Qian Liu
| Snapshot Date: 2026-04-10 13:40 -0400 (Fri, 10 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 Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-11 11:36 -0400 (Sat, 11 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4919 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4631 |
| 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 1793/2390 | 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 | | ||||||||
| 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: 2026-04-11 03:40:29 -0400 (Sat, 11 Apr 2026) |
| EndedAt: 2026-04-11 03:43:16 -0400 (Sat, 11 Apr 2026) |
| EllapsedTime: 167.4 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* 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: 2026-04-11 07:40:29 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 6.19 0.385 6.578
* 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 alpha (2026-04-05 r89794)
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...
2fbb5557e50c8_GRCh38.primary_assembly.genome.fa.1.bt2 added
2fbb554fd68478_GRCh38.primary_assembly.genome.fa.2.bt2 added
2fbb5548494b92_GRCh38.primary_assembly.genome.fa.3.bt2 added
2fbb5566ec9167_GRCh38.primary_assembly.genome.fa.4.bt2 added
2fbb551970e0cc_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2fbb55234b389f_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2fbb5529b5cfdd_outfile.txt added
2fbb552ea8e931_GRCh37_to_GRCh38.chain added
2fbb5575f674a7_GRCh37_to_NCBI34.chain added
2fbb55771ac1e_GRCh37_to_NCBI35.chain added
2fbb552ecabefa_GRCh37_to_NCBI36.chain added
2fbb55422e8c2c_GRCh38_to_GRCh37.chain added
2fbb5576c86c94_GRCh38_to_NCBI34.chain added
2fbb551eac394_GRCh38_to_NCBI35.chain added
2fbb55691a05b0_GRCh38_to_NCBI36.chain added
2fbb551ab9c484_NCBI34_to_GRCh37.chain added
2fbb55472672b6_NCBI34_to_GRCh38.chain added
2fbb55d3720fe_NCBI35_to_GRCh37.chain added
2fbb55e023f69_NCBI35_to_GRCh38.chain added
2fbb5556f1c0b0_NCBI36_to_GRCh37.chain added
2fbb552bf47b81_NCBI36_to_GRCh38.chain added
2fbb5567d2413e_GRCm38_to_NCBIM36.chain added
2fbb5564f7f8_GRCm38_to_NCBIM37.chain added
2fbb551bf2752e_NCBIM36_to_GRCm38.chain added
2fbb55e945b48_NCBIM37_to_GRCm38.chain added
2fbb5571b2d31d_1000G_omni2.5.b37.vcf.gz added
2fbb5557ee293_1000G_omni2.5.b37.vcf.gz.tbi added
2fbb5522ce5442_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2fbb557640a38c_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2fbb554f0717ee_1000G_omni2.5.hg38.vcf.gz added
2fbb55323300c8_1000G_omni2.5.hg38.vcf.gz.tbi added
2fbb557bbef454_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2fbb551edd9c67_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2fbb557a7c4c5a_af-only-gnomad.raw.sites.vcf added
2fbb5562ab85bc_af-only-gnomad.raw.sites.vcf.idx added
2fbb55384e7d33_Mutect2-exome-panel.vcf.idx added
2fbb551dc784f9_Mutect2-WGS-panel-b37.vcf added
2fbb55c615599_Mutect2-WGS-panel-b37.vcf.idx added
2fbb5566f76664_small_exac_common_3.vcf added
2fbb5513bdf9a0_small_exac_common_3.vcf.idx added
2fbb5513d301b7_1000g_pon.hg38.vcf.gz added
2fbb5515c2255e_1000g_pon.hg38.vcf.gz.tbi added
2fbb5555ec85cc_af-only-gnomad.hg38.vcf.gz added
2fbb55a9b6e4b_af-only-gnomad.hg38.vcf.gz.tbi added
2fbb5517ace8f2_small_exac_common_3.hg38.vcf.gz added
2fbb553f068b7c_small_exac_common_3.hg38.vcf.gz.tbi added
2fbb55255532d0_gencode.v41.annotation.gtf added
2fbb555ed35ba9_gencode.v42.annotation.gtf added
2fbb554c3dac7a_gencode.vM30.annotation.gtf added
2fbb5533577239_gencode.vM31.annotation.gtf added
2fbb5535c51c59_gencode.v41.transcripts.fa added
2fbb55783227fb_gencode.v41.transcripts.fa.fai added
2fbb551b29b377_gencode.v42.transcripts.fa added
2fbb55362a1451_gencode.v42.transcripts.fa.fai added
2fbb5514249d2a_gencode.vM30.pc_transcripts.fa added
