Qian Liu
| Snapshot Date: 2026-02-02 13:45 -0500 (Mon, 02 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 2026-02-05 11:57 -0500 (Thu, 05 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" | 4888 |
| 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: 2026-02-04 03:40:34 -0500 (Wed, 04 Feb 2026) |
| EndedAt: 2026-02-04 03:43:20 -0500 (Wed, 04 Feb 2026) |
| EllapsedTime: 165.2 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 5.709 0.231 5.945
* 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...
7af7642ba3005_GRCh38.primary_assembly.genome.fa.1.bt2 added
7af76250e3b74_GRCh38.primary_assembly.genome.fa.2.bt2 added
7af767110b210_GRCh38.primary_assembly.genome.fa.3.bt2 added
7af761d8fe481_GRCh38.primary_assembly.genome.fa.4.bt2 added
7af7613e30354_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
7af7668e9002f_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
7af76fb4977d_outfile.txt added
7af767d222996_GRCh37_to_GRCh38.chain added
7af76f634e20_GRCh37_to_NCBI34.chain added
7af766088fa70_GRCh37_to_NCBI35.chain added
7af7625f29d8a_GRCh37_to_NCBI36.chain added
7af7666ca924d_GRCh38_to_GRCh37.chain added
7af765cf6980c_GRCh38_to_NCBI34.chain added
7af763b4872ff_GRCh38_to_NCBI35.chain added
7af764fe8f089_GRCh38_to_NCBI36.chain added
7af76500c2390_NCBI34_to_GRCh37.chain added
7af766c68a9a5_NCBI34_to_GRCh38.chain added
7af7616739bec_NCBI35_to_GRCh37.chain added
7af765100824e_NCBI35_to_GRCh38.chain added
7af764bc56802_NCBI36_to_GRCh37.chain added
7af761806d0c0_NCBI36_to_GRCh38.chain added
7af765cbbcbb5_GRCm38_to_NCBIM36.chain added
7af761e0e0ff_GRCm38_to_NCBIM37.chain added
7af767ebb434b_NCBIM36_to_GRCm38.chain added
7af7671e5fe7d_NCBIM37_to_GRCm38.chain added
7af761735f46b_1000G_omni2.5.b37.vcf.gz added
7af76e0ade33_1000G_omni2.5.b37.vcf.gz.tbi added
7af76483eab0a_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
7af76752dd7f4_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
7af76724f9bc8_1000G_omni2.5.hg38.vcf.gz added
7af76386ed10f_1000G_omni2.5.hg38.vcf.gz.tbi added
7af7637e807f9_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
7af76175dd73c_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
7af76297f831f_af-only-gnomad.raw.sites.vcf added
7af765577ec7a_af-only-gnomad.raw.sites.vcf.idx added
7af762b40da91_Mutect2-exome-panel.vcf.idx added
7af761268834e_Mutect2-WGS-panel-b37.vcf added
7af76652c83f7_Mutect2-WGS-panel-b37.vcf.idx added
7af7628630427_small_exac_common_3.vcf added
7af7621cbd16f_small_exac_common_3.vcf.idx added
7af7645b57e67_1000g_pon.hg38.vcf.gz added
7af764e55a1b2_1000g_pon.hg38.vcf.gz.tbi added
7af7689663bc_af-only-gnomad.hg38.vcf.gz added
7af7622ac1673_af-only-gnomad.hg38.vcf.gz.tbi added
7af7699e14b1_small_exac_common_3.hg38.vcf.gz added
7af76587f5446_small_exac_common_3.hg38.vcf.gz.tbi added
7af7672b83a03_gencode.v41.annotation.gtf added
7af767606be57_gencode.v42.annotation.gtf added
7af766ef2f032_gencode.vM30.annotation.gtf added
7af7643b8bc52_gencode.vM31.annotation.gtf added
7af7641cc2659_gencode.v41.transcripts.fa added
7af766f9c0f3_gencode.v41.transcripts.fa.fai added
7af7620748807_gencode.v42.transcripts.fa added
7af7643ad0758_gencode.v42.transcripts.fa.fai added
7af765b5043e_gencode.vM30.pc_transcripts.fa added
7af76125a8684_gencode.vM30.pc_transcripts.fa.fai added
7af765ae2fbc4_gencode.vM31.pc_transcripts.fa added
7af7613bfe271_gencode.vM31.pc_transcripts.fa.fai added
7af765a99318e_GRCh38.primary_assembly.genome.fa.1.ht2 added
