Qian Liu
| Snapshot Date: 2026-02-12 13:45 -0500 (Thu, 12 Feb 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 2026-02-16 11:58 -0500 (Mon, 16 Feb 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" | 4889 |
| 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: 2026-02-13 04:23:59 -0500 (Fri, 13 Feb 2026) |
| EndedAt: 2026-02-13 04:34:19 -0500 (Fri, 13 Feb 2026) |
| EllapsedTime: 620.4 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 24.04.3 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 ...Warning: unable to access index for repository https://bioconductor.org/packages/3.22/bioc/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.22/data/annotation/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/PACKAGES'
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 5.860 0.225 6.091
getCloudData 2.712 0.178 7.924
* 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...
3041935d559990_GRCh38.primary_assembly.genome.fa.1.bt2 added
3041933344938b_GRCh38.primary_assembly.genome.fa.2.bt2 added
3041937a71b95c_GRCh38.primary_assembly.genome.fa.3.bt2 added
3041936a0dee09_GRCh38.primary_assembly.genome.fa.4.bt2 added
30419332967a82_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3041937c69cee0_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
304193185ffa0d_outfile.txt added
3041934f84a09c_GRCh37_to_GRCh38.chain added
3041936d6f595a_GRCh37_to_NCBI34.chain added
3041931749874e_GRCh37_to_NCBI35.chain added
3041931af78008_GRCh37_to_NCBI36.chain added
304193599e04b4_GRCh38_to_GRCh37.chain added
3041934fb8a89e_GRCh38_to_NCBI34.chain added
3041936dcbd9cb_GRCh38_to_NCBI35.chain added
3041936f62aaf5_GRCh38_to_NCBI36.chain added
30419325d35ce0_NCBI34_to_GRCh37.chain added
3041932486ee51_NCBI34_to_GRCh38.chain added
3041931da38c5b_NCBI35_to_GRCh37.chain added
3041933608ec82_NCBI35_to_GRCh38.chain added
30419355835fb8_NCBI36_to_GRCh37.chain added
304193132d615b_NCBI36_to_GRCh38.chain added
304193565f3dff_GRCm38_to_NCBIM36.chain added
30419337018d84_GRCm38_to_NCBIM37.chain added
30419340f03e8c_NCBIM36_to_GRCm38.chain added
30419327790bec_NCBIM37_to_GRCm38.chain added
3041936d98873f_1000G_omni2.5.b37.vcf.gz added
30419355de56f9_1000G_omni2.5.b37.vcf.gz.tbi added
304193173aeac8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
30419366be07a9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3041933ce44ad9_1000G_omni2.5.hg38.vcf.gz added
30419329951c98_1000G_omni2.5.hg38.vcf.gz.tbi added
3041934413a139_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3041937028de64_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3041932406d5f4_af-only-gnomad.raw.sites.vcf added
3041932e218f42_af-only-gnomad.raw.sites.vcf.idx added
30419322bf58e6_Mutect2-exome-panel.vcf.idx added
3041932070a4d4_Mutect2-WGS-panel-b37.vcf added
3041934681894f_Mutect2-WGS-panel-b37.vcf.idx added
3041937243f982_small_exac_common_3.vcf added
304193ddffe2e_small_exac_common_3.vcf.idx added
3041935dcb109e_1000g_pon.hg38.vcf.gz added
304193d3b798a_1000g_pon.hg38.vcf.gz.tbi added
304193677e02e2_af-only-gnomad.hg38.vcf.gz added
3041932d83b93c_af-only-gnomad.hg38.vcf.gz.tbi added
3041937b075356_small_exac_common_3.hg38.vcf.gz added
30419356e0add7_small_exac_common_3.hg38.vcf.gz.tbi added
3041935357161c_gencode.v41.annotation.gtf added
3041931f8e41a7_gencode.v42.annotation.gtf added
30419374843a32_gencode.vM30.annotation.gtf added
304193960029e_gencode.vM31.annotation.gtf added
3041937511a15f_gencode.v41.transcripts.fa added
3041937b19b8d_gencode.v41.transcripts.fa.fai added
3041935fbf409d_gencode.v42.transcripts.fa added
3041932c132ee3_gencode.v42.transcripts.fa.fai added
30419348a1da19_gencode.vM30.pc_transcripts.fa added
3041937384c8a_gencode.vM30.pc_transcripts.fa.fai added
