Qian Liu
| Snapshot Date: 2026-02-05 13:45 -0500 (Thu, 05 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 2026-02-09 11:58 -0500 (Mon, 09 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" | 4888 |
| 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: 2026-02-06 03:12:19 -0500 (Fri, 06 Feb 2026) |
| EndedAt: 2026-02-06 03:15:02 -0500 (Fri, 06 Feb 2026) |
| EllapsedTime: 162.2 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 5.594 0.237 5.835
* 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...
6577f323b1e9c_GRCh38.primary_assembly.genome.fa.1.bt2 added
6577f6a2341ec_GRCh38.primary_assembly.genome.fa.2.bt2 added
6577f43d22276_GRCh38.primary_assembly.genome.fa.3.bt2 added
6577f4ac8382_GRCh38.primary_assembly.genome.fa.4.bt2 added
6577f2cec798f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
6577f2ded055c_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
6577f2e6334ec_outfile.txt added
6577f666be969_GRCh37_to_GRCh38.chain added
6577f48ccf6f9_GRCh37_to_NCBI34.chain added
6577f3543188a_GRCh37_to_NCBI35.chain added
6577f9019017_GRCh37_to_NCBI36.chain added
6577f2c0870d1_GRCh38_to_GRCh37.chain added
6577f7988a67f_GRCh38_to_NCBI34.chain added
6577f79169a6_GRCh38_to_NCBI35.chain added
6577f6ad113a9_GRCh38_to_NCBI36.chain added
6577f502e55d9_NCBI34_to_GRCh37.chain added
6577f4b3ee5c0_NCBI34_to_GRCh38.chain added
6577f54924a79_NCBI35_to_GRCh37.chain added
6577f4b3451b4_NCBI35_to_GRCh38.chain added
6577f6bb4ddb_NCBI36_to_GRCh37.chain added
6577f46b0e6d4_NCBI36_to_GRCh38.chain added
6577f156cf55c_GRCm38_to_NCBIM36.chain added
6577f3322edd1_GRCm38_to_NCBIM37.chain added
6577f747fc901_NCBIM36_to_GRCm38.chain added
6577f3dc87753_NCBIM37_to_GRCm38.chain added
6577f13303f91_1000G_omni2.5.b37.vcf.gz added
6577ffa64657_1000G_omni2.5.b37.vcf.gz.tbi added
6577f3a8f1a9a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
6577f64e3527b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
6577f7f5f9e4d_1000G_omni2.5.hg38.vcf.gz added
6577f7d080825_1000G_omni2.5.hg38.vcf.gz.tbi added
6577f171e7117_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
6577f6982e039_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
6577f40da2a9b_af-only-gnomad.raw.sites.vcf added
6577f1bcaf49a_af-only-gnomad.raw.sites.vcf.idx added
6577f166f59c8_Mutect2-exome-panel.vcf.idx added
6577f6ec72ff7_Mutect2-WGS-panel-b37.vcf added
6577f4a2e2986_Mutect2-WGS-panel-b37.vcf.idx added
6577f7cdb4331_small_exac_common_3.vcf added
6577f379426f0_small_exac_common_3.vcf.idx added
6577f7f714210_1000g_pon.hg38.vcf.gz added
6577f5dcd349_1000g_pon.hg38.vcf.gz.tbi added
6577f639c97c1_af-only-gnomad.hg38.vcf.gz added
6577f78f9e88f_af-only-gnomad.hg38.vcf.gz.tbi added
6577fd6e3cef_small_exac_common_3.hg38.vcf.gz added
6577f4e6dab6a_small_exac_common_3.hg38.vcf.gz.tbi added
6577f49283e68_gencode.v41.annotation.gtf added
6577f58ad22b0_gencode.v42.annotation.gtf added
6577f22fff5e3_gencode.vM30.annotation.gtf added
6577f145c901c_gencode.vM31.annotation.gtf added
6577f5f68708b_gencode.v41.transcripts.fa added
6577f69b0dcb7_gencode.v41.transcripts.fa.fai added
6577f29c98579_gencode.v42.transcripts.fa added
6577f128b5e5c_gencode.v42.transcripts.fa.fai added
6577f5e30a5b9_gencode.vM30.pc_transcripts.fa added
6577f6791fccc_gencode.vM30.pc_transcripts.fa.fai added
6577f25bb9ded_gencode.vM31.pc_transcripts.fa added
6577f6dd6ec10_gencode.vM31.pc_transcripts.fa.fai added
6577f22211766_GRCh38.primary_assembly.genome.fa.1.ht2 added
