Qian Liu
| Snapshot Date: 2026-03-25 13:45 -0400 (Wed, 25 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 2026-03-26 11:57 -0400 (Thu, 26 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" | 4893 |
| 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: 2026-03-26 03:12:28 -0400 (Thu, 26 Mar 2026) |
| EndedAt: 2026-03-26 03:15:14 -0400 (Thu, 26 Mar 2026) |
| EllapsedTime: 166.2 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 24.04.4 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 6.286 0.518 6.807
* 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...
948b32f6a083e_GRCh38.primary_assembly.genome.fa.1.bt2 added
948b36d4b5cfc_GRCh38.primary_assembly.genome.fa.2.bt2 added
948b36078fc6_GRCh38.primary_assembly.genome.fa.3.bt2 added
948b37299bce3_GRCh38.primary_assembly.genome.fa.4.bt2 added
948b36a0856a6_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
948b321d35933_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
948b36c1f6357_outfile.txt added
948b342e8a6cf_GRCh37_to_GRCh38.chain added
948b37c939711_GRCh37_to_NCBI34.chain added
948b31382e445_GRCh37_to_NCBI35.chain added
948b35a7f0d99_GRCh37_to_NCBI36.chain added
948b344812e43_GRCh38_to_GRCh37.chain added
948b3737f802_GRCh38_to_NCBI34.chain added
948b3363225ec_GRCh38_to_NCBI35.chain added
948b36d194f86_GRCh38_to_NCBI36.chain added
948b359ec3fe_NCBI34_to_GRCh37.chain added
948b3f942861_NCBI34_to_GRCh38.chain added
948b35b248c91_NCBI35_to_GRCh37.chain added
948b37731a5d3_NCBI35_to_GRCh38.chain added
948b35195ee94_NCBI36_to_GRCh37.chain added
948b32a3cda95_NCBI36_to_GRCh38.chain added
948b33487d670_GRCm38_to_NCBIM36.chain added
948b3c093ea6_GRCm38_to_NCBIM37.chain added
948b3a47398b_NCBIM36_to_GRCm38.chain added
948b36bd5d8c5_NCBIM37_to_GRCm38.chain added
948b36ffadc28_1000G_omni2.5.b37.vcf.gz added
948b32a696f62_1000G_omni2.5.b37.vcf.gz.tbi added
948b31fce2d14_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
948b36500be8e_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
948b37d72a21a_1000G_omni2.5.hg38.vcf.gz added
948b3d11739e_1000G_omni2.5.hg38.vcf.gz.tbi added
948b3146ac6cd_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
948b36abdff16_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
948b313190365_af-only-gnomad.raw.sites.vcf added
948b370483b0_af-only-gnomad.raw.sites.vcf.idx added
948b354c655bd_Mutect2-exome-panel.vcf.idx added
948b334ec5c98_Mutect2-WGS-panel-b37.vcf added
948b37323e708_Mutect2-WGS-panel-b37.vcf.idx added
948b317aefc8c_small_exac_common_3.vcf added
948b3317ff3aa_small_exac_common_3.vcf.idx added
948b36a6cb4d_1000g_pon.hg38.vcf.gz added
948b3722e0a25_1000g_pon.hg38.vcf.gz.tbi added
948b3760121ed_af-only-gnomad.hg38.vcf.gz added
948b3ddec34f_af-only-gnomad.hg38.vcf.gz.tbi added
948b328603011_small_exac_common_3.hg38.vcf.gz added
948b3631a7173_small_exac_common_3.hg38.vcf.gz.tbi added
948b3137d874d_gencode.v41.annotation.gtf added
948b337f45872_gencode.v42.annotation.gtf added
948b33e3efe05_gencode.vM30.annotation.gtf added
948b3aaf2d21_gencode.vM31.annotation.gtf added
948b398a4706_gencode.v41.transcripts.fa added
948b3687bd89a_gencode.v41.transcripts.fa.fai added
948b33f370391_gencode.v42.transcripts.fa added
948b3159385ac_gencode.v42.transcripts.fa.fai added
948b372c31225_gencode.vM30.pc_transcripts.fa added
948b32b0cdc56_gencode.vM30.pc_transcripts.fa.fai added
948b358e61d4_gencode.vM31.pc_transcripts.fa added
948b31d2c8187_gencode.vM31.pc_transcripts.fa.fai added
948b34adb096a_GRCh38.primary_assembly.genome.fa.1.ht2 added
948b36a8f2062_GRCh38.primary_assembly.genome.fa.2.ht2 added
948b31a9f23a2_GRCh38.primary_assembly.genome.fa.3.ht2 added
948b357ec7d09_GRCh38.primary_assembly.genome.fa.4.ht2 added
948b37ef9e72f_GRCh38.primary_assembly.genome.fa.5.ht2 added
948b355d22b8_GRCh38.primary_assembly.genome.fa.6.ht2 added
948b36b05806e_GRCh38.primary_assembly.genome.fa.7.ht2 added
948b35fe6ae0_GRCh38.primary_assembly.genome.fa.8.ht2 added
948b35a237875_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
948b31ff1dd06_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
948b3792251e8_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
948b371d27501_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
948b35171d0b0_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
948b37fc91d35_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
948b364007f26_GRCh38_full_analysis_set_plus_decoy_hla.fa added
948b34772f29e_GRCh38.primary_assembly.genome.fa.fai added
948b3da7e085_GRCh38.primary_assembly.genome.fa.amb added
948b3c60af37_GRCh38.primary_assembly.genome.fa.ann added
948b32a8d6411_GRCh38.primary_assembly.genome.fa.bwt added
948b3212567d2_GRCh38.primary_assembly.genome.fa.pac added
948b3445507a9_GRCh38.primary_assembly.genome.fa.sa added
948b368cc6216_GRCh38.primary_assembly.genome.fa added
948b32bd494f3_hs37d5.fa.fai added
948b34ddf4eaf_hs37d5.fa.amb added
948b351483ab0_hs37d5.fa.ann added
948b36b0b9885_hs37d5.fa.bwt added
948b36372d45b_hs37d5.fa.pac added
948b3440b4cd5_hs37d5.fa.sa added
948b3161874db_hs37d5.fa added
948b36901362f_complete_ref_lens.bin added
948b36137ce5d_ctable.bin added
948b360f37e46_ctg_offsets.bin added
948b353905692_duplicate_clusters.tsv added
948b37bd6f1ff_info.json added
948b338dffb4f_mphf.bin added
948b3528a3dc1_pos.bin added
948b313414b7_pre_indexing.log added
948b323e57bbd_rank.bin added
948b35888a8a1_ref_indexing.log added
948b35b578d2d_refAccumLengths.bin added
948b343d758c3_reflengths.bin added
948b351aafa89_refseq.bin added
948b34d2a022e_seq.bin added
948b315492974_versionInfo.json added
948b3517417bf_salmon_index added
948b3312a8155_chrLength.txt added
948b35cbc1c12_chrName.txt added
948b35f1bf844_chrNameLength.txt added
948b33d8b308c_chrStart.txt added
948b37498023_exonGeTrInfo.tab added
948b3416016_exonInfo.tab added
948b31e03836_geneInfo.tab added
948b37015e23a_Genome added
948b32c15f50a_genomeParameters.txt added
948b34fbf86e5_Log.out added
948b3415e1cea_SA added
948b317218d8f_SAindex added
948b333325b41_sjdbInfo.txt added
948b356969c0_sjdbList.fromGTF.out.tab added
948b32d3a026a_sjdbList.out.tab added
948b31c339170_transcriptInfo.tab added
948b366a1381d_GRCh38.GENCODE.v42_100 added
948b3e2d80b0_knownGene_hg38.sql added
948b36fc3e802_knownGene_hg38.txt added
948b362782a1c_refGene_hg38.sql added
948b3470d7bff_refGene_hg38.txt added
948b3424e25c4_knownGene_mm39.sql added
948b363ac3ed3_knownGene_mm39.txt added
948b36af2f7bc_refGene_mm39.sql added
948b31ad6ce65_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/RtmpK0rUfr/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
18.922 1.535 20.994
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.286 | 0.518 | 6.807 | |
| dataSearch | 1.139 | 0.019 | 1.159 | |
| dataUpdate | 0.000 | 0.000 | 0.001 | |
| getCloudData | 2.750 | 0.157 | 3.506 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.124 | 0.001 | 0.126 | |
| recipeLoad | 1.287 | 0.068 | 1.356 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.570 | 0.018 | 0.587 | |
| recipeUpdate | 0 | 0 | 0 | |