Qian Liu
| Snapshot Date: 2026-05-13 13:40 -0400 (Wed, 13 May 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_23 |
| git_last_commit: bb3489b |
| git_last_commit_date: 2026-04-28 08:59:39 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-14 11:33 -0400 (Thu, 14 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4994 |
| 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 1815/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.12.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.4 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: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2026-05-14 04:00:41 -0400 (Thu, 14 May 2026) |
| EndedAt: 2026-05-14 04:03:27 -0400 (Thu, 14 May 2026) |
| EllapsedTime: 166.3 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-14 08:00:41 UTC
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.12.0’
* 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 6.308 0.433 6.743
* 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 ‘1.12.0’ ** 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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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...
102ab61dc35986_GRCh38.primary_assembly.genome.fa.1.bt2 added
102ab63b25c65c_GRCh38.primary_assembly.genome.fa.2.bt2 added
102ab642b6bf9c_GRCh38.primary_assembly.genome.fa.3.bt2 added
102ab6283744bf_GRCh38.primary_assembly.genome.fa.4.bt2 added
102ab668f68958_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
102ab63c201990_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
102ab6d20413e_outfile.txt added
102ab63aa8955e_GRCh37_to_GRCh38.chain added
102ab61675c26d_GRCh37_to_NCBI34.chain added
102ab642b10cf3_GRCh37_to_NCBI35.chain added
102ab611dd5d5e_GRCh37_to_NCBI36.chain added
102ab667ac46e5_GRCh38_to_GRCh37.chain added
102ab67896d770_GRCh38_to_NCBI34.chain added
102ab6657573b2_GRCh38_to_NCBI35.chain added
102ab6e9ead86_GRCh38_to_NCBI36.chain added
102ab61b908537_NCBI34_to_GRCh37.chain added
102ab67f9a3229_NCBI34_to_GRCh38.chain added
102ab6660504e_NCBI35_to_GRCh37.chain added
102ab6582e02f7_NCBI35_to_GRCh38.chain added
102ab6394b2b9c_NCBI36_to_GRCh37.chain added
102ab616a2c4a4_NCBI36_to_GRCh38.chain added
102ab6119ae82d_GRCm38_to_NCBIM36.chain added
102ab645995d03_GRCm38_to_NCBIM37.chain added
102ab65454cdfb_NCBIM36_to_GRCm38.chain added
102ab648955d21_NCBIM37_to_GRCm38.chain added
102ab6544dfcc3_1000G_omni2.5.b37.vcf.gz added
102ab61c92390_1000G_omni2.5.b37.vcf.gz.tbi added
102ab6150f9e32_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
102ab655bc78ef_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
102ab67348f701_1000G_omni2.5.hg38.vcf.gz added
102ab62efbe297_1000G_omni2.5.hg38.vcf.gz.tbi added
102ab6737fd275_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
102ab62e6ebd5d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
102ab671b2a233_af-only-gnomad.raw.sites.vcf added
102ab61bb71735_af-only-gnomad.raw.sites.vcf.idx added
102ab6176546b6_Mutect2-exome-panel.vcf.idx added
102ab62dd2bbc3_Mutect2-WGS-panel-b37.vcf added
102ab628d75873_Mutect2-WGS-panel-b37.vcf.idx added
102ab6520ddc14_small_exac_common_3.vcf added
102ab644487e30_small_exac_common_3.vcf.idx added
102ab66b886566_1000g_pon.hg38.vcf.gz added
102ab663eb3972_1000g_pon.hg38.vcf.gz.tbi added
102ab62bf4c516_af-only-gnomad.hg38.vcf.gz added
102ab6641f3cd7_af-only-gnomad.hg38.vcf.gz.tbi added
102ab64960ad25_small_exac_common_3.hg38.vcf.gz added
102ab63a93729c_small_exac_common_3.hg38.vcf.gz.tbi added
102ab67fafc20e_gencode.v41.annotation.gtf added
102ab648fadf4e_gencode.v42.annotation.gtf added
102ab640f3c2ea_gencode.vM30.annotation.gtf added
102ab657ddc505_gencode.vM31.annotation.gtf added
102ab62460aeb_gencode.v41.transcripts.fa added
102ab65796878e_gencode.v41.transcripts.fa.fai added
102ab66978ad32_gencode.v42.transcripts.fa added
102ab647df67ee_gencode.v42.transcripts.fa.fai added
102ab62beb558a_gencode.vM30.pc_transcripts.fa added
102ab6320e0a53_gencode.vM30.pc_transcripts.fa.fai added
102ab61c2d64b1_gencode.vM31.pc_transcripts.fa added
102ab62db4791a_gencode.vM31.pc_transcripts.fa.fai added
102ab6471da885_GRCh38.primary_assembly.genome.fa.1.ht2 added
102ab671e9dda0_GRCh38.primary_assembly.genome.fa.2.ht2 added
102ab620fd701b_GRCh38.primary_assembly.genome.fa.3.ht2 added
102ab676198b1c_GRCh38.primary_assembly.genome.fa.4.ht2 added
102ab66569b016_GRCh38.primary_assembly.genome.fa.5.ht2 added
102ab64f6c2d79_GRCh38.primary_assembly.genome.fa.6.ht2 added
102ab667cc2d4f_GRCh38.primary_assembly.genome.fa.7.ht2 added
102ab6120c74b_GRCh38.primary_assembly.genome.fa.8.ht2 added
102ab666d1742f_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
102ab6159ee913_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
102ab629f81fbe_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
102ab638df5043_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
102ab659e76743_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
102ab615808525_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
102ab61cca89b6_GRCh38_full_analysis_set_plus_decoy_hla.fa added
102ab65dc2c59_GRCh38.primary_assembly.genome.fa.fai added
102ab6799fc1fc_GRCh38.primary_assembly.genome.fa.amb added
102ab6662b36db_GRCh38.primary_assembly.genome.fa.ann added
102ab6406f9ef5_GRCh38.primary_assembly.genome.fa.bwt added
102ab6794f840a_GRCh38.primary_assembly.genome.fa.pac added
102ab62f261629_GRCh38.primary_assembly.genome.fa.sa added
102ab616361e0_GRCh38.primary_assembly.genome.fa added
102ab6512d4910_hs37d5.fa.fai added
102ab6316c2114_hs37d5.fa.amb added
102ab658f9e96e_hs37d5.fa.ann added
102ab63aa5f642_hs37d5.fa.bwt added
102ab6794b8903_hs37d5.fa.pac added
102ab64e53ef8_hs37d5.fa.sa added
102ab66cb40096_hs37d5.fa added
102ab61578edb4_complete_ref_lens.bin added
102ab63299b812_ctable.bin added
102ab633d1a91b_ctg_offsets.bin added
102ab6762cb55_duplicate_clusters.tsv added
102ab65397282e_info.json added
102ab629eb3438_mphf.bin added
102ab66ccc7b6b_pos.bin added
102ab6230355a7_pre_indexing.log added
102ab611b76187_rank.bin added
102ab66ded42b6_ref_indexing.log added
102ab69d4c9d6_refAccumLengths.bin added
102ab627564a9a_reflengths.bin added
102ab617e56274_refseq.bin added
102ab642b41a19_seq.bin added
102ab613db1de_versionInfo.json added
102ab62d65e799_salmon_index added
102ab65f7ea3cf_chrLength.txt added
102ab6719de37_chrName.txt added
102ab62705a995_chrNameLength.txt added
102ab645a9daaa_chrStart.txt added
102ab647897d2d_exonGeTrInfo.tab added
102ab620552da0_exonInfo.tab added
102ab674cff0d4_geneInfo.tab added
102ab648ecdf0d_Genome added
102ab6718276b0_genomeParameters.txt added
102ab6263c11e8_Log.out added
102ab621e6c87b_SA added
102ab62c286cf2_SAindex added
102ab61f879aeb_sjdbInfo.txt added
102ab626cc0774_sjdbList.fromGTF.out.tab added
102ab618dc6d88_sjdbList.out.tab added
102ab6350088a0_transcriptInfo.tab added
102ab65965bf86_GRCh38.GENCODE.v42_100 added
102ab64cae16a4_knownGene_hg38.sql added
102ab63c6353f5_knownGene_hg38.txt added
102ab62cfce7b4_refGene_hg38.sql added
102ab676994adc_refGene_hg38.txt added
102ab6292fcf60_knownGene_mm39.sql added
102ab650003d5b_knownGene_mm39.txt added
102ab6850ac63_refGene_mm39.sql added
102ab6171d1216_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/Rtmpq7eomC/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
18.107 1.390 19.739
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.308 | 0.433 | 6.743 | |
| dataSearch | 1.141 | 0.049 | 1.190 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 2.702 | 0.117 | 3.309 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.121 | 0.005 | 0.126 | |
| recipeLoad | 1.264 | 0.056 | 1.323 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.558 | 0.014 | 0.572 | |
| recipeUpdate | 0 | 0 | 0 | |