Qian Liu
| Snapshot Date: 2026-04-26 13:40 -0400 (Sun, 26 Apr 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 Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-27 11:33 -0400 (Mon, 27 Apr 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" | 4980 |
| 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 1814/2417 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.11.0 (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: 1.11.0 |
| 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: 2026-04-27 03:51:59 -0400 (Mon, 27 Apr 2026) |
| EndedAt: 2026-04-27 03:54:49 -0400 (Mon, 27 Apr 2026) |
| EllapsedTime: 169.7 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 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: 2026-04-27 07:51:59 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 6.294 0.384 6.68
* 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 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...
3ab7271426e408_GRCh38.primary_assembly.genome.fa.1.bt2 added
3ab727574b2e15_GRCh38.primary_assembly.genome.fa.2.bt2 added
3ab7272f2b21df_GRCh38.primary_assembly.genome.fa.3.bt2 added
3ab72773e9f148_GRCh38.primary_assembly.genome.fa.4.bt2 added
3ab72795399ac_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3ab727717741af_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3ab7272b28d775_outfile.txt added
3ab727129a0402_GRCh37_to_GRCh38.chain added
3ab7272c295167_GRCh37_to_NCBI34.chain added
3ab7274808618d_GRCh37_to_NCBI35.chain added
3ab727487ded5e_GRCh37_to_NCBI36.chain added
3ab7276f96dba9_GRCh38_to_GRCh37.chain added
3ab7276770fdb2_GRCh38_to_NCBI34.chain added
3ab727166d0703_GRCh38_to_NCBI35.chain added
3ab727a05cd12_GRCh38_to_NCBI36.chain added
3ab7277baffa90_NCBI34_to_GRCh37.chain added
3ab7277c935448_NCBI34_to_GRCh38.chain added
3ab7272afcf14d_NCBI35_to_GRCh37.chain added
3ab72776754e_NCBI35_to_GRCh38.chain added
3ab7273d6fea68_NCBI36_to_GRCh37.chain added
3ab72741fd599e_NCBI36_to_GRCh38.chain added
3ab7271e66c7bf_GRCm38_to_NCBIM36.chain added
3ab72757c5f9a0_GRCm38_to_NCBIM37.chain added
3ab7276ea76fb2_NCBIM36_to_GRCm38.chain added
3ab7273a365c13_NCBIM37_to_GRCm38.chain added
3ab7277bc2b765_1000G_omni2.5.b37.vcf.gz added
3ab7275dfee7c2_1000G_omni2.5.b37.vcf.gz.tbi added
3ab7272227461a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3ab727398af29a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3ab7277d282b6f_1000G_omni2.5.hg38.vcf.gz added
3ab727663868fa_1000G_omni2.5.hg38.vcf.gz.tbi added
3ab7274db1d6a2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3ab72754735984_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3ab72715638ad9_af-only-gnomad.raw.sites.vcf added
3ab727419bc7ea_af-only-gnomad.raw.sites.vcf.idx added
3ab7275dc6f330_Mutect2-exome-panel.vcf.idx added
3ab7276dacc88_Mutect2-WGS-panel-b37.vcf added
3ab7276cc49f60_Mutect2-WGS-panel-b37.vcf.idx added
3ab7277060f732_small_exac_common_3.vcf added
3ab72733041def_small_exac_common_3.vcf.idx added
3ab72734cd00ed_1000g_pon.hg38.vcf.gz added
3ab72738dee490_1000g_pon.hg38.vcf.gz.tbi added
3ab727229af999_af-only-gnomad.hg38.vcf.gz added
3ab7271c3dfe9f_af-only-gnomad.hg38.vcf.gz.tbi added
3ab7274f4beb93_small_exac_common_3.hg38.vcf.gz added
3ab7272ca0c6ab_small_exac_common_3.hg38.vcf.gz.tbi added
3ab72717edf92f_gencode.v41.annotation.gtf added
3ab7274bdf3fdb_gencode.v42.annotation.gtf added
3ab727579db7f8_gencode.vM30.annotation.gtf added
3ab72718646e7e_gencode.vM31.annotation.gtf added
3ab72794f2a44_gencode.v41.transcripts.fa added
3ab727199b1196_gencode.v41.transcripts.fa.fai added
3ab72736cb363d_gencode.v42.transcripts.fa added
3ab727611523e4_gencode.v42.transcripts.fa.fai added
3ab7278428148_gencode.vM30.pc_transcripts.fa added
3ab72771019250_gencode.vM30.pc_transcripts.fa.fai added
3ab7275cd7db49_gencode.vM31.pc_transcripts.fa added
3ab7276641690a_gencode.vM31.pc_transcripts.fa.fai added
3ab7271328d86b_GRCh38.primary_assembly.genome.fa.1.ht2 added
3ab7271662cde3_GRCh38.primary_assembly.genome.fa.2.ht2 added
3ab72763699479_GRCh38.primary_assembly.genome.fa.3.ht2 added
3ab72779614165_GRCh38.primary_assembly.genome.fa.4.ht2 added
3ab7276414a486_GRCh38.primary_assembly.genome.fa.5.ht2 added
3ab72737dcedfd_GRCh38.primary_assembly.genome.fa.6.ht2 added
3ab727ec4cc3e_GRCh38.primary_assembly.genome.fa.7.ht2 added
3ab72725b06c70_GRCh38.primary_assembly.genome.fa.8.ht2 added
3ab72715a3e12d_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3ab727159f98c7_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3ab72712750bd0_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3ab727604d85f_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3ab72748a3b6b6_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3ab72747420cbd_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3ab7273ee3bcef_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3ab7276b3eb04f_GRCh38.primary_assembly.genome.fa.fai added
3ab72763800b5d_GRCh38.primary_assembly.genome.fa.amb added
3ab727e2fa883_GRCh38.primary_assembly.genome.fa.ann added
3ab72717df76fa_GRCh38.primary_assembly.genome.fa.bwt added
3ab7277b6e048c_GRCh38.primary_assembly.genome.fa.pac added
3ab7275a0ee85e_GRCh38.primary_assembly.genome.fa.sa added
3ab7276f7d2ef2_GRCh38.primary_assembly.genome.fa added
3ab72713d2730a_hs37d5.fa.fai added
3ab727635e12a2_hs37d5.fa.amb added
3ab7279184088_hs37d5.fa.ann added
3ab7274a9da947_hs37d5.fa.bwt added
3ab72744733686_hs37d5.fa.pac added
3ab727115ac1d0_hs37d5.fa.sa added
3ab7273b9f3b98_hs37d5.fa added
3ab727214b11cf_complete_ref_lens.bin added
3ab727779c2adb_ctable.bin added
3ab7274ec81403_ctg_offsets.bin added
3ab72737addfb3_duplicate_clusters.tsv added
3ab7275b05bf54_info.json added
3ab72748295568_mphf.bin added
3ab7271bc28439_pos.bin added
3ab72712e2ad52_pre_indexing.log added
3ab72756ee21a6_rank.bin added
3ab7274172f0a9_ref_indexing.log added
3ab72728868e7f_refAccumLengths.bin added
3ab7276c8dba6d_reflengths.bin added
3ab72753e7fc7a_refseq.bin added
3ab7272e8b66df_seq.bin added
3ab72735317124_versionInfo.json added
3ab7271b2a0937_salmon_index added
3ab7276d6f23ce_chrLength.txt added
3ab72720702173_chrName.txt added
3ab7277eaa1494_chrNameLength.txt added
3ab7277b9ecc51_chrStart.txt added
3ab727384f986e_exonGeTrInfo.tab added
3ab7277a181921_exonInfo.tab added
3ab72755adb4b0_geneInfo.tab added
3ab72727ccc760_Genome added
3ab727dea8c2b_genomeParameters.txt added
3ab727390bc752_Log.out added
3ab72730e507e9_SA added
3ab72758883573_SAindex added
3ab7277d7efdd9_sjdbInfo.txt added
3ab727423fc9b9_sjdbList.fromGTF.out.tab added
3ab7271427710b_sjdbList.out.tab added
3ab7271eca0fa8_transcriptInfo.tab added
3ab72739dbf494_GRCh38.GENCODE.v42_100 added
3ab72762ef850e_knownGene_hg38.sql added
3ab7275677ef5b_knownGene_hg38.txt added
3ab72714e1b3e9_refGene_hg38.sql added
3ab7272b18da76_refGene_hg38.txt added
3ab727723a7394_knownGene_mm39.sql added
3ab72727c4613b_knownGene_mm39.txt added
3ab727206fc1c_refGene_mm39.sql added
3ab72733ad643e_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/RtmpliI23I/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
18.307 1.402 20.252
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.294 | 0.384 | 6.680 | |
| dataSearch | 1.159 | 0.040 | 1.203 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.702 | 0.063 | 3.389 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.132 | 0.001 | 0.134 | |
| recipeLoad | 1.304 | 0.021 | 1.325 | |
| recipeMake | 0.000 | 0.001 | 0.000 | |
| recipeSearch | 0.521 | 0.010 | 0.531 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |