Qian Liu
| Snapshot Date: 2026-03-11 13:40 -0400 (Wed, 11 Mar 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 Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-12 11:34 -0400 (Thu, 12 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4806 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4049 |
| 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 1776/2360 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.11.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 2026-03-12 02:58:44 -0400 (Thu, 12 Mar 2026) |
| EndedAt: 2026-03-12 03:01:34 -0400 (Thu, 12 Mar 2026) |
| EllapsedTime: 169.6 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 Under development (unstable) (2026-03-05 r89546)
* 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
* current time: 2026-03-12 06:58:44 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 5.837 0.374 6.213
* 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 Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
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...
b68f5754f362d_GRCh38.primary_assembly.genome.fa.1.bt2 added
b68f5639f6dd5_GRCh38.primary_assembly.genome.fa.2.bt2 added
b68f5720322f4_GRCh38.primary_assembly.genome.fa.3.bt2 added
b68f5198e0e9b_GRCh38.primary_assembly.genome.fa.4.bt2 added
b68f51ee41179_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
b68f571688e13_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
b68f55498caf4_outfile.txt added
b68f55035e534_GRCh37_to_GRCh38.chain added
b68f513dacc03_GRCh37_to_NCBI34.chain added
b68f57acd7d0d_GRCh37_to_NCBI35.chain added
b68f57445392c_GRCh37_to_NCBI36.chain added
b68f55116e67e_GRCh38_to_GRCh37.chain added
b68f545bdb9a9_GRCh38_to_NCBI34.chain added
b68f5130e702c_GRCh38_to_NCBI35.chain added
b68f5121b25a5_GRCh38_to_NCBI36.chain added
b68f531f3454f_NCBI34_to_GRCh37.chain added
b68f548e25444_NCBI34_to_GRCh38.chain added
b68f570d4012d_NCBI35_to_GRCh37.chain added
b68f52be5724b_NCBI35_to_GRCh38.chain added
b68f51c23b567_NCBI36_to_GRCh37.chain added
b68f56c300adb_NCBI36_to_GRCh38.chain added
b68f577c566f5_GRCm38_to_NCBIM36.chain added
b68f5da8e266_GRCm38_to_NCBIM37.chain added
b68f558a13ea_NCBIM36_to_GRCm38.chain added
b68f53fa1042b_NCBIM37_to_GRCm38.chain added
b68f57af2787d_1000G_omni2.5.b37.vcf.gz added
b68f577fbba2b_1000G_omni2.5.b37.vcf.gz.tbi added
b68f57abc91c3_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
b68f575b16bb_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
b68f5114079b3_1000G_omni2.5.hg38.vcf.gz added
b68f531a0ded3_1000G_omni2.5.hg38.vcf.gz.tbi added
b68f57caa4ce9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
b68f574dfe788_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
b68f523a401c7_af-only-gnomad.raw.sites.vcf added
b68f516385b84_af-only-gnomad.raw.sites.vcf.idx added
b68f513c3f901_Mutect2-exome-panel.vcf.idx added
b68f5150c8fda_Mutect2-WGS-panel-b37.vcf added
b68f56ad12678_Mutect2-WGS-panel-b37.vcf.idx added
b68f563f9de35_small_exac_common_3.vcf added
b68f528e75bde_small_exac_common_3.vcf.idx added
b68f5659ea385_1000g_pon.hg38.vcf.gz added
b68f5583f1761_1000g_pon.hg38.vcf.gz.tbi added
b68f579fe425c_af-only-gnomad.hg38.vcf.gz added
b68f52b5c5d2e_af-only-gnomad.hg38.vcf.gz.tbi added
b68f56b4d878d_small_exac_common_3.hg38.vcf.gz added
b68f5c196801_small_exac_common_3.hg38.vcf.gz.tbi added
b68f55d4fa27e_gencode.v41.annotation.gtf added
b68f5342fdbd2_gencode.v42.annotation.gtf added
b68f57ced692e_gencode.vM30.annotation.gtf added
b68f593514c9_gencode.vM31.annotation.gtf added
b68f550539139_gencode.v41.transcripts.fa added
b68f5691d7409_gencode.v41.transcripts.fa.fai added
b68f5fa7bbe_gencode.v42.transcripts.fa added
b68f55dfc739f_gencode.v42.transcripts.fa.fai added
b68f56ea787f4_gencode.vM30.pc_transcripts.fa added
