Qian Liu
| Snapshot Date: 2026-02-16 13:45 -0500 (Mon, 16 Feb 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 Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-18 11:58 -0500 (Wed, 18 Feb 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" | 4890 |
| 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: 2026-02-17 04:21:38 -0500 (Tue, 17 Feb 2026) |
| EndedAt: 2026-02-17 04:24:29 -0500 (Tue, 17 Feb 2026) |
| EllapsedTime: 171.2 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 5.705 0.228 5.936
getCloudData 2.580 0.149 7.477
* 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...
36ada975310a67_GRCh38.primary_assembly.genome.fa.1.bt2 added
36ada9602d9069_GRCh38.primary_assembly.genome.fa.2.bt2 added
36ada95c4c4523_GRCh38.primary_assembly.genome.fa.3.bt2 added
36ada9701fd5b9_GRCh38.primary_assembly.genome.fa.4.bt2 added
36ada95183a781_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
36ada95d3ce6f3_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
36ada92737314b_outfile.txt added
36ada940d5d2c6_GRCh37_to_GRCh38.chain added
36ada920d5256_GRCh37_to_NCBI34.chain added
36ada938bbe59_GRCh37_to_NCBI35.chain added
36ada91094a0a5_GRCh37_to_NCBI36.chain added
36ada96d5378e4_GRCh38_to_GRCh37.chain added
36ada95866d39a_GRCh38_to_NCBI34.chain added
36ada954374963_GRCh38_to_NCBI35.chain added
36ada96c458d70_GRCh38_to_NCBI36.chain added
36ada91ad320b7_NCBI34_to_GRCh37.chain added
36ada96e167923_NCBI34_to_GRCh38.chain added
36ada950f4736c_NCBI35_to_GRCh37.chain added
36ada934464c70_NCBI35_to_GRCh38.chain added
36ada970ae968e_NCBI36_to_GRCh37.chain added
36ada9c3c72e0_NCBI36_to_GRCh38.chain added
36ada933977386_GRCm38_to_NCBIM36.chain added
36ada95ca8392b_GRCm38_to_NCBIM37.chain added
36ada96b6ca81b_NCBIM36_to_GRCm38.chain added
36ada95845a3e3_NCBIM37_to_GRCm38.chain added
36ada938e98236_1000G_omni2.5.b37.vcf.gz added
36ada969c72931_1000G_omni2.5.b37.vcf.gz.tbi added
36ada97392d9a7_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
36ada92a9890c8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
36ada96b43d67b_1000G_omni2.5.hg38.vcf.gz added
36ada945222fe6_1000G_omni2.5.hg38.vcf.gz.tbi added
36ada91fc99b2f_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
36ada94b7166e4_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
36ada9216e750a_af-only-gnomad.raw.sites.vcf added
36ada9fe970e8_af-only-gnomad.raw.sites.vcf.idx added
36ada91cf50e65_Mutect2-exome-panel.vcf.idx added
36ada97eab5bfd_Mutect2-WGS-panel-b37.vcf added
36ada93720a234_Mutect2-WGS-panel-b37.vcf.idx added
36ada95dcae12c_small_exac_common_3.vcf added
36ada9b8ae53_small_exac_common_3.vcf.idx added
36ada93aac608d_1000g_pon.hg38.vcf.gz added
36ada96e5f81d1_1000g_pon.hg38.vcf.gz.tbi added
36ada96e0c2737_af-only-gnomad.hg38.vcf.gz added
36ada913133428_af-only-gnomad.hg38.vcf.gz.tbi added
36ada94296cb34_small_exac_common_3.hg38.vcf.gz added
36ada95a51b4a8_small_exac_common_3.hg38.vcf.gz.tbi added
36ada92de654df_gencode.v41.annotation.gtf added
36ada930ad4458_gencode.v42.annotation.gtf added
36ada92b462814_gencode.vM30.annotation.gtf added
36ada9622ca150_gencode.vM31.annotation.gtf added
36ada9215bdae6_gencode.v41.transcripts.fa added
36ada937829af4_gencode.v41.transcripts.fa.fai added
36ada915c414d6_gencode.v42.transcripts.fa added
36ada97e041411_gencode.v42.transcripts.fa.fai added
36ada922ef4310_gencode.vM30.pc_transcripts.fa added
36ada96e09b8b9_gencode.vM30.pc_transcripts.fa.fai added
36ada936ed9648_gencode.vM31.pc_transcripts.fa added
36ada9cb66c41_gencode.vM31.pc_transcripts.fa.fai added
36ada9619c9261_GRCh38.primary_assembly.genome.fa.1.ht2 added
36ada961862710_GRCh38.primary_assembly.genome.fa.2.ht2 added
36ada977fa42bc_GRCh38.primary_assembly.genome.fa.3.ht2 added
36ada926bec247_GRCh38.primary_assembly.genome.fa.4.ht2 added
36ada914fc240_GRCh38.primary_assembly.genome.fa.5.ht2 added
36ada9436ba9a1_GRCh38.primary_assembly.genome.fa.6.ht2 added
36ada9482d3751_GRCh38.primary_assembly.genome.fa.7.ht2 added
36ada911393328_GRCh38.primary_assembly.genome.fa.8.ht2 added
36ada96060b806_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
36ada946d8934e_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
36ada94859d55c_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
36ada93e2b9932_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
36ada9479141a1_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
36ada930635ea_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
36ada92c8b1b03_GRCh38_full_analysis_set_plus_decoy_hla.fa added
36ada9359d68d9_GRCh38.primary_assembly.genome.fa.fai added
36ada916196a12_GRCh38.primary_assembly.genome.fa.amb added
36ada96f21e638_GRCh38.primary_assembly.genome.fa.ann added
36ada9fef1d81_GRCh38.primary_assembly.genome.fa.bwt added
36ada943ffbef1_GRCh38.primary_assembly.genome.fa.pac added
36ada91fcf2a90_GRCh38.primary_assembly.genome.fa.sa added
36ada93b354595_GRCh38.primary_assembly.genome.fa added
36ada9262c6041_hs37d5.fa.fai added
36ada9412b0576_hs37d5.fa.amb added
36ada972b7e089_hs37d5.fa.ann added
36ada93bf07518_hs37d5.fa.bwt added
36ada93f2f1987_hs37d5.fa.pac added
36ada915a72399_hs37d5.fa.sa added
36ada929fa2dd1_hs37d5.fa added
36ada9761cafcf_complete_ref_lens.bin added
36ada9225d8fdb_ctable.bin added
36ada9b96c032_ctg_offsets.bin added
36ada957a2d6e0_duplicate_clusters.tsv added
36ada91a57d297_info.json added
36ada93255827a_mphf.bin added
36ada958f29920_pos.bin added
36ada95dc37c38_pre_indexing.log added
36ada97a82b9cb_rank.bin added
36ada96a2bcc48_ref_indexing.log added
36ada93e24343f_refAccumLengths.bin added
36ada9415b4d1a_reflengths.bin added
36ada93285a1a5_refseq.bin added
36ada97c4fcd71_seq.bin added
36ada98ec8ebb_versionInfo.json added
36ada9358bd78f_salmon_index added
36ada928dae875_chrLength.txt added
36ada93e89f794_chrName.txt added
36ada94ba541a1_chrNameLength.txt added
36ada917fccead_chrStart.txt added
36ada94e791515_exonGeTrInfo.tab added
36ada9fa50092_exonInfo.tab added
36ada937cbf93d_geneInfo.tab added
36ada99ae5aaa_Genome added
36ada935d160d4_genomeParameters.txt added
36ada978f6feb3_Log.out added
36ada97c663b34_SA added
36ada971c1d5ec_SAindex added
36ada93826183a_sjdbInfo.txt added
36ada9120d5ecd_sjdbList.fromGTF.out.tab added
36ada91bbc03bd_sjdbList.out.tab added
36ada92e42c80a_transcriptInfo.tab added
36ada9346aeea8_GRCh38.GENCODE.v42_100 added
36ada92752c3f0_knownGene_hg38.sql added
36ada95e59eea_knownGene_hg38.txt added
36ada94ec2c140_refGene_hg38.sql added
36ada959a8466a_refGene_hg38.txt added
36ada95ed8380a_knownGene_mm39.sql added
36ada92c863d78_knownGene_mm39.txt added
36ada9542b0035_refGene_mm39.sql added
36ada949040452_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/RtmpG9WRa6/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
18.015 1.600 22.269
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.705 | 0.228 | 5.936 | |
| dataSearch | 1.060 | 0.012 | 1.072 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.580 | 0.149 | 7.477 | |
| getData | 0.000 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.114 | 0.002 | 0.117 | |
| recipeLoad | 1.203 | 0.009 | 1.213 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.508 | 0.004 | 0.511 | |
| recipeUpdate | 0 | 0 | 0 | |