6577fa9ef069_GRCh38.primary_assembly.genome.fa.2.ht2 added
6577f6d368a5d_GRCh38.primary_assembly.genome.fa.3.ht2 added
6577f1f291f8b_GRCh38.primary_assembly.genome.fa.4.ht2 added
6577f21bd6180_GRCh38.primary_assembly.genome.fa.5.ht2 added
6577f56b96a97_GRCh38.primary_assembly.genome.fa.6.ht2 added
6577f60034a26_GRCh38.primary_assembly.genome.fa.7.ht2 added
6577f3d88561a_GRCh38.primary_assembly.genome.fa.8.ht2 added
6577f6d28c45f_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
6577f4eca7a1d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
6577f7b67fa0_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
6577f6a040791_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
6577f65ea10d_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
6577f727c1b0_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
6577f6fe0dada_GRCh38_full_analysis_set_plus_decoy_hla.fa added
6577f69fb38cf_GRCh38.primary_assembly.genome.fa.fai added
6577f21aa3f_GRCh38.primary_assembly.genome.fa.amb added
6577f7d4f17c9_GRCh38.primary_assembly.genome.fa.ann added
6577f3868e439_GRCh38.primary_assembly.genome.fa.bwt added
6577f4949e8a8_GRCh38.primary_assembly.genome.fa.pac added
6577f55fc3a79_GRCh38.primary_assembly.genome.fa.sa added
6577f5b68da1d_GRCh38.primary_assembly.genome.fa added
6577f5da678c4_hs37d5.fa.fai added
6577f3564ab04_hs37d5.fa.amb added
6577f4519b6d4_hs37d5.fa.ann added
6577f76ffe3d_hs37d5.fa.bwt added
6577f47f00960_hs37d5.fa.pac added
6577f234a5c8d_hs37d5.fa.sa added
6577f6f01fb09_hs37d5.fa added
6577f6daba74e_complete_ref_lens.bin added
6577f1121489d_ctable.bin added
6577f1123126f_ctg_offsets.bin added
6577f784a97b7_duplicate_clusters.tsv added
6577f7e57d2fb_info.json added
6577f304c31fa_mphf.bin added
6577f1a07f937_pos.bin added
6577f55113d92_pre_indexing.log added
6577f104f7c20_rank.bin added
6577f57904f52_ref_indexing.log added
6577f423a01f1_refAccumLengths.bin added
6577f5f19f63d_reflengths.bin added
6577f5f46cef2_refseq.bin added
6577f2c3e0982_seq.bin added
6577f6578974b_versionInfo.json added
6577f666e90a3_salmon_index added
6577f1c1ee45c_chrLength.txt added
6577f4f73d01a_chrName.txt added
6577f66903ae2_chrNameLength.txt added
6577f196dfc26_chrStart.txt added
6577f7dcb453_exonGeTrInfo.tab added
6577f2fda238a_exonInfo.tab added
6577f6f6a369f_geneInfo.tab added
6577f63458e70_Genome added
6577fd809c4f_genomeParameters.txt added
6577f24cee1a4_Log.out added
6577f285f4545_SA added
6577f14f09a8c_SAindex added
6577f6cbeeb04_sjdbInfo.txt added
6577f4ba9a1d2_sjdbList.fromGTF.out.tab added
6577f3f29596_sjdbList.out.tab added
6577f5a6a9252_transcriptInfo.tab added
6577f5ccaea70_GRCh38.GENCODE.v42_100 added
6577f1515a805_knownGene_hg38.sql added
6577f52b52a09_knownGene_hg38.txt added
6577f5b22bd6b_refGene_hg38.sql added
6577f4561da00_refGene_hg38.txt added
6577f6cbd2341_knownGene_mm39.sql added
6577f3033fafd_knownGene_mm39.txt added
6577f55b15620_refGene_mm39.sql added
6577f444d7293_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/Rtmp5AD6gm/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
18.200 1.881 20.581
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.594 | 0.237 | 5.835 | |
| dataSearch | 1.093 | 0.004 | 1.097 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.603 | 0.092 | 3.514 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.122 | 0.000 | 0.123 | |
| recipeLoad | 1.229 | 0.012 | 1.240 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.528 | 0.008 | 0.536 | |
| recipeUpdate | 0 | 0 | 0 | |