Qian Liu
| Snapshot Date: 2026-01-01 13:45 -0500 (Thu, 01 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 Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-01-05 11:58 -0500 (Mon, 05 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" | 4883 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
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: 2026-01-02 03:02:52 -0500 (Fri, 02 Jan 2026) |
| EndedAt: 2026-01-02 03:05:40 -0500 (Fri, 02 Jan 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 5.884 0.247 6.134
getCloudData 2.924 0.234 5.579
* 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...
daf3b1e74d31f_GRCh38.primary_assembly.genome.fa.1.bt2 added
daf3b1b98f585_GRCh38.primary_assembly.genome.fa.2.bt2 added
daf3b732c9aa5_GRCh38.primary_assembly.genome.fa.3.bt2 added
daf3b5baf639c_GRCh38.primary_assembly.genome.fa.4.bt2 added
daf3b14d8fedf_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
daf3b2fade3cd_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
daf3b6664f192_outfile.txt added
daf3b4f0f1bcb_GRCh37_to_GRCh38.chain added
daf3b692a1d32_GRCh37_to_NCBI34.chain added
daf3b7de27b1f_GRCh37_to_NCBI35.chain added
daf3b764256f8_GRCh37_to_NCBI36.chain added
daf3b5a3b11f5_GRCh38_to_GRCh37.chain added
daf3b4abba437_GRCh38_to_NCBI34.chain added
daf3b20d7b3e1_GRCh38_to_NCBI35.chain added
daf3bc96079b_GRCh38_to_NCBI36.chain added
daf3b126a9831_NCBI34_to_GRCh37.chain added
daf3b7c485167_NCBI34_to_GRCh38.chain added
daf3b4b9cea06_NCBI35_to_GRCh37.chain added
daf3b5344f0c1_NCBI35_to_GRCh38.chain added
daf3b5964285b_NCBI36_to_GRCh37.chain added
daf3b6b98b2e1_NCBI36_to_GRCh38.chain added
daf3b22ee895d_GRCm38_to_NCBIM36.chain added
daf3bb851809_GRCm38_to_NCBIM37.chain added
daf3b130e958_NCBIM36_to_GRCm38.chain added
daf3b7d634de8_NCBIM37_to_GRCm38.chain added
daf3b72c3042b_1000G_omni2.5.b37.vcf.gz added
daf3b1b3349d8_1000G_omni2.5.b37.vcf.gz.tbi added
daf3b36187b72_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
daf3b5b66c171_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
daf3b62cf0089_1000G_omni2.5.hg38.vcf.gz added
daf3b167ae81e_1000G_omni2.5.hg38.vcf.gz.tbi added
daf3b79db9490_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
daf3b7e67f60e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
daf3b9a782c3_af-only-gnomad.raw.sites.vcf added
daf3b558af82c_af-only-gnomad.raw.sites.vcf.idx added
daf3b1340f4ed_Mutect2-exome-panel.vcf.idx added
daf3b39556690_Mutect2-WGS-panel-b37.vcf added
daf3b3befe9be_Mutect2-WGS-panel-b37.vcf.idx added
daf3b625010b8_small_exac_common_3.vcf added
daf3b227f83c3_small_exac_common_3.vcf.idx added
daf3b39d264de_1000g_pon.hg38.vcf.gz added
daf3b589267b0_1000g_pon.hg38.vcf.gz.tbi added
daf3b7cba95b8_af-only-gnomad.hg38.vcf.gz added
daf3b48e0915_af-only-gnomad.hg38.vcf.gz.tbi added
daf3b796a1b92_small_exac_common_3.hg38.vcf.gz added
daf3b9509d53_small_exac_common_3.hg38.vcf.gz.tbi added
daf3b16f8a147_gencode.v41.annotation.gtf added
daf3b75b26cf9_gencode.v42.annotation.gtf added
daf3b54ed8759_gencode.vM30.annotation.gtf added
daf3b6a3d9208_gencode.vM31.annotation.gtf added
daf3b4f169554_gencode.v41.transcripts.fa added
daf3b40863a3b_gencode.v41.transcripts.fa.fai added
daf3bd2c1b66_gencode.v42.transcripts.fa added
daf3b5a9bad5e_gencode.v42.transcripts.fa.fai added
daf3b41b72393_gencode.vM30.pc_transcripts.fa added
daf3ba8f694e_gencode.vM30.pc_transcripts.fa.fai added
daf3b4d5eb189_gencode.vM31.pc_transcripts.fa added
daf3b5cea6d6c_gencode.vM31.pc_transcripts.fa.fai added
daf3b40a7e4c1_GRCh38.primary_assembly.genome.fa.1.ht2 added
daf3b28c572fa_GRCh38.primary_assembly.genome.fa.2.ht2 added
daf3b3fb96df5_GRCh38.primary_assembly.genome.fa.3.ht2 added
daf3b5722ccdf_GRCh38.primary_assembly.genome.fa.4.ht2 added
daf3b22a1078a_GRCh38.primary_assembly.genome.fa.5.ht2 added
daf3b3e216403_GRCh38.primary_assembly.genome.fa.6.ht2 added
daf3b60ca4fa2_GRCh38.primary_assembly.genome.fa.7.ht2 added
daf3b782bffb7_GRCh38.primary_assembly.genome.fa.8.ht2 added
daf3b516258f0_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
daf3b1a1fb633_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
daf3b341be975_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
daf3b33b269a8_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
daf3b3c9f39f6_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
daf3b6dee4e53_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
daf3bc44d158_GRCh38_full_analysis_set_plus_decoy_hla.fa added
daf3b3959cfae_GRCh38.primary_assembly.genome.fa.fai added
daf3b727c5769_GRCh38.primary_assembly.genome.fa.amb added
daf3b5aeecea_GRCh38.primary_assembly.genome.fa.ann added
daf3b42aa6d01_GRCh38.primary_assembly.genome.fa.bwt added
daf3b974f8b0_GRCh38.primary_assembly.genome.fa.pac added
daf3b7b6159e4_GRCh38.primary_assembly.genome.fa.sa added
daf3b1797f45a_GRCh38.primary_assembly.genome.fa added
daf3b73b28ab8_hs37d5.fa.fai added
daf3b4a77ef38_hs37d5.fa.amb added
daf3b581e2e95_hs37d5.fa.ann added
daf3bdea61e_hs37d5.fa.bwt added
daf3b25139c96_hs37d5.fa.pac added
daf3b19d55229_hs37d5.fa.sa added
daf3bb6e0f6d_hs37d5.fa added
daf3b72724e20_complete_ref_lens.bin added
daf3b76bfbf95_ctable.bin added
daf3b4c15f42e_ctg_offsets.bin added
daf3b1b37c11a_duplicate_clusters.tsv added
daf3b36792d8a_info.json added
daf3b2338c10d_mphf.bin added
daf3b3dd8c8a5_pos.bin added
daf3b749a918d_pre_indexing.log added
daf3b40310af_rank.bin added
daf3b3604c85c_ref_indexing.log added
daf3b45fcea7d_refAccumLengths.bin added
daf3b1e22c6e2_reflengths.bin added
daf3b6a20b1d1_refseq.bin added
daf3b79af5425_seq.bin added
daf3b5ac200d8_versionInfo.json added
daf3b580f0025_salmon_index added
daf3b5f4257d_chrLength.txt added
daf3b141bd086_chrName.txt added
daf3b4a8b578e_chrNameLength.txt added
daf3bba31268_chrStart.txt added
daf3b56c63d87_exonGeTrInfo.tab added
daf3b5400503e_exonInfo.tab added
daf3b7046c4c_geneInfo.tab added
daf3b6e5e31e2_Genome added
daf3b47b2daf6_genomeParameters.txt added
daf3b517c5b84_Log.out added
daf3b467c6077_SA added
daf3b48918115_SAindex added
daf3b768ff81b_sjdbInfo.txt added
daf3b6051b2a0_sjdbList.fromGTF.out.tab added
daf3b53ff9082_sjdbList.out.tab added
daf3b6902463b_transcriptInfo.tab added
daf3b57117235_GRCh38.GENCODE.v42_100 added
daf3b201584b0_knownGene_hg38.sql added
daf3b43a0755_knownGene_hg38.txt added
daf3bd8a9fbf_refGene_hg38.sql added
daf3b434e45bd_refGene_hg38.txt added
daf3b4212cffa_knownGene_mm39.sql added
daf3b225314c_knownGene_mm39.txt added
daf3b4751566c_refGene_mm39.sql added
daf3b78179856_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/RtmpiMx23m/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
18.034 0.916 19.514
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.884 | 0.247 | 6.134 | |
| dataSearch | 1.074 | 0.009 | 1.082 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.924 | 0.234 | 5.579 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.127 | 0.000 | 0.127 | |
| recipeLoad | 1.303 | 0.041 | 1.345 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.556 | 0.032 | 0.588 | |
| recipeUpdate | 0 | 0 | 0 | |