Qian Liu
| Snapshot Date: 2026-05-28 13:40 -0400 (Thu, 28 May 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: RELEASE_3_23 |
| git_last_commit: bb3489b |
| git_last_commit_date: 2026-04-28 08:59:39 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-29 11:32 -0400 (Fri, 29 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4997 |
| 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 1815/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.12.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.4 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: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2026-05-29 04:02:49 -0400 (Fri, 29 May 2026) |
| EndedAt: 2026-05-29 04:05:37 -0400 (Fri, 29 May 2026) |
| EllapsedTime: 167.3 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-29 08:02:50 UTC
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.12.0’
* 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 6.507 0.442 6.971
* 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 ‘1.12.0’ ** 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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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...
1c220f3c478c3_GRCh38.primary_assembly.genome.fa.1.bt2 added
1c220f69d26a97_GRCh38.primary_assembly.genome.fa.2.bt2 added
1c220fc16b7dc_GRCh38.primary_assembly.genome.fa.3.bt2 added
1c220f13532420_GRCh38.primary_assembly.genome.fa.4.bt2 added
1c220fdb84fb8_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1c220f3b21d8c7_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1c220f4676901c_outfile.txt added
1c220f49082df7_GRCh37_to_GRCh38.chain added
1c220f40ee5bbb_GRCh37_to_NCBI34.chain added
1c220f617d89a6_GRCh37_to_NCBI35.chain added
1c220f29e088cc_GRCh37_to_NCBI36.chain added
1c220f4636fb34_GRCh38_to_GRCh37.chain added
1c220f1aec3743_GRCh38_to_NCBI34.chain added
1c220f260c0f08_GRCh38_to_NCBI35.chain added
1c220f606d7c49_GRCh38_to_NCBI36.chain added
1c220f4142e79c_NCBI34_to_GRCh37.chain added
1c220f3b765362_NCBI34_to_GRCh38.chain added
1c220f5e71872f_NCBI35_to_GRCh37.chain added
1c220f790e5eb0_NCBI35_to_GRCh38.chain added
1c220f3519dc67_NCBI36_to_GRCh37.chain added
1c220f2d7300f8_NCBI36_to_GRCh38.chain added
1c220f43f097_GRCm38_to_NCBIM36.chain added
1c220f5ee40553_GRCm38_to_NCBIM37.chain added
1c220f353dfb5f_NCBIM36_to_GRCm38.chain added
1c220f3445a051_NCBIM37_to_GRCm38.chain added
1c220f69a87e56_1000G_omni2.5.b37.vcf.gz added
1c220f4808c57b_1000G_omni2.5.b37.vcf.gz.tbi added
1c220f7d8fd5ae_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1c220f277e8095_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1c220f78d2c422_1000G_omni2.5.hg38.vcf.gz added
1c220f641aba29_1000G_omni2.5.hg38.vcf.gz.tbi added
1c220f2b42f958_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1c220f62a52eb9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1c220f70317205_af-only-gnomad.raw.sites.vcf added
1c220f3e961d78_af-only-gnomad.raw.sites.vcf.idx added
1c220f705d7e71_Mutect2-exome-panel.vcf.idx added
1c220f2b534acc_Mutect2-WGS-panel-b37.vcf added
1c220f50cad94_Mutect2-WGS-panel-b37.vcf.idx added
1c220f3965ac68_small_exac_common_3.vcf added
1c220f6c41a688_small_exac_common_3.vcf.idx added
1c220f668a373a_1000g_pon.hg38.vcf.gz added
1c220f63463534_1000g_pon.hg38.vcf.gz.tbi added
1c220f3278a1bc_af-only-gnomad.hg38.vcf.gz added
1c220f1766e7d_af-only-gnomad.hg38.vcf.gz.tbi added
1c220f952443c_small_exac_common_3.hg38.vcf.gz added
1c220f12e61e06_small_exac_common_3.hg38.vcf.gz.tbi added
1c220f42b95619_gencode.v41.annotation.gtf added
1c220f44c8979f_gencode.v42.annotation.gtf added
1c220f7157a535_gencode.vM30.annotation.gtf added
1c220f3bc7b4ca_gencode.vM31.annotation.gtf added
1c220f79e27406_gencode.v41.transcripts.fa added
1c220f1ecaa62e_gencode.v41.transcripts.fa.fai added
1c220f3c0ba561_gencode.v42.transcripts.fa added
1c220f58c67959_gencode.v42.transcripts.fa.fai added
1c220f5408a18d_gencode.vM30.pc_transcripts.fa added
1c220f705145b2_gencode.vM30.pc_transcripts.fa.fai added
1c220f426ef7af_gencode.vM31.pc_transcripts.fa added
1c220f1c116708_gencode.vM31.pc_transcripts.fa.fai added
1c220f6de11b60_GRCh38.primary_assembly.genome.fa.1.ht2 added
1c220f69ed7844_GRCh38.primary_assembly.genome.fa.2.ht2 added
1c220f14e42b2a_GRCh38.primary_assembly.genome.fa.3.ht2 added
1c220f51fbd589_GRCh38.primary_assembly.genome.fa.4.ht2 added
1c220f1530719c_GRCh38.primary_assembly.genome.fa.5.ht2 added
1c220f778959e3_GRCh38.primary_assembly.genome.fa.6.ht2 added
1c220f422d478f_GRCh38.primary_assembly.genome.fa.7.ht2 added
1c220f53c68f14_GRCh38.primary_assembly.genome.fa.8.ht2 added
1c220f67e6d854_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1c220f6d80925b_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1c220f58d33ca8_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1c220f214c84bd_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1c220f59c238e3_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1c220f3f5d73e3_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1c220f492b9f1_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1c220fc3adaa0_GRCh38.primary_assembly.genome.fa.fai added
1c220f40d3e260_GRCh38.primary_assembly.genome.fa.amb added
1c220fde4fe2e_GRCh38.primary_assembly.genome.fa.ann added
1c220f1f20f8a6_GRCh38.primary_assembly.genome.fa.bwt added
1c220f38d387a_GRCh38.primary_assembly.genome.fa.pac added
1c220f52ad95cd_GRCh38.primary_assembly.genome.fa.sa added
1c220f10789ddb_GRCh38.primary_assembly.genome.fa added
1c220f3f54ed44_hs37d5.fa.fai added
1c220f4c9009d3_hs37d5.fa.amb added
1c220f2f434409_hs37d5.fa.ann added
1c220f7b6092a5_hs37d5.fa.bwt added
1c220f2556832c_hs37d5.fa.pac added
1c220f34be597_hs37d5.fa.sa added
1c220f6bb1d857_hs37d5.fa added
1c220f67c57adb_complete_ref_lens.bin added
1c220f1f5d4c9f_ctable.bin added
1c220f5992f3b7_ctg_offsets.bin added
1c220f51b2f320_duplicate_clusters.tsv added
1c220f344177ca_info.json added
1c220f2b8ec940_mphf.bin added
1c220f66e364bc_pos.bin added
1c220f2bcad1ad_pre_indexing.log added
1c220f6dbc10cf_rank.bin added
1c220f3aa9f3d1_ref_indexing.log added
1c220f13b1aa02_refAccumLengths.bin added
1c220f5b3ca32b_reflengths.bin added
1c220f137d3079_refseq.bin added
1c220f34fe2ebf_seq.bin added
1c220f34fedc0e_versionInfo.json added
1c220f52daa45c_salmon_index added
1c220f3990e8b0_chrLength.txt added
1c220f4139b6ae_chrName.txt added
1c220f13ae86bd_chrNameLength.txt added
1c220f4775e6de_chrStart.txt added
1c220f605aaf54_exonGeTrInfo.tab added
1c220f173bbf37_exonInfo.tab added
1c220f1a237cab_geneInfo.tab added
1c220f70d34d30_Genome added
1c220f5690ac7b_genomeParameters.txt added
1c220f66b3867e_Log.out added
1c220f20169139_SA added
1c220f51f13f20_SAindex added
1c220fc0a09aa_sjdbInfo.txt added
1c220f236276d0_sjdbList.fromGTF.out.tab added
1c220f3da31777_sjdbList.out.tab added
1c220f73cf8486_transcriptInfo.tab added
1c220f42bfc370_GRCh38.GENCODE.v42_100 added
1c220f17360b2e_knownGene_hg38.sql added
1c220f458277a6_knownGene_hg38.txt added
1c220f77013b3a_refGene_hg38.sql added
1c220f42c4d46e_refGene_hg38.txt added
1c220f2c65dc62_knownGene_mm39.sql added
1c220f22cc0ce7_knownGene_mm39.txt added
1c220f3080e53e_refGene_mm39.sql added
1c220f670fd033_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/RtmpC0yo5H/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
18.859 1.327 21.001
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.507 | 0.442 | 6.971 | |
| dataSearch | 1.169 | 0.058 | 1.228 | |
| dataUpdate | 0.001 | 0.000 | 0.001 | |
| getCloudData | 2.629 | 0.150 | 3.282 | |
| getData | 0.000 | 0.001 | 0.001 | |
| meta_data | 0.000 | 0.001 | 0.001 | |
| recipeHub-class | 0.129 | 0.002 | 0.131 | |
| recipeLoad | 1.314 | 0.068 | 1.384 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.535 | 0.026 | 0.560 | |
| recipeUpdate | 0.000 | 0.001 | 0.000 | |