Qian Liu
| Snapshot Date: 2026-01-28 13:40 -0500 (Wed, 28 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: 4a5d06b |
| git_last_commit_date: 2025-10-29 11:20:44 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-29 11:32 -0500 (Thu, 29 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4851 |
| 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 1766/2347 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.11.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
|
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: 1.11.0 |
| 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_1.11.0.tar.gz |
| StartedAt: 2026-01-29 04:07:13 -0500 (Thu, 29 Jan 2026) |
| EndedAt: 2026-01-29 04:09:58 -0500 (Thu, 29 Jan 2026) |
| EllapsedTime: 165.3 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘1.11.0’
* 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 5.757 0.357 6.115
* 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 ‘1.11.0’ ** 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 Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
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...
26ff2f605d5b4c_GRCh38.primary_assembly.genome.fa.1.bt2 added
26ff2f133782fc_GRCh38.primary_assembly.genome.fa.2.bt2 added
26ff2f1fa80c85_GRCh38.primary_assembly.genome.fa.3.bt2 added
26ff2f7253b24d_GRCh38.primary_assembly.genome.fa.4.bt2 added
26ff2f32e12db6_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
26ff2f5e096722_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
26ff2f55af3232_outfile.txt added
26ff2f44378094_GRCh37_to_GRCh38.chain added
26ff2f6a441056_GRCh37_to_NCBI34.chain added
26ff2f59dfd96c_GRCh37_to_NCBI35.chain added
26ff2f248de0e6_GRCh37_to_NCBI36.chain added
26ff2f75913e19_GRCh38_to_GRCh37.chain added
26ff2f1f7bb35f_GRCh38_to_NCBI34.chain added
26ff2f66a74d4c_GRCh38_to_NCBI35.chain added
26ff2fc875c11_GRCh38_to_NCBI36.chain added
26ff2f33ed797c_NCBI34_to_GRCh37.chain added
26ff2fe4616a9_NCBI34_to_GRCh38.chain added
26ff2f668f30bf_NCBI35_to_GRCh37.chain added
26ff2f6af14198_NCBI35_to_GRCh38.chain added
26ff2f7755de20_NCBI36_to_GRCh37.chain added
26ff2f6792ee90_NCBI36_to_GRCh38.chain added
26ff2f1747d100_GRCm38_to_NCBIM36.chain added
26ff2f65dc92a6_GRCm38_to_NCBIM37.chain added
26ff2f166d2ab2_NCBIM36_to_GRCm38.chain added
26ff2f49df5ba_NCBIM37_to_GRCm38.chain added
26ff2f479cfdcf_1000G_omni2.5.b37.vcf.gz added
26ff2f2c8d3b2f_1000G_omni2.5.b37.vcf.gz.tbi added
26ff2f27c90399_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
26ff2f3313d1eb_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
26ff2f390ac4a6_1000G_omni2.5.hg38.vcf.gz added
26ff2f1d3c7717_1000G_omni2.5.hg38.vcf.gz.tbi added
26ff2f13712d38_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
26ff2f4c4247a2_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
26ff2f3ce4839c_af-only-gnomad.raw.sites.vcf added
26ff2f5c4df85_af-only-gnomad.raw.sites.vcf.idx added
26ff2f7f237558_Mutect2-exome-panel.vcf.idx added
26ff2f1aedeabe_Mutect2-WGS-panel-b37.vcf added
26ff2f5b7411b7_Mutect2-WGS-panel-b37.vcf.idx added
26ff2f435af5ed_small_exac_common_3.vcf added
26ff2f531fb14_small_exac_common_3.vcf.idx added
26ff2f3553eb23_1000g_pon.hg38.vcf.gz added
26ff2f67e8d6d3_1000g_pon.hg38.vcf.gz.tbi added
26ff2f7ac3392e_af-only-gnomad.hg38.vcf.gz added
26ff2f54cf9e82_af-only-gnomad.hg38.vcf.gz.tbi added
26ff2f4e90241f_small_exac_common_3.hg38.vcf.gz added
26ff2f74a953f_small_exac_common_3.hg38.vcf.gz.tbi added
26ff2f8bd17ff_gencode.v41.annotation.gtf added
26ff2f5cd63ac8_gencode.v42.annotation.gtf added
26ff2f6dd9c5fe_gencode.vM30.annotation.gtf added
26ff2f73ae5997_gencode.vM31.annotation.gtf added
26ff2f542c18e8_gencode.v41.transcripts.fa added
26ff2f556cb48e_gencode.v41.transcripts.fa.fai added
26ff2faf62a98_gencode.v42.transcripts.fa added
26ff2f3a08ab8f_gencode.v42.transcripts.fa.fai added
