Qian Liu
| Snapshot Date: 2026-03-30 13:45 -0400 (Mon, 30 Mar 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-31 11:57 -0400 (Tue, 31 Mar 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" | 4893 |
| 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: 2026-03-31 03:03:56 -0400 (Tue, 31 Mar 2026) |
| EndedAt: 2026-03-31 03:06:43 -0400 (Tue, 31 Mar 2026) |
| EllapsedTime: 167.2 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 24.04.4 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 6.322 0.289 6.616
* 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...
208c9661c9b9b4_GRCh38.primary_assembly.genome.fa.1.bt2 added
208c96797b2ca4_GRCh38.primary_assembly.genome.fa.2.bt2 added
208c96690da4bb_GRCh38.primary_assembly.genome.fa.3.bt2 added
208c96415da6fb_GRCh38.primary_assembly.genome.fa.4.bt2 added
208c9644352983_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
208c96a872edc_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
208c96777b6da4_outfile.txt added
208c9645d192e7_GRCh37_to_GRCh38.chain added
208c9676bb52ab_GRCh37_to_NCBI34.chain added
208c962b987fc_GRCh37_to_NCBI35.chain added
208c962c94df81_GRCh37_to_NCBI36.chain added
208c962ef142de_GRCh38_to_GRCh37.chain added
208c9655126d3b_GRCh38_to_NCBI34.chain added
208c961098cea_GRCh38_to_NCBI35.chain added
208c96b5ddab8_GRCh38_to_NCBI36.chain added
208c966a71c252_NCBI34_to_GRCh37.chain added
208c9622729e6a_NCBI34_to_GRCh38.chain added
208c966d98dfe6_NCBI35_to_GRCh37.chain added
208c96427257b_NCBI35_to_GRCh38.chain added
208c963a97b2f5_NCBI36_to_GRCh37.chain added
208c9632789868_NCBI36_to_GRCh38.chain added
208c964d4ad381_GRCm38_to_NCBIM36.chain added
208c966967aaf4_GRCm38_to_NCBIM37.chain added
208c961a45bee6_NCBIM36_to_GRCm38.chain added
208c9656b94213_NCBIM37_to_GRCm38.chain added
208c963859bc70_1000G_omni2.5.b37.vcf.gz added
208c96740fd806_1000G_omni2.5.b37.vcf.gz.tbi added
208c9655e1c25c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
208c963180524_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
208c96359e0853_1000G_omni2.5.hg38.vcf.gz added
208c96147cb789_1000G_omni2.5.hg38.vcf.gz.tbi added
208c9664e1bed8_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
208c962f1934f7_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
208c967d8a5c44_af-only-gnomad.raw.sites.vcf added
208c96263f65d3_af-only-gnomad.raw.sites.vcf.idx added
208c96734e5e7b_Mutect2-exome-panel.vcf.idx added
208c968118b20_Mutect2-WGS-panel-b37.vcf added
208c961dbad378_Mutect2-WGS-panel-b37.vcf.idx added
208c96391ff162_small_exac_common_3.vcf added
208c967eccddcb_small_exac_common_3.vcf.idx added
208c9620745b74_1000g_pon.hg38.vcf.gz added
208c9665b4d0e3_1000g_pon.hg38.vcf.gz.tbi added
208c962dbe20a9_af-only-gnomad.hg38.vcf.gz added
208c967586c8af_af-only-gnomad.hg38.vcf.gz.tbi added
208c9666be5dce_small_exac_common_3.hg38.vcf.gz added
208c96391bfb61_small_exac_common_3.hg38.vcf.gz.tbi added
208c965ff88b02_gencode.v41.annotation.gtf added
208c96930fc38_gencode.v42.annotation.gtf added
208c9626b4db48_gencode.vM30.annotation.gtf added
208c96641fb07d_gencode.vM31.annotation.gtf added
208c9643c8af2d_gencode.v41.transcripts.fa added
208c96592d73b0_gencode.v41.transcripts.fa.fai added
208c96316a83fe_gencode.v42.transcripts.fa added
208c962d305a21_gencode.v42.transcripts.fa.fai added
208c9673733296_gencode.vM30.pc_transcripts.fa added
208c96823c611_gencode.vM30.pc_transcripts.fa.fai added
208c96658a1692_gencode.vM31.pc_transcripts.fa added
208c9667830a9c_gencode.vM31.pc_transcripts.fa.fai added
208c965e05886d_GRCh38.primary_assembly.genome.fa.1.ht2 added
