Qian Liu
| Snapshot Date: 2026-02-26 13:45 -0500 (Thu, 26 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 2026-02-27 11:58 -0500 (Fri, 27 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" | 4891 |
| 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: 2026-02-27 03:11:31 -0500 (Fri, 27 Feb 2026) |
| EndedAt: 2026-02-27 03:14:16 -0500 (Fri, 27 Feb 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 24.04.3 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 5.903 0.252 6.161
* 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...
3bcc521d4e4b7b_GRCh38.primary_assembly.genome.fa.1.bt2 added
3bcc523a19e121_GRCh38.primary_assembly.genome.fa.2.bt2 added
3bcc5220f43290_GRCh38.primary_assembly.genome.fa.3.bt2 added
3bcc52454609f1_GRCh38.primary_assembly.genome.fa.4.bt2 added
3bcc522d83ba16_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3bcc52519081cd_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3bcc523d421f9d_outfile.txt added
3bcc527efd0452_GRCh37_to_GRCh38.chain added
3bcc526ebc1b00_GRCh37_to_NCBI34.chain added
3bcc5254bc3344_GRCh37_to_NCBI35.chain added
3bcc52350e580a_GRCh37_to_NCBI36.chain added
3bcc523d6d6189_GRCh38_to_GRCh37.chain added
3bcc521dff6472_GRCh38_to_NCBI34.chain added
3bcc52518b6f4d_GRCh38_to_NCBI35.chain added
3bcc5221d7dc6a_GRCh38_to_NCBI36.chain added
3bcc527bcebd24_NCBI34_to_GRCh37.chain added
3bcc5227656bdc_NCBI34_to_GRCh38.chain added
3bcc523475c3a1_NCBI35_to_GRCh37.chain added
3bcc5286a802b_NCBI35_to_GRCh38.chain added
3bcc5247caeb84_NCBI36_to_GRCh37.chain added
3bcc5275fb8dd7_NCBI36_to_GRCh38.chain added
3bcc5217dc6788_GRCm38_to_NCBIM36.chain added
3bcc526ff0d01d_GRCm38_to_NCBIM37.chain added
3bcc52687f8874_NCBIM36_to_GRCm38.chain added
3bcc524fd6852f_NCBIM37_to_GRCm38.chain added
3bcc524105142_1000G_omni2.5.b37.vcf.gz added
3bcc526dad77b4_1000G_omni2.5.b37.vcf.gz.tbi added
3bcc526b4bbc4d_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3bcc52697a89bd_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3bcc52488e76c5_1000G_omni2.5.hg38.vcf.gz added
3bcc5219928253_1000G_omni2.5.hg38.vcf.gz.tbi added
3bcc526c8d538_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3bcc522a857e7_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3bcc523a86b4e3_af-only-gnomad.raw.sites.vcf added
3bcc524c0edf29_af-only-gnomad.raw.sites.vcf.idx added
3bcc52302c11fd_Mutect2-exome-panel.vcf.idx added
3bcc52c1736b1_Mutect2-WGS-panel-b37.vcf added
3bcc52950fec6_Mutect2-WGS-panel-b37.vcf.idx added
3bcc522f291650_small_exac_common_3.vcf added
3bcc527ad351b1_small_exac_common_3.vcf.idx added
3bcc525e0d320a_1000g_pon.hg38.vcf.gz added
3bcc5264376e5a_1000g_pon.hg38.vcf.gz.tbi added
3bcc523840b33a_af-only-gnomad.hg38.vcf.gz added
3bcc527c0c967d_af-only-gnomad.hg38.vcf.gz.tbi added
3bcc5235c2dda7_small_exac_common_3.hg38.vcf.gz added
3bcc525a188fa4_small_exac_common_3.hg38.vcf.gz.tbi added
3bcc5277db53a1_gencode.v41.annotation.gtf added
3bcc525d284983_gencode.v42.annotation.gtf added
3bcc52e8e5346_gencode.vM30.annotation.gtf added
3bcc5245d3cd_gencode.vM31.annotation.gtf added
3bcc5224f33508_gencode.v41.transcripts.fa added
3bcc52489e11d_gencode.v41.transcripts.fa.fai added
3bcc5218223b55_gencode.v42.transcripts.fa added
3bcc5214e40525_gencode.v42.transcripts.fa.fai added
3bcc526d096992_gencode.vM30.pc_transcripts.fa added
3bcc5267f8c084_gencode.vM30.pc_transcripts.fa.fai added
3bcc5218f45667_gencode.vM31.pc_transcripts.fa added
3bcc525ab6e146_gencode.vM31.pc_transcripts.fa.fai added
3bcc5253447cd2_GRCh38.primary_assembly.genome.fa.1.ht2 added