2fbb5529be0ec0_gencode.vM30.pc_transcripts.fa.fai added
2fbb5527dce76e_gencode.vM31.pc_transcripts.fa added
2fbb5519a37fbd_gencode.vM31.pc_transcripts.fa.fai added
2fbb554c8c6302_GRCh38.primary_assembly.genome.fa.1.ht2 added
2fbb551e1d8afa_GRCh38.primary_assembly.genome.fa.2.ht2 added
2fbb5568aa97ac_GRCh38.primary_assembly.genome.fa.3.ht2 added
2fbb557ebf63cb_GRCh38.primary_assembly.genome.fa.4.ht2 added
2fbb5519dc7f4f_GRCh38.primary_assembly.genome.fa.5.ht2 added
2fbb557883413_GRCh38.primary_assembly.genome.fa.6.ht2 added
2fbb55793bb025_GRCh38.primary_assembly.genome.fa.7.ht2 added
2fbb557c88050b_GRCh38.primary_assembly.genome.fa.8.ht2 added
2fbb553fd6b146_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2fbb551703351f_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2fbb558e95aa4_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2fbb5526ce17aa_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2fbb552ac12ebf_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2fbb551cbc5c5c_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2fbb553c903d08_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2fbb55adb48c_GRCh38.primary_assembly.genome.fa.fai added
2fbb552757caa7_GRCh38.primary_assembly.genome.fa.amb added
2fbb55543d25fa_GRCh38.primary_assembly.genome.fa.ann added
2fbb553fb44008_GRCh38.primary_assembly.genome.fa.bwt added
2fbb554cacfd77_GRCh38.primary_assembly.genome.fa.pac added
2fbb55331081a3_GRCh38.primary_assembly.genome.fa.sa added
2fbb55bf1ec83_GRCh38.primary_assembly.genome.fa added
2fbb5546fb0_hs37d5.fa.fai added
2fbb5568d59dfc_hs37d5.fa.amb added
2fbb55424147e_hs37d5.fa.ann added
2fbb551b2e2328_hs37d5.fa.bwt added
2fbb551effb24e_hs37d5.fa.pac added
2fbb551848b1a8_hs37d5.fa.sa added
2fbb5544ec31e8_hs37d5.fa added
2fbb5546dc99bc_complete_ref_lens.bin added
2fbb5531ec3166_ctable.bin added
2fbb55117894ea_ctg_offsets.bin added
2fbb5564fa24b7_duplicate_clusters.tsv added
2fbb551a96c912_info.json added
2fbb551037f8b5_mphf.bin added
2fbb557ed6a406_pos.bin added
2fbb55221efd25_pre_indexing.log added
2fbb55973a8db_rank.bin added
2fbb557b5ea911_ref_indexing.log added
2fbb5561f5ae6b_refAccumLengths.bin added
2fbb552076ddfa_reflengths.bin added
2fbb5544803b5_refseq.bin added
2fbb558c3c615_seq.bin added
2fbb554b380cb9_versionInfo.json added
2fbb5521046011_salmon_index added
2fbb554554031d_chrLength.txt added
2fbb554be5c145_chrName.txt added
2fbb55485c2ab9_chrNameLength.txt added
2fbb5519912917_chrStart.txt added
2fbb55b9a014e_exonGeTrInfo.tab added
2fbb5515092830_exonInfo.tab added
2fbb554ca1aabb_geneInfo.tab added
2fbb55178bedd1_Genome added
2fbb55150d97e1_genomeParameters.txt added
2fbb55357748b7_Log.out added
2fbb551bb0024f_SA added
2fbb55303bbb09_SAindex added
2fbb555476fb05_sjdbInfo.txt added
2fbb5533f8b3f8_sjdbList.fromGTF.out.tab added
2fbb557527ecf1_sjdbList.out.tab added
2fbb551b5394c2_transcriptInfo.tab added
2fbb5565e4e55e_GRCh38.GENCODE.v42_100 added
2fbb556a081db_knownGene_hg38.sql added
2fbb554db979_knownGene_hg38.txt added
2fbb557bae70_refGene_hg38.sql added
2fbb5516d87a91_refGene_hg38.txt added
2fbb557f245d7f_knownGene_mm39.sql added
2fbb55229aab95_knownGene_mm39.txt added
2fbb55204c236c_refGene_mm39.sql added
2fbb557a830690_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/RtmpAbmW01/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
20.290 1.463 23.014
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.190 | 0.385 | 6.578 | |
| dataSearch | 1.137 | 0.024 | 1.162 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.624 | 0.098 | 3.231 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.130 | 0.004 | 0.135 | |
| recipeLoad | 1.305 | 0.079 | 1.392 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.512 | 0.013 | 0.524 | |
| recipeUpdate | 0 | 0 | 0 | |