Qian Liu
| Snapshot Date: 2026-03-13 13:40 -0400 (Fri, 13 Mar 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 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-14 11:34 -0400 (Sat, 14 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4837 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4050 |
| 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 1777/2361 | 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 | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 2026-03-14 03:08:26 -0400 (Sat, 14 Mar 2026) |
| EndedAt: 2026-03-14 03:11:09 -0400 (Sat, 14 Mar 2026) |
| EllapsedTime: 163.5 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) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-14 07:08:26 UTC
* 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 6.338 0.397 6.74
* 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) (2026-03-05 r89546) -- "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...
2f3c97539ebd0e_GRCh38.primary_assembly.genome.fa.1.bt2 added
2f3c973a8ece03_GRCh38.primary_assembly.genome.fa.2.bt2 added
2f3c977ec9aaf4_GRCh38.primary_assembly.genome.fa.3.bt2 added
2f3c97214d6b0f_GRCh38.primary_assembly.genome.fa.4.bt2 added
2f3c975bf9fd60_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2f3c9753d56ed7_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2f3c972f4509da_outfile.txt added
2f3c9743a9acad_GRCh37_to_GRCh38.chain added
2f3c97455f01d9_GRCh37_to_NCBI34.chain added
2f3c97573e5639_GRCh37_to_NCBI35.chain added
2f3c975b8784fd_GRCh37_to_NCBI36.chain added
2f3c974188151a_GRCh38_to_GRCh37.chain added
2f3c972ab470e3_GRCh38_to_NCBI34.chain added
2f3c97357cb3e2_GRCh38_to_NCBI35.chain added
2f3c97b16a76a_GRCh38_to_NCBI36.chain added
2f3c9736538a15_NCBI34_to_GRCh37.chain added
2f3c977f3bce76_NCBI34_to_GRCh38.chain added
2f3c975515d8e3_NCBI35_to_GRCh37.chain added
2f3c977becc63_NCBI35_to_GRCh38.chain added
2f3c9748fd1098_NCBI36_to_GRCh37.chain added
2f3c9777b24e10_NCBI36_to_GRCh38.chain added
2f3c9765b49dd_GRCm38_to_NCBIM36.chain added
2f3c9768917618_GRCm38_to_NCBIM37.chain added
2f3c971fb2b5bd_NCBIM36_to_GRCm38.chain added
2f3c9742c2771f_NCBIM37_to_GRCm38.chain added
2f3c9749e04e2c_1000G_omni2.5.b37.vcf.gz added
2f3c972a6ce53d_1000G_omni2.5.b37.vcf.gz.tbi added
2f3c9754ba85c5_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2f3c973ee5ecee_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2f3c976b227d26_1000G_omni2.5.hg38.vcf.gz added
2f3c977a8eb64d_1000G_omni2.5.hg38.vcf.gz.tbi added
2f3c971284a9fd_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2f3c9725b14b2a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2f3c9779586142_af-only-gnomad.raw.sites.vcf added
2f3c9733d2150c_af-only-gnomad.raw.sites.vcf.idx added
2f3c971ab488a_Mutect2-exome-panel.vcf.idx added
2f3c974d2dd019_Mutect2-WGS-panel-b37.vcf added
2f3c9763171ee6_Mutect2-WGS-panel-b37.vcf.idx added
2f3c974554f538_small_exac_common_3.vcf added
2f3c97128cd1f2_small_exac_common_3.vcf.idx added
2f3c973a55751f_1000g_pon.hg38.vcf.gz added
2f3c9720dc7a35_1000g_pon.hg38.vcf.gz.tbi added
2f3c975414e70d_af-only-gnomad.hg38.vcf.gz added
2f3c976509e602_af-only-gnomad.hg38.vcf.gz.tbi added
2f3c9756592e18_small_exac_common_3.hg38.vcf.gz added
2f3c975f2b8e77_small_exac_common_3.hg38.vcf.gz.tbi added
2f3c971b5d7017_gencode.v41.annotation.gtf added
2f3c975594fc8e_gencode.v42.annotation.gtf added
2f3c973441675b_gencode.vM30.annotation.gtf added
2f3c97231c3c7b_gencode.vM31.annotation.gtf added
2f3c971e920d27_gencode.v41.transcripts.fa added
2f3c972bf3b56b_gencode.v41.transcripts.fa.fai added
2f3c9729778658_gencode.v42.transcripts.fa added
2f3c97723833f_gencode.v42.transcripts.fa.fai added
2f3c974ba66b28_gencode.vM30.pc_transcripts.fa added
2f3c976c39fd78_gencode.vM30.pc_transcripts.fa.fai added
2f3c975103d16c_gencode.vM31.pc_transcripts.fa added
2f3c9776135065_gencode.vM31.pc_transcripts.fa.fai added
2f3c9740f4833d_GRCh38.primary_assembly.genome.fa.1.ht2 added
2f3c97fe9be5a_GRCh38.primary_assembly.genome.fa.2.ht2 added
2f3c976135cd8c_GRCh38.primary_assembly.genome.fa.3.ht2 added
2f3c973b83398b_GRCh38.primary_assembly.genome.fa.4.ht2 added
2f3c97226e6857_GRCh38.primary_assembly.genome.fa.5.ht2 added
2f3c976e718b6_GRCh38.primary_assembly.genome.fa.6.ht2 added
2f3c9734db9acd_GRCh38.primary_assembly.genome.fa.7.ht2 added
2f3c9756407d64_GRCh38.primary_assembly.genome.fa.8.ht2 added
2f3c978926140_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2f3c972096ae6_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2f3c9739579c4a_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2f3c974de75678_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2f3c9714963cd8_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2f3c9773ad116a_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2f3c976ec3d0ae_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2f3c9768ab23e5_GRCh38.primary_assembly.genome.fa.fai added
2f3c9758b6f76c_GRCh38.primary_assembly.genome.fa.amb added
2f3c97451cfec6_GRCh38.primary_assembly.genome.fa.ann added
2f3c9747d6b25d_GRCh38.primary_assembly.genome.fa.bwt added
2f3c9774146784_GRCh38.primary_assembly.genome.fa.pac added
2f3c971ab1fb54_GRCh38.primary_assembly.genome.fa.sa added
2f3c977c1819b8_GRCh38.primary_assembly.genome.fa added
2f3c971730a3ff_hs37d5.fa.fai added
2f3c973944087b_hs37d5.fa.amb added
2f3c97280bcf23_hs37d5.fa.ann added
2f3c9740a82a57_hs37d5.fa.bwt added
2f3c9740678bbb_hs37d5.fa.pac added
2f3c9773b23a4b_hs37d5.fa.sa added
2f3c972ce227cf_hs37d5.fa added
2f3c97116b5d27_complete_ref_lens.bin added
2f3c9769c58ab1_ctable.bin added
2f3c976dd6ab0d_ctg_offsets.bin added
2f3c9721551b81_duplicate_clusters.tsv added
2f3c974afb583d_info.json added
2f3c972959e498_mphf.bin added
2f3c9743c383d9_pos.bin added
2f3c9751e270f3_pre_indexing.log added
2f3c975e357f65_rank.bin added
2f3c971a04013d_ref_indexing.log added
2f3c975a74d233_refAccumLengths.bin added
2f3c97603eea4b_reflengths.bin added
2f3c97535b9d87_refseq.bin added
2f3c97285c28ac_seq.bin added
2f3c9774d52723_versionInfo.json added
2f3c974708aef1_salmon_index added
2f3c97171ff95a_chrLength.txt added
2f3c975d804b09_chrName.txt added
2f3c971fbfa65e_chrNameLength.txt added
2f3c975c3cf820_chrStart.txt added
2f3c972556fd66_exonGeTrInfo.tab added
2f3c9713d40de2_exonInfo.tab added
2f3c9776eef374_geneInfo.tab added
2f3c97216f171e_Genome added
2f3c972b04b1e1_genomeParameters.txt added
2f3c973032fbf0_Log.out added
2f3c97497ae641_SA added
2f3c976bacdc38_SAindex added
2f3c97709a87ab_sjdbInfo.txt added
2f3c973d2d208c_sjdbList.fromGTF.out.tab added
2f3c97188f0408_sjdbList.out.tab added
2f3c97205e4d2_transcriptInfo.tab added
2f3c9726f2ab3d_GRCh38.GENCODE.v42_100 added
2f3c97665af15_knownGene_hg38.sql added
2f3c97235b0053_knownGene_hg38.txt added
2f3c9771ee037a_refGene_hg38.sql added
2f3c972fbf93ad_refGene_hg38.txt added
2f3c97671e842c_knownGene_mm39.sql added
2f3c9743d0746d_knownGene_mm39.txt added
2f3c97df51312_refGene_mm39.sql added
2f3c971228569_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/RtmpzxMChd/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
18.142 1.142 19.464
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.338 | 0.397 | 6.740 | |
| dataSearch | 1.137 | 0.057 | 1.194 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.722 | 0.167 | 3.530 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.000 | 0.001 | 0.001 | |
| recipeHub-class | 0.124 | 0.002 | 0.127 | |
| recipeLoad | 1.352 | 0.080 | 1.433 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.563 | 0.041 | 0.604 | |
| recipeUpdate | 0 | 0 | 0 | |