3bcc5226ee024_GRCh38.primary_assembly.genome.fa.2.ht2 added
3bcc522345580b_GRCh38.primary_assembly.genome.fa.3.ht2 added
3bcc526cd6ff25_GRCh38.primary_assembly.genome.fa.4.ht2 added
3bcc52937b55d_GRCh38.primary_assembly.genome.fa.5.ht2 added
3bcc5225edaff2_GRCh38.primary_assembly.genome.fa.6.ht2 added
3bcc52275db408_GRCh38.primary_assembly.genome.fa.7.ht2 added
3bcc5255469486_GRCh38.primary_assembly.genome.fa.8.ht2 added
3bcc525619c1f0_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3bcc523374eab9_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3bcc525e97934d_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3bcc52542d840_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3bcc522e483c6a_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3bcc523ca4c557_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3bcc52697a469a_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3bcc526688efa4_GRCh38.primary_assembly.genome.fa.fai added
3bcc5238b15bd4_GRCh38.primary_assembly.genome.fa.amb added
3bcc521f3d2441_GRCh38.primary_assembly.genome.fa.ann added
3bcc5240a17f49_GRCh38.primary_assembly.genome.fa.bwt added
3bcc52308caf76_GRCh38.primary_assembly.genome.fa.pac added
3bcc527c656dc5_GRCh38.primary_assembly.genome.fa.sa added
3bcc524f2fd28f_GRCh38.primary_assembly.genome.fa added
3bcc5230d28343_hs37d5.fa.fai added
3bcc522158a2cd_hs37d5.fa.amb added
3bcc5253b9b3ac_hs37d5.fa.ann added
3bcc5248f4be98_hs37d5.fa.bwt added
3bcc52363ca7f2_hs37d5.fa.pac added
3bcc5240c31d3e_hs37d5.fa.sa added
3bcc5230ed7f1d_hs37d5.fa added
3bcc524f30fe59_complete_ref_lens.bin added
3bcc521b79fe84_ctable.bin added
3bcc52431fbef_ctg_offsets.bin added
3bcc52519fde7e_duplicate_clusters.tsv added
3bcc523ebf5690_info.json added
3bcc527108fb14_mphf.bin added
3bcc525ad793db_pos.bin added
3bcc5264ad0682_pre_indexing.log added
3bcc521866af1c_rank.bin added
3bcc52301e2861_ref_indexing.log added
3bcc523ac6c872_refAccumLengths.bin added
3bcc524bdb99d6_reflengths.bin added
3bcc52eb5bbae_refseq.bin added
3bcc524009a0b2_seq.bin added
3bcc527a23d640_versionInfo.json added
3bcc524b5a8106_salmon_index added
3bcc522983e74c_chrLength.txt added
3bcc5260acc5e5_chrName.txt added
3bcc5240bdcda_chrNameLength.txt added
3bcc5248c10b8e_chrStart.txt added
3bcc52214e452e_exonGeTrInfo.tab added
3bcc5234988c50_exonInfo.tab added
3bcc5245267953_geneInfo.tab added
3bcc52707e17bd_Genome added
3bcc52656b0f93_genomeParameters.txt added
3bcc52667f1c20_Log.out added
3bcc524437cb69_SA added
3bcc522e5fce2c_SAindex added
3bcc521cbbc412_sjdbInfo.txt added
3bcc524fae8a8_sjdbList.fromGTF.out.tab added
3bcc525f4d4d49_sjdbList.out.tab added
3bcc526becc26b_transcriptInfo.tab added
3bcc522074e72c_GRCh38.GENCODE.v42_100 added
3bcc52637f4938_knownGene_hg38.sql added
3bcc523d8ca0e9_knownGene_hg38.txt added
3bcc525f343dbc_refGene_hg38.sql added
3bcc525488444c_refGene_hg38.txt added
3bcc52186434c4_knownGene_mm39.sql added
3bcc5243e1443f_knownGene_mm39.txt added
3bcc526ceef368_refGene_mm39.sql added
3bcc5248825d26_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/RtmpKjEQtv/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
18.052 1.001 19.516
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.903 | 0.252 | 6.161 | |
| dataSearch | 1.129 | 0.028 | 1.157 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.784 | 0.176 | 4.109 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0 | 0 | 0 | |
| recipeHub-class | 0.124 | 0.000 | 0.125 | |
| recipeLoad | 1.266 | 0.058 | 1.325 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.545 | 0.019 | 0.565 | |
| recipeUpdate | 0 | 0 | 0 | |