_3.hg38.vcf.gz added
1d26f43343fd37_small_exac_common_3.hg38.vcf.gz.tbi added
1d26f45ce19c9c_gencode.v41.annotation.gtf added
1d26f41d9cb354_gencode.v42.annotation.gtf added
1d26f41549bbe8_gencode.vM30.annotation.gtf added
1d26f46bdb2e87_gencode.vM31.annotation.gtf added
1d26f46d684a1e_gencode.v41.transcripts.fa added
1d26f432757f69_gencode.v41.transcripts.fa.fai added
1d26f43f4e492a_gencode.v42.transcripts.fa added
1d26f42fc16012_gencode.v42.transcripts.fa.fai added
1d26f451b08390_gencode.vM30.pc_transcripts.fa added
1d26f432c4a68_gencode.vM30.pc_transcripts.fa.fai added
1d26f434f35654_gencode.vM31.pc_transcripts.fa added
1d26f4227bb26_gencode.vM31.pc_transcripts.fa.fai added
1d26f44a4e801e_GRCh38.primary_assembly.genome.fa.1.ht2 added
1d26f46898ca7f_GRCh38.primary_assembly.genome.fa.2.ht2 added
1d26f44776fc71_GRCh38.primary_assembly.genome.fa.3.ht2 added
1d26f47880b08b_GRCh38.primary_assembly.genome.fa.4.ht2 added
1d26f441fc5aba_GRCh38.primary_assembly.genome.fa.5.ht2 added
1d26f44a914589_GRCh38.primary_assembly.genome.fa.6.ht2 added
1d26f4103801de_GRCh38.primary_assembly.genome.fa.7.ht2 added
1d26f438152f50_GRCh38.primary_assembly.genome.fa.8.ht2 added
1d26f4531fd53_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1d26f46696fef6_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1d26f45a598059_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1d26f47e155206_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1d26f4654d730c_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1d26f4b4b1a84_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1d26f442f3918a_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1d26f4e941222_GRCh38.primary_assembly.genome.fa.fai added
1d26f414b2a551_GRCh38.primary_assembly.genome.fa.amb added
1d26f45173911_GRCh38.primary_assembly.genome.fa.ann added
1d26f441d80f59_GRCh38.primary_assembly.genome.fa.bwt added
1d26f4719441ed_GRCh38.primary_assembly.genome.fa.pac added
1d26f422b3ec66_GRCh38.primary_assembly.genome.fa.sa added
1d26f45721cb41_GRCh38.primary_assembly.genome.fa added
1d26f45d6f7074_hs37d5.fa.fai added
1d26f4101c3684_hs37d5.fa.amb added
1d26f49974aaa_hs37d5.fa.ann added
1d26f41cbdb99e_hs37d5.fa.bwt added
1d26f43fdd9696_hs37d5.fa.pac added
1d26f45b47ce3a_hs37d5.fa.sa added
1d26f41fea0406_hs37d5.fa added
1d26f474d0eceb_complete_ref_lens.bin added
1d26f45d6f8960_ctable.bin added
1d26f46a388424_ctg_offsets.bin added
1d26f45d69b76a_duplicate_clusters.tsv added
1d26f424e685d1_info.json added
1d26f462b934b0_mphf.bin added
1d26f41f661225_pos.bin added
1d26f46f77cb5a_pre_indexing.log added
1d26f472f1368e_rank.bin added
1d26f4577b4175_ref_indexing.log added
1d26f474a9c8ae_refAccumLengths.bin added
1d26f459883585_reflengths.bin added
1d26f431d4c1ce_refseq.bin added
1d26f472bf1ab4_seq.bin added
1d26f43ed5a891_versionInfo.json added
1d26f43d1fdc53_salmon_index added
1d26f435b2ac3f_chrLength.txt added
1d26f44d69bab3_chrName.txt added
1d26f451d281a4_chrNameLength.txt added
1d26f43ac9e550_chrStart.txt added
1d26f4f41ca0c_exonGeTrInfo.tab added
1d26f44366c391_exonInfo.tab added
1d26f45d7dd1b6_geneInfo.tab added
1d26f46663954d_Genome added
1d26f420d63405_genomeParameters.txt added
1d26f46d9a083b_Log.out added
1d26f46ffadff7_SA added
1d26f43d93eda4_SAindex added
1d26f42d779ed1_sjdbInfo.txt added
1d26f44b42ae31_sjdbList.fromGTF.out.tab added
1d26f45d7df1aa_sjdbList.out.tab added
1d26f422488bbc_transcriptInfo.tab added
1d26f428b23791_GRCh38.GENCODE.v42_100 added
1d26f447b675cf_knownGene_hg38.sql added
1d26f47fb24327_knownGene_hg38.txt added
1d26f44d98bd63_refGene_hg38.sql added
1d26f42a6faa7f_refGene_hg38.txt added
1d26f41f18554c_knownGene_mm39.sql added
1d26f43d1088bd_knownGene_mm39.txt added
1d26f41d60e10d_refGene_mm39.sql added
1d26f4769396c1_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/RtmpzxIhL3/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
17.758 1.123 19.248
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.832 | 0.320 | 6.155 | |
| dataSearch | 1.090 | 0.023 | 1.113 | |
| dataUpdate | 0.001 | 0.001 | 0.001 | |
| getCloudData | 2.540 | 0.114 | 3.307 | |
| getData | 0.001 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.125 | 0.002 | 0.128 | |
| recipeLoad | 1.262 | 0.087 | 1.350 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.524 | 0.030 | 0.555 | |
| recipeUpdate | 0 | 0 | 0 | |