b68f5409b7fe9_gencode.vM30.pc_transcripts.fa.fai added
b68f558eeec1c_gencode.vM31.pc_transcripts.fa added
b68f566a3421f_gencode.vM31.pc_transcripts.fa.fai added
b68f53b5811ad_GRCh38.primary_assembly.genome.fa.1.ht2 added
b68f5604a02d8_GRCh38.primary_assembly.genome.fa.2.ht2 added
b68f577e3bbd2_GRCh38.primary_assembly.genome.fa.3.ht2 added
b68f56cf8f080_GRCh38.primary_assembly.genome.fa.4.ht2 added
b68f55cf44fc1_GRCh38.primary_assembly.genome.fa.5.ht2 added
b68f56cc3a35a_GRCh38.primary_assembly.genome.fa.6.ht2 added
b68f5109cf247_GRCh38.primary_assembly.genome.fa.7.ht2 added
b68f5732cab45_GRCh38.primary_assembly.genome.fa.8.ht2 added
b68f5879c5b_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
b68f525a98221_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
b68f55dfdd1bd_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
b68f564817a90_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
b68f54e90ddff_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
b68f5439c7542_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
b68f53cc091f2_GRCh38_full_analysis_set_plus_decoy_hla.fa added
b68f5488f205b_GRCh38.primary_assembly.genome.fa.fai added
b68f56ef8d271_GRCh38.primary_assembly.genome.fa.amb added
b68f5280e197f_GRCh38.primary_assembly.genome.fa.ann added
b68f554a8885d_GRCh38.primary_assembly.genome.fa.bwt added
b68f54c4874ef_GRCh38.primary_assembly.genome.fa.pac added
b68f55c3df551_GRCh38.primary_assembly.genome.fa.sa added
b68f55195f18b_GRCh38.primary_assembly.genome.fa added
b68f5557d89b8_hs37d5.fa.fai added
b68f52c91868a_hs37d5.fa.amb added
b68f53ab36595_hs37d5.fa.ann added
b68f556780577_hs37d5.fa.bwt added
b68f5a8dfa29_hs37d5.fa.pac added
b68f5295aed89_hs37d5.fa.sa added
b68f517138560_hs37d5.fa added
b68f5637ce646_complete_ref_lens.bin added
b68f5ffe2fa8_ctable.bin added
b68f5526b970d_ctg_offsets.bin added
b68f543c6e91e_duplicate_clusters.tsv added
b68f57e1eb7b_info.json added
b68f53f64878d_mphf.bin added
b68f520bb38df_pos.bin added
b68f574a58ed5_pre_indexing.log added
b68f5500179d4_rank.bin added
b68f513e7e424_ref_indexing.log added
b68f5752d2b31_refAccumLengths.bin added
b68f575aafbf6_reflengths.bin added
b68f571e5b5e1_refseq.bin added
b68f559aea5c1_seq.bin added
b68f5443bd9f5_versionInfo.json added
b68f535822b23_salmon_index added
b68f5166f37b3_chrLength.txt added
b68f5ccafa51_chrName.txt added
b68f5247afd94_chrNameLength.txt added
b68f53e7d5133_chrStart.txt added
b68f5617382ae_exonGeTrInfo.tab added
b68f570c37283_exonInfo.tab added
b68f51abb4684_geneInfo.tab added
b68f533097439_Genome added
b68f54640fc3c_genomeParameters.txt added
b68f5474ccd0f_Log.out added
b68f56dbcd9ce_SA added
b68f51cb901b3_SAindex added
b68f551dac738_sjdbInfo.txt added
b68f51717c757_sjdbList.fromGTF.out.tab added
b68f533cc8713_sjdbList.out.tab added
b68f53557ad7e_transcriptInfo.tab added
b68f52715f700_GRCh38.GENCODE.v42_100 added
b68f56381e21_knownGene_hg38.sql added
b68f5791e969c_knownGene_hg38.txt added
b68f52ef7e27b_refGene_hg38.sql added
b68f5459ca5ae_refGene_hg38.txt added
b68f519d9cf7b_knownGene_mm39.sql added
b68f5239d7150_knownGene_mm39.txt added
b68f5159e1f83_refGene_mm39.sql added
b68f52dc1b39f_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/Rtmpd1ZkV2/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
18.569 1.546 20.438
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.837 | 0.374 | 6.213 | |
| dataSearch | 1.155 | 0.038 | 1.193 | |
| dataUpdate | 0.001 | 0.000 | 0.001 | |
| getCloudData | 2.626 | 0.152 | 3.667 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.123 | 0.004 | 0.128 | |
| recipeLoad | 1.274 | 0.071 | 1.346 | |
| recipeMake | 0.001 | 0.000 | 0.001 | |
| recipeSearch | 0.542 | 0.011 | 0.554 | |
| recipeUpdate | 0.000 | 0.000 | 0.001 | |