Qian Liu
| Snapshot Date: 2026-03-29 13:45 -0400 (Sun, 29 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-30 11:57 -0400 (Mon, 30 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" | 4893 |
| 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: 2026-03-30 03:38:18 -0400 (Mon, 30 Mar 2026) |
| EndedAt: 2026-03-30 03:41:06 -0400 (Mon, 30 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 24.04.4 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 5.98 0.24 6.226
* 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...
e3d6d22d71e4c_GRCh38.primary_assembly.genome.fa.1.bt2 added
e3d6d45e09b6e_GRCh38.primary_assembly.genome.fa.2.bt2 added
e3d6d5b484085_GRCh38.primary_assembly.genome.fa.3.bt2 added
e3d6d3217a1de_GRCh38.primary_assembly.genome.fa.4.bt2 added
e3d6d99e1cf3_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
e3d6d6b82a4b6_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
e3d6d3de00e39_outfile.txt added
e3d6d7dade79c_GRCh37_to_GRCh38.chain added
e3d6d15c661f5_GRCh37_to_NCBI34.chain added
e3d6d17c6d8a3_GRCh37_to_NCBI35.chain added
e3d6dbb39657_GRCh37_to_NCBI36.chain added
e3d6d477e8fff_GRCh38_to_GRCh37.chain added
e3d6d5a79a1ef_GRCh38_to_NCBI34.chain added
e3d6d9593b85_GRCh38_to_NCBI35.chain added
e3d6d57fac8a_GRCh38_to_NCBI36.chain added
e3d6d46b20c40_NCBI34_to_GRCh37.chain added
e3d6d4d382c12_NCBI34_to_GRCh38.chain added
e3d6d5c909915_NCBI35_to_GRCh37.chain added
e3d6dca6680_NCBI35_to_GRCh38.chain added
e3d6d602a9da6_NCBI36_to_GRCh37.chain added
e3d6dc4e908a_NCBI36_to_GRCh38.chain added
e3d6d534bdb14_GRCm38_to_NCBIM36.chain added
e3d6d1b63607d_GRCm38_to_NCBIM37.chain added
e3d6dea9a0dc_NCBIM36_to_GRCm38.chain added
e3d6d37793131_NCBIM37_to_GRCm38.chain added
e3d6d228af523_1000G_omni2.5.b37.vcf.gz added
e3d6d6f449b7b_1000G_omni2.5.b37.vcf.gz.tbi added
e3d6d344fbd3b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
e3d6d2714aadb_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
e3d6d55cbf044_1000G_omni2.5.hg38.vcf.gz added
e3d6d21c81fef_1000G_omni2.5.hg38.vcf.gz.tbi added
e3d6d49ebc927_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
e3d6d1bac8bb2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
e3d6d7d106074_af-only-gnomad.raw.sites.vcf added
e3d6d7c036b05_af-only-gnomad.raw.sites.vcf.idx added
e3d6d254aa8a5_Mutect2-exome-panel.vcf.idx added
e3d6d6893052b_Mutect2-WGS-panel-b37.vcf added
e3d6d39e3793f_Mutect2-WGS-panel-b37.vcf.idx added
e3d6d22f89042_small_exac_common_3.vcf added
e3d6d7e596720_small_exac_common_3.vcf.idx added
e3d6d51aa51e2_1000g_pon.hg38.vcf.gz added
e3d6d2eac2699_1000g_pon.hg38.vcf.gz.tbi added
e3d6d45d7f71f_af-only-gnomad.hg38.vcf.gz added
e3d6d2c23f3d1_af-only-gnomad.hg38.vcf.gz.tbi added
e3d6d3805621e_small_exac_common_3.hg38.vcf.gz added
e3d6d4b57a3a9_small_exac_common_3.hg38.vcf.gz.tbi added
e3d6d72d60011_gencode.v41.annotation.gtf added
e3d6d53d8e30_gencode.v42.annotation.gtf added
e3d6d27e83cbe_gencode.vM30.annotation.gtf added
e3d6d73a06691_gencode.vM31.annotation.gtf added
e3d6d65682bd6_gencode.v41.transcripts.fa added
e3d6d3436cd49_gencode.v41.transcripts.fa.fai added
e3d6d46ec41a6_gencode.v42.transcripts.fa added
e3d6dcb8c53_gencode.v42.transcripts.fa.fai added
e3d6d42e06e25_gencode.vM30.pc_transcripts.fa added
e3d6d7e6572d7_gencode.vM30.pc_transcripts.fa.fai added
e3d6d23568176_gencode.vM31.pc_transcripts.fa added
e3d6d322509a1_gencode.vM31.pc_transcripts.fa.fai added
e3d6d32b53013_GRCh38.primary_assembly.genome.fa.1.ht2 added
