Qian Liu
| Snapshot Date: 2026-05-19 13:40 -0400 (Tue, 19 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 2026-05-20 11:32 -0400 (Wed, 20 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" | 4995 |
| 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: 2026-05-20 04:06:03 -0400 (Wed, 20 May 2026) |
| EndedAt: 2026-05-20 04:08:52 -0400 (Wed, 20 May 2026) |
| EllapsedTime: 169.4 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_1.12.0.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: 2026-05-20 08:06:03 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 6.321 0.431 6.755
* 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...
3634de6e3a55ca_GRCh38.primary_assembly.genome.fa.1.bt2 added
3634de2b033697_GRCh38.primary_assembly.genome.fa.2.bt2 added
3634dec0df437_GRCh38.primary_assembly.genome.fa.3.bt2 added
3634de125ec1e6_GRCh38.primary_assembly.genome.fa.4.bt2 added
3634de54fee781_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3634de9798be_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3634dea50054b_outfile.txt added
3634de6bebfa76_GRCh37_to_GRCh38.chain added
3634de47c83a8_GRCh37_to_NCBI34.chain added
3634de251fe798_GRCh37_to_NCBI35.chain added
3634de286a0297_GRCh37_to_NCBI36.chain added
3634de3406bf97_GRCh38_to_GRCh37.chain added
3634de574ec85b_GRCh38_to_NCBI34.chain added
3634de7c6352b2_GRCh38_to_NCBI35.chain added
3634de3cf665db_GRCh38_to_NCBI36.chain added
3634de2afb0edb_NCBI34_to_GRCh37.chain added
3634de76d06697_NCBI34_to_GRCh38.chain added
3634de7b263548_NCBI35_to_GRCh37.chain added
3634de4d30fb28_NCBI35_to_GRCh38.chain added
3634de31c0065b_NCBI36_to_GRCh37.chain added
3634de244284f7_NCBI36_to_GRCh38.chain added
3634de31205157_GRCm38_to_NCBIM36.chain added
3634de70ee4c0d_GRCm38_to_NCBIM37.chain added
3634de7251024_NCBIM36_to_GRCm38.chain added
3634de3546ce1a_NCBIM37_to_GRCm38.chain added
3634de155c5914_1000G_omni2.5.b37.vcf.gz added
3634de25061ae9_1000G_omni2.5.b37.vcf.gz.tbi added
3634de7233ace7_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3634de3a65352c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3634de504e716f_1000G_omni2.5.hg38.vcf.gz added
3634de115bbf1e_1000G_omni2.5.hg38.vcf.gz.tbi added
3634de289f8af7_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3634de7b51a807_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3634de1d69b355_af-only-gnomad.raw.sites.vcf added
3634de3afe4cdd_af-only-gnomad.raw.sites.vcf.idx added
3634de50508f88_Mutect2-exome-panel.vcf.idx added
3634de1e014c14_Mutect2-WGS-panel-b37.vcf added
3634de454e5228_Mutect2-WGS-panel-b37.vcf.idx added
3634de3c3c89fe_small_exac_common_3.vcf added
3634de227dcfbc_small_exac_common_3.vcf.idx added
3634de6a6e39c1_1000g_pon.hg38.vcf.gz added
3634de64a68c95_1000g_pon.hg38.vcf.gz.tbi added
3634de56848f53_af-only-gnomad.hg38.vcf.gz added
3634de41bd021c_af-only-gnomad.hg38.vcf.gz.tbi added
3634de6109df47_small_exac_common_3.hg38.vcf.gz added
3634de137af52f_small_exac_common_3.hg38.vcf.gz.tbi added
3634de6cb810f7_gencode.v41.annotation.gtf added
3634de57da45de_gencode.v42.annotation.gtf added
3634deea12a77_gencode.vM30.annotation.gtf added
3634de39e90c1f_gencode.vM31.annotation.gtf added
3634de99a4c39_gencode.v41.transcripts.fa added
3634de32e3af6e_gencode.v41.transcripts.fa.fai added
3634de6b095d76_gencode.v42.transcripts.fa added
3634de7a889847_gencode.v42.transcripts.fa.fai added
3634de3a08bf93_gencode.vM30.pc_transcripts.fa added
3634de20502b91_gencode.vM30.pc_transcripts.fa.fai added
3634defe4f15b_gencode.vM31.pc_transcripts.fa added
3634de5f0eda7c_gencode.vM31.pc_transcripts.fa.fai added
3634de1283d878_GRCh38.primary_assembly.genome.fa.1.ht2 added
3634de4a4a2687_GRCh38.primary_assembly.genome.fa.2.ht2 added
3634de2f5d4bec_GRCh38.primary_assembly.genome.fa.3.ht2 added
3634de23df9797_GRCh38.primary_assembly.genome.fa.4.ht2 added
3634de72e9b17e_GRCh38.primary_assembly.genome.fa.5.ht2 added
3634de2aaef3f3_GRCh38.primary_assembly.genome.fa.6.ht2 added
3634de41494aec_GRCh38.primary_assembly.genome.fa.7.ht2 added
3634de2de7fe5c_GRCh38.primary_assembly.genome.fa.8.ht2 added
3634de7aff837b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3634de5f4a9700_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3634de73365084_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3634de373c0d79_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3634de1c866bd_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3634de5da48a45_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3634de1be29a0f_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3634de584cf610_GRCh38.primary_assembly.genome.fa.fai added
3634de1f618c62_GRCh38.primary_assembly.genome.fa.amb added
3634de7cec7956_GRCh38.primary_assembly.genome.fa.ann added
3634de6bc7eb3f_GRCh38.primary_assembly.genome.fa.bwt added
3634dec199d59_GRCh38.primary_assembly.genome.fa.pac added
3634de54c6bf35_GRCh38.primary_assembly.genome.fa.sa added
3634de7a6915b7_GRCh38.primary_assembly.genome.fa added
3634de4602a979_hs37d5.fa.fai added
3634de5e610b6e_hs37d5.fa.amb added
3634de2d4cc525_hs37d5.fa.ann added
3634de310c06ef_hs37d5.fa.bwt added
3634de58e9a3b5_hs37d5.fa.pac added
3634de675584b8_hs37d5.fa.sa added
3634de515c3280_hs37d5.fa added
3634de68ce9510_complete_ref_lens.bin added
3634de46645f35_ctable.bin added
3634de63e00af9_ctg_offsets.bin added
3634de3318bb98_duplicate_clusters.tsv added
3634de75c1ab21_info.json added
3634de7bfa290_mphf.bin added
3634de26026d16_pos.bin added
3634de20709f14_pre_indexing.log added
3634de4908ed7c_rank.bin added
3634de53ea6b72_ref_indexing.log added
3634de1b70228f_refAccumLengths.bin added
3634de2853847d_reflengths.bin added
3634de4720bbf7_refseq.bin added
3634de52ac3008_seq.bin added
3634de2a1beb3a_versionInfo.json added
3634de24c5463c_salmon_index added
3634de6e8eca17_chrLength.txt added
3634de268e14a_chrName.txt added
3634de4426d29e_chrNameLength.txt added
3634de6b7b436e_chrStart.txt added
3634de6e30cc8a_exonGeTrInfo.tab added
3634de50406ff8_exonInfo.tab added
3634de404202a3_geneInfo.tab added
3634de6899e241_Genome added
3634de16431971_genomeParameters.txt added
3634de1ea30e11_Log.out added
3634de15e6a766_SA added
3634de474f2060_SAindex added
3634de778cb1c7_sjdbInfo.txt added
3634de7d3c2c1f_sjdbList.fromGTF.out.tab added
3634de18ab52e1_sjdbList.out.tab added
3634de605b46d7_transcriptInfo.tab added
3634de43a08b54_GRCh38.GENCODE.v42_100 added
3634de7c8b5dda_knownGene_hg38.sql added
3634de1374026f_knownGene_hg38.txt added
3634de39623675_refGene_hg38.sql added
3634de44b006a_refGene_hg38.txt added
3634de39766f86_knownGene_mm39.sql added
3634de59d2d589_knownGene_mm39.txt added
3634de4d53ede6_refGene_mm39.sql added
3634ded60daf8_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/Rtmp7YFRvl/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
18.944 1.219 20.397
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.321 | 0.431 | 6.755 | |
| dataSearch | 1.183 | 0.040 | 1.224 | |
| dataUpdate | 0.000 | 0.001 | 0.001 | |
| getCloudData | 2.721 | 0.192 | 3.357 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.132 | 0.003 | 0.135 | |
| recipeLoad | 1.353 | 0.052 | 1.407 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.537 | 0.043 | 0.580 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |