Qian Liu
| Snapshot Date: 2025-11-16 13:45 -0500 (Sun, 16 Nov 2025) |
| 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 2025-11-17 11:58 -0500 (Mon, 17 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4903 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 | 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: 2025-11-17 03:24:22 -0500 (Mon, 17 Nov 2025) |
| EndedAt: 2025-11-17 03:27:03 -0500 (Mon, 17 Nov 2025) |
| EllapsedTime: 160.2 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 4.5.1 Patched (2025-08-23 r88802)
* 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 5.734 0.215 5.952
* 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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...
1e11962ae2a4ae_GRCh38.primary_assembly.genome.fa.1.bt2 added
1e119647b7593b_GRCh38.primary_assembly.genome.fa.2.bt2 added
1e1196309c9e08_GRCh38.primary_assembly.genome.fa.3.bt2 added
1e11967d59ea00_GRCh38.primary_assembly.genome.fa.4.bt2 added
1e119630e59fb8_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1e11964c2dda45_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1e11964697b811_outfile.txt added
1e119628bae4e3_GRCh37_to_GRCh38.chain added
1e119670b261e9_GRCh37_to_NCBI34.chain added
1e11963ff114d3_GRCh37_to_NCBI35.chain added
1e1196415beb1_GRCh37_to_NCBI36.chain added
1e1196522fa75f_GRCh38_to_GRCh37.chain added
1e11964eec623e_GRCh38_to_NCBI34.chain added
1e11962f3ab598_GRCh38_to_NCBI35.chain added
1e119611bce836_GRCh38_to_NCBI36.chain added
1e1196a4d2047_NCBI34_to_GRCh37.chain added
1e119626907189_NCBI34_to_GRCh38.chain added
1e11966d1543f1_NCBI35_to_GRCh37.chain added
1e11964404601a_NCBI35_to_GRCh38.chain added
1e11966a81ea57_NCBI36_to_GRCh37.chain added
1e1196292c427d_NCBI36_to_GRCh38.chain added
1e119633b3199_GRCm38_to_NCBIM36.chain added
1e11965e84e99e_GRCm38_to_NCBIM37.chain added
1e1196b408297_NCBIM36_to_GRCm38.chain added
1e119651c2df35_NCBIM37_to_GRCm38.chain added
1e119663f5138a_1000G_omni2.5.b37.vcf.gz added
1e11962310ad14_1000G_omni2.5.b37.vcf.gz.tbi added
1e11967cef4e1b_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1e11965b64d016_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1e11961e6d61af_1000G_omni2.5.hg38.vcf.gz added
1e11967ac1c989_1000G_omni2.5.hg38.vcf.gz.tbi added
1e119664774c4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1e11966624baea_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1e11962b5e6791_af-only-gnomad.raw.sites.vcf added
1e11963a15ec5_af-only-gnomad.raw.sites.vcf.idx added
1e1196170a5aa2_Mutect2-exome-panel.vcf.idx added
1e1196778c41d6_Mutect2-WGS-panel-b37.vcf added
1e11964a3916d6_Mutect2-WGS-panel-b37.vcf.idx added
1e11963fc53f86_small_exac_common_3.vcf added
1e1196683ea3bf_small_exac_common_3.vcf.idx added
1e1196a2a2ba9_1000g_pon.hg38.vcf.gz added
1e119643dafe37_1000g_pon.hg38.vcf.gz.tbi added
1e11963a6e4b1e_af-only-gnomad.hg38.vcf.gz added
1e119659168de7_af-only-gnomad.hg38.vcf.gz.tbi added
1e11967315b3cf_small_exac_common_3.hg38.vcf.gz added
1e11964c2b3354_small_exac_common_3.hg38.vcf.gz.tbi added
1e11966363ae2e_gencode.v41.annotation.gtf added
1e119619a62558_gencode.v42.annotation.gtf added
1e119639407746_gencode.vM30.annotation.gtf added
1e119627680e49_gencode.vM31.annotation.gtf added
1e11964280fb0_gencode.v41.transcripts.fa added
1e1196626cb9c3_gencode.v41.transcripts.fa.fai added
1e11962aa33fe2_gencode.v42.transcripts.fa added
1e119662acf94e_gencode.v42.transcripts.fa.fai added
1e11966dad3c5b_gencode.vM30.pc_transcripts.fa added
1e11967c661f17_gencode.vM30.pc_transcripts.fa.fai added
1e119646a20cd8_gencode.vM31.pc_transcripts.fa added
1e119610bde96f_gencode.vM31.pc_transcripts.fa.fai added
1e119679556d32_GRCh38.primary_assembly.genome.fa.1.ht2 added
1e11962206dcee_GRCh38.primary_assembly.genome.fa.2.ht2 added
1e11962f2b4b1f_GRCh38.primary_assembly.genome.fa.3.ht2 added
1e1196741736bb_GRCh38.primary_assembly.genome.fa.4.ht2 added
1e1196284e51b3_GRCh38.primary_assembly.genome.fa.5.ht2 added
1e119615500609_GRCh38.primary_assembly.genome.fa.6.ht2 added
1e11961f759e4c_GRCh38.primary_assembly.genome.fa.7.ht2 added
1e11962befb078_GRCh38.primary_assembly.genome.fa.8.ht2 added
1e11962c5a60ac_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1e11961701e023_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1e11967628c74e_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1e11966c1fa032_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1e11967f4083e2_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1e119652f2f8_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1e11962ffa9e69_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1e119639aecf01_GRCh38.primary_assembly.genome.fa.fai added
1e1196596980df_GRCh38.primary_assembly.genome.fa.amb added
1e119623105239_GRCh38.primary_assembly.genome.fa.ann added
1e11965da0255_GRCh38.primary_assembly.genome.fa.bwt added
1e11963ccd2f0e_GRCh38.primary_assembly.genome.fa.pac added
1e11963cb67791_GRCh38.primary_assembly.genome.fa.sa added
1e11963f1a799b_GRCh38.primary_assembly.genome.fa added
1e119664353d57_hs37d5.fa.fai added
1e119640de8741_hs37d5.fa.amb added
1e11962187335f_hs37d5.fa.ann added
1e1196ed87d39_hs37d5.fa.bwt added
1e1196238b808f_hs37d5.fa.pac added
1e1196f346fba_hs37d5.fa.sa added
1e1196b3e9c50_hs37d5.fa added
1e11966a2d8d67_complete_ref_lens.bin added
1e11961ff25929_ctable.bin added
1e11964940983_ctg_offsets.bin added
1e1196c346a56_duplicate_clusters.tsv added
1e11964f1da448_info.json added
1e119678ab403e_mphf.bin added
1e11963482bc09_pos.bin added
1e1196646daa52_pre_indexing.log added
1e11961820de8b_rank.bin added
1e119660726c81_ref_indexing.log added
1e119610c80afe_refAccumLengths.bin added
1e11962f22beae_reflengths.bin added
1e1196569b33cf_refseq.bin added
1e11967ce7ab30_seq.bin added
1e11962e634290_versionInfo.json added
1e119656ee26c7_salmon_index added
1e11962ce24999_chrLength.txt added
1e119668121191_chrName.txt added
1e11963057a7a7_chrNameLength.txt added
1e11964ff29bd2_chrStart.txt added
1e11966dec13e7_exonGeTrInfo.tab added
1e11966d24d6b5_exonInfo.tab added
1e1196ca91364_geneInfo.tab added
1e11962d068d82_Genome added
1e1196515a140c_genomeParameters.txt added
1e11964d879aa5_Log.out added
1e11964e8dc0e1_SA added
1e119660329145_SAindex added
1e119671131b35_sjdbInfo.txt added
1e11965dc2309b_sjdbList.fromGTF.out.tab added
1e11966b712d95_sjdbList.out.tab added
1e11965b40a89c_transcriptInfo.tab added
1e11967db489c5_GRCh38.GENCODE.v42_100 added
1e119670053718_knownGene_hg38.sql added
1e1196677512f2_knownGene_hg38.txt added
1e11964cd22e0d_refGene_hg38.sql added
1e119668b07757_refGene_hg38.txt added
1e11961bf7cefb_knownGene_mm39.sql added
1e1196313fd85f_knownGene_mm39.txt added
1e1196d155e2_refGene_mm39.sql added
1e11967c6a3b7c_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/RtmpR1AiNh/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
17.326 0.968 19.069
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.734 | 0.215 | 5.952 | |
| dataSearch | 1.091 | 0.008 | 1.099 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.642 | 0.212 | 4.272 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.121 | 0.015 | 0.137 | |
| recipeLoad | 1.241 | 0.053 | 1.294 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.513 | 0.037 | 0.549 | |
| recipeUpdate | 0 | 0 | 0 | |