e3d6d4a6b2c51_GRCh38.primary_assembly.genome.fa.2.ht2 added
e3d6d7f0f9e5_GRCh38.primary_assembly.genome.fa.3.ht2 added
e3d6d547d5002_GRCh38.primary_assembly.genome.fa.4.ht2 added
e3d6d1456f579_GRCh38.primary_assembly.genome.fa.5.ht2 added
e3d6d239d8598_GRCh38.primary_assembly.genome.fa.6.ht2 added
e3d6d518db077_GRCh38.primary_assembly.genome.fa.7.ht2 added
e3d6d105a607e_GRCh38.primary_assembly.genome.fa.8.ht2 added
e3d6d48e82e3d_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
e3d6d3a20b5a2_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
e3d6d4a3dd9bd_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
e3d6d6be0be7f_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
e3d6d387a1cc2_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
e3d6d1be82b9f_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
e3d6d1a8ce518_GRCh38_full_analysis_set_plus_decoy_hla.fa added
e3d6d7e5213e1_GRCh38.primary_assembly.genome.fa.fai added
e3d6d480c1f71_GRCh38.primary_assembly.genome.fa.amb added
e3d6d52924736_GRCh38.primary_assembly.genome.fa.ann added
e3d6d49a9b78b_GRCh38.primary_assembly.genome.fa.bwt added
e3d6d3ae21f82_GRCh38.primary_assembly.genome.fa.pac added
e3d6d57cfd566_GRCh38.primary_assembly.genome.fa.sa added
e3d6d7191f449_GRCh38.primary_assembly.genome.fa added
e3d6d2e828614_hs37d5.fa.fai added
e3d6d3d38013d_hs37d5.fa.amb added
e3d6d25c8c192_hs37d5.fa.ann added
e3d6d756ec7ba_hs37d5.fa.bwt added
e3d6d3e038d90_hs37d5.fa.pac added
e3d6d68a92fb8_hs37d5.fa.sa added
e3d6d73d43a91_hs37d5.fa added
e3d6d615a0f07_complete_ref_lens.bin added
e3d6d1ace3959_ctable.bin added
e3d6d26896aa4_ctg_offsets.bin added
e3d6d2bc53b58_duplicate_clusters.tsv added
e3d6d22bf333e_info.json added
e3d6d7b06baa7_mphf.bin added
e3d6d401c30d1_pos.bin added
e3d6d465cb8d6_pre_indexing.log added
e3d6d4c946b1e_rank.bin added
e3d6d50769150_ref_indexing.log added
e3d6df44e714_refAccumLengths.bin added
e3d6d6b520c0_reflengths.bin added
e3d6d1ab46b0d_refseq.bin added
e3d6d7b25a593_seq.bin added
e3d6d3f2f3d82_versionInfo.json added
e3d6d369c96ad_salmon_index added
e3d6d15b28aac_chrLength.txt added
e3d6d3d815163_chrName.txt added
e3d6d7ea8b61e_chrNameLength.txt added
e3d6d6844d1e2_chrStart.txt added
e3d6d72b08ee_exonGeTrInfo.tab added
e3d6d398ad5a0_exonInfo.tab added
e3d6d4014a749_geneInfo.tab added
e3d6d78bcfd38_Genome added
e3d6d680d5bb4_genomeParameters.txt added
e3d6d7d4ca886_Log.out added
e3d6d1e85beca_SA added
e3d6d5d7c236e_SAindex added
e3d6d3b503616_sjdbInfo.txt added
e3d6d72eee82_sjdbList.fromGTF.out.tab added
e3d6d51505e00_sjdbList.out.tab added
e3d6d1caa451d_transcriptInfo.tab added
e3d6d21fd27db_GRCh38.GENCODE.v42_100 added
e3d6d77d9c8a4_knownGene_hg38.sql added
e3d6d486f8076_knownGene_hg38.txt added
e3d6d44bc5b1a_refGene_hg38.sql added
e3d6d72e0834b_refGene_hg38.txt added
e3d6d88bb147_knownGene_mm39.sql added
e3d6db1913f0_knownGene_mm39.txt added
e3d6d3f74ee69_refGene_mm39.sql added
e3d6d59024297_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/RtmpWxfhmY/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
18.469 1.937 20.825
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.980 | 0.240 | 6.226 | |
| dataSearch | 1.105 | 0.012 | 1.118 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.677 | 0.133 | 3.336 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.136 | 0.001 | 0.138 | |
| recipeLoad | 1.314 | 0.059 | 1.374 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.555 | 0.026 | 0.581 | |
| recipeUpdate | 0 | 0 | 0 | |