Qian Liu
| Snapshot Date: 2026-03-05 13:45 -0500 (Thu, 05 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 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-06 11:58 -0500 (Fri, 06 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" | 4894 |
| 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: 2026-03-06 03:25:44 -0500 (Fri, 06 Mar 2026) |
| EndedAt: 2026-03-06 03:28:32 -0500 (Fri, 06 Mar 2026) |
| EllapsedTime: 168.2 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 24.04.3 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 5.937 0.256 6.199
getCloudData 2.605 0.196 5.332
* 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...
36f0243514bcfe_GRCh38.primary_assembly.genome.fa.1.bt2 added
36f024690f911d_GRCh38.primary_assembly.genome.fa.2.bt2 added
36f0247c5ae21d_GRCh38.primary_assembly.genome.fa.3.bt2 added
36f024327734f2_GRCh38.primary_assembly.genome.fa.4.bt2 added
36f024350f12b7_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
36f0243b3dc5d9_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
36f0243e0d798a_outfile.txt added
36f0242048f4de_GRCh37_to_GRCh38.chain added
36f024463ae5ba_GRCh37_to_NCBI34.chain added
36f024139f8359_GRCh37_to_NCBI35.chain added
36f02412f0d4d5_GRCh37_to_NCBI36.chain added
36f0244e5c000f_GRCh38_to_GRCh37.chain added
36f024569ab550_GRCh38_to_NCBI34.chain added
36f024320484bf_GRCh38_to_NCBI35.chain added
36f0244b8e816c_GRCh38_to_NCBI36.chain added
36f02451389891_NCBI34_to_GRCh37.chain added
36f0243b63b877_NCBI34_to_GRCh38.chain added
36f024793bb8b6_NCBI35_to_GRCh37.chain added
36f0246e156bc8_NCBI35_to_GRCh38.chain added
36f0247bc61e5a_NCBI36_to_GRCh37.chain added
36f0245a66e439_NCBI36_to_GRCh38.chain added
36f0242756bce3_GRCm38_to_NCBIM36.chain added
36f0244f5b3c26_GRCm38_to_NCBIM37.chain added
36f0244f29d7d5_NCBIM36_to_GRCm38.chain added
36f0243c3d821c_NCBIM37_to_GRCm38.chain added
36f02466870801_1000G_omni2.5.b37.vcf.gz added
36f0249cf05d_1000G_omni2.5.b37.vcf.gz.tbi added
36f0241b8fa062_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
36f0241734966e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
36f02446124844_1000G_omni2.5.hg38.vcf.gz added
36f02426724aee_1000G_omni2.5.hg38.vcf.gz.tbi added
36f0244c49536d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
36f0242f21d961_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
36f02422cd2d0c_af-only-gnomad.raw.sites.vcf added
36f0247ec0885f_af-only-gnomad.raw.sites.vcf.idx added
36f0246430ec19_Mutect2-exome-panel.vcf.idx added
36f0245e0af2e5_Mutect2-WGS-panel-b37.vcf added
36f0243cce01e9_Mutect2-WGS-panel-b37.vcf.idx added
36f024479e0f7_small_exac_common_3.vcf added
36f0242445d8a0_small_exac_common_3.vcf.idx added
36f024506d8542_1000g_pon.hg38.vcf.gz added
36f024176ab5cd_1000g_pon.hg38.vcf.gz.tbi added
36f02472a1d8af_af-only-gnomad.hg38.vcf.gz added
36f02427083a92_af-only-gnomad.hg38.vcf.gz.tbi added
36f024496f3a8c_small_exac_common_3.hg38.vcf.gz added
36f0243e305a1b_small_exac_common_3.hg38.vcf.gz.tbi added
36f0247840d324_gencode.v41.annotation.gtf added
36f0244d2f303_gencode.v42.annotation.gtf added
36f024376c12d2_gencode.vM30.annotation.gtf added
36f02466563eec_gencode.vM31.annotation.gtf added
36f02499115d_gencode.v41.transcripts.fa added
36f02411d2f70b_gencode.v41.transcripts.fa.fai added
36f024dacfbcf_gencode.v42.transcripts.fa added
36f0244ff44d83_gencode.v42.transcripts.fa.fai added
36f02460fccee0_gencode.vM30.pc_transcripts.fa added
36f02449ea7deb_gencode.vM30.pc_transcripts.fa.fai added
36f024367b5585_gencode.vM31.pc_transcripts.fa added
36f0246199bf3d_gencode.vM31.pc_transcripts.fa.fai added
