Qian Liu
| Snapshot Date: 2026-05-24 13:40 -0400 (Sun, 24 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 2026-05-25 11:32 -0400 (Mon, 25 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: 2026-05-25 04:04:49 -0400 (Mon, 25 May 2026) |
| EndedAt: 2026-05-25 04:07:38 -0400 (Mon, 25 May 2026) |
| EllapsedTime: 169.5 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_1.12.0.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: 2026-05-25 08:04:49 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 6.388 0.431 6.822
* 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...
3bbabf5ac40c39_GRCh38.primary_assembly.genome.fa.1.bt2 added
3bbabf5c533e01_GRCh38.primary_assembly.genome.fa.2.bt2 added
3bbabf2d88bac_GRCh38.primary_assembly.genome.fa.3.bt2 added
3bbabf6854f573_GRCh38.primary_assembly.genome.fa.4.bt2 added
3bbabf366c346c_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3bbabf73418534_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
3bbabf46a43eed_outfile.txt added
3bbabfe5774a_GRCh37_to_GRCh38.chain added
3bbabf669c577e_GRCh37_to_NCBI34.chain added
3bbabf4538046d_GRCh37_to_NCBI35.chain added
3bbabf22802159_GRCh37_to_NCBI36.chain added
3bbabf5faad224_GRCh38_to_GRCh37.chain added
3bbabf29d375c4_GRCh38_to_NCBI34.chain added
3bbabf12f7fb68_GRCh38_to_NCBI35.chain added
3bbabf5b0e9313_GRCh38_to_NCBI36.chain added
3bbabf15c23ee4_NCBI34_to_GRCh37.chain added
3bbabf4682c29_NCBI34_to_GRCh38.chain added
3bbabf678798e6_NCBI35_to_GRCh37.chain added
3bbabf76d0f539_NCBI35_to_GRCh38.chain added
3bbabf2c6c924b_NCBI36_to_GRCh37.chain added
3bbabf4123785d_NCBI36_to_GRCh38.chain added
3bbabf6d0f2659_GRCm38_to_NCBIM36.chain added
3bbabf1f4110e2_GRCm38_to_NCBIM37.chain added
3bbabfdd14ab9_NCBIM36_to_GRCm38.chain added
3bbabf4f6df8d7_NCBIM37_to_GRCm38.chain added
3bbabf4d4fa760_1000G_omni2.5.b37.vcf.gz added
3bbabf27970054_1000G_omni2.5.b37.vcf.gz.tbi added
3bbabf2c120650_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
3bbabf5581a7d7_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3bbabfdfb328_1000G_omni2.5.hg38.vcf.gz added
3bbabf2d117bf3_1000G_omni2.5.hg38.vcf.gz.tbi added
3bbabf3045b410_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
3bbabf5d32f12a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3bbabf2fea079f_af-only-gnomad.raw.sites.vcf added
3bbabf189aa984_af-only-gnomad.raw.sites.vcf.idx added
3bbabf139f2596_Mutect2-exome-panel.vcf.idx added
3bbabf232b8cd3_Mutect2-WGS-panel-b37.vcf added
3bbabf5f3ee871_Mutect2-WGS-panel-b37.vcf.idx added
3bbabf14849ce0_small_exac_common_3.vcf added
3bbabf9c7e452_small_exac_common_3.vcf.idx added
3bbabf2476ecdf_1000g_pon.hg38.vcf.gz added
3bbabf3704be3a_1000g_pon.hg38.vcf.gz.tbi added
3bbabf6972b676_af-only-gnomad.hg38.vcf.gz added
3bbabf4e4a62a3_af-only-gnomad.hg38.vcf.gz.tbi added
3bbabf49fcb9a2_small_exac_common_3.hg38.vcf.gz added
3bbabf44814989_small_exac_common_3.hg38.vcf.gz.tbi added
3bbabf640ca188_gencode.v41.annotation.gtf added
3bbabf4e64e5cc_gencode.v42.annotation.gtf added
3bbabf2c08e270_gencode.vM30.annotation.gtf added
3bbabf5add96c1_gencode.vM31.annotation.gtf added
3bbabf7ad17817_gencode.v41.transcripts.fa added
3bbabf6d2c5acd_gencode.v41.transcripts.fa.fai added
3bbabf47ecbd1a_gencode.v42.transcripts.fa added
3bbabf1a1288f9_gencode.v42.transcripts.fa.fai added
3bbabf7afda586_gencode.vM30.pc_transcripts.fa added
3bbabf175ab5f1_gencode.vM30.pc_transcripts.fa.fai added
3bbabf6762305a_gencode.vM31.pc_transcripts.fa added
3bbabf2294a5db_gencode.vM31.pc_transcripts.fa.fai added
3bbabf436cbc41_GRCh38.primary_assembly.genome.fa.1.ht2 added
