Qian Liu
| Snapshot Date: 2026-01-29 13:40 -0500 (Thu, 29 Jan 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 2026-01-30 13:21 -0500 (Fri, 30 Jan 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" | 4852 |
| 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 1766/2347 | 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: 2026-01-30 03:17:09 -0500 (Fri, 30 Jan 2026) |
| EndedAt: 2026-01-30 03:19:54 -0500 (Fri, 30 Jan 2026) |
| EllapsedTime: 164.4 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 5.813 0.362 6.177
* 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...
2d6a6b7345c95e_GRCh38.primary_assembly.genome.fa.1.bt2 added
2d6a6b70127b9f_GRCh38.primary_assembly.genome.fa.2.bt2 added
2d6a6b6b2be0bd_GRCh38.primary_assembly.genome.fa.3.bt2 added
2d6a6b38a9e1e8_GRCh38.primary_assembly.genome.fa.4.bt2 added
2d6a6ba6149a1_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2d6a6b3c3bb57f_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2d6a6b157ffc62_outfile.txt added
2d6a6b67455087_GRCh37_to_GRCh38.chain added
2d6a6b3ea09d4a_GRCh37_to_NCBI34.chain added
2d6a6b23e4960d_GRCh37_to_NCBI35.chain added
2d6a6b63684ab6_GRCh37_to_NCBI36.chain added
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2d6a6bf670aa9_NCBI34_to_GRCh37.chain added
2d6a6b23882fb8_NCBI34_to_GRCh38.chain added
2d6a6b514b835b_NCBI35_to_GRCh37.chain added
2d6a6b3a2e3564_NCBI35_to_GRCh38.chain added
2d6a6b704581ea_NCBI36_to_GRCh37.chain added
2d6a6b2ecda03c_NCBI36_to_GRCh38.chain added
2d6a6b78f9e360_GRCm38_to_NCBIM36.chain added
2d6a6b3cdf4715_GRCm38_to_NCBIM37.chain added
2d6a6b10ec1374_NCBIM36_to_GRCm38.chain added
2d6a6b1524d6a1_NCBIM37_to_GRCm38.chain added
2d6a6b691f6a6f_1000G_omni2.5.b37.vcf.gz added
2d6a6b5db8bf1a_1000G_omni2.5.b37.vcf.gz.tbi added
2d6a6b9a82979_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2d6a6be247913_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2d6a6b3b76760a_1000G_omni2.5.hg38.vcf.gz added
2d6a6b7301f68b_1000G_omni2.5.hg38.vcf.gz.tbi added
2d6a6b16a4271_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2d6a6b2b88f1aa_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2d6a6b5e2dd748_af-only-gnomad.raw.sites.vcf added
2d6a6b3a14245a_af-only-gnomad.raw.sites.vcf.idx added
2d6a6b35ea3b4b_Mutect2-exome-panel.vcf.idx added
2d6a6b1a698cc8_Mutect2-WGS-panel-b37.vcf added
2d6a6b4f9420bc_Mutect2-WGS-panel-b37.vcf.idx added
2d6a6b1d2f8bd3_small_exac_common_3.vcf added
2d6a6b590a2a12_small_exac_common_3.vcf.idx added
2d6a6b7378b6c9_1000g_pon.hg38.vcf.gz added
2d6a6b97d689_1000g_pon.hg38.vcf.gz.tbi added
2d6a6b6093b4f4_af-only-gnomad.hg38.vcf.gz added
2d6a6b3ba1e58c_af-only-gnomad.hg38.vcf.gz.tbi added
2d6a6b218ec8a2_small_exac_common_3.hg38.vcf.gz added
2d6a6b7046e6a1_small_exac_common_3.hg38.vcf.gz.tbi added
2d6a6b4b08f035_gencode.v41.annotation.gtf added
2d6a6b4516f85a_gencode.v42.annotation.gtf added
2d6a6b419269fc_gencode.vM30.annotation.gtf added
2d6a6b5372599_gencode.vM31.annotation.gtf added
2d6a6b355c7a44_gencode.v41.transcripts.fa added
2d6a6b70600a39_gencode.v41.transcripts.fa.fai added
2d6a6b7e3108fa_gencode.v42.transcripts.fa added
2d6a6b723bc159_gencode.v42.transcripts.fa.fai added
2d6a6b14c1dad_gencode.vM30.pc_transcripts.fa added
2d6a6b1355df9b_gencode.vM30.pc_transcripts.fa.fai added
2d6a6b5b5b2bc8_gencode.vM31.pc_transcripts.fa added
2d6a6b5f04dcc7_gencode.vM31.pc_transcripts.fa.fai added
2d6a6b1cfe0915_GRCh38.primary_assembly.genome.fa.1.ht2 added
2d6a6b697fa4db_GRCh38.primary_assembly.genome.fa.2.ht2 added
2d6a6b1a7b52d2_GRCh38.primary_assembly.genome.fa.3.ht2 added
2d6a6bfffffa0_GRCh38.primary_assembly.genome.fa.4.ht2 added
2d6a6b6ae9e74d_GRCh38.primary_assembly.genome.fa.5.ht2 added
2d6a6b4604447c_GRCh38.primary_assembly.genome.fa.6.ht2 added
2d6a6b6e2dd6e8_GRCh38.primary_assembly.genome.fa.7.ht2 added
2d6a6b24fe0ba7_GRCh38.primary_assembly.genome.fa.8.ht2 added
2d6a6b7bee7fc7_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2d6a6b89763b0_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2d6a6b74922c63_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2d6a6b191e0b9a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2d6a6b61a18dc3_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2d6a6b680ae32d_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2d6a6b19b5e223_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2d6a6b423542b7_GRCh38.primary_assembly.genome.fa.fai added
2d6a6b23acc8b9_GRCh38.primary_assembly.genome.fa.amb added
2d6a6b3b44aac5_GRCh38.primary_assembly.genome.fa.ann added
2d6a6b327c2958_GRCh38.primary_assembly.genome.fa.bwt added
2d6a6b6eb5b8ef_GRCh38.primary_assembly.genome.fa.pac added
2d6a6b5ba31f_GRCh38.primary_assembly.genome.fa.sa added
2d6a6b740e9355_GRCh38.primary_assembly.genome.fa added
2d6a6b73ecde88_hs37d5.fa.fai added
2d6a6b35b81d63_hs37d5.fa.amb added
2d6a6b646e9d8e_hs37d5.fa.ann added
2d6a6b721de782_hs37d5.fa.bwt added
2d6a6b27f3debd_hs37d5.fa.pac added
2d6a6b65babb3b_hs37d5.fa.sa added
2d6a6b573c71e_hs37d5.fa added
2d6a6b34f0a85_complete_ref_lens.bin added
2d6a6b44bf9802_ctable.bin added
2d6a6b2271d033_ctg_offsets.bin added
2d6a6b6cceaf61_duplicate_clusters.tsv added
2d6a6b5f3aead4_info.json added
2d6a6b3271cfd3_mphf.bin added
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2d6a6b253f2f50_pre_indexing.log added
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2d6a6b212daf18_refAccumLengths.bin added
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2d6a6b7148ceb8_refseq.bin added
2d6a6b3a4bbab2_seq.bin added
2d6a6bad8982f_versionInfo.json added
2d6a6b5953b1e5_salmon_index added
2d6a6b54019cd6_chrLength.txt added
2d6a6b4d0ddae6_chrName.txt added
2d6a6b7d007a9f_chrNameLength.txt added
2d6a6bf46479b_chrStart.txt added
2d6a6b7f8a043e_exonGeTrInfo.tab added
2d6a6b6bb6338e_exonInfo.tab added
2d6a6bfa1eabb_geneInfo.tab added
2d6a6b73989793_Genome added
2d6a6b5fa31216_genomeParameters.txt added
2d6a6b455a081e_Log.out added
2d6a6b58073521_SA added
2d6a6b51c0f999_SAindex added
2d6a6b6d4de6db_sjdbInfo.txt added
2d6a6b3dc1f05c_sjdbList.fromGTF.out.tab added
2d6a6b5734c0b7_sjdbList.out.tab added
2d6a6b709cf161_transcriptInfo.tab added
2d6a6b281885f_GRCh38.GENCODE.v42_100 added
2d6a6b79a690ea_knownGene_hg38.sql added
2d6a6b5d6ba0c2_knownGene_hg38.txt added
2d6a6b61bc7333_refGene_hg38.sql added
2d6a6b2c1860bd_refGene_hg38.txt added
2d6a6b35243770_knownGene_mm39.sql added
2d6a6b6fba284_knownGene_mm39.txt added
2d6a6b4cb80778_refGene_mm39.sql added
2d6a6b31dad9c5_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/RtmpBZJwLd/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
17.624 1.187 19.674
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.813 | 0.362 | 6.177 | |
| dataSearch | 1.114 | 0.036 | 1.151 | |
| dataUpdate | 0.001 | 0.000 | 0.001 | |
| getCloudData | 2.577 | 0.114 | 3.733 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.122 | 0.018 | 0.140 | |
| recipeLoad | 1.262 | 0.084 | 1.347 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.526 | 0.011 | 0.537 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |