Qian Liu
| Snapshot Date: 2025-12-01 13:45 -0500 (Mon, 01 Dec 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 2025-12-04 12:01 -0500 (Thu, 04 Dec 2025).
| 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" | 4878 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4624 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | 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: 2025-12-02 03:37:31 -0500 (Tue, 02 Dec 2025) |
| EndedAt: 2025-12-02 03:40:20 -0500 (Tue, 02 Dec 2025) |
| 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 5.772 0.212 5.988
getCloudData 2.875 0.109 5.500
* 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...
229e0b5695dd3e_GRCh38.primary_assembly.genome.fa.1.bt2 added
229e0b43355f2_GRCh38.primary_assembly.genome.fa.2.bt2 added
229e0b69626c3f_GRCh38.primary_assembly.genome.fa.3.bt2 added
229e0b6c4c5ccd_GRCh38.primary_assembly.genome.fa.4.bt2 added
229e0b4c3f3c31_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
229e0b11c9b066_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
229e0b36243482_outfile.txt added
229e0b165d278f_GRCh37_to_GRCh38.chain added
229e0b3531f96e_GRCh37_to_NCBI34.chain added
229e0b38cd7a85_GRCh37_to_NCBI35.chain added
229e0b2e0cdb32_GRCh37_to_NCBI36.chain added
229e0b11524b49_GRCh38_to_GRCh37.chain added
229e0b3418a60c_GRCh38_to_NCBI34.chain added
229e0b7ffaa5cd_GRCh38_to_NCBI35.chain added
229e0b42ec607a_GRCh38_to_NCBI36.chain added
229e0b457546e7_NCBI34_to_GRCh37.chain added
229e0b5349f6d_NCBI34_to_GRCh38.chain added
229e0bc7bd99b_NCBI35_to_GRCh37.chain added
229e0b42820ef6_NCBI35_to_GRCh38.chain added
229e0b2925aa1b_NCBI36_to_GRCh37.chain added
229e0b4a15bbcd_NCBI36_to_GRCh38.chain added
229e0b7e15d351_GRCm38_to_NCBIM36.chain added
229e0b746c9deb_GRCm38_to_NCBIM37.chain added
229e0b3c6dea5f_NCBIM36_to_GRCm38.chain added
229e0b6e196a93_NCBIM37_to_GRCm38.chain added
229e0b5c99dae8_1000G_omni2.5.b37.vcf.gz added
229e0b55a3b262_1000G_omni2.5.b37.vcf.gz.tbi added
229e0b4b50b9c0_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
229e0b37f4af26_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
229e0b24f1effd_1000G_omni2.5.hg38.vcf.gz added
229e0b36b6de83_1000G_omni2.5.hg38.vcf.gz.tbi added
229e0be8a8c64_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
229e0b292545ef_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
229e0b20194ac3_af-only-gnomad.raw.sites.vcf added
229e0b7ad6e932_af-only-gnomad.raw.sites.vcf.idx added
229e0b75648220_Mutect2-exome-panel.vcf.idx added
229e0b31e2fb29_Mutect2-WGS-panel-b37.vcf added
229e0b30fb1db4_Mutect2-WGS-panel-b37.vcf.idx added
229e0bbc1a9af_small_exac_common_3.vcf added
229e0b6714f498_small_exac_common_3.vcf.idx added
229e0b69c89839_1000g_pon.hg38.vcf.gz added
229e0b39ce84e1_1000g_pon.hg38.vcf.gz.tbi added
229e0b78673fe1_af-only-gnomad.hg38.vcf.gz added
229e0b1de13e45_af-only-gnomad.hg38.vcf.gz.tbi added
229e0b39c92aae_small_exac_common_3.hg38.vcf.gz added
229e0b3b53a05b_small_exac_common_3.hg38.vcf.gz.tbi added
229e0b6356852d_gencode.v41.annotation.gtf added
229e0b3efdca1c_gencode.v42.annotation.gtf added
229e0b47cf79f6_gencode.vM30.annotation.gtf added
229e0b25d89423_gencode.vM31.annotation.gtf added
229e0b68237437_gencode.v41.transcripts.fa added
229e0b11e535c3_gencode.v41.transcripts.fa.fai added
229e0b23ee6775_gencode.v42.transcripts.fa added
229e0b5c901222_gencode.v42.transcripts.fa.fai added
229e0b4e532022_gencode.vM30.pc_transcripts.fa added
229e0b1207d208_gencode.vM30.pc_transcripts.fa.fai added
229e0b3929ed0b_gencode.vM31.pc_transcripts.fa added
229e0b23f6d285_gencode.vM31.pc_transcripts.fa.fai added
229e0b5d588bc8_GRCh38.primary_assembly.genome.fa.1.ht2 added
229e0b711e9c31_GRCh38.primary_assembly.genome.fa.2.ht2 added
229e0b48e8c282_GRCh38.primary_assembly.genome.fa.3.ht2 added
229e0b140f6a4c_GRCh38.primary_assembly.genome.fa.4.ht2 added
229e0b7fa92896_GRCh38.primary_assembly.genome.fa.5.ht2 added
229e0b720e0871_GRCh38.primary_assembly.genome.fa.6.ht2 added
229e0b3428b50f_GRCh38.primary_assembly.genome.fa.7.ht2 added
229e0b7a8011c8_GRCh38.primary_assembly.genome.fa.8.ht2 added
229e0b67728a91_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
229e0b660bb038_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
229e0b2b7b2f7c_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
229e0b73343441_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
229e0b4d20a4d0_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
229e0b1543c7b5_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
229e0b2d02b922_GRCh38_full_analysis_set_plus_decoy_hla.fa added
229e0b4587e4b2_GRCh38.primary_assembly.genome.fa.fai added
229e0b332505fb_GRCh38.primary_assembly.genome.fa.amb added
229e0b66cbe3d1_GRCh38.primary_assembly.genome.fa.ann added
229e0bdb850d_GRCh38.primary_assembly.genome.fa.bwt added
229e0b167b8b28_GRCh38.primary_assembly.genome.fa.pac added
229e0b25c9aded_GRCh38.primary_assembly.genome.fa.sa added
229e0b48aaff04_GRCh38.primary_assembly.genome.fa added
229e0b3c541f4b_hs37d5.fa.fai added
229e0bded2224_hs37d5.fa.amb added
229e0b5a9034c7_hs37d5.fa.ann added
229e0b604286c0_hs37d5.fa.bwt added
229e0b6a7d3446_hs37d5.fa.pac added
229e0b28e354ea_hs37d5.fa.sa added
229e0b724a58c8_hs37d5.fa added
229e0b23a72151_complete_ref_lens.bin added
229e0b4cda276f_ctable.bin added
229e0b4fa2e491_ctg_offsets.bin added
229e0b14c5bd83_duplicate_clusters.tsv added
229e0b15c2e9f1_info.json added
229e0b63b24edd_mphf.bin added
229e0b146ee619_pos.bin added
229e0b7d0f262_pre_indexing.log added
229e0b17db03ec_rank.bin added
229e0beeef7e1_ref_indexing.log added
229e0b6f437cf3_refAccumLengths.bin added
229e0b7de6b424_reflengths.bin added
229e0b3a6a275d_refseq.bin added
229e0b6277b134_seq.bin added
229e0b4b0758f5_versionInfo.json added
229e0b4fadef12_salmon_index added
229e0bf7a6a57_chrLength.txt added
229e0b108f3da7_chrName.txt added
229e0b2d2f50d_chrNameLength.txt added
229e0b76464e28_chrStart.txt added
229e0b116ac2b4_exonGeTrInfo.tab added
229e0b194e8035_exonInfo.tab added
229e0b1c0ffc15_geneInfo.tab added
229e0b5a15c1b8_Genome added
229e0b55a29f81_genomeParameters.txt added
229e0b29fd1e39_Log.out added
229e0b34a5f680_SA added
229e0b35e52641_SAindex added
229e0b147a527f_sjdbInfo.txt added
229e0b5d894b6a_sjdbList.fromGTF.out.tab added
229e0b282f7f0a_sjdbList.out.tab added
229e0b382173d1_transcriptInfo.tab added
229e0b2a6372d9_GRCh38.GENCODE.v42_100 added
229e0b77d2639b_knownGene_hg38.sql added
229e0b4ce73154_knownGene_hg38.txt added
229e0b40265cca_refGene_hg38.sql added
229e0b5b84b278_refGene_hg38.txt added
229e0b6156176d_knownGene_mm39.sql added
229e0b47f74f2c_knownGene_mm39.txt added
229e0b735fb664_refGene_mm39.sql added
229e0b70450f4e_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/RtmpX7WZ4J/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
17.744 0.939 19.601
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.772 | 0.212 | 5.988 | |
| dataSearch | 1.149 | 0.004 | 1.153 | |
| dataUpdate | 0.001 | 0.000 | 0.001 | |
| getCloudData | 2.875 | 0.109 | 5.500 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.121 | 0.000 | 0.122 | |
| recipeLoad | 1.247 | 0.015 | 1.262 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.522 | 0.006 | 0.528 | |
| recipeUpdate | 0 | 0 | 0 | |