Qian Liu
| Snapshot Date: 2026-03-08 13:45 -0400 (Sun, 08 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 2026-03-09 11:57 -0400 (Mon, 09 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: 2026-03-09 03:04:57 -0400 (Mon, 09 Mar 2026) |
| EndedAt: 2026-03-09 03:07:44 -0400 (Mon, 09 Mar 2026) |
| EllapsedTime: 167.2 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 5.917 0.267 6.189
getCloudData 2.744 0.216 5.177
* 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...
19716a3109474f_GRCh38.primary_assembly.genome.fa.1.bt2 added
19716a52917ac_GRCh38.primary_assembly.genome.fa.2.bt2 added
19716af267784_GRCh38.primary_assembly.genome.fa.3.bt2 added
19716a463b56bb_GRCh38.primary_assembly.genome.fa.4.bt2 added
19716a2b979fba_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
19716a31bbdd30_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
19716a3d52f6b4_outfile.txt added
19716a68f5d7ee_GRCh37_to_GRCh38.chain added
19716a7f0a48ed_GRCh37_to_NCBI34.chain added
19716a77d8c169_GRCh37_to_NCBI35.chain added
19716a685e3065_GRCh37_to_NCBI36.chain added
19716a276edde3_GRCh38_to_GRCh37.chain added
19716a1d7a3e93_GRCh38_to_NCBI34.chain added
19716a5d13c8e_GRCh38_to_NCBI35.chain added
19716a2920eac_GRCh38_to_NCBI36.chain added
19716a2f303d1d_NCBI34_to_GRCh37.chain added
19716a12cde41a_NCBI34_to_GRCh38.chain added
19716a417b0c7c_NCBI35_to_GRCh37.chain added
19716a30d4043f_NCBI35_to_GRCh38.chain added
19716a3727cbb_NCBI36_to_GRCh37.chain added
19716a16772206_NCBI36_to_GRCh38.chain added
19716a4afede45_GRCm38_to_NCBIM36.chain added
19716a12c9c7d2_GRCm38_to_NCBIM37.chain added
19716a7c58c6a6_NCBIM36_to_GRCm38.chain added
19716a22571252_NCBIM37_to_GRCm38.chain added
19716a545705f5_1000G_omni2.5.b37.vcf.gz added
19716a61100cb4_1000G_omni2.5.b37.vcf.gz.tbi added
19716a8f44062_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
19716a4e223cbc_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
19716a50ee6f70_1000G_omni2.5.hg38.vcf.gz added
19716a792b62c5_1000G_omni2.5.hg38.vcf.gz.tbi added
19716a7f2b840b_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
19716a5617871c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
19716a851da49_af-only-gnomad.raw.sites.vcf added
19716a4566dac7_af-only-gnomad.raw.sites.vcf.idx added
19716a1af26d6_Mutect2-exome-panel.vcf.idx added
19716a3a0db779_Mutect2-WGS-panel-b37.vcf added
19716a2b9d17b_Mutect2-WGS-panel-b37.vcf.idx added
19716a6aa4fec5_small_exac_common_3.vcf added
19716a39180067_small_exac_common_3.vcf.idx added
19716a7a9292e4_1000g_pon.hg38.vcf.gz added
19716a53032f2a_1000g_pon.hg38.vcf.gz.tbi added
19716a6086de4a_af-only-gnomad.hg38.vcf.gz added
19716a180cd178_af-only-gnomad.hg38.vcf.gz.tbi added
19716a58d46bb8_small_exac_common_3.hg38.vcf.gz added
19716a6318ecf7_small_exac_common_3.hg38.vcf.gz.tbi added
19716a473d0e95_gencode.v41.annotation.gtf added
19716a6ba24fd2_gencode.v42.annotation.gtf added
19716a2493f973_gencode.vM30.annotation.gtf added
19716a781112d4_gencode.vM31.annotation.gtf added
19716a6f14cc8e_gencode.v41.transcripts.fa added
19716a3b0b1b7a_gencode.v41.transcripts.fa.fai added
19716a430ff11a_gencode.v42.transcripts.fa added
19716a1de9460_gencode.v42.transcripts.fa.fai added
19716a3763e220_gencode.vM30.pc_transcripts.fa added
19716a6567036c_gencode.vM30.pc_transcripts.fa.fai added
19716a56359a55_gencode.vM31.pc_transcripts.fa added
19716a1873eed4_gencode.vM31.pc_transcripts.fa.fai added
19716a6e5b43ce_GRCh38.primary_assembly.genome.fa.1.ht2 added
19716a2457d712_GRCh38.primary_assembly.genome.fa.2.ht2 added
19716a69625e44_GRCh38.primary_assembly.genome.fa.3.ht2 added
19716a6786a693_GRCh38.primary_assembly.genome.fa.4.ht2 added
19716a23835b1d_GRCh38.primary_assembly.genome.fa.5.ht2 added
19716a3f79e560_GRCh38.primary_assembly.genome.fa.6.ht2 added
19716a6fd880dd_GRCh38.primary_assembly.genome.fa.7.ht2 added
19716a68ea35e4_GRCh38.primary_assembly.genome.fa.8.ht2 added
19716a41290c37_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
19716a29e63856_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
19716a6ba40760_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
19716a2bce0afc_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
19716a62fe38bd_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
19716a66369a44_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
19716a7ed13a26_GRCh38_full_analysis_set_plus_decoy_hla.fa added
19716a43851708_GRCh38.primary_assembly.genome.fa.fai added
19716a7e436bbc_GRCh38.primary_assembly.genome.fa.amb added
19716a57a5a5df_GRCh38.primary_assembly.genome.fa.ann added
19716a269e03ff_GRCh38.primary_assembly.genome.fa.bwt added
19716a45807a51_GRCh38.primary_assembly.genome.fa.pac added
19716a4347f5b1_GRCh38.primary_assembly.genome.fa.sa added
19716a4b31fd72_GRCh38.primary_assembly.genome.fa added
19716a3d918d26_hs37d5.fa.fai added
19716a325cc23f_hs37d5.fa.amb added
19716a63d18ec_hs37d5.fa.ann added
19716aa17e40_hs37d5.fa.bwt added
19716a343b56a0_hs37d5.fa.pac added
19716a3da0fb0c_hs37d5.fa.sa added
19716a660881ac_hs37d5.fa added
19716aa70f0f5_complete_ref_lens.bin added
19716a5614e9e1_ctable.bin added
19716a5463c57a_ctg_offsets.bin added
19716a2ec8c807_duplicate_clusters.tsv added
19716a3f774825_info.json added
19716a3bea6c0d_mphf.bin added
19716a524c2325_pos.bin added
19716a7ef12d86_pre_indexing.log added
19716a2bc2ecea_rank.bin added
19716a3b365909_ref_indexing.log added
19716a401a39bd_refAccumLengths.bin added
19716a55a92541_reflengths.bin added
19716a26da6069_refseq.bin added
19716a6be844b9_seq.bin added
19716a38a75dfe_versionInfo.json added
19716ad10faae_salmon_index added
19716a6ab97edf_chrLength.txt added
19716a7c2c7506_chrName.txt added
19716ab54666a_chrNameLength.txt added
19716a425f24be_chrStart.txt added
19716a22ca7905_exonGeTrInfo.tab added
19716a50d4e0bc_exonInfo.tab added
19716a5a71a70_geneInfo.tab added
19716a6dfc7678_Genome added
19716ae666de2_genomeParameters.txt added
19716a3803dcaf_Log.out added
19716a74398f64_SA added
19716af07ec22_SAindex added
19716a6c3f334f_sjdbInfo.txt added
19716a31da8a71_sjdbList.fromGTF.out.tab added
19716a75106dce_sjdbList.out.tab added
19716a76b02445_transcriptInfo.tab added
19716a7ef7452_GRCh38.GENCODE.v42_100 added
19716a49743348_knownGene_hg38.sql added
19716a2578ec4c_knownGene_hg38.txt added
19716a4766bc77_refGene_hg38.sql added
19716a55e9f55_refGene_hg38.txt added
19716a77c50f71_knownGene_mm39.sql added
19716a4657e9fd_knownGene_mm39.txt added
19716a31218c40_refGene_mm39.sql added
19716a32fb687b_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/Rtmpr640pX/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
18.357 1.719 20.866
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.917 | 0.267 | 6.189 | |
| dataSearch | 1.114 | 0.019 | 1.133 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.744 | 0.216 | 5.177 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.123 | 0.003 | 0.126 | |
| recipeLoad | 1.279 | 0.040 | 1.334 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.519 | 0.029 | 0.547 | |
| recipeUpdate | 0 | 0 | 0 | |