3bbabf3ce3d831_GRCh38.primary_assembly.genome.fa.2.ht2 added
3bbabf23745903_GRCh38.primary_assembly.genome.fa.3.ht2 added
3bbabf707e3834_GRCh38.primary_assembly.genome.fa.4.ht2 added
3bbabf6d298c42_GRCh38.primary_assembly.genome.fa.5.ht2 added
3bbabfa74a2d_GRCh38.primary_assembly.genome.fa.6.ht2 added
3bbabf20683fd4_GRCh38.primary_assembly.genome.fa.7.ht2 added
3bbabf5c435c6_GRCh38.primary_assembly.genome.fa.8.ht2 added
3bbabf14466fc3_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3bbabf4393cca7_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3bbabf65031e37_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3bbabf28cb0ca4_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
3bbabf4d5bb0f9_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3bbabf97a0b16_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
3bbabf5fcfcade_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3bbabf36ce6770_GRCh38.primary_assembly.genome.fa.fai added
3bbabf57c46dba_GRCh38.primary_assembly.genome.fa.amb added
3bbabf29cc8480_GRCh38.primary_assembly.genome.fa.ann added
3bbabf7b4fb0f9_GRCh38.primary_assembly.genome.fa.bwt added
3bbabf3bd10f42_GRCh38.primary_assembly.genome.fa.pac added
3bbabf78316a4c_GRCh38.primary_assembly.genome.fa.sa added
3bbabf27589369_GRCh38.primary_assembly.genome.fa added
3bbabf16aea603_hs37d5.fa.fai added
3bbabf7302e264_hs37d5.fa.amb added
3bbabf1484ee37_hs37d5.fa.ann added
3bbabf5e9b631e_hs37d5.fa.bwt added
3bbabfd156b5d_hs37d5.fa.pac added
3bbabff8293bd_hs37d5.fa.sa added
3bbabf75f6190f_hs37d5.fa added
3bbabf74779bb7_complete_ref_lens.bin added
3bbabf32173998_ctable.bin added
3bbabf3962d551_ctg_offsets.bin added
3bbabf315b73e9_duplicate_clusters.tsv added
3bbabf558b929c_info.json added
3bbabf29e10d85_mphf.bin added
3bbabf1e85002b_pos.bin added
3bbabf5632dcc9_pre_indexing.log added
3bbabf4a494d59_rank.bin added
3bbabf244935f1_ref_indexing.log added
3bbabf6a794c8d_refAccumLengths.bin added
3bbabfddd1a01_reflengths.bin added
3bbabf94c5428_refseq.bin added
3bbabf13445931_seq.bin added
3bbabf5b38cafa_versionInfo.json added
3bbabf12c65f3f_salmon_index added
3bbabf7314240f_chrLength.txt added
3bbabf1207326a_chrName.txt added
3bbabf6a8accf9_chrNameLength.txt added
3bbabf1ce0a88f_chrStart.txt added
3bbabfd56e364_exonGeTrInfo.tab added
3bbabf265bdc3b_exonInfo.tab added
3bbabf151212dc_geneInfo.tab added
3bbabf34af76cd_Genome added
3bbabf3d0a823e_genomeParameters.txt added
3bbabf814f540_Log.out added
3bbabf49346504_SA added
3bbabf1ba5e55c_SAindex added
3bbabf152a609d_sjdbInfo.txt added
3bbabf58b6f8c2_sjdbList.fromGTF.out.tab added
3bbabf119bfe6c_sjdbList.out.tab added
3bbabf9a1fc55_transcriptInfo.tab added
3bbabface325a_GRCh38.GENCODE.v42_100 added
3bbabf4afed3bd_knownGene_hg38.sql added
3bbabf3afd703e_knownGene_hg38.txt added
3bbabf6059c4f6_refGene_hg38.sql added
3bbabf74dfe142_refGene_hg38.txt added
3bbabf59827069_knownGene_mm39.sql added
3bbabf368ca1c0_knownGene_mm39.txt added
3bbabf3f292e9c_refGene_mm39.sql added
3bbabf7dcba65a_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/Rtmp68J6Os/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
18.641 1.168 19.989
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.388 | 0.431 | 6.822 | |
| dataSearch | 1.168 | 0.060 | 1.229 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.725 | 0.109 | 3.243 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.130 | 0.003 | 0.134 | |
| recipeLoad | 1.391 | 0.025 | 1.420 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.539 | 0.013 | 0.552 | |
| recipeUpdate | 0 | 0 | 0 | |