Qian Liu
| Snapshot Date: 2026-03-06 13:45 -0500 (Fri, 06 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 2026-03-07 11:57 -0500 (Sat, 07 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" | 4892 |
| 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: 2026-03-07 03:27:43 -0500 (Sat, 07 Mar 2026) |
| EndedAt: 2026-03-07 03:30:31 -0500 (Sat, 07 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 5.661 0.249 5.915
getCloudData 2.879 0.191 5.819
* 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...
18310f2dbc9d38_GRCh38.primary_assembly.genome.fa.1.bt2 added
18310ff8a3ad1_GRCh38.primary_assembly.genome.fa.2.bt2 added
18310f1a7f692_GRCh38.primary_assembly.genome.fa.3.bt2 added
18310f717abc4e_GRCh38.primary_assembly.genome.fa.4.bt2 added
18310f3efb3fd9_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
18310f3035e431_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
18310f29fc052c_outfile.txt added
18310f79926eb3_GRCh37_to_GRCh38.chain added
18310f7e749b44_GRCh37_to_NCBI34.chain added
18310f1c8ac6cf_GRCh37_to_NCBI35.chain added
18310f5f5764dd_GRCh37_to_NCBI36.chain added
18310f4568aa31_GRCh38_to_GRCh37.chain added
18310f3601431e_GRCh38_to_NCBI34.chain added
18310f749de109_GRCh38_to_NCBI35.chain added
18310f497e3238_GRCh38_to_NCBI36.chain added
18310f7be774c6_NCBI34_to_GRCh37.chain added
18310f2a2176f1_NCBI34_to_GRCh38.chain added
18310f480849e2_NCBI35_to_GRCh37.chain added
18310f4e08d137_NCBI35_to_GRCh38.chain added
18310f14fa7d1a_NCBI36_to_GRCh37.chain added
18310f1558a82f_NCBI36_to_GRCh38.chain added
18310f10c44d45_GRCm38_to_NCBIM36.chain added
18310f6e358d75_GRCm38_to_NCBIM37.chain added
18310f41fde108_NCBIM36_to_GRCm38.chain added
18310f54407100_NCBIM37_to_GRCm38.chain added
18310f34a30ff2_1000G_omni2.5.b37.vcf.gz added
18310f66f24c54_1000G_omni2.5.b37.vcf.gz.tbi added
18310f318a919b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
18310f53681911_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
18310f58e82636_1000G_omni2.5.hg38.vcf.gz added
18310f71f862df_1000G_omni2.5.hg38.vcf.gz.tbi added
18310f124b64a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
18310f68726108_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
18310f73a05971_af-only-gnomad.raw.sites.vcf added
18310f729f7298_af-only-gnomad.raw.sites.vcf.idx added
18310f276da0e1_Mutect2-exome-panel.vcf.idx added
18310f23d63da3_Mutect2-WGS-panel-b37.vcf added
18310f1c9b77c5_Mutect2-WGS-panel-b37.vcf.idx added
18310f21000f94_small_exac_common_3.vcf added
18310f224ad8e7_small_exac_common_3.vcf.idx added
18310f39263e94_1000g_pon.hg38.vcf.gz added
18310f577471_1000g_pon.hg38.vcf.gz.tbi added
18310f67b38318_af-only-gnomad.hg38.vcf.gz added
18310f6f2781b2_af-only-gnomad.hg38.vcf.gz.tbi added
18310f74f5557b_small_exac_common_3.hg38.vcf.gz added
18310f3131b550_small_exac_common_3.hg38.vcf.gz.tbi added
18310f6b0ef678_gencode.v41.annotation.gtf added
18310f1f16cc6c_gencode.v42.annotation.gtf added
18310f7939ff33_gencode.vM30.annotation.gtf added
18310f3917c7af_gencode.vM31.annotation.gtf added
18310f34114986_gencode.v41.transcripts.fa added
18310fe92a762_gencode.v41.transcripts.fa.fai added
18310f49dc14f4_gencode.v42.transcripts.fa added
18310f2246d6fb_gencode.v42.transcripts.fa.fai added
18310f5090886a_gencode.vM30.pc_transcripts.fa added
18310f1e1c85f5_gencode.vM30.pc_transcripts.fa.fai added
18310f56e9e6ed_gencode.vM31.pc_transcripts.fa added
18310f3782d4bf_gencode.vM31.pc_transcripts.fa.fai added
18310f4fa71790_GRCh38.primary_assembly.genome.fa.1.ht2 added
18310f2a51ffff_GRCh38.primary_assembly.genome.fa.2.ht2 added
18310f106afaf5_GRCh38.primary_assembly.genome.fa.3.ht2 added
18310f419f7a70_GRCh38.primary_assembly.genome.fa.4.ht2 added
18310f2b76b649_GRCh38.primary_assembly.genome.fa.5.ht2 added
18310f78dd5bfd_GRCh38.primary_assembly.genome.fa.6.ht2 added
18310f353fd3e1_GRCh38.primary_assembly.genome.fa.7.ht2 added
18310f1e1628e1_GRCh38.primary_assembly.genome.fa.8.ht2 added
18310f204afcde_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
18310f59161184_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
18310f3ab1a0a6_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
18310f414b0c73_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
18310f7b60ea6b_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
18310f73d7df3b_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
18310f41a280e4_GRCh38_full_analysis_set_plus_decoy_hla.fa added
18310f63146d83_GRCh38.primary_assembly.genome.fa.fai added
18310f62ff60ed_GRCh38.primary_assembly.genome.fa.amb added
18310f3697d65f_GRCh38.primary_assembly.genome.fa.ann added
18310f144622d4_GRCh38.primary_assembly.genome.fa.bwt added
18310f4e0e5766_GRCh38.primary_assembly.genome.fa.pac added
18310f55aea2cb_GRCh38.primary_assembly.genome.fa.sa added
18310fd802207_GRCh38.primary_assembly.genome.fa added
18310f7261f15_hs37d5.fa.fai added
18310f9bfec52_hs37d5.fa.amb added
18310f1c12c969_hs37d5.fa.ann added
18310f5102340a_hs37d5.fa.bwt added
18310f2c06c34d_hs37d5.fa.pac added
18310f6ca351d3_hs37d5.fa.sa added
18310f6f1eb9ff_hs37d5.fa added
18310f2f0aa3b_complete_ref_lens.bin added
18310f24262692_ctable.bin added
18310f3ec5d18f_ctg_offsets.bin added
18310f2d42aa3a_duplicate_clusters.tsv added
18310f34912188_info.json added
18310f654bff_mphf.bin added
18310f58b96083_pos.bin added
18310f2d6e7d85_pre_indexing.log added
18310f35a51fe1_rank.bin added
18310f76cf8964_ref_indexing.log added
18310f4db97a64_refAccumLengths.bin added
18310febb3165_reflengths.bin added
18310f31812a0b_refseq.bin added
18310ff0486d7_seq.bin added
18310fa1c1bd1_versionInfo.json added
18310f25590946_salmon_index added
18310f50a707bb_chrLength.txt added
18310f6d308954_chrName.txt added
18310f8586a33_chrNameLength.txt added
18310f73ede1b_chrStart.txt added
18310f176ac28_exonGeTrInfo.tab added
18310f5666c199_exonInfo.tab added
18310f5ced80e6_geneInfo.tab added
18310fef6ce2f_Genome added
18310f5d8ce0af_genomeParameters.txt added
18310f66ad6d38_Log.out added
18310f2b099798_SA added
18310f2e8f14b9_SAindex added
18310f12b43086_sjdbInfo.txt added
18310f17ace96c_sjdbList.fromGTF.out.tab added
18310f1dadceb8_sjdbList.out.tab added
18310f15a4dac1_transcriptInfo.tab added
18310f3bd30ffe_GRCh38.GENCODE.v42_100 added
18310f5c73a047_knownGene_hg38.sql added
18310f42e784fb_knownGene_hg38.txt added
18310f70643186_refGene_hg38.sql added
18310f5cd8ec47_refGene_hg38.txt added
18310f1ba0e57e_knownGene_mm39.sql added
18310f1dd2af0c_knownGene_mm39.txt added
18310f127e0c28_refGene_mm39.sql added
18310f12706ee2_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/RtmpGANwit/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
18.160 1.837 21.495
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.661 | 0.249 | 5.915 | |
| dataSearch | 1.117 | 0.003 | 1.121 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.879 | 0.191 | 5.819 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.118 | 0.003 | 0.121 | |
| recipeLoad | 1.254 | 0.049 | 1.304 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.517 | 0.003 | 0.520 | |
| recipeUpdate | 0 | 0 | 0 | |