7af765010d3b8_GRCh38.primary_assembly.genome.fa.2.ht2 added
7af7660f7e39_GRCh38.primary_assembly.genome.fa.3.ht2 added
7af761308029d_GRCh38.primary_assembly.genome.fa.4.ht2 added
7af767f8dbb2_GRCh38.primary_assembly.genome.fa.5.ht2 added
7af761d6d5576_GRCh38.primary_assembly.genome.fa.6.ht2 added
7af763c8785bc_GRCh38.primary_assembly.genome.fa.7.ht2 added
7af765d70c82c_GRCh38.primary_assembly.genome.fa.8.ht2 added
7af7648ae3007_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
7af764ef0090b_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
7af76429d4c24_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
7af767111342e_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
7af7670bbda7a_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
7af76852ca8b_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
7af763f66d5e0_GRCh38_full_analysis_set_plus_decoy_hla.fa added
7af7679523e36_GRCh38.primary_assembly.genome.fa.fai added
7af762afee0ff_GRCh38.primary_assembly.genome.fa.amb added
7af764904ea92_GRCh38.primary_assembly.genome.fa.ann added
7af7651d1927c_GRCh38.primary_assembly.genome.fa.bwt added
7af761db71b02_GRCh38.primary_assembly.genome.fa.pac added
7af763f0ba8e9_GRCh38.primary_assembly.genome.fa.sa added
7af7640c482af_GRCh38.primary_assembly.genome.fa added
7af76616fd754_hs37d5.fa.fai added
7af76d7cf42_hs37d5.fa.amb added
7af7647be43a2_hs37d5.fa.ann added
7af761e45f5c_hs37d5.fa.bwt added
7af764484d69b_hs37d5.fa.pac added
7af764d7347e0_hs37d5.fa.sa added
7af76143ee5e0_hs37d5.fa added
7af761f67d25f_complete_ref_lens.bin added
7af7661332a51_ctable.bin added
7af766ed8176f_ctg_offsets.bin added
7af766f78a617_duplicate_clusters.tsv added
7af766742a88a_info.json added
7af761e01a0c_mphf.bin added
7af76777181c9_pos.bin added
7af764affe00_pre_indexing.log added
7af763e679fc9_rank.bin added
7af7654e249f6_ref_indexing.log added
7af764d5e2e07_refAccumLengths.bin added
7af76d57a8d4_reflengths.bin added
7af76177f961a_refseq.bin added
7af763e6f6236_seq.bin added
7af767e13834e_versionInfo.json added
7af761fd260a5_salmon_index added
7af767dd63816_chrLength.txt added
7af767765c184_chrName.txt added
7af764ad141a4_chrNameLength.txt added
7af7646db22a8_chrStart.txt added
7af7649375401_exonGeTrInfo.tab added
7af7668885ca7_exonInfo.tab added
7af765e6cb91_geneInfo.tab added
7af769fbd6b0_Genome added
7af7649f833fb_genomeParameters.txt added
7af766be9ad4_Log.out added
7af7651ba1a52_SA added
7af764bdc9357_SAindex added
7af764b43716f_sjdbInfo.txt added
7af761f2d6232_sjdbList.fromGTF.out.tab added
7af76601b7938_sjdbList.out.tab added
7af766aab43ce_transcriptInfo.tab added
7af76608c83_GRCh38.GENCODE.v42_100 added
7af764ef390a7_knownGene_hg38.sql added
7af765a23e9e5_knownGene_hg38.txt added
7af7667a3350d_refGene_hg38.sql added
7af7650d3aab3_refGene_hg38.txt added
7af7651956baf_knownGene_mm39.sql added
7af766c53330e_knownGene_mm39.txt added
7af76f3b4a7c_refGene_mm39.sql added
7af762677b5a5_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/RtmpcJEDZk/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
19.536 1.164 21.387
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.709 | 0.231 | 5.945 | |
| dataSearch | 1.073 | 0.014 | 1.087 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.666 | 0.118 | 3.596 | |
| getData | 0 | 0 | 0 | |
| meta_data | 0.000 | 0.000 | 0.001 | |
| recipeHub-class | 0.123 | 0.000 | 0.124 | |
| recipeLoad | 1.260 | 0.013 | 1.274 | |
| recipeMake | 0 | 0 | 0 | |
| recipeSearch | 0.536 | 0.003 | 0.540 | |
| recipeUpdate | 0 | 0 | 0 | |