Qian Liu
| Snapshot Date: 2026-03-12 13:45 -0400 (Thu, 12 Mar 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-13 11:58 -0400 (Fri, 13 Mar 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" | 4892 |
| 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: 2026-03-13 03:34:54 -0400 (Fri, 13 Mar 2026) |
| EndedAt: 2026-03-13 03:37:37 -0400 (Fri, 13 Mar 2026) |
| EllapsedTime: 163.2 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 5.765 0.229 5.998
* 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...
1e383147929bc_GRCh38.primary_assembly.genome.fa.1.bt2 added
1e383162d38a3a_GRCh38.primary_assembly.genome.fa.2.bt2 added
1e38314e936020_GRCh38.primary_assembly.genome.fa.3.bt2 added
1e38314b595b37_GRCh38.primary_assembly.genome.fa.4.bt2 added
1e38312507de10_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1e3831670b56db_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1e38315b780130_outfile.txt added
1e38314dd6d46d_GRCh37_to_GRCh38.chain added
1e383160aca6c2_GRCh37_to_NCBI34.chain added
1e383159ed086f_GRCh37_to_NCBI35.chain added
1e38312cc18bd2_GRCh37_to_NCBI36.chain added
1e3831400b0c0_GRCh38_to_GRCh37.chain added
1e38314a9adbfe_GRCh38_to_NCBI34.chain added
1e3831253cc2d4_GRCh38_to_NCBI35.chain added
1e383123374e8a_GRCh38_to_NCBI36.chain added
1e383133cd3c3f_NCBI34_to_GRCh37.chain added
1e38316c98d640_NCBI34_to_GRCh38.chain added
1e3831771211c6_NCBI35_to_GRCh37.chain added
1e38313554f54_NCBI35_to_GRCh38.chain added
1e38315c33b251_NCBI36_to_GRCh37.chain added
1e38317a5c531f_NCBI36_to_GRCh38.chain added
1e383163f41d90_GRCm38_to_NCBIM36.chain added
1e383173de3b9c_GRCm38_to_NCBIM37.chain added
1e38312c3d8055_NCBIM36_to_GRCm38.chain added
1e38316564e90a_NCBIM37_to_GRCm38.chain added
1e38312866cdda_1000G_omni2.5.b37.vcf.gz added
1e3831a7ddae9_1000G_omni2.5.b37.vcf.gz.tbi added
1e38313d829e08_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1e383138bbd4b4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1e3831778b953c_1000G_omni2.5.hg38.vcf.gz added
1e383150135821_1000G_omni2.5.hg38.vcf.gz.tbi added
1e38313d34fe71_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1e38315a5f1f77_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1e38311ea6b841_af-only-gnomad.raw.sites.vcf added
1e383188e59a8_af-only-gnomad.raw.sites.vcf.idx added
1e38317f66fd87_Mutect2-exome-panel.vcf.idx added
1e38315b20f1c_Mutect2-WGS-panel-b37.vcf added
1e383164065ad8_Mutect2-WGS-panel-b37.vcf.idx added
1e38314d3dd1f4_small_exac_common_3.vcf added
1e3831665eb5df_small_exac_common_3.vcf.idx added
1e38313df36348_1000g_pon.hg38.vcf.gz added
1e383179ff5dc7_1000g_pon.hg38.vcf.gz.tbi added
1e38316a5f669f_af-only-gnomad.hg38.vcf.gz added
1e383188e3f46_af-only-gnomad.hg38.vcf.gz.tbi added
1e38311f3c209b_small_exac_common_3.hg38.vcf.gz added
1e3831d96b529_small_exac_common_3.hg38.vcf.gz.tbi added
1e38313c5b7b85_gencode.v41.annotation.gtf added
1e3831bd4f6db_gencode.v42.annotation.gtf added
1e38314a8c6ef_gencode.vM30.annotation.gtf added
1e38313fb0cad9_gencode.vM31.annotation.gtf added
1e38316808a92d_gencode.v41.transcripts.fa added
1e38317f051a0e_gencode.v41.transcripts.fa.fai added
1e383123a4e869_gencode.v42.transcripts.fa added
1e38315be6e4c9_gencode.v42.transcripts.fa.fai added
1e38312b429a64_gencode.vM30.pc_transcripts.fa added
1e3831909d173_gencode.vM30.pc_transcripts.fa.fai added
1e383144db2a3_gencode.vM31.pc_transcripts.fa added
1e383135c0754d_gencode.vM31.pc_transcripts.fa.fai added
1e3831468c6f7c_GRCh38.primary_assembly.genome.fa.1.ht2 added
1e38313d098758_GRCh38.primary_assembly.genome.fa.2.ht2 added
1e38312d4c0a8a_GRCh38.primary_assembly.genome.fa.3.ht2 added
1e3831169fc79d_GRCh38.primary_assembly.genome.fa.4.ht2 added
1e38317a3e85c9_GRCh38.primary_assembly.genome.fa.5.ht2 added
1e38317ab2a01_GRCh38.primary_assembly.genome.fa.6.ht2 added
1e383135467fde_GRCh38.primary_assembly.genome.fa.7.ht2 added
1e38312ccdf71_GRCh38.primary_assembly.genome.fa.8.ht2 added
1e38317122788_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1e38313af88efb_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1e383166d33a49_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1e3831544ff97c_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1e3831215744da_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1e383124c69d91_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1e38314e4f5743_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1e3831bb6ab79_GRCh38.primary_assembly.genome.fa.fai added
1e38312d54dcd8_GRCh38.primary_assembly.genome.fa.amb added
1e38316d8b77de_GRCh38.primary_assembly.genome.fa.ann added
1e3831194d60a2_GRCh38.primary_assembly.genome.fa.bwt added
1e383169b0585d_GRCh38.primary_assembly.genome.fa.pac added
1e383179606eba_GRCh38.primary_assembly.genome.fa.sa added
1e38311df62791_GRCh38.primary_assembly.genome.fa added
1e383129612337_hs37d5.fa.fai added
1e3831616917e7_hs37d5.fa.amb added
1e38311cfb41a0_hs37d5.fa.ann added
1e38314d060ba0_hs37d5.fa.bwt added
1e38313d4ffcb0_hs37d5.fa.pac added
1e3831483ddc04_hs37d5.fa.sa added
1e3831560fdd14_hs37d5.fa added
1e3831419daf54_complete_ref_lens.bin added
1e38317dfe5151_ctable.bin added
1e38311c9c4c90_ctg_offsets.bin added
1e38317ea736ac_duplicate_clusters.tsv added
1e38312b4a5bdb_info.json added
1e3831333c142d_mphf.bin added
1e383178e5bc75_pos.bin added
1e383132f585dc_pre_indexing.log added
1e38316882940b_rank.bin added
1e38317bb29be6_ref_indexing.log added
1e38313a07ad64_refAccumLengths.bin added
1e3831237b2306_reflengths.bin added
1e38316285d62f_refseq.bin added
1e3831e57a6e1_seq.bin added
1e383144d267e0_versionInfo.json added
1e383174c73c1_salmon_index added
1e38315ca6fe24_chrLength.txt added
1e383150891359_chrName.txt added
1e383134a15099_chrNameLength.txt added
1e38314a327603_chrStart.txt added
1e383169d673fb_exonGeTrInfo.tab added
1e38311e51a8f6_exonInfo.tab added
1e38314392e4bd_geneInfo.tab added
1e38317cc9b8d_Genome added
1e383147b2cc2d_genomeParameters.txt added
1e383124fbfca4_Log.out added
1e383124c7dd2d_SA added
1e383114b8d7ce_SAindex added
1e3831624bf954_sjdbInfo.txt added
1e38316d05b931_sjdbList.fromGTF.out.tab added
1e38316ac8b4e2_sjdbList.out.tab added
1e383123e9a8a8_transcriptInfo.tab added
1e38316b040a82_GRCh38.GENCODE.v42_100 added
1e38317650172_knownGene_hg38.sql added
1e38312290df54_knownGene_hg38.txt added
1e3831164e665e_refGene_hg38.sql added
1e38313aa1159f_refGene_hg38.txt added
1e38311b769bc9_knownGene_mm39.sql added
1e38314943ec3a_knownGene_mm39.txt added
1e38312323a9aa_refGene_mm39.sql added
1e3831172937af_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/RtmpMMqZof/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
18.146 1.247 19.894
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.765 | 0.229 | 5.998 | |
| dataSearch | 1.106 | 0.024 | 1.131 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.725 | 0.135 | 3.555 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.125 | 0.002 | 0.128 | |
| recipeLoad | 1.277 | 0.075 | 1.353 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.567 | 0.039 | 0.605 | |
| recipeUpdate | 0 | 0 | 0 | |