Qian Liu
| Snapshot Date: 2026-01-19 13:45 -0500 (Mon, 19 Jan 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 2026-01-22 11:58 -0500 (Thu, 22 Jan 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" | 4886 |
| 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 | | ||||||||
|
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: 2026-01-20 03:18:37 -0500 (Tue, 20 Jan 2026) |
| EndedAt: 2026-01-20 03:21:21 -0500 (Tue, 20 Jan 2026) |
| EllapsedTime: 164.2 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 5.921 0.245 6.17
* 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...
3174216477a1d7_GRCh38.primary_assembly.genome.fa.1.bt2 added
3174214d9da048_GRCh38.primary_assembly.genome.fa.2.bt2 added
317421910a970_GRCh38.primary_assembly.genome.fa.3.bt2 added
31742161474bba_GRCh38.primary_assembly.genome.fa.4.bt2 added
31742129445a54_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
3174212e74d39a_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
31742124fc9338_outfile.txt added
31742151864f59_GRCh37_to_GRCh38.chain added
31742132c558c3_GRCh37_to_NCBI34.chain added
3174217b211bc1_GRCh37_to_NCBI35.chain added
317421413a472d_GRCh37_to_NCBI36.chain added
3174215f5d6bd4_GRCh38_to_GRCh37.chain added
3174215b146c3e_GRCh38_to_NCBI34.chain added
317421cf1155c_GRCh38_to_NCBI35.chain added
3174211171e0f5_GRCh38_to_NCBI36.chain added
317421863c9af_NCBI34_to_GRCh37.chain added
317421b9301dd_NCBI34_to_GRCh38.chain added
317421609345b4_NCBI35_to_GRCh37.chain added
3174217f038c3c_NCBI35_to_GRCh38.chain added
31742145f68cd6_NCBI36_to_GRCh37.chain added
31742159b811f9_NCBI36_to_GRCh38.chain added
3174211274045c_GRCm38_to_NCBIM36.chain added
3174215dcd1fb_GRCm38_to_NCBIM37.chain added
317421e7431e9_NCBIM36_to_GRCm38.chain added
317421187c5bd9_NCBIM37_to_GRCm38.chain added
31742115b89a6_1000G_omni2.5.b37.vcf.gz added
3174216b54e99_1000G_omni2.5.b37.vcf.gz.tbi added
3174219e1273e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
317421779362f9_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
3174211a4582e8_1000G_omni2.5.hg38.vcf.gz added
3174212d754582_1000G_omni2.5.hg38.vcf.gz.tbi added
3174215c0b04d0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
31742167e32330_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
3174213685eef2_af-only-gnomad.raw.sites.vcf added
3174213d52508b_af-only-gnomad.raw.sites.vcf.idx added
31742111277d84_Mutect2-exome-panel.vcf.idx added
31742164fac28c_Mutect2-WGS-panel-b37.vcf added
317421624ee3c3_Mutect2-WGS-panel-b37.vcf.idx added
31742162adccde_small_exac_common_3.vcf added
31742117c01b50_small_exac_common_3.vcf.idx added
3174215d6fff84_1000g_pon.hg38.vcf.gz added
31742123e8140b_1000g_pon.hg38.vcf.gz.tbi added
317421771d8724_af-only-gnomad.hg38.vcf.gz added
31742138846bc2_af-only-gnomad.hg38.vcf.gz.tbi added
31742130d92967_small_exac_common_3.hg38.vcf.gz added
31742188f6819_small_exac_common_3.hg38.vcf.gz.tbi added
31742140e83571_gencode.v41.annotation.gtf added
3174213c6c2b45_gencode.v42.annotation.gtf added
3174216922adce_gencode.vM30.annotation.gtf added
3174213febc1ae_gencode.vM31.annotation.gtf added
317421262b81b_gencode.v41.transcripts.fa added
31742142dabfc7_gencode.v41.transcripts.fa.fai added
317421525fc60a_gencode.v42.transcripts.fa added
31742183f8a17_gencode.v42.transcripts.fa.fai added
317421514ef1b0_gencode.vM30.pc_transcripts.fa added
3174216adc21e3_gencode.vM30.pc_transcripts.fa.fai added
31742199b13bd_gencode.vM31.pc_transcripts.fa added
3174215804404a_gencode.vM31.pc_transcripts.fa.fai added
31742174bd4921_GRCh38.primary_assembly.genome.fa.1.ht2 added
31742112e76b6_GRCh38.primary_assembly.genome.fa.2.ht2 added
