Qian Liu
| Snapshot Date: 2025-12-02 13:40 -0500 (Tue, 02 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: 4a5d06b |
| git_last_commit_date: 2025-10-29 11:20:44 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-03 11:34 -0500 (Wed, 03 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4575 |
| 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 1753/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.11.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.11.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz |
| StartedAt: 2025-12-03 03:19:32 -0500 (Wed, 03 Dec 2025) |
| EndedAt: 2025-12-03 03:22:18 -0500 (Wed, 03 Dec 2025) |
| EllapsedTime: 166.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.11.0’
* 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 5.986 0.364 6.351
* 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-3.23-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.11.0’ ** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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...
369de253fa356c_GRCh38.primary_assembly.genome.fa.1.bt2 added
369de22f48d368_GRCh38.primary_assembly.genome.fa.2.bt2 added
369de2786c9361_GRCh38.primary_assembly.genome.fa.3.bt2 added
369de2272c16ed_GRCh38.primary_assembly.genome.fa.4.bt2 added
369de2736a5a2f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
369de244c0132e_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
369de2589340d6_outfile.txt added
369de254e686c3_GRCh37_to_GRCh38.chain added
369de2553be64_GRCh37_to_NCBI34.chain added
369de27f9dec7b_GRCh37_to_NCBI35.chain added
369de22febefce_GRCh37_to_NCBI36.chain added
369de219d56cde_GRCh38_to_GRCh37.chain added
369de22957cfc_GRCh38_to_NCBI34.chain added
369de27dabc386_GRCh38_to_NCBI35.chain added
369de220b435fb_GRCh38_to_NCBI36.chain added
369de256d404c3_NCBI34_to_GRCh37.chain added
369de26231e870_NCBI34_to_GRCh38.chain added
369de273804a87_NCBI35_to_GRCh37.chain added
369de24211799b_NCBI35_to_GRCh38.chain added
369de241a4fea3_NCBI36_to_GRCh37.chain added
369de24c070eb_NCBI36_to_GRCh38.chain added
369de24fcd84a5_GRCm38_to_NCBIM36.chain added
369de27bc9051e_GRCm38_to_NCBIM37.chain added
369de24f43e091_NCBIM36_to_GRCm38.chain added
369de21c1f8ad8_NCBIM37_to_GRCm38.chain added
369de2656e427a_1000G_omni2.5.b37.vcf.gz added
369de254cdc894_1000G_omni2.5.b37.vcf.gz.tbi added
369de25c7a5f22_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
369de2f849038_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
369de246de6a57_1000G_omni2.5.hg38.vcf.gz added
369de26452ba38_1000G_omni2.5.hg38.vcf.gz.tbi added
369de2637ec5a5_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
369de276273dbf_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
369de25cbf4d99_af-only-gnomad.raw.sites.vcf added
369de2aaadc92_af-only-gnomad.raw.sites.vcf.idx added
369de2699197ee_Mutect2-exome-panel.vcf.idx added
369de2217f60c7_Mutect2-WGS-panel-b37.vcf added
369de2633e1d69_Mutect2-WGS-panel-b37.vcf.idx added
369de23e781eb1_small_exac_common_3.vcf added
369de226d31f2b_small_exac_common_3.vcf.idx added
369de262dc09e4_1000g_pon.hg38.vcf.gz added
369de26e640e7f_1000g_pon.hg38.vcf.gz.tbi added
369de240a88c09_af-only-gnomad.hg38.vcf.gz added
369de2657186e0_af-only-gnomad.hg38.vcf.gz.tbi added
369de26c0fd206_small_exac_common_3.hg38.vcf.gz added
369de2615cc204_small_exac_common_3.hg38.vcf.gz.tbi added
369de23c458ba4_gencode.v41.annotation.gtf added
369de24e41ba76_gencode.v42.annotation.gtf added
369de254dd0c8c_gencode.vM30.annotation.gtf added
369de27e57053f_gencode.vM31.annotation.gtf added
369de2fe6b91a_gencode.v41.transcripts.fa added
369de2599d7d77_gencode.v41.transcripts.fa.fai added
369de24e2489e4_gencode.v42.transcripts.fa added
369de2bafbe38_gencode.v42.transcripts.fa.fai added
369de228e15e09_gencode.vM30.pc_transcripts.fa added