30419319abb622_gencode.vM31.pc_transcripts.fa added
3041931e803113_gencode.vM31.pc_transcripts.fa.fai added
3041931e733752_GRCh38.primary_assembly.genome.fa.1.ht2 added
30419369bdcc_GRCh38.primary_assembly.genome.fa.2.ht2 added
3041935b647bec_GRCh38.primary_assembly.genome.fa.3.ht2 added
304193480853eb_GRCh38.primary_assembly.genome.fa.4.ht2 added
304193447d5f05_GRCh38.primary_assembly.genome.fa.5.ht2 added
3041934b8d5a50_GRCh38.primary_assembly.genome.fa.6.ht2 added
3041936c0f29df_GRCh38.primary_assembly.genome.fa.7.ht2 added
304193729eee48_GRCh38.primary_assembly.genome.fa.8.ht2 added
3041936e4cb336_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
304193c7fceb4_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
30419339207797_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3041936090acb8_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3041931a5fcce2_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
30419316eb8835_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3041936dcc2643_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3041931ddcfc5_GRCh38.primary_assembly.genome.fa.fai added
304193446f4171_GRCh38.primary_assembly.genome.fa.amb added
30419368d37999_GRCh38.primary_assembly.genome.fa.ann added
30419358be7d9c_GRCh38.primary_assembly.genome.fa.bwt added
30419317c6578d_GRCh38.primary_assembly.genome.fa.pac added
304193861bb40_GRCh38.primary_assembly.genome.fa.sa added
3041934d42b7cf_GRCh38.primary_assembly.genome.fa added
30419321265a2b_hs37d5.fa.fai added
3041937d735c9f_hs37d5.fa.amb added
30419354f4535c_hs37d5.fa.ann added
304193e59ac9_hs37d5.fa.bwt added
30419329868b82_hs37d5.fa.pac added
3041931d962d76_hs37d5.fa.sa added
30419381de753_hs37d5.fa added
304193433241a5_complete_ref_lens.bin added
3041933c165e89_ctable.bin added
30419326911ea5_ctg_offsets.bin added
304193439bff71_duplicate_clusters.tsv added
304193177ada75_info.json added
3041936e997290_mphf.bin added
3041938195e76_pos.bin added
304193630834c5_pre_indexing.log added
3041935aa89c70_rank.bin added
3041937ab84cbe_ref_indexing.log added
3041935154e7fb_refAccumLengths.bin added
30419367286b24_reflengths.bin added
30419333d8c456_refseq.bin added
30419331e594b3_seq.bin added
3041931883806_versionInfo.json added
3041934ac44c8b_salmon_index added
3041931fb1baf6_chrLength.txt added
30419336607cb_chrName.txt added
304193f338dfd_chrNameLength.txt added
304193885348f_chrStart.txt added
3041935c248568_exonGeTrInfo.tab added
30419326f9e58a_exonInfo.tab added
30419310e6efcf_geneInfo.tab added
30419329673d37_Genome added
30419348203fb6_genomeParameters.txt added
304193e5a4c6e_Log.out added
3041937e5b9093_SA added
3041934905da7f_SAindex added
30419337e0d7f1_sjdbInfo.txt added
3041931bf1be09_sjdbList.fromGTF.out.tab added
3041935123c1d2_sjdbList.out.tab added
3041937b131996_transcriptInfo.tab added
30419358081c92_GRCh38.GENCODE.v42_100 added
30419377b4e077_knownGene_hg38.sql added
3041933eaf1907_knownGene_hg38.txt added
3041936f82f707_refGene_hg38.sql added
304193664e5308_refGene_hg38.txt added
30419346c8777d_knownGene_mm39.sql added
304193528b2bcc_knownGene_mm39.txt added
30419340f6ef78_refGene_mm39.sql added
3041934180c43c_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/RtmpdTR4Nx/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
18.243 1.426 21.844
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.860 | 0.225 | 6.091 | |
| dataSearch | 1.073 | 0.008 | 1.081 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.712 | 0.178 | 7.924 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.001 | 0.001 | |
| recipeHub-class | 0.123 | 0.010 | 0.134 | |
| recipeLoad | 1.262 | 0.044 | 1.307 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.561 | 0.016 | 0.578 | |
| recipeUpdate | 0 | 0 | 0 | |