3174217249c332_GRCh38.primary_assembly.genome.fa.3.ht2 added
31742122328ea3_GRCh38.primary_assembly.genome.fa.4.ht2 added
3174215d397b87_GRCh38.primary_assembly.genome.fa.5.ht2 added
3174215a2ce662_GRCh38.primary_assembly.genome.fa.6.ht2 added
31742158b87d95_GRCh38.primary_assembly.genome.fa.7.ht2 added
3174211a8bcc12_GRCh38.primary_assembly.genome.fa.8.ht2 added
3174216b5463e6_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
3174213db34022_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
3174217cdaafd5_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
3174214e0230c4_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
31742155735b72_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
3174215a4aaf59_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
31742171ea44cf_GRCh38_full_analysis_set_plus_decoy_hla.fa added
3174214c90e296_GRCh38.primary_assembly.genome.fa.fai added
31742112cf1b1b_GRCh38.primary_assembly.genome.fa.amb added
31742122c36e37_GRCh38.primary_assembly.genome.fa.ann added
31742155204ab0_GRCh38.primary_assembly.genome.fa.bwt added
31742153b7508d_GRCh38.primary_assembly.genome.fa.pac added
3174215f2f997c_GRCh38.primary_assembly.genome.fa.sa added
3174213e42f87e_GRCh38.primary_assembly.genome.fa added
31742113a3123b_hs37d5.fa.fai added
31742161925197_hs37d5.fa.amb added
31742111db845_hs37d5.fa.ann added
3174216602d845_hs37d5.fa.bwt added
31742169d1dbae_hs37d5.fa.pac added
317421526ca9f6_hs37d5.fa.sa added
31742150defa28_hs37d5.fa added
317421736cef6c_complete_ref_lens.bin added
3174212a70ea40_ctable.bin added
317421459c4349_ctg_offsets.bin added
317421749b6622_duplicate_clusters.tsv added
3174211cbaad72_info.json added
31742167ced1ed_mphf.bin added
31742151d4e1a9_pos.bin added
31742176e793d4_pre_indexing.log added
31742140874f82_rank.bin added
3174216c60adbb_ref_indexing.log added
317421623bf7ba_refAccumLengths.bin added
3174217e3a8fa4_reflengths.bin added
317421693b5d90_refseq.bin added
317421303e287f_seq.bin added
31742153adeb16_versionInfo.json added
31742143860ce9_salmon_index added
31742122286d4e_chrLength.txt added
317421203ecdad_chrName.txt added
31742156552805_chrNameLength.txt added
31742144ebdb85_chrStart.txt added
317421755f185d_exonGeTrInfo.tab added
3174212a0c7892_exonInfo.tab added
317421241b7501_geneInfo.tab added
31742133a210db_Genome added
3174213daf8acd_genomeParameters.txt added
3174215adc699_Log.out added
31742134bfc920_SA added
31742123b26312_SAindex added
3174216f7fa247_sjdbInfo.txt added
31742172c7316_sjdbList.fromGTF.out.tab added
31742174915d3a_sjdbList.out.tab added
31742162ec91b3_transcriptInfo.tab added
317421319d5d56_GRCh38.GENCODE.v42_100 added
3174213a2da083_knownGene_hg38.sql added
3174215787f7d6_knownGene_hg38.txt added
3174214e580ac8_refGene_hg38.sql added
31742121fc7270_refGene_hg38.txt added
317421295cd97f_knownGene_mm39.sql added
317421453f9e9c_knownGene_mm39.txt added
3174216283c1f3_refGene_mm39.sql added
31742115bd873b_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/Rtmp5VVUdb/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 0 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
>
>
>
> proc.time()
user system elapsed
18.223 1.524 20.089
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.921 | 0.245 | 6.170 | |
| dataSearch | 1.110 | 0.025 | 1.135 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.955 | 0.568 | 4.513 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.13 | 0.00 | 0.13 | |
| recipeLoad | 1.321 | 0.053 | 1.375 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.556 | 0.033 | 0.589 | |
| recipeUpdate | 0.001 | 0.000 | 0.000 | |