369de26a4414bd_gencode.vM30.pc_transcripts.fa.fai added
369de2711e00b2_gencode.vM31.pc_transcripts.fa added
369de27daf269d_gencode.vM31.pc_transcripts.fa.fai added
369de246be73df_GRCh38.primary_assembly.genome.fa.1.ht2 added
369de2a290eb_GRCh38.primary_assembly.genome.fa.2.ht2 added
369de2448d90f4_GRCh38.primary_assembly.genome.fa.3.ht2 added
369de22b112e17_GRCh38.primary_assembly.genome.fa.4.ht2 added
369de264215690_GRCh38.primary_assembly.genome.fa.5.ht2 added
369de23ab4ceb3_GRCh38.primary_assembly.genome.fa.6.ht2 added
369de27d07bb0_GRCh38.primary_assembly.genome.fa.7.ht2 added
369de26ecc3322_GRCh38.primary_assembly.genome.fa.8.ht2 added
369de2244666a1_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
369de2294fdc77_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
369de2520a508b_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
369de262be8552_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
369de25022fba2_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
369de234e65a6f_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
369de2512293d2_GRCh38_full_analysis_set_plus_decoy_hla.fa added
369de210cb87ab_GRCh38.primary_assembly.genome.fa.fai added
369de21a57e150_GRCh38.primary_assembly.genome.fa.amb added
369de23d3265d8_GRCh38.primary_assembly.genome.fa.ann added
369de2722849b0_GRCh38.primary_assembly.genome.fa.bwt added
369de2569d6cf4_GRCh38.primary_assembly.genome.fa.pac added
369de2b74204e_GRCh38.primary_assembly.genome.fa.sa added
369de24705563c_GRCh38.primary_assembly.genome.fa added
369de254f47233_hs37d5.fa.fai added
369de21b5ad968_hs37d5.fa.amb added
369de220a2d3b3_hs37d5.fa.ann added
369de22318fc18_hs37d5.fa.bwt added
369de2270a97a1_hs37d5.fa.pac added
369de2498431bc_hs37d5.fa.sa added
369de2d5d10d5_hs37d5.fa added
369de218289853_complete_ref_lens.bin added
369de24733585a_ctable.bin added
369de2541b84b4_ctg_offsets.bin added
369de218cb293e_duplicate_clusters.tsv added
369de2bc0e94e_info.json added
369de27f2cb2cc_mphf.bin added
369de27cec7fce_pos.bin added
369de24675b802_pre_indexing.log added
369de26fd2e7c_rank.bin added
369de26bb8b2f1_ref_indexing.log added
369de26abc1ea3_refAccumLengths.bin added
369de2304d0af4_reflengths.bin added
369de23dc3037c_refseq.bin added
369de24d7aa3f6_seq.bin added
369de2700696_versionInfo.json added
369de272a95dec_salmon_index added
369de21e9d37c8_chrLength.txt added
369de2113b8e42_chrName.txt added
369de2d013f3c_chrNameLength.txt added
369de25bcf9da0_chrStart.txt added
369de2363d7f2_exonGeTrInfo.tab added
369de2639eac30_exonInfo.tab added
369de26743bdee_geneInfo.tab added
369de24a692e2e_Genome added
369de238931e63_genomeParameters.txt added
369de229e9757_Log.out added
369de26b0c01e1_SA added
369de25bac1a7b_SAindex added
369de229a92ef8_sjdbInfo.txt added
369de23490339e_sjdbList.fromGTF.out.tab added
369de269092b50_sjdbList.out.tab added
369de241d1c74b_transcriptInfo.tab added
369de27bc38bf8_GRCh38.GENCODE.v42_100 added
369de23d24b005_knownGene_hg38.sql added
369de25a9cf08a_knownGene_hg38.txt added
369de27847546_refGene_hg38.sql added
369de23c5162d1_refGene_hg38.txt added
369de257897058_knownGene_mm39.sql added
369de24dfa2d48_knownGene_mm39.txt added
369de2434e914d_refGene_mm39.sql added
369de243422349_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/RtmpPeI200/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
17.813 1.117 19.789
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.986 | 0.364 | 6.351 | |
| dataSearch | 1.085 | 0.037 | 1.121 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.693 | 0.113 | 4.250 | |
| getData | 0.000 | 0.001 | 0.000 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.117 | 0.011 | 0.129 | |
| recipeLoad | 1.205 | 0.044 | 1.251 | |
| recipeMake | 0.000 | 0.001 | 0.001 | |
| recipeSearch | 0.515 | 0.011 | 0.528 | |
| recipeUpdate | 0 | 0 | 0 | |