36f024657a1e4d_GRCh38.primary_assembly.genome.fa.1.ht2 added
36f0244dafebf3_GRCh38.primary_assembly.genome.fa.2.ht2 added
36f02427ac0781_GRCh38.primary_assembly.genome.fa.3.ht2 added
36f024bec693c_GRCh38.primary_assembly.genome.fa.4.ht2 added
36f02419f93f60_GRCh38.primary_assembly.genome.fa.5.ht2 added
36f02456cde0e3_GRCh38.primary_assembly.genome.fa.6.ht2 added
36f0242eb99648_GRCh38.primary_assembly.genome.fa.7.ht2 added
36f02418b9c7bf_GRCh38.primary_assembly.genome.fa.8.ht2 added
36f0243afeccfc_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
36f024cc4892d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
36f0245587c9a8_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
36f0243f78adf3_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
36f024310a61cd_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
36f02425f54eea_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
36f02456e363c0_GRCh38_full_analysis_set_plus_decoy_hla.fa added
36f02423ac3a7c_GRCh38.primary_assembly.genome.fa.fai added
36f0244cfd897d_GRCh38.primary_assembly.genome.fa.amb added
36f02420529e4c_GRCh38.primary_assembly.genome.fa.ann added
36f02461dc9498_GRCh38.primary_assembly.genome.fa.bwt added
36f024453e5ca1_GRCh38.primary_assembly.genome.fa.pac added
36f0242525914f_GRCh38.primary_assembly.genome.fa.sa added
36f0241948a76a_GRCh38.primary_assembly.genome.fa added
36f0242b949b8d_hs37d5.fa.fai added
36f02425bea2ac_hs37d5.fa.amb added
36f0242b1b9e75_hs37d5.fa.ann added
36f0243941975c_hs37d5.fa.bwt added
36f02475b2f030_hs37d5.fa.pac added
36f024c186d55_hs37d5.fa.sa added
36f02432c1547_hs37d5.fa added
36f0242c2e45b5_complete_ref_lens.bin added
36f0246db22c93_ctable.bin added
36f02468a63395_ctg_offsets.bin added
36f02479de31a8_duplicate_clusters.tsv added
36f024155e3414_info.json added
36f02474929cd1_mphf.bin added
36f02413d77109_pos.bin added
36f0246c2c14f7_pre_indexing.log added
36f024234c3319_rank.bin added
36f0242c9138c8_ref_indexing.log added
36f024272ae1f3_refAccumLengths.bin added
36f0243010bc46_reflengths.bin added
36f0242190271_refseq.bin added
36f02466a38fe7_seq.bin added
36f024611b1e14_versionInfo.json added
36f024280e515b_salmon_index added
36f0243d86f3a7_chrLength.txt added
36f0244c75890_chrName.txt added
36f024750bdad8_chrNameLength.txt added
36f0245dd991f4_chrStart.txt added
36f02466a3ed28_exonGeTrInfo.tab added
36f0243a4a3779_exonInfo.tab added
36f0242ff2343_geneInfo.tab added
36f0247fec9492_Genome added
36f02465ded306_genomeParameters.txt added
36f02428bdc5f0_Log.out added
36f0242b083307_SA added
36f0241f206a62_SAindex added
36f0241e70b620_sjdbInfo.txt added
36f0243720a05d_sjdbList.fromGTF.out.tab added
36f024224c7faa_sjdbList.out.tab added
36f0244a9efbd5_transcriptInfo.tab added
36f02424d2ccf0_GRCh38.GENCODE.v42_100 added
36f024af2b33f_knownGene_hg38.sql added
36f024447d2d7d_knownGene_hg38.txt added
36f0243a310104_refGene_hg38.sql added
36f0247f855010_refGene_hg38.txt added
36f02458549e86_knownGene_mm39.sql added
36f024265d15fc_knownGene_mm39.txt added
36f02422d18329_refGene_mm39.sql added
36f0244e5d74f_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/RtmpXtOPoh/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
17.933 1.001 20.170
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.937 | 0.256 | 6.199 | |
| dataSearch | 1.088 | 0.024 | 1.111 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.605 | 0.196 | 5.332 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.111 | 0.002 | 0.114 | |
| recipeLoad | 1.195 | 0.055 | 1.251 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.54 | 0.02 | 0.56 | |
| recipeUpdate | 0 | 0 | 0 | |