208c9668a21bb6_GRCh38.primary_assembly.genome.fa.2.ht2 added
208c961d2112ef_GRCh38.primary_assembly.genome.fa.3.ht2 added
208c9672823ff6_GRCh38.primary_assembly.genome.fa.4.ht2 added
208c964d83da8f_GRCh38.primary_assembly.genome.fa.5.ht2 added
208c964c3a47e6_GRCh38.primary_assembly.genome.fa.6.ht2 added
208c96700c9c3a_GRCh38.primary_assembly.genome.fa.7.ht2 added
208c9673c34062_GRCh38.primary_assembly.genome.fa.8.ht2 added
208c963f88a661_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
208c96781e275a_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
208c96117e13da_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
208c9678a897c3_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
208c9676eb0525_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
208c9631f26f4f_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
208c965e5d68a7_GRCh38_full_analysis_set_plus_decoy_hla.fa added
208c9624a925cf_GRCh38.primary_assembly.genome.fa.fai added
208c96277937fe_GRCh38.primary_assembly.genome.fa.amb added
208c96451bc675_GRCh38.primary_assembly.genome.fa.ann added
208c965dc52130_GRCh38.primary_assembly.genome.fa.bwt added
208c96771c300_GRCh38.primary_assembly.genome.fa.pac added
208c964e4cc2ad_GRCh38.primary_assembly.genome.fa.sa added
208c96479fc78_GRCh38.primary_assembly.genome.fa added
208c966b91737d_hs37d5.fa.fai added
208c96121571db_hs37d5.fa.amb added
208c965da77028_hs37d5.fa.ann added
208c961cfbf77b_hs37d5.fa.bwt added
208c963f45cbfc_hs37d5.fa.pac added
208c96511aa2be_hs37d5.fa.sa added
208c96251fbd8d_hs37d5.fa added
208c9624cfe28e_complete_ref_lens.bin added
208c96389dad5a_ctable.bin added
208c9632545fa_ctg_offsets.bin added
208c96d71fe45_duplicate_clusters.tsv added
208c9655bec049_info.json added
208c9675a785f1_mphf.bin added
208c965af5d8d4_pos.bin added
208c9621f90830_pre_indexing.log added
208c9665b4222b_rank.bin added
208c964eb91936_ref_indexing.log added
208c966181ae91_refAccumLengths.bin added
208c965dd24986_reflengths.bin added
208c9660372d11_refseq.bin added
208c965a2a4655_seq.bin added
208c9654bd4eab_versionInfo.json added
208c9612299c60_salmon_index added
208c963887aefc_chrLength.txt added
208c967966747a_chrName.txt added
208c9639a2d45e_chrNameLength.txt added
208c967da37571_chrStart.txt added
208c96572b95ab_exonGeTrInfo.tab added
208c964114975f_exonInfo.tab added
208c964bf0381e_geneInfo.tab added
208c965ba59223_Genome added
208c962ca60adc_genomeParameters.txt added
208c965e05a9f9_Log.out added
208c96394d024c_SA added
208c9649a20258_SAindex added
208c961d4b75f6_sjdbInfo.txt added
208c96a67a50a_sjdbList.fromGTF.out.tab added
208c966ec1bfe5_sjdbList.out.tab added
208c96421b5884_transcriptInfo.tab added
208c9643055265_GRCh38.GENCODE.v42_100 added
208c9671e705df_knownGene_hg38.sql added
208c964f8d56c9_knownGene_hg38.txt added
208c9618c412ae_refGene_hg38.sql added
208c96678e8bd0_refGene_hg38.txt added
208c962a832f9d_knownGene_mm39.sql added
208c963abd1ade_knownGene_mm39.txt added
208c964d42adfc_refGene_mm39.sql added
208c96793c48d4_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/RtmpJp85UQ/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
18.640 1.015 20.117
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.322 | 0.289 | 6.616 | |
| dataSearch | 1.181 | 0.052 | 1.233 | |
| dataUpdate | 0.001 | 0.000 | 0.000 | |
| getCloudData | 2.906 | 0.230 | 3.740 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.124 | 0.003 | 0.127 | |
| recipeLoad | 1.320 | 0.067 | 1.389 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.558 | 0.004 | 0.563 | |
| recipeUpdate | 0 | 0 | 0 | |