26ff2f6bd9df40_gencode.vM30.pc_transcripts.fa added
26ff2ff942052_gencode.vM30.pc_transcripts.fa.fai added
26ff2f1a5a95e_gencode.vM31.pc_transcripts.fa added
26ff2f18671a6f_gencode.vM31.pc_transcripts.fa.fai added
26ff2f375d23eb_GRCh38.primary_assembly.genome.fa.1.ht2 added
26ff2f34b97b49_GRCh38.primary_assembly.genome.fa.2.ht2 added
26ff2f5171df16_GRCh38.primary_assembly.genome.fa.3.ht2 added
26ff2f54999b02_GRCh38.primary_assembly.genome.fa.4.ht2 added
26ff2f482aa881_GRCh38.primary_assembly.genome.fa.5.ht2 added
26ff2f1db426b8_GRCh38.primary_assembly.genome.fa.6.ht2 added
26ff2f117e1e9f_GRCh38.primary_assembly.genome.fa.7.ht2 added
26ff2f4def8806_GRCh38.primary_assembly.genome.fa.8.ht2 added
26ff2f1cd79c11_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
26ff2f2c6c095d_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
26ff2f296399be_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
26ff2f603291fe_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
26ff2f319e0472_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
26ff2f5eb784e1_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
26ff2f481b68d1_GRCh38_full_analysis_set_plus_decoy_hla.fa added
26ff2f2c613da0_GRCh38.primary_assembly.genome.fa.fai added
26ff2f33872364_GRCh38.primary_assembly.genome.fa.amb added
26ff2f16ab8cf1_GRCh38.primary_assembly.genome.fa.ann added
26ff2f33abd2df_GRCh38.primary_assembly.genome.fa.bwt added
26ff2f3c443b63_GRCh38.primary_assembly.genome.fa.pac added
26ff2f7381c7b9_GRCh38.primary_assembly.genome.fa.sa added
26ff2f218598de_GRCh38.primary_assembly.genome.fa added
26ff2f2ff294fa_hs37d5.fa.fai added
26ff2f47ade0a2_hs37d5.fa.amb added
26ff2f76f24d6c_hs37d5.fa.ann added
26ff2f3ae8bf92_hs37d5.fa.bwt added
26ff2f1b68c31_hs37d5.fa.pac added
26ff2f62cc2cad_hs37d5.fa.sa added
26ff2f4a7cdfe4_hs37d5.fa added
26ff2f35c358f_complete_ref_lens.bin added
26ff2f7b33471c_ctable.bin added
26ff2f1da03cf_ctg_offsets.bin added
26ff2f3815b0d8_duplicate_clusters.tsv added
26ff2f4ca52632_info.json added
26ff2f56739ed2_mphf.bin added
26ff2f40595a_pos.bin added
26ff2f6a594ceb_pre_indexing.log added
26ff2f67f1bd71_rank.bin added
26ff2f4e2fe160_ref_indexing.log added
26ff2f730e8fc_refAccumLengths.bin added
26ff2f145dc6ce_reflengths.bin added
26ff2f77937b1e_refseq.bin added
26ff2f67637afa_seq.bin added
26ff2f45fbcb40_versionInfo.json added
26ff2f564b0000_salmon_index added
26ff2f2f7ee3cb_chrLength.txt added
26ff2f725d08e0_chrName.txt added
26ff2f9d22364_chrNameLength.txt added
26ff2f462a70bc_chrStart.txt added
26ff2f2608dbc0_exonGeTrInfo.tab added
26ff2f46165ec7_exonInfo.tab added
26ff2f39ac3876_geneInfo.tab added
26ff2f478e749e_Genome added
26ff2f7608f3c1_genomeParameters.txt added
26ff2f15a1918_Log.out added
26ff2f3e80c20a_SA added
26ff2f30f1b354_SAindex added
26ff2f310a549_sjdbInfo.txt added
26ff2f214ceeb7_sjdbList.fromGTF.out.tab added
26ff2f7b6e9338_sjdbList.out.tab added
26ff2f66cdad8_transcriptInfo.tab added
26ff2f1c8035d4_GRCh38.GENCODE.v42_100 added
26ff2f7d489708_knownGene_hg38.sql added
26ff2f3e828bb0_knownGene_hg38.txt added
26ff2f69255c06_refGene_hg38.sql added
26ff2f53bc35da_refGene_hg38.txt added
26ff2f3ec2e50a_knownGene_mm39.sql added
26ff2f537ea8f1_knownGene_mm39.txt added
26ff2f3badf34b_refGene_mm39.sql added
26ff2fcf2c66b_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/RtmpRWPgZj/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
18.758 1.930 21.314
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.757 | 0.357 | 6.115 | |
| dataSearch | 1.089 | 0.023 | 1.113 | |
| dataUpdate | 0.001 | 0.001 | 0.000 | |
| getCloudData | 2.715 | 0.162 | 4.142 | |
| getData | 0.001 | 0.000 | 0.001 | |
| meta_data | 0.001 | 0.000 | 0.001 | |
| recipeHub-class | 0.124 | 0.003 | 0.128 | |
| recipeLoad | 1.273 | 0.115 | 1.390 | |
| recipeMake | 0.001 | 0.000 | 0.000 | |
| recipeSearch | 0.518 | 0.011 | 0.529 | |
| recipeUpdate | 0